scatterplot3d/0000755000175100001440000000000011544601042013060 5ustar hornikusersscatterplot3d/CHANGES0000744000175100001440000000734211542111402014054 0ustar hornikusersChanges in 0.3-x releases of scatterplot3d: ======= 0.3.0: New design: box, pretty() for ticks, ... 0.3.1: par("las") bug patched, scale.y is changed (code and default) 0.3.2: all angles will work again (default: 40) tick mark labeling changed (using mtext) par("mar") is set in the first line, not very general! 0.3.3: new argument "mar", more details in the help files 0.3.4: new arguments x/y/z.ticklabs, thanks to Ben Bolker! bug fix: adj for tick.mark.labels corrected 0.3-5: new argument y.margin.add for manual fixing scaling problems (e.g. some y-tickmarks dissapear after rescaling the window) 0.3-6: cex.symbols introduced to solve magnification errors 0.3-7: added function plane3d, which will be returned, (e.g. for overlaying a regression plane) 0.3-8: bugfix: some magnification errors for y.ticklabs 0.3-9: bugfix: pch works vectorized again (error with y-sorting) 0.3-10: added function box3d(), which will be returned, to draw the box surrounding the plot again after additions * added a function s3d.persp() - somehow joining s3d and persp() * 0.3-11: * s3d.persp() deleted again, because of various reasons * Created this file to reduce the size of the R code. 0.3-12: bug fix: tick.mark.labels of y axis were sometimes raised by a constant or vice versa format() is used to print tick.mark.labels pretty, and smarter calculation of desired (for y axis tick.mark.labels) plot margins 0.3-13: typos in help file box3d() refreshes the right lines for an arbitrary angle now. calculation of space for tick.mark.labels fixed (bug was introduced with 0.3-12 ?) Extending s3d requires to set par(mar) to those settings s3d was generated with, which will be done for points3d(), plane3d(), and box3d() automatically. A "Note" has been added to the help file. 0.3-14: Reference changed in help file. Suggestions by Martin Maechler (thank you!): - clean up a lot of code - Added note on unfixed bug to help file. - Added Martin's great examples 6 a/b: "color cube" 0.3-15: Allow for just 1 point (was 2 before) to be plotted Allow all points to be within a major plane Argument lty.hide introduced (for plotting of in-visible edges) plane3d() allows to plot the box-intersecting lines in a different line style 0.3-16: bug fix: non-finite or NA values of y did not work. 0.3-17: bug fix: Example 6 fixed by Martin Maechler 0.3-18: bug fix: non-finite or NA values of y still did not work, if highlight.3d=TRUE 0.3-19: CITATION file and package vignette added 0.3-20: NAMESPACE added, translation support for warnings/erorrs added, srcltx.sty added 0.3-21: chicago.* added 0.3-22: bugfix: returned closures have to set par("usr") and par("mar") internally as the former call to scatterplot3d did! 0.3-23: bugfix: must not reset mar in scatterplot3d! 0.3-24: par("type") does no longer exist for R >= 2.3.0 x.prty, y.prty, z.prty are no longer removed in the s3d environment (user request) 0.3-25: bugfix: $ depreceated ... 0.3-26: CITATION in UTF-8 0.3-27: CITATION in latin1 and declaration to be latin1 package 0.3-28: bugfix: y sorted revserse (and hence had also wrong tick labels) for angles > 180. 0.3-29: bugfix: retunred function points3d()/xyz.convert()/plane3d can deal with angle > 180 0.3-30: added argument lty.hplot for controllling horizontal line style, by Jari Oksanen 0.3-31: fix cex.symbols reordering bug 0.3-32: some qpdf compression in ./inst/doc known UNfixed bug: xlim, ylim, zlim don't work *exactly* for enlarged areas scatterplot3d/DESCRIPTION0000744000175100001440000000061311544625757014612 0ustar hornikusersPackage: scatterplot3d Version: 0.3-33 Date: 2011-03-30 Title: 3D Scatter Plot Author: Uwe Ligges Maintainer: Uwe Ligges Description: Plots a three dimensional (3D) point cloud. Depends: R (>= 2.7.0) License: GPL-2 Encoding: latin1 Packaged: 2011-03-30 10:12:51 UTC; CRAN Repository: CRAN Date/Publication: 2011-03-30 13:11:11 scatterplot3d/inst/0000755000175100001440000000000011544601042014035 5ustar hornikusersscatterplot3d/inst/CITATION0000744000175100001440000000135311010547270015175 0ustar hornikuserscitHeader("To cite scatterplot3d in publications use:") citEntry(entry = "article", title = "Scatterplot3d - an R Package for Visualizing Multivariate Data", author = personList(person(first="Uwe", last="Ligges", email="Uwe.Ligges@R-project.org"), person(first="Martin", last='M{\\"a}chler', email="Martin.Maechler@R-project.org")), journal = "Journal of Statistical Software", year = 2003, pages = "1--20", number = 11, volume = 8, url = "http://www.jstatsoft.org", textVersion = paste("Ligges, U. and Mchler, M. 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"Data Structuring Group %%% Department of Computer Science %%% University of Waterloo %%% Waterloo, Ontario, Canada %%% N2L 3G1", %%% telephone = "(519) 885-1211", %%% FAX = "(519) 885-1208", %%% checksum = "26323 1654 5143 37417", %%% email = "gnpaulle@bluebox.uwaterloo.ca", %%% codetable = "ISO/ASCII", %%% keywords = "", %%% supported = "yes", %%% abstract = "A BibTeX bibliography style that follows the %%% `B' reference style of the 13th Edition of %%% the Chicago Manual of Style. A detailed %%% feature list is given below.", %%% docstring = "The checksum field above contains a CRC-16 %%% checksum as the first value, followed by the %%% equivalent of the standard UNIX wc (word %%% count) utility output of lines, words, and %%% characters. This is produced by Robert %%% Solovay's checksum utility.", %%% } %%% ==================================================================== % % "Chicago" BibTeX style, chicago.bst % =================================== % % BibTeX `chicago' style file for BibTeX version 0.99c, LaTeX version 2.09 % Place it in a file called chicago.bst in the BibTeX search path. % You need to include chicago.sty as a \documentstyle option. % (Placing it in the same directory as the LaTeX document should also work.) % This "chicago" style is based on newapa.bst (American Psych. Assoc.) % found at ymir.claremont.edu. % % Citation format: (author-last-name year) % (author-last-name and author-last-name year) % (author-last-name, author-last-name, and author-last-name year) % (author-last-name et al. year) % (author-last-name) % author-last-name (year) % (author-last-name and author-last-name) % (author-last-name et al.) % (year) or (year,year) % year or year,year % % Reference list ordering: alphabetical by author or whatever passes % for author in the absence of one. % % This BibTeX style has support for abbreviated author lists and for % year-only citations. This is done by having the citations % actually look like % % \citeauthoryear{full-author-info}{abbrev-author-info}{year} % % The LaTeX style has to have the following (or similar) % % \let\@internalcite\cite % \def\fullcite{\def\citeauthoryear##1##2##3{##1, ##3}\@internalcite} % \def\fullciteA{\def\citeauthoryear##1##2##3{##1}\@internalcite} % \def\shortcite{\def\citeauthoryear##1##2##3{##2, ##3}\@internalcite} % \def\shortciteA{\def\citeauthoryear##1##2##3{##2}\@internalcite} % \def\citeyear{\def\citeauthoryear##1##2##3{##3}\@internalcite} % % These TeX macro definitions are found in chicago.sty. Additional % commands to manipulate different components of a citation can be defined % so that, for example, you can list author's names without parentheses % if using a citation as a noun or object in a sentence. % % This file was originally copied from newapa.bst at ymir.claremont.edu. % % Features of chicago.bst: % ======================= % % - full names used in citations, but abbreviated citations are available % (see above) % - if an entry has a "month", then the month and year are also printed % as part of that bibitem. % - all conjunctions use "and" instead of "\&" % - major modification from Chicago Manual of Style (13th ed.) is that % only the first author in a reference appears last name first- % additional authors appear as J. Q. Public. % - pages are listed as "pp. xx-xx" in all entry types except % article entries. % - book, inbook, and manual use "location: publisher" (or organization) % for address and publisher. All other types list publishers separately. % - "pp." are used to identify page numbers for all entry types except % articles. % - organization is used as a citation label if neither author nor editor % is present (for manuals). % - "et al." is used for long author and editor lists, or when "others" % is used. % % Modifications and bug fixes from newapa.bst: % =========================================== % % - added month, year to bib entries if month is present % - fixed bug with In proceedings, added necessary comma after title % - all conjunctions changed to "and" from "\&" % - fixed bug with author labels in my.full.label: "et al." now is % generated when "others" is an author name % - major modification from Chicago Manual of Style (13th ed.) is that % only the first author in a reference appears last name first- % additional authors appear as J. Q. Public. % - pages are listed as "pp. xx-xx" in all entry types except % article entries. Unnecessary (IMHO) "()" around page numbers % were removed, and page numbers now don't end with a period. % - created chicago.sty for use with this bibstyle (required). % - fixed bugs in FUNCTION {format.vol.num.pages} for missing volume, % number, and /or pages. Renamed to format.jour.vol. % - fixed bug in formatting booktitles: additional period an error if % book has a volume. % - fixed bug: editors usually given redundant period before next clause % (format.editors.dot) removed. % - added label support for organizations, if both author and editor % are missing (from alpha.bst). If organization is too long, then % the key field is used for abbreviated citations. % - In proceedings or books of several volumes, no comma was written % between the "Volume x" and the page numbers (this was intentional % in newapa.bst). Fixed. % - Some journals may not have volumes/numbers, only month/year (eg. % IEEE Computer). Fixed bug in article style that assumed volume/number % was always present. % % Original documentation for newapa.sty: % ===================================== % % This version was made by modifying the master file made by % Oren Patashnik (PATASHNIK@SCORE.STANFORD.EDU), and the 'named' BibTeX % style of Peter F. Patel-Schneider. % % Copyright (C) 1985, all rights reserved. % Copying of this file is authorized only if either % (1) you make absolutely no changes to your copy, including name, or % (2) if you do make changes, you name it something other than 'newapa.bst'. % There are undoubtably bugs in this style. If you make bug fixes, % improvements, etc. please let me know. My e-mail address is: % spencer@cgrg.ohio.state.edu or 71160.3141@compuserve.com % % This style was made from 'plain.bst', 'named.bst', and 'apalike.bst', % with lots of tweaking to make it look like APA style, along with tips % from Young Ryu and Brian Reiser's modifications of 'apalike.bst'. ENTRY { address author booktitle chapter edition editor howpublished institution journal key month note number organization pages publisher school series title type volume year } {} { label.year extra.label sort.year sort.label } INTEGERS { output.state before.all mid.sentence after.sentence after.block } FUNCTION {init.state.consts} { #0 'before.all := #1 'mid.sentence := #2 'after.sentence := #3 'after.block := } STRINGS { s t u } FUNCTION {output.nonnull} { 's := output.state mid.sentence = { ", " * write$ } { output.state after.block = { add.period$ write$ newline$ "\newblock " write$ } { output.state before.all = 'write$ { add.period$ " " * write$ } if$ } if$ mid.sentence 'output.state := } if$ s } % Use a colon to separate output. Used only for address/publisher % combination in book/inbook types, address/institution for manuals, % and organization:publisher for proceedings (inproceedings). % FUNCTION {output.nonnull.colon} { 's := output.state mid.sentence = { ": " * write$ } { output.state after.block = { add.period$ write$ newline$ "\newblock " write$ } { output.state before.all = 'write$ { add.period$ " " * write$ } if$ } if$ mid.sentence 'output.state := } if$ s } FUNCTION {output} { duplicate$ empty$ 'pop$ 'output.nonnull if$ } FUNCTION {output.colon} { duplicate$ empty$ 'pop$ 'output.nonnull.colon if$ } FUNCTION {output.check} { 't := duplicate$ empty$ { pop$ "empty " t * " in " * cite$ * warning$ } 'output.nonnull if$ } FUNCTION {output.check.colon} { 't := duplicate$ empty$ { pop$ "empty " t * " in " * cite$ * warning$ } 'output.nonnull.colon if$ } FUNCTION {output.year.check} { year empty$ { "empty year in " cite$ * warning$ } { write$ " (" year * extra.label * month empty$ { ")" * } { ", " * month * ")" * } if$ mid.sentence 'output.state := } if$ } FUNCTION {fin.entry} { add.period$ write$ newline$ } FUNCTION {new.block} { output.state before.all = 'skip$ { after.block 'output.state := } if$ } FUNCTION {new.sentence} { output.state after.block = 'skip$ { output.state before.all = 'skip$ { after.sentence 'output.state := } if$ } if$ } FUNCTION {not} { { #0 } { #1 } if$ } FUNCTION {and} { 'skip$ { pop$ #0 } if$ } FUNCTION {or} { { pop$ #1 } 'skip$ if$ } FUNCTION {new.block.checka} { empty$ 'skip$ 'new.block if$ } FUNCTION {new.block.checkb} { empty$ swap$ empty$ and 'skip$ 'new.block if$ } FUNCTION {new.sentence.checka} { empty$ 'skip$ 'new.sentence if$ } FUNCTION {new.sentence.checkb} { empty$ swap$ empty$ and 'skip$ 'new.sentence if$ } FUNCTION {field.or.null} { duplicate$ empty$ { pop$ "" } 'skip$ if$ } % % Emphasize the top string on the stack. % FUNCTION {emphasize} { duplicate$ empty$ { pop$ "" } { "{\em " swap$ * "}" * } if$ } % % Emphasize the top string on the stack, but add a trailing space. % FUNCTION {emphasize.space} { duplicate$ empty$ { pop$ "" } { "{\em " swap$ * "\/}" * } if$ } INTEGERS { nameptr namesleft numnames } % % Format bibliographical entries with the first author last name first, % and subsequent authors with initials followed by last name. % All names are formatted in this routine. % FUNCTION {format.names} { 's := #1 'nameptr := % nameptr = 1; s num.names$ 'numnames := % numnames = num.name$(s); numnames 'namesleft := { namesleft #0 > } { nameptr #1 = {s nameptr "{vv~}{ll}{, jj}{, f.}" format.name$ 't := } {s nameptr "{f.~}{vv~}{ll}{, jj}" format.name$ 't := } if$ nameptr #1 > { namesleft #1 > { ", " * t * } { numnames #2 > { "," * } 'skip$ if$ t "others" = { " et~al." * } { " and " * t * } % from Chicago Manual of Style if$ } if$ } 't if$ nameptr #1 + 'nameptr := % nameptr += 1; namesleft #1 - 'namesleft := % namesleft =- 1; } while$ } FUNCTION {my.full.label} { 's := #1 'nameptr := % nameptr = 1; s num.names$ 'numnames := % numnames = num.name$(s); numnames 'namesleft := { namesleft #0 > } { s nameptr "{vv~}{ll}" format.name$ 't := % get the next name nameptr #1 > { namesleft #1 > { ", " * t * } { numnames #2 > { "," * } 'skip$ if$ t "others" = { " et~al." * } { " and " * t * } % from Chicago Manual of Style if$ } if$ } 't if$ nameptr #1 + 'nameptr := % nameptr += 1; namesleft #1 - 'namesleft := % namesleft =- 1; } while$ } FUNCTION {format.names.fml} % % Format names in "familiar" format, with first initial followed by % last name. Like format.names, ALL names are formatted. % { 's := #1 'nameptr := % nameptr = 1; s num.names$ 'numnames := % numnames = num.name$(s); numnames 'namesleft := { namesleft #0 > } { s nameptr "{f.~}{vv~}{ll}{, jj}" format.name$ 't := nameptr #1 > { namesleft #1 > { ", " * t * } { numnames #2 > { "," * } 'skip$ if$ t "others" = { " et~al." * } { " and " * t * } % { " \& " * t * } if$ } if$ } 't if$ nameptr #1 + 'nameptr := % nameptr += 1; namesleft #1 - 'namesleft := % namesleft =- 1; } while$ } FUNCTION {format.authors} { author empty$ { "" } { author format.names } if$ } FUNCTION {format.key} { empty$ { key field.or.null } { "" } if$ } % % Format editor names for use in the "in" types: inbook, incollection, % inproceedings: first initial, then last names. When editors are the % LABEL for an entry, then format.editor is used which lists editors % by last name first. % FUNCTION {format.editors.fml} { editor empty$ { "" } { editor format.names.fml editor num.names$ #1 > { " (Eds.)" * } { " (Ed.)" * } if$ } if$ } % % Format editor names for use in labels, last names first. % FUNCTION {format.editors} { editor empty$ { "" } { editor format.names editor num.names$ #1 > { " (Eds.)" * } { " (Ed.)" * } if$ } if$ } FUNCTION {format.title} { title empty$ { "" } { title "t" change.case$ } if$ } % Note that the APA style requres case changes % in article titles. The following does not % change cases. If you perfer it, uncomment the % following and comment out the above. %FUNCTION {format.title} %{ title empty$ % { "" } % { title } % if$ %} FUNCTION {n.dashify} { 't := "" { t empty$ not } { t #1 #1 substring$ "-" = { t #1 #2 substring$ "--" = not { "--" * t #2 global.max$ substring$ 't := } { { t #1 #1 substring$ "-" = } { "-" * t #2 global.max$ substring$ 't := } while$ } if$ } { t #1 #1 substring$ * t #2 global.max$ substring$ 't := } if$ } while$ } FUNCTION {format.btitle} { edition empty$ { title emphasize } { title empty$ { title emphasize } { volume empty$ % gnp - check for volume, then don't need period { "{\em " title * "\/} (" * edition * " ed.)" * "." * } { "{\em " title * "\/} (" * edition * " ed.)" * } if$ } if$ } if$ } FUNCTION {format.emphasize.booktitle} { edition empty$ { booktitle emphasize } { booktitle empty$ { booktitle emphasize } { volume empty$ % gnp - extra period an error if book has a volume { "{\em " booktitle * "\/} (" * edition * " ed.)" * "." *} { "{\em " booktitle * "\/} (" * edition * " ed.)" * } if$ } if$ } if$ } FUNCTION {tie.or.space.connect} { duplicate$ text.length$ #3 < { "~" } { " " } if$ swap$ * * } FUNCTION {either.or.check} { empty$ 'pop$ { "can't use both " swap$ * " fields in " * cite$ * warning$ } if$ } FUNCTION {format.bvolume} { volume empty$ { "" } { "Volume" volume tie.or.space.connect % gnp - changed to mixed case series empty$ 'skip$ { " of " * series emphasize * } if$ "volume and number" number either.or.check } if$ } FUNCTION {format.number.series} { volume empty$ { number empty$ { series field.or.null } { output.state mid.sentence = { "Number" } % gnp - changed to mixed case always { "Number" } if$ number tie.or.space.connect series empty$ { "there's a number but no series in " cite$ * warning$ } { " in " * series * } if$ } if$ } { "" } if$ } INTEGERS { multiresult } FUNCTION {multi.page.check} { 't := #0 'multiresult := { multiresult not t empty$ not and } { t #1 #1 substring$ duplicate$ "-" = swap$ duplicate$ "," = swap$ "+" = or or { #1 'multiresult := } { t #2 global.max$ substring$ 't := } if$ } while$ multiresult } FUNCTION {format.pages} { pages empty$ { "" } { pages multi.page.check { "pp.\ " pages n.dashify tie.or.space.connect } % gnp - removed () { "pp.\ " pages tie.or.space.connect } if$ } if$ } % By Young (and Spencer) % GNP - fixed bugs with missing volume, number, and/or pages % % Format journal, volume, number, pages for article types. % FUNCTION {format.jour.vol} { journal empty$ { "no journal in " cite$ * warning$ "" } { journal emphasize.space } if$ number empty$ { volume empty$ { "no number and no volume in " cite$ * warning$ "" * } { "~{\em " * Volume * "}" * } if$ } { volume empty$ {"no volume for " cite$ * warning$ "~(" * number * ")" * } { "~" * volume emphasize.space "(" * number * ")" * * } if$ } if$ pages empty$ {"page numbers missing in " cite$ * warning$ "" * } % gnp - place a null string on the stack for output { duplicate$ empty$ { pop$ format.pages } { ", " * pages n.dashify * } % gnp - removed pp. for articles if$ } if$ } FUNCTION {format.chapter.pages} { chapter empty$ 'format.pages { type empty$ { "Chapter" } % gnp - changed to mixed case { type "t" change.case$ } if$ chapter tie.or.space.connect pages empty$ {"page numbers missing in " cite$ * warning$} % gnp - added check { ", " * format.pages * } if$ } if$ } FUNCTION {format.in.ed.booktitle} { booktitle empty$ { "" } { editor empty$ { "In " format.emphasize.booktitle * } { "In " format.editors.fml * ", " * format.emphasize.booktitle * } if$ } if$ } FUNCTION {format.thesis.type} { type empty$ 'skip$ { pop$ type "t" change.case$ } if$ } FUNCTION {format.tr.number} { type empty$ { "Technical Report" } 'type if$ number empty$ { "t" change.case$ } { number tie.or.space.connect } if$ } FUNCTION {format.article.crossref} { "See" "\citeN{" * crossref * "}" * } FUNCTION {format.crossref.editor} { editor #1 "{vv~}{ll}" format.name$ editor num.names$ duplicate$ #2 > { pop$ " et~al." * } { #2 < 'skip$ { editor #2 "{ff }{vv }{ll}{ jj}" format.name$ "others" = { " et~al." * } { " and " * editor #2 "{vv~}{ll}" format.name$ * } if$ } if$ } if$ } FUNCTION {format.book.crossref} { volume empty$ { "empty volume in " cite$ * "'s crossref of " * crossref * warning$ "In " } { "Volume" volume tie.or.space.connect % gnp - changed to mixed case " of " * } if$ editor empty$ editor field.or.null author field.or.null = or { key empty$ { series empty$ { "need editor, key, or series for " cite$ * " to crossref " * crossref * warning$ "" * } { "{\em " * series * "\/}" * } if$ } { key * } if$ } { format.crossref.editor * } if$ " \citeN{" * crossref * "}" * } FUNCTION {format.incoll.inproc.crossref} { "See" " \citeN{" * crossref * "}" * } % format.lab.names: % % determines "short" names for the abbreviated author information. % "Long" labels are created in calc.label, using the routine my.full.label % to format author and editor fields. % % There are 4 cases for labels. (n=3 in the example) % a) one author Foo % b) one to n Foo, Bar and Baz % c) use of "and others" Foo, Bar et al. % d) more than n Foo et al. % FUNCTION {format.lab.names} { 's := s num.names$ 'numnames := numnames #2 > % change number to number of others allowed before % forcing "et al". { s #1 "{vv~}{ll}" format.name$ " et~al." * } { numnames #1 - 'namesleft := #2 'nameptr := s #1 "{vv~}{ll}" format.name$ { namesleft #0 > } { nameptr numnames = { s nameptr "{ff }{vv }{ll}{ jj}" format.name$ "others" = { " et~al." * } { " and " * s nameptr "{vv~}{ll}" format.name$ * } if$ } { ", " * s nameptr "{vv~}{ll}" format.name$ * } if$ nameptr #1 + 'nameptr := namesleft #1 - 'namesleft := } while$ } if$ } FUNCTION {author.key.label} { author empty$ { key empty$ { "no key, author in " cite$ * warning$ cite$ #1 #3 substring$ } 'key if$ } { author format.lab.names } if$ } FUNCTION {editor.key.label} { editor empty$ { key empty$ { "no key, editor in " cite$ * warning$ cite$ #1 #3 substring$ } 'key if$ } { editor format.lab.names } if$ } FUNCTION {author.key.organization.label} % % added - gnp. Provide label formatting by organization if author is null. % { author empty$ { organization empty$ { key empty$ { "no key, author or organization in " cite$ * warning$ cite$ #1 #3 substring$ } 'key if$ } { organization } if$ } { author format.lab.names } if$ } FUNCTION {editor.key.organization.label} % % added - gnp. Provide label formatting by organization if editor is null. % { editor empty$ { organization empty$ { key empty$ { "no key, editor or organization in " cite$ * warning$ cite$ #1 #3 substring$ } 'key if$ } { organization } if$ } { editor format.lab.names } if$ } FUNCTION {author.editor.key.label} { author empty$ { editor empty$ { key empty$ { "no key, author, or editor in " cite$ * warning$ cite$ #1 #3 substring$ } 'key if$ } { editor format.lab.names } if$ } { author format.lab.names } if$ } FUNCTION {calc.label} % % Changed - GNP. See also author.organization.sort, editor.organization.sort % Form label for BibTeX entry. The classification of which fields are used % for which type of entry (book, inbook, etc.) are taken from alpha.bst. % The change here from newapa is to also include organization as a % citation label if author or editor is missing. % { type$ "book" = type$ "inbook" = or 'author.editor.key.label { type$ "proceedings" = 'editor.key.organization.label { type$ "manual" = 'author.key.organization.label 'author.key.label if$ } if$ } if$ author empty$ % generate the full label citation information. { editor empty$ { organization empty$ { "no author, editor, or organization in " cite$ * warning$ "??" } { organization } if$ } { editor my.full.label } if$ } { author my.full.label } if$ % leave label on the stack, to be popped when required. "}{" * swap$ * "}{" * % year field.or.null purify$ #-1 #4 substring$ * % % save the year for sort processing afterwards (adding a, b, c, etc.) % year field.or.null purify$ #-1 #4 substring$ 'label.year := } FUNCTION {output.bibitem} { newline$ "\bibitem[\protect\citeauthoryear{" write$ calc.label write$ sort.year write$ "}]{" write$ cite$ write$ "}" write$ newline$ "" before.all 'output.state := } FUNCTION {article} { output.bibitem format.authors "author" output.check author format.key output % added output.year.check % added new.block format.title "title" output.check new.block crossref missing$ { format.jour.vol output } { format.article.crossref output.nonnull format.pages output } if$ new.block note output fin.entry } FUNCTION {book} { output.bibitem author empty$ { format.editors "author and editor" output.check } { format.authors output.nonnull crossref missing$ { "author and editor" editor either.or.check } 'skip$ if$ } if$ output.year.check % added new.block format.btitle "title" output.check crossref missing$ { format.bvolume output new.block format.number.series output new.sentence address output publisher "publisher" output.check.colon } { new.block format.book.crossref output.nonnull } if$ new.block note output fin.entry } FUNCTION {booklet} { output.bibitem format.authors output author format.key output % added output.year.check % added new.block format.title "title" output.check new.block howpublished output address output new.block note output fin.entry } FUNCTION {inbook} { output.bibitem author empty$ { format.editors "author and editor" output.check } { format.authors output.nonnull crossref missing$ { "author and editor" editor either.or.check } 'skip$ if$ } if$ output.year.check % added new.block format.btitle "title" output.check crossref missing$ { format.bvolume output format.chapter.pages "chapter and pages" output.check new.block format.number.series output new.sentence address output publisher "publisher" output.check.colon } { format.chapter.pages "chapter and pages" output.check new.block format.book.crossref output.nonnull } if$ new.block note output fin.entry } FUNCTION {incollection} { output.bibitem format.authors "author" output.check author format.key output % added output.year.check % added new.block format.title "title" output.check new.block crossref missing$ { format.in.ed.booktitle "booktitle" output.check format.bvolume output format.number.series output format.chapter.pages output % gnp - was special.output.nonnull % left out comma before page numbers new.sentence address output publisher "publisher" output.check.colon } { format.incoll.inproc.crossref output.nonnull format.chapter.pages output } if$ new.block note output fin.entry } FUNCTION {inproceedings} { output.bibitem format.authors "author" output.check author format.key output % added output.year.check % added new.block format.title "title" output.check new.block crossref missing$ { format.in.ed.booktitle "booktitle" output.check format.bvolume output format.number.series output address output format.pages output new.sentence organization output publisher output.colon } { format.incoll.inproc.crossref output.nonnull format.pages output } if$ new.block note output fin.entry } FUNCTION {conference} { inproceedings } FUNCTION {manual} { output.bibitem author empty$ { editor empty$ { organization "organization" output.check organization format.key output } % if all else fails, use key { format.editors "author and editor" output.check } if$ } { format.authors output.nonnull } if$ output.year.check % added new.block format.btitle "title" output.check organization address new.block.checkb % Reversed the order of "address" and "organization", added the ":". address output organization "organization" output.check.colon % address output % ":" output % organization output new.block note output fin.entry } FUNCTION {mastersthesis} { output.bibitem format.authors "author" output.check author format.key output % added output.year.check % added new.block format.title "title" output.check new.block "Master's thesis" format.thesis.type output.nonnull school "school" output.check address output new.block note output fin.entry } FUNCTION {misc} { output.bibitem format.authors output author format.key output % added output.year.check % added title howpublished new.block.checkb format.title output new.block howpublished output new.block note output fin.entry } FUNCTION {phdthesis} { output.bibitem format.authors "author" output.check author format.key output % added output.year.check % added new.block format.btitle "title" output.check new.block "Ph.\ D. thesis" format.thesis.type output.nonnull school "school" output.check address output new.block note output fin.entry } FUNCTION {proceedings} { output.bibitem editor empty$ { organization output organization format.key output } % gnp - changed from author format.key { format.editors output.nonnull } if$ % author format.key output % gnp - removed (should be either % editor or organization output.year.check % added (newapa) new.block format.btitle "title" output.check format.bvolume output format.number.series output address output new.sentence organization output publisher output.colon new.block note output fin.entry } FUNCTION {techreport} { output.bibitem format.authors "author" output.check author format.key output % added output.year.check % added new.block format.title "title" output.check new.block format.tr.number output.nonnull institution "institution" output.check address output new.block note output fin.entry } FUNCTION {unpublished} { output.bibitem format.authors "author" output.check author format.key output % added output.year.check % added new.block format.title "title" output.check new.block note "note" output.check fin.entry } FUNCTION {default.type} { misc } MACRO {jan} {"January"} MACRO {feb} {"February"} MACRO {mar} {"March"} MACRO {apr} {"April"} MACRO {may} {"May"} MACRO {jun} {"June"} MACRO {jul} {"July"} MACRO {aug} {"August"} MACRO {sep} {"September"} MACRO {oct} {"October"} MACRO {nov} {"November"} MACRO {dec} {"December"} MACRO {acmcs} {"ACM Computing Surveys"} MACRO {acta} {"Acta Informatica"} MACRO {ai} {"Artificial Intelligence"} MACRO {cacm} {"Communications of the ACM"} MACRO {ibmjrd} {"IBM Journal of Research and Development"} MACRO {ibmsj} {"IBM Systems Journal"} MACRO {ieeese} {"IEEE Transactions on Software Engineering"} MACRO {ieeetc} {"IEEE Transactions on Computers"} MACRO {ieeetcad} {"IEEE Transactions on Computer-Aided Design of Integrated Circuits"} MACRO {ipl} {"Information Processing Letters"} MACRO {jacm} {"Journal of the ACM"} MACRO {jcss} {"Journal of Computer and System Sciences"} MACRO {scp} {"Science of Computer Programming"} MACRO {sicomp} {"SIAM Journal on Computing"} MACRO {tocs} {"ACM Transactions on Computer Systems"} MACRO {tods} {"ACM Transactions on Database Systems"} MACRO {tog} {"ACM Transactions on Graphics"} MACRO {toms} {"ACM Transactions on Mathematical Software"} MACRO {toois} {"ACM Transactions on Office Information Systems"} MACRO {toplas} {"ACM Transactions on Programming Languages and Systems"} MACRO {tcs} {"Theoretical Computer Science"} READ FUNCTION {sortify} { purify$ "l" change.case$ } INTEGERS { len } FUNCTION {chop.word} { 's := 'len := s #1 len substring$ = { s len #1 + global.max$ substring$ } 's if$ } FUNCTION {sort.format.names} { 's := #1 'nameptr := "" s num.names$ 'numnames := numnames 'namesleft := { namesleft #0 > } { nameptr #1 > { " " * } 'skip$ if$ s nameptr "{vv{ } }{ll{ }}{ f{ }}{ jj{ }}" format.name$ 't := nameptr numnames = t "others" = and { " et~al" * } { t sortify * } if$ nameptr #1 + 'nameptr := namesleft #1 - 'namesleft := } while$ } FUNCTION {sort.format.title} { 't := "A " #2 "An " #3 "The " #4 t chop.word chop.word chop.word sortify #1 global.max$ substring$ } FUNCTION {author.sort} { author empty$ { key empty$ { "to sort, need author or key in " cite$ * warning$ "" } { key sortify } if$ } { author sort.format.names } if$ } FUNCTION {editor.sort} { editor empty$ { key empty$ { "to sort, need editor or key in " cite$ * warning$ "" } { key sortify } if$ } { editor sort.format.names } if$ } FUNCTION {author.editor.sort} { author empty$ { "missing author in " cite$ * warning$ editor empty$ { key empty$ { "to sort, need author, editor, or key in " cite$ * warning$ "" } { key sortify } if$ } { editor sort.format.names } if$ } { author sort.format.names } if$ } FUNCTION {author.organization.sort} % % added - GNP. Stack author or organization for sorting (from alpha.bst). % Unlike alpha.bst, we need entire names, not abbreviations % { author empty$ { organization empty$ { key empty$ { "to sort, need author, organization, or key in " cite$ * warning$ "" } { key sortify } if$ } { organization sortify } if$ } { author sort.format.names } if$ } FUNCTION {editor.organization.sort} % % added - GNP. Stack editor or organization for sorting (from alpha.bst). % Unlike alpha.bst, we need entire names, not abbreviations % { editor empty$ { organization empty$ { key empty$ { "to sort, need editor, organization, or key in " cite$ * warning$ "" } { key sortify } if$ } { organization sortify } if$ } { editor sort.format.names } if$ } FUNCTION {presort} % % Presort creates the bibentry's label via a call to calc.label, and then % sorts the entries based on entry type. Chicago.bst adds support for % including organizations as the sort key; the following is stolen from % alpha.bst. % { calc.label sortify % recalculate bibitem label year field.or.null purify$ #-1 #4 substring$ * % add year " " * type$ "book" = type$ "inbook" = or 'author.editor.sort { type$ "proceedings" = 'editor.organization.sort { type$ "manual" = 'author.organization.sort 'author.sort if$ } if$ } if$ #1 entry.max$ substring$ % added for newapa 'sort.label := % added for newapa sort.label % added for newapa * " " * title field.or.null sort.format.title * #1 entry.max$ substring$ 'sort.key$ := } ITERATE {presort} SORT % by label, year, author/editor, title STRINGS { last.label next.extra } INTEGERS { last.extra.num } FUNCTION {initialize.extra.label.stuff} { #0 int.to.chr$ 'last.label := "" 'next.extra := #0 'last.extra.num := } FUNCTION {forward.pass} % % Pass through all entries, comparing current entry to last one. % Need to concatenate year to the stack (done by calc.label) to determine % if two entries are the same (see presort) % { last.label calc.label year field.or.null purify$ #-1 #4 substring$ * % add year #1 entry.max$ substring$ = % are they equal? { last.extra.num #1 + 'last.extra.num := last.extra.num int.to.chr$ 'extra.label := } { "a" chr.to.int$ 'last.extra.num := "" 'extra.label := calc.label year field.or.null purify$ #-1 #4 substring$ * % add year #1 entry.max$ substring$ 'last.label := % assign to last.label } if$ } FUNCTION {reverse.pass} { next.extra "b" = { "a" 'extra.label := } 'skip$ if$ label.year extra.label * 'sort.year := extra.label 'next.extra := } EXECUTE {initialize.extra.label.stuff} ITERATE {forward.pass} REVERSE {reverse.pass} FUNCTION {bib.sort.order} { sort.label " " * year field.or.null sortify * " " * title field.or.null sort.format.title * #1 entry.max$ substring$ 'sort.key$ := } ITERATE {bib.sort.order} SORT % by sort.label, year, title --- giving final bib. order. FUNCTION {begin.bib} { preamble$ empty$ 'skip$ { preamble$ write$ newline$ } if$ "\begin{thebibliography}{}" write$ newline$ } EXECUTE {begin.bib} EXECUTE {init.state.consts} ITERATE {call.type$} FUNCTION {end.bib} { newline$ "\end{thebibliography}" write$ newline$ } EXECUTE {end.bib} scatterplot3d/inst/doc/chicago.sty0000744000175100001440000002474407460735513016771 0ustar hornikusers% -*- LaTeX -*- %%% ==================================================================== %%% @LaTeX-style-file{ %%% author = "Glenn Paulley", %%% version = "4", %%% date = "31 August 1992", %%% time = "09:42:44 199", %%% filename = "chicago.sty", %%% address = "Data Structuring Group %%% Department of Computer Science %%% University of Waterloo %%% Waterloo, Ontario, Canada %%% N2L 3G1", %%% telephone = "(519) 885-1211", %%% FAX = "(519) 885-1208", %%% checksum = "44674 264 1050 10394", %%% email = "gnpaulle@bluebox.uwaterloo.ca", %%% codetable = "ISO/ASCII", %%% keywords = "", %%% supported = "yes", %%% abstract = "Contains the LaTeX style command definitions %%% for the Chicago BibTeX styles chicago.bst and %%% chicagoa.bst. For details, see below.", %%% docstring = "The checksum field above contains a CRC-16 %%% checksum as the first value, followed by the %%% equivalent of the standard UNIX wc (word %%% count) utility output of lines, words, and %%% characters. This is produced by Robert %%% Solovay's checksum utility.", %%% } %%% ==================================================================== % % chicago.sty: Style file for use with bibtex style chicago.bst, for % bibliographies formatted according to the 13th Edition of the Chicago % Manual of Style. % % 'newapa.bst' was made from 'plain.bst', 'named.bst', and 'apalike.bst', % with lots of tweaking to make it look like APA style, along with tips % from Young Ryu and Brian Reiser's modifications of 'apalike.bst'. % newapa.sty formed the basis of this style, chicago.sty. Author-date % references in newapa.bst formed the basis for chicago.bst. Chicagoa.bst % supports annotations. % % Version 4 (August, 1992): % - fixed chicago.bst and chicagoa.bst to handle long author lists in % sorting % - fixed chicago.bst and chicagoa.bst so that missing page numbers in % ``article'' entries are handled correctly % - modified chicago.sty to format entries with 2nd and subsequent lines % indented. % % Citation format: (author-last-name year) % (author-last-name and author-last-name year) % (author-last-name et al. year) % (author-last-name) % author-last-name % author-last-name (year) % (author-last-name and author-last-name) % (author-last-name et al.) % (year) or (year,year) % year or year,year % % Reference list ordering: alphabetical by author or whatever passes % for author in the absence of one. % % This BibTeX style has support for abbreviated author lists and for % year-only citations. This is done by having the citations % actually look like % % \citeauthoryear{full-author-info}{abbrev-author-info}{year} % % The LaTeX style has to have the following (or similar) % % \let\@internalcite\cite % \def\fullcite{\def\citeauthoryear##1##2##3{##1, ##3}\@internalcite} % \def\fullciteA{\def\citeauthoryear##1##2##3{##1}\@internalcite} % \def\shortcite{\def\citeauthoryear##1##2##3{##2, ##3}\@internalcite} % \def\shortciteA{\def\citeauthoryear##1##2##3{##2}\@internalcite} % \def\citeyear{\def\citeauthoryear##1##2##3{##3}\@internalcite} % % ------------------------------------------------------------------------- % This file implements citations for the ``chicago'' bibliography style. % Place it in a file called chicago.sty in the TeX search path. %(Placing it in the same directory as the LaTeX document should also work.) % % This file is a modification of the ``newapa'' LaTeX style, % originally adapted by Steven Spencer from the ``apalike'' LaTeX style. % It was originally modified by Stephen N. Spencer, with further % modifications by Young U. Ryu. % % The ``chicago'' BibTeX bibliography style creates citations with labels: % \citeauthoryear{author-info}{abbrev. author-info}{year} % % These labels are processed by the following LaTeX commands: % % \cite{key} % which produces citations with full author list and year. % eg. (Brown 1978; Jarke, Turner, Stohl, et al. 1985) % \citeNP{key} % which produces citations with full author list and year, but without % enclosing parentheses: % eg. Brown 1978; Jarke, Turner and Stohl 1985 % \citeA{key} % which produces citations with only the full author list. % eg. (Brown; Jarke, Turner and Stohl) % \citeANP{key} % which produces citations with only the full author list, without % parentheses eg. Brown; Jarke, Turner and Stohl % \citeN{key} % which produces citations with the full author list and year, but % can be used as nouns in a sentence; no parentheses appear around % the author names, but only around the year. % eg. Shneiderman (1978) states that...... % \citeN should only be used for a single citation. % \shortcite{key} % which produces citations with abbreviated author list and year. % \shortciteNP{key} % which produces citations with abbreviated author list and year. % \shortciteA{key} % which produces only the abbreviated author list. % \shortciteANP{key} % which produces only the abbreviated author list. % \shortciteN{key} % which produces the abbreviated author list and year, with only the % year in parentheses. Use with only one citation. % \citeyear{key} % which produces the year information only, within parentheses. % \citeyearNP{key} % which produces the year information only. % % Abbreviated author lists use the ``et al.'' construct. % % `NP' means `no parentheses'. % % This LaTeX style file must be used with the ``chicago'' or ``chicagoa'' % (annotated chicago style) BibTeX styles. % \typeout{Using Chicago Manual of Style bibliography: 31 August 1992} % % ------------------------------------------------------------------------- % % Citation macros. % \let\@internalcite\cite % \def\cite{\def\@citeseppen{-1000}% \def\@cite##1##2{(##1\if@tempswa , ##2\fi)}% \def\citeauthoryear##1##2##3{##1 ##3}\@internalcite} \def\citeNP{\def\@citeseppen{-1000}% \def\@cite##1##2{##1\if@tempswa , ##2\fi}% \def\citeauthoryear##1##2##3{##1 ##3}\@internalcite} \def\citeN{\def\@citeseppen{-1000}% \def\@cite##1##2{##1\if@tempswa , ##2)\else{)}\fi}% \def\citeauthoryear##1##2##3{##1 (##3}\@citedata} \def\citeA{\def\@citeseppen{-1000}% \def\@cite##1##2{(##1\if@tempswa , ##2\fi)}% \def\citeauthoryear##1##2##3{##1}\@internalcite} \def\citeANP{\def\@citeseppen{-1000}% \def\@cite##1##2{##1\if@tempswa , ##2\fi}% \def\citeauthoryear##1##2##3{##1}\@internalcite} % \def\shortcite{\def\@citeseppen{-1000}% \def\@cite##1##2{(##1\if@tempswa , ##2\fi)}% \def\citeauthoryear##1##2##3{##2 ##3}\@internalcite} \def\shortciteNP{\def\@citeseppen{-1000}% \def\@cite##1##2{##1\if@tempswa , ##2\fi}% \def\citeauthoryear##1##2##3{##2 ##3}\@internalcite} \def\shortciteN{\def\@citeseppen{-1000}% \def\@cite##1##2{##1\if@tempswa , ##2)\else{)}\fi}% \def\citeauthoryear##1##2##3{##2 (##3}\@citedata} \def\shortciteA{\def\@citeseppen{-1000}% \def\@cite##1##2{(##1\if@tempswa , ##2\fi)}% \def\citeauthoryear##1##2##3{##2}\@internalcite} \def\shortciteANP{\def\@citeseppen{-1000}% \def\@cite##1##2{##1\if@tempswa , ##2\fi}% \def\citeauthoryear##1##2##3{##2}\@internalcite} % \def\citeyear{\def\@citeseppen{-1000}% \def\@cite##1##2{(##1\if@tempswa , ##2\fi)}% \def\citeauthoryear##1##2##3{##3}\@citedata} \def\citeyearNP{\def\@citeseppen{-1000}% \def\@cite##1##2{##1\if@tempswa , ##2\fi}% \def\citeauthoryear##1##2##3{##3}\@citedata} % % \@citedata and \@citedatax: % % Place commas in-between citations in the same \citeyear, \citeyearNP, % \citeN, or \shortciteN command. % Use something like \citeN{ref1,ref2,ref3} and \citeN{ref4} for a list. % \def\@citedata{% \@ifnextchar [{\@tempswatrue\@citedatax}% {\@tempswafalse\@citedatax[]}% } \def\@citedatax[#1]#2{% \if@filesw\immediate\write\@auxout{\string\citation{#2}}\fi% \def\@citea{}\@cite{\@for\@citeb:=#2\do% {\@citea\def\@citea{, }\@ifundefined% by Young {b@\@citeb}{{\bf ?}% \@warning{Citation `\@citeb' on page \thepage \space undefined}}% {\csname b@\@citeb\endcsname}}}{#1}}% % don't box citations, separate with ; and a space % also, make the penalty between citations negative: a good place to break. % \def\@citex[#1]#2{% \if@filesw\immediate\write\@auxout{\string\citation{#2}}\fi% \def\@citea{}\@cite{\@for\@citeb:=#2\do% {\@citea\def\@citea{; }\@ifundefined% by Young {b@\@citeb}{{\bf ?}% \@warning{Citation `\@citeb' on page \thepage \space undefined}}% {\csname b@\@citeb\endcsname}}}{#1}}% % (from apalike.sty) % No labels in the bibliography. % \def\@biblabel#1{} % (from apalike.sty) % Set length of hanging indentation for bibliography entries. % \newlength{\bibhang} \setlength{\bibhang}{2em} % Indent second and subsequent lines of bibliographic entries. Stolen % from openbib.sty: \newblock is set to {}. \newdimen\bibindent \bibindent=1.5em \@ifundefined{refname}% {\@ifundefined{chapter}% {\newcommand{\refname}{References}}% {\newcommand{\refname}{Bibliography}}% }% {}% \@ifundefined{chapter}% {\def\thebibliography#1{\section*{\refname\@mkboth %% {\uppercase{\refname}}{\uppercase{\refname}}}\list {\refname}{\refname}}\list {[\arabic{enumi}]}{\settowidth\labelwidth{[#1]} \leftmargin\labelwidth \advance\leftmargin\labelsep \advance\leftmargin\bibindent \itemindent -\bibindent \listparindent \itemindent \parsep \z@ \usecounter{enumi}} \def\newblock{} \sloppy \sfcode`\.=1000\relax}} {\def\thebibliography#1{\chapter*{\refname\@mkboth {\refname}{\refname}}\list %% {\uppercase{\refname}}{\uppercase{\refname}}}\list {[\arabic{enumi}]}{\settowidth\labelwidth{[#1]} \leftmargin\labelwidth \advance\leftmargin\labelsep \advance\leftmargin\bibindent \itemindent -\bibindent \listparindent \itemindent \parsep \z@ \usecounter{enumi}} \def\newblock{} \sloppy \sfcode`\.=1000\relax}} scatterplot3d/inst/doc/colorcube.pdf0000744000175100001440000003551711542111246017266 0ustar hornikusers%PDF-1.1 % 1 0 obj << /Pages 3 0 R /Type /Catalog >> endobj 2 0 obj << /CreationDate (D:20030116170439) /Producer (R Graphics) >> endobj 3 0 obj << /Count 1 /Kids [ 4 0 R ] /MediaBox [ 0 0 864 432 ] /Type /Pages >> endobj 4 0 obj << /Contents 5 0 R /Parent 3 0 R /Resources 6 0 R /Type /Page >> endobj 5 0 obj << /Length 13578 /Filter /FlateDecode >> stream x}I,;rZڋ.qZ x!Z܀݀ A2YA2X&/'81|׿z[)z8k~ϯPk|/R?m+tO/;_^#5^kIV]DNh&R2oL~'o|z'3~YȏuLo_ٽM s+5 %o,o_TNDٿkۖz3@*/}R*k:6}h񋏶 C{6XxVz( sA\77cMXX|*~ o\ψyߖFTi(~PhRӮJV>:r}[Nן}}y}?{FLo*_ןR%~xO?KR㪿?!sUS_2_۟?';|o1B~k寯zwb8$dZ2鴒+;1P^ptF( t2yƔdt.oKP2aaNAE! ]i[b0w|S,B :ac&}_(jTT nj!)ZwP'ʪvjF-3WT4ANr6yJNƕjS)e{Kt463}Gɘۯ:c~ܶ-YPW&d<~oo >k~'o& _׃kW/Y~!s-=7i׿}B/kV1eOL:lv0e2qwOXZ~Z9]j*-MV&gazێV%\rږԖ@9F_=>;iP:2!>il!L넟ֆUx8 >!>FY˞l!jV٘M\fִSح |۵L'1A\t>.U˺{2 C - * P&hގ铱筬6;kTKYf> }^dl9E˄x:lkc6N;P&ШS.\(QA"'zn[dYK-DAr/P0^9-U/iK`a[PyaIC?6†ˣ vpZ6yϧD'nw41WEž֭3" twZ&a#rdI7N,RWQؙC^\ͮy<_&AK8` 2y+_GQh t ɼnxbJR8CZy\.kIöa ? *q[d=vA}K 9iXFּM?Jsf -yX ghm]ht96+-JʄV6@aWѨ u-k4z s=`5˄tV(XW~IP̢i#AOLP|SIF8O-'&ZeJ0e*NLת dS6el뢏h)O1)D?hՃewlӯž!ThtOnA83F_>nXA􉖒kLGe[*2̿2@hm1 ;3*!mB9Q35(T1Ǽh^#LVk8Kvaf6Io7ra{`a[덶{5$`ۃ7\AW\=*&)R-PE/JײZEtѾBG'-"t,N/ǘ8yZp6_PH2p=^TSg*ao뚗1ۆfhƝ znC0r6O9f:a~^Ѳ"!d;^nkÀW *a0_lZJ=y:$ 7k)woRث"!ޱvax)v)];hܪ7E-XC &aq v lJH* (،Y Gh6:A#)ԒUo)F(6z'U}gkJW974r^L֞m>p9#Š쭫5-ZR]3IN Wa\$S,N* O.FSt4~ЎChZ4<&Eڡ64O#,Nb :pj4Ώ W\RR>(c3ڂ"+4t{l@Gȫ6Ma(3-@~i o$j[8 ̌s8reMbfedi)b6ț# 4؜bRĦ_!qFd"֛{[PȒ.,AK˺7+o 6`xdX֛ަȚC$P{ o??j;(*λ&W M (&*T,ǛĽ{֠"%{~ S,9BxY?1oAVf ˱ zHmlSb4mQ=Ȣnʟi!V1 Iieɧy3s՟!ϖUf"óڤt^oMϸzUhZe%4Plf%_V暴:C&; ~`)p4e=t^%,yj k;ΨIkF!e.九@Z6ltW m"^@,Y#WМhgꔙ#^J%)g[X4}Wx\e^V8}qV 'i]LBlmQ G:( FvfM38 Ehãf h"%?GߙaycR6`fC`"=Jܷ Lb@ܘBǿ=$rJ8vV D*rhxtջBSe)N`l:Ӭ3#VD6*!gǧ!foz߬ŨUVM.g)(G^4ٜMk SBӂ8SB8}Ki@>-eSY;TR}b-:=BPS` V.{sm]bA}zn a lخ8eʆd(:n'xK9Ma6p±O l t&Αb uX=㷱)R;,Ep3ZYŸ<_'hRbasbq/He|2L~fZbKkțnRup4 @;MD, I3ߢXG2C>w2mC$cpڀڙ]J󁟆pm{QF0e*yMS))j9pBeE[&pےK}2KsӅfv[B_'J؜p:XXK%+Jx6s N&Pk8xO>>;`':L̀:=y@Iysxq{O{1ZB?Adn?DvP6ҴM1GP 5cϭEPPCPA+й |INHIgx'ˬ3|tT *ț+[ Z;8Bk퐴4$2a\ v  4*LP#g0ue_Oւ@Ės* lpV6"l%?%0O x[{nUDh{-aD{{EÛj}TbբД9 4HB9icy`:SDŇ1ISxvqIB"^Sxz:kyڮx"k'F}I0Ӌ⵬#hC4&Sy*d+2:q }M2ۗ 2_n p0Dpnm=yg)hQk_'lS0gkɋWA6.5p7B+XȈƝ ȶY1uD!4 O6i!Mr;v]&a/,hAc<۔e+AZDdVf '-C:Nkz!` ]a 1BqZ}b͕(H7[-Sw@Q&n֪[VCdٯ6)я"!Mq-k1a~*zKP)O#AX8VST{?ڀ&9\q̗JB-kB]~C&Q 8:#ˉb vMt$^5\eԣ/ ?+\INCTᚏPIv\ڸE 6lUzQ9k7#֊:O&:8`}-£1k8 Cmg,蠏 uPI&dd輮S-@wAAQ?ay?76Q܎m چg޾N8reF(ͧF4~E3]s)Z{b ՝Y SzLhzxjGY"E)$:\%MN[yiq]1` auBM-՞lhh\Y L^sO @7tRkg@4+H2xk2 />yE%Ԡ埫ڋ2F =XDoڣœ?o|M̓"Giu#LzbmbhcDz*:*Tps=%oԟs;2 * ow.pPüc_'$I6M6V dJ][Iۀso#\mjyj dCl3Sq?# )(,Som f>\-jMh_Ѳg;䧣 ΰp*m s=͇XWfoT.{*4Y ex*6]=5k o5+ZRN{6綆`/4E_'[]*Pʁ Dʴ "s7 6]uP$2#{ǒ&tǧbjǼILjH p_O&&Vگ6##v0uzٳhFpJ! 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American Statistical Association}} } @STRING{JCGS = {{Journal of Computational and Graphical Statistics}} } @STRING{SFB475 = {{SFB 475, Department of Statistics, University of Dortmund, Germany}} } @STRING{NY = {{New York}} } @INPROCEEDINGS{AdlerNenadic2003, AUTHOR = "Adler,~D. and Nenadic,~O. and Zucchini,~W.", YEAR = "2003", TITLE = "RGL: A R-library for 3D visualization with OpenGL.", BOOKTITLE = {{Proceedings of the 35th Symposium of the Interface: Computing Science and Statistics}}, ADDRESS = "Salt Lake City", } @BOOK{becker84, AUTHOR = "Becker,~R.~A. and Chambers,~J.~M.", TITLE = {S. {A}n Interactive Environment for Data Analysis and Graphics}, PUBLISHER = "Wadsworth and Brooks/Cole", address = "Monterey", YEAR = 1984, NOTE = "[the 'brown book']" } @BOOK{becker85, AUTHOR = "Becker,~R.~A. and Chambers,~J.~M.", TITLE = {Extending the S--System}, PUBLISHER = "Wadsworth and Brooks/Cole", address = "Monterey", YEAR = 1985 } @BOOK{becker88, AUTHOR = "Becker,~R.~A. and Chambers,~J.~M. and Wilks,~A.~R.", TITLE = {The {NEW S} Language --- a Programming Environment for Data Analysis and Graphics}, PUBLISHER = "Chapman \& Hall", address = NY, YEAR = 1988, NOTE = "[the 'blue book']" } @ARTICLE{becker96, AUTHOR = "Becker,~R.~A. and Cleveland,~W.~S. and Shyu,~M.", TITLE = {The Visual Design and Control of Trellis Display}, JOURNAL = JCGS, YEAR = 1996, VOLUME = 5, NUMBER = 2, pages = "123--155" } @BOOK{brockwell, AUTHOR = "Brockwell,~P.~J. and Davis,~R.~A.", TITLE = {Time Series: Theory and Methods}, PUBLISHER = "Springer", ADDRESS = NY, YEAR = "1991", EDITION = "2nd" } @TECHREPORT{busse, AUTHOR = {Busse,~A.~M. and H{\"u}sken,~M. and Stagge,~P.}, TITLE = {{Offline-Analyse eines BTA-Tiefbohrprozesses}}, INSTITUTION = SFB475, YEAR = "2001", number = "16/2001", NOTE = {See also: \url{http://www.statistik.tu-dortmund.de/sfb475/en/tr-e.html}} } @BOOK{chambers92, AUTHOR = "Chambers,~J.~M. and Hastie,~T.~J.", YEAR = 1992, TITLE = {Statistical Models in {S}}, ADDRESS = NY, PUBLISHER = "Chapman \& Hall", NOTE = "[the 'white book']" } @BOOK{chambers98, AUTHOR = "Chambers,~J.~M.", YEAR = "1998", TITLE = {Programming with Data. A Guide to the {S} Language.}, ADDRESS = NY, PUBLISHER = "Springer", NOTE = "[the 'green book']" } @BOOK{cleveland, AUTHOR = "Cleveland,~W.~S.", TITLE = {{Visualizing Data}}, PUBLISHER = "Hobart Press", ADDRESS = "Summit, NJ", YEAR = "1993" } @ARTICLE{gentleman, AUTHOR = "Gentleman,~R. and Ihaka,~R.", TITLE = {{Lexical Scope and Statistical Computing}}, JOURNAL = JCGS, YEAR = "2000", VOLUME = "9", NUMBER = "3", pages = "491--508" } @conference{heilemann, author = {Heilemann,~U. and M\"{u}nch,~H.~J.}, title = {{West German Business Cycles 1963--1994: A Multivariate Discriminant Analysis}}, booktitle = {{CIRET--Conference in Singapore, CIRET--Studien 50}}, year = "1996" } @ARTICLE{ihaka, AUTHOR = "Ihaka,~R. and Gentleman,~R.", TITLE = {{R: A Language for Data Analysis and Graphics}}, JOURNAL = JCGS, YEAR = "1996", VOLUME = "5", NUMBER = "3", pages = "299--314" } @ARTICLE{knapp02, AUTHOR = "Knapp,~G. and Hartung,~J.", YEAR = "2003", TITLE = {Improved Tests for a Random Effects Meta-Regression with a Single Covariate}, JOURNAL = {Statistics in Medicine}, VOLUME = "22", NUMBER = "17", PAGES = "2693--2710" } @BOOK{knuth, author = "Knuth,~D.~E.", title= {{The {\TeX}book}}, publisher = "Addison-Wesley", year = "1984", benutzt = "NEIN" } @MASTERSTHESIS{ligges00, author = "Ligges,~U.", title = {{Identifikation lokal station{\"a}rer Anteile in Gesangszeitreihen}}, school = {{F}achbereich {S}tatistik, {U}niversit{\"a}t {D}ortmund}, year = "2000", type = {{Diploma Thesis}}, address = {Germany}, benutzt = "ja" } @TECHREPORT{ligges02, AUTHOR = "Ligges,~U. and Weihs,~C. and Hasse-Becker,~P.", TITLE = {{Detection of Locally Stationary Segments in Time Series -- Algorithms and Applications}}, INSTITUTION = SFB475, YEAR = "2002", number = "11/2002", NOTE = {See also: \url{http://www.statistik.tu-dortmund.de/sfb475/en/tr-e.html}}, benutzt = "ja" } @INPROCEEDINGS{ligges:cs02, AUTHOR = "Ligges,~U. and Weihs,~C. and Hasse-Becker,~P.", TITLE = {{Detection of Locally Stationary Segments in Time Series}}, YEAR = "2002", booktitle = {{Proceedings of CompStat2002}}, organization ={{Humboldt Universit{\"a}t zu Berlin}}, ADDRESS = "Berlin", benutzt = "ja" } @book{lucas87, author = "Lucas,~R.~E.", year = "1987", title = {{Models of Business Cycles}}, publisher = "Basil Blackwell", address = NY, benutzt = "ja" } @INPROCEEDINGS{murdoch, author = {Duncan Murdoch}, title = {{RGL: An R Interface to OpenGL}}, booktitle = {{Proceedings of the 2nd International Workshop on Distributed Statistical Computing, March 15--17}}, organization= {{Technische Universit\"at Wien}}, ADDRESS = "Vienna", editor = {Kurt Hornik and Friedrich Leisch}, year = {2001}, note = {ISSN~1609-395X, \url{http://www.ci.tuwien.ac.at/Conferences/DSC-2001/Proceedings/}} } @ARTICLE{murrell00, AUTHOR = "Murrell,~P. and Ihaka,~R.", TITLE = {An Approach to Providing Mathematical Annotation in Plots}, JOURNAL = JCGS, YEAR = 2000, VOLUME = 9, NUMBER = 3, pages = "582--599" } @INPROCEEDINGS{murrell01, AUTHOR = "Murrell,~P.", title = {{R Lattice Graphics}}, booktitle = {{Proceedings of the 2nd International Workshop on Distributed Statistical Computing, March 15--17}}, organization= {{Technische Universit\"at Wien}}, ADDRESS = "Vienna", editor = {Kurt Hornik and Friedrich Leisch}, year = {2001}, note = {ISSN~1609-395X, \url{http://www.ci.tuwien.ac.at/Conferences/DSC-2001/Proceedings/}} } @ARTICLE{picard, AUTHOR = "Picard,~D.", YEAR = "1985", TITLE = {Testing and Estimating Change--Points in Time Series}, JOURNAL = {Advances in Applied Probability}, VOLUME = "17", PAGES = "841--867" } @ARTICLE{priestley, AUTHOR = "Priestley,~M.~B. and Subba Rao,~T.", YEAR = "1969", TITLE = {A Test for Non-Stationarity of Time Series}, JOURNAL = {Journal of the Royal Statistical Society, Series B}, VOLUME = "31", PAGES = "140--149" } @MANUAL{r-data150, author = {R Development Core Team}, title = {R Data Import/Export, {\upshape Version 1.5.0}}, YEAR = 2002, ORGANIZATION = {{R--Project}}, NOTE = {ISBN~3-901167-53-6, \url{http://CRAN.R-project.org/manuals.html}}, benutzt = "NEIN" } @MANUAL{r-ext, author = {{R Development Core Team}}, title = {Writing {R} Extensions, {\upshape Version 2.0.1}}, YEAR = 2004, ORGANIZATION ={{R--Project}}, NOTE = {ISBN~3-900051-11-9, \url{http://CRAN.R-project.org/manuals.html}} } @MANUAL{r-faq, author = "Hornik,~K.", title = {{R FAQ}, {\upshape Version 2.0.2004-11-14}}, YEAR = 2004, ORGANIZATION ={{R--Project}}, NOTE = {ISBN~3-900051-08-9, \url{http://CRAN.R-project.org/manuals.html}} } @MANUAL{r-inst150, author = {{R Development Core Team}}, title = {R Installation and Administration, {\upshape Version 1.5.0}}, YEAR = 2002, ORGANIZATION ={{R--Project}}, NOTE = {ISBN~3-901167-52-8, \url{http://CRAN.R-project.org/manuals.html}}, benutzt = "NEIN" } @MANUAL{r-intro150, author = "Venables,~W.~N. and Smith,~D.~M. and {the R Development Core Team}", title = {An Introduction to {R}, {\upshape Version 1.5.0}}, subtitle = {{Notes on R: A Programming Environment for Data Analysis and Graphics}}, YEAR = 2002, ORGANIZATION ={{R--Project}}, NOTE = {ISBN~3-901167-55-2, \url{http://CRAN.R-project.org/manuals.html}}, benutzt = "NEIN" } @MANUAL{r-lang, author = {{R Development Core Team}}, title = {{R Language Definition,} {\upshape Version 2.0.1}}, YEAR = 2004, ORGANIZATION ={{R--Project}}, NOTE = {ISBN~3-900051-13-5, \url{http://CRAN.R-project.org/manuals.html}} } @Manual{r-ref, title = {R: A language and environment for statistical computing}, author = {{R Development Core Team}}, organization = {R Foundation for Statistical Computing}, address = {Vienna, Austria}, year = {2004}, note = {{ISBN} 3-900051-07-0}, url = {http://www.R-project.org}, } @BOOK{ripley98, AUTHOR = {Venables,~W.~N. and Ripley,~B.~D.}, TITLE = {Modern Applied Statistics with {S-PLUS}}, EDITION = 2, YEAR = 1998, ADDRESS = NY, PUBLISHER = "Springer", benutzt = "NEIN" } @BOOK{ripley00, AUTHOR = {Venables,~W.~N. and Ripley,~B.~D.}, TITLE = {{S Programming}}, YEAR = "2000", ADDRESS = NY, PUBLISHER = "Springer", benutzt = "NEIN" } @ARTICLE{sarkar02, AUTHOR = "Sarkar,~D.", YEAR = "2002", TITLE = {{Lattice: An Implementation of Trellis Graphics in R}}, JOURNAL = {{R News}}, VOLUME = "2", NUMBER = "2", pages = {19--23}, ISSN = {1609-3631}, URL = {http://CRAN.R-project.org/doc/Rnews/} } @BOOK{schlittgen, AUTHOR = {Schlittgen,~R. and Streitberg,~B.}, YEAR = "1997", TITLE = {Zeitreihenanalyse}, ADDRESS = "M{\"u}nchen", PUBLISHER = {Oldenbourg}, benutzt = "ja" } @INPROCEEDINGS{scholkopf, AUTHOR = "Sch{\"o}lkopf,~B.", YEAR = 1998, TITLE = {{Support-Vektor-Lernen}}, BOOKTITLE = {{G. Hotz et al. (ed.): Ausgezeichnete Informatikdissertationen}}, PAGES = "135--150", ADDRESS = "Stuttgart", PUBLISHER = "Teubner" , benutzt = "ja" } @MANUAL{schwaighofer, AUTHOR = "Schwaighofer,~A.", YEAR = "2002", TITLE = {{SVM toolbox for Matlab}}, NOTE = {\url{http://www.igi.tugraz.at/aschwaig/software.html}}, benutzt = "ja" } @BOOK{seidner, AUTHOR = "Seidner,~W. and Wendler,~J.", TITLE = {{D}ie {S}{\"a}ngerstimme}, PUBLISHER = "Henschel", address = "Berlin", YEAR = "1997", benutzt = "ja" } @TECHREPORT{sondhauss, AUTHOR = "Sondhau{\ss},~U. and Weihs,~C. and Ligges,~U.", YEAR = 2002, TITLE = {Prediction of Notes from Vocal Time Series}, INSTITUTION = SFB475, NOTE = {See also: \url{http://www.statistik.tu-dortmund.de/sfb475/en/tr-e.html}}, benutzt = "ja" } @INPROCEEDINGS{swayne91, AUTHOR = "Swayne,~D.~F. and Buja,~A. and Hubbell,~N.", TITLE = {{XG}obi meets {S}: Integrating Software for Data Analysis}, BOOKTITLE = {Computing Science and Statistics: Proceedings of the 23rd Symposium on the Interface}, YEAR = 1991, pages = "430--434", ORGANIZATION ={Interface Foundation of North America, Inc.}, ADDRESS = {Fairfax Station, VA}, benutzt = "ja" } @ARTICLE{swayne98, AUTHOR = "Swayne,~D.~F. and Cook,~D. and Buja,~A.", TITLE = {XGobi: Interactive Dynamic Graphics in the {X} Window System}, JOURNAL = JCGS, YEAR = 1998, VOLUME = 7, NUMBER = 1, pages = "113--130", NOTE = "See also \url{http://www.research.att.com/areas/stat/xgobi/}" } @article{swayne02, Author = "Swayne,~D.~F. and Temple Lang,~D. and Buja,~A. and Cook,~D.", Year = 2002, Title = {{GGobi}: Evolving from {XGobi} into an Extensible Framework for Interactive Data Visualization}, Journal= JCGS, Note= "(To appear)" } @article{temple00, author = "Temple Lang,~D.", title = {{The Omegahat Environment: New Possibilities for Statistical Computing}}, journal = JCGS, year = 2000, volume = 9, number = 3, pages = "423--451", benutzt = "ja" } @InProceedings{temple01, Author = "Temple Lang,~D. and Swayne,~D.~F.", Title = {{GGobi meets R}: an Extensible Environment for Interactive Dynamic Data Visualization}, booktitle = {Proceedings of the 2nd International Workshop on Distributed Statistical Computing}, date = {March 15--17}, year = 2001, organization = {{Technische Universit\"at Wien}}, ADDRESS = "Vienna", editor = {Kurt Hornik and Friedrich Leisch}, note = {ISSN~1609-395X, \url{http://www.ci.tuwien.ac.at/Conferences/DSC-2001/Proceedings/}}, benutzt = "ja" } @TECHREPORT{theis99, AUTHOR = {Theis,~W. and Vogtl{\"a}nder,~K. and Weihs,~C.}, TITLE = {Descriptive Studies on Stylized Facts of the German Business Cycle}, INSTITUTION = SFB475, YEAR = "1999", number = "45/1999", NOTE = {See also: \url{http://www.statistik.tu-dortmund.de/sfb475/en/tr-e.html}}, benutzt = "ja" } @book{tong93, author = "Tong,~H.", title = {Non-linear Time Series, A Dynamical System Approach}, series = "Oxford Statistical Science Series", publisher = "Oxford University Press", address = NY, year = 1993, benutzt = "ja" } @BOOK{trenkler, AUTHOR = "B{\"u}ning,~H. and Trenkler,~G.", YEAR = 1994, TITLE = {{Nichtparametrische statistische Methoden}}, ADDRESS = "Berlin", PUBLISHER = {{de~Gruyter}}, benutzt = "ja" } @BOOK{vapnik, AUTHOR = "Vapnik,~V.", YEAR = 1995, TITLE = {The Nature of Statistical Learning Theory}, ADDRESS = NY, PUBLISHER = "Springer", benutzt = "ja" } @INPROCEEDINGS{weihs, AUTHOR = "Weihs,~C. and Berghoff,~S. and Hasse-Becker,~P. and Ligges,~U.", EDITOR = "Kunert,~J. and Trenkler,~G.", BOOKTITLE = {{Mathematical Statistics and Biometrical Applications}}, TITLE = {{Assessment of Purity of Intonation in Singing Presentations by Discriminant Analysis}}, pages = "395--410", PUBLISHER = "Lohmar: Josef Eul Verlag", YEAR = 2001, benutzt = "ja" } @ARTICLE{weinert, AUTHOR = "Weinert,~K. and Webber,~O. and Busse,~A.~M. and H{\"u}sken,~M. and Mehnen,~J. and Stagge~P.", TITLE = {{In die Tiefe: Koordinierter Einsatz von Sensorik und Statistik zur Analyse und Modellierung von BTA-Tiefbohrprozessen}}, JOURNAL = {{Spur,~G. (ed.): ZWF, Zeitschrift f{\"u}r wirtschaftlichen Fabrikbetrieb}}, YEAR = 2001, volume = 5, pages = "299--314", address = "M{\"u}nchen", PUBLISHER = "Carl Hanser Verlag", benutzt = "ja" } scatterplot3d/inst/doc/meta.pdf0000744000175100001440000004730407476774072016263 0ustar hornikusers%PDF-1.1 % 1 0 obj << /CreationDate (D:20020604001402) /Producer (R Graphics) >> endobj 2 0 obj << /Type /Catalog /Pages 3 0 R >> endobj 4 0 obj << /ProcSet [/PDF /Text] /Font << /F1 6 0 R /F2 7 0 R /F3 8 0 R /F4 9 0 R /F5 10 0 R /F6 11 0 R >> >> endobj 5 0 obj << /Type /Encoding /BaseEncoding /PDFDocEncoding /Differences [ 45/minus 96/quoteleft 144/dotlessi /grave /acute /circumflex /tilde /macron /breve /dotaccent /dieresis /.notdef /ring /cedilla /.notdef /hungarumlaut /ogonek /caron /space] >> endobj 6 0 obj << /Type /Font /Subtype /Type1 /Name /F1 /BaseFont /Helvetica /Encoding 5 0 R >> endobj 7 0 obj << /Type /Font /Subtype /Type1 /Name /F2 /BaseFont /Helvetica-Bold /Encoding 5 0 R >> endobj 8 0 obj 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scatterplot3d/inst/doc/s3d.Rnw0000744000175100001440000000346211544577566016020 0ustar hornikusers%\VignetteIndexEntry{Scatterplot3d - an R Package for Visualizing Multivariate Data} \include{SFBs3d_Def} \begin{document} \begin{center} \vspace*{7 mm}{\Large\bf Scatterplot3d -- an \RR\ package for Visualizing Multivariate Data} \vspace{22 mm}{\large Uwe Ligges and Martin M\"achler}\vspace{7 mm} \emph{\small \begin{tabular}{c@{\extracolsep{5mm}}cc} Fachbereich Statistik & & Seminar f\"ur Statistik\\ Universit\"at Dortmund & & ETH Z\"urich \\ 44221 Dortmund & & CH-8092 Z\"urich\\ Germany & & Switzerland \end{tabular}}\end{center}\vspace{30 mm} Parts of this vignette have been published previously by the Journal of Statistical Software:\\ Ligges, U. and M\"achler, M. (2003): Scatterplot3d -- an \RR\ Package for Visualizing Multivariate Data. {\em Journal of Statistical Software} 8(11), 1--20. \vspace{5 mm} {\bf Abstract \label{abstract}} \emph{Scatterplot3d} is an \RR\ package for the visualization of multivariate data in a three dimensional space. \RR\ is a ``language for data analysis and graphics''. %% kein Paragraph in kurzem Abstract In this paper we discuss the features % advantages of the package. It is designed by exclusively making use of already existing functions of \RR\ and its graphics system and thus shows the extensibility of the \RR\ graphics system. Additionally some examples on generated and real world data are provided, as well as the source code and the help page of \sdd . \input{SFBs3d_Intro} \input{SFBs3d_Design} \input{SFBs3d_Extend} \input{SFBs3d_Examples} \input{SFBs3d_Related} \input{SFBs3d_Conclusion} \bibliographystyle{chicago} \bibliography{ligges} \clearpage \begin{appendix} \section*{Appendix -- help page} \small \input{scatterplot3d-help} \end{appendix} \end{document} scatterplot3d/inst/doc/scatterplot3d-help.tex0000744000175100001440000002354510743373763021077 0ustar hornikusers\HeaderA{scatterplot3d}{3D Scatter Plot}{scatterplot3d} \keyword{hplot}{scatterplot3d} \begin{Description}\relax Plots a three dimensional (3D) point cloud. \end{Description} \begin{Usage} \begin{verbatim} scatterplot3d(x, y=NULL, z=NULL, color=par("col"), pch=NULL, main=NULL, sub=NULL, xlim=NULL, ylim=NULL, zlim=NULL, xlab=NULL, ylab=NULL, zlab=NULL, scale.y=1, angle=40, axis=TRUE, tick.marks=TRUE, label.tick.marks=TRUE, x.ticklabs=NULL, y.ticklabs=NULL, z.ticklabs=NULL, y.margin.add=0, grid=TRUE, box=TRUE, lab=par("lab"), lab.z=mean(lab[1:2]), type=par("type"), highlight.3d=FALSE, mar=c(5,3,4,3)+0.1, col.axis=par("col.axis"), col.grid="grey", col.lab=par("col.lab"), cex.symbols=par("cex"), cex.axis=par("cex.axis"), cex.lab=0.8 * par("cex.lab"), font.axis=par("font.axis"), font.lab=par("font.lab"), lty.axis=par("lty"), lty.grid=par("lty"), lty.hide=NULL, log="", ...) \end{verbatim} \end{Usage} \begin{Arguments} \begin{ldescription} \item[\code{x}] the coordinates of points in the plot. \item[\code{y}] the y coordinates of points in the plot, optional if \code{x} is an appropriate structure. \item[\code{z}] the z coordinates of points in the plot, optional if \code{x} is an appropriate structure. \item[\code{color}] colors of points in the plot, optional if \code{x} is an appropriate structure. Will be ignored if \code{highlight.3d = TRUE}. \item[\code{pch}] plotting "character", i.e. symbol to use. \item[\code{main}] an overall title for the plot. \item[\code{sub}] sub-title. \item[\code{xlim, ylim, zlim}] the x, y and z limits (min, max) of the plot. Note that setting enlarged limits may not work as exactly as expected (a known but unfixed bug). \item[\code{xlab, ylab, zlab}] titles for the x, y and z axis. \item[\code{scale.y}] scale of y axis related to x- and z axis. \item[\code{angle}] angle between x and y axis (Attention: result depends on scaling. For 180 < angle < 360 the returned functions \code{xyz.convert} and \code{points3d} will not work properly.). \item[\code{axis}] a logical value indicating whether axes should be drawn on the plot. \item[\code{tick.marks}] a logical value indicating whether tick marks should be drawn on the plot (only if \code{axis = TRUE}). \item[\code{label.tick.marks}] a logical value indicating whether tick marks should be labeled on the plot (only if \code{axis = TRUE} and \code{tick.marks = TRUE}). \item[\code{x.ticklabs, y.ticklabs, z.ticklabs}] vector of tick mark labels. \item[\code{y.margin.add}] add additional space between tick mark labels and axis label of the y axis \item[\code{grid}] a logical value indicating whether a grid should be drawn on the plot. \item[\code{box}] a logical value indicating whether a box should be drawn around the plot. \item[\code{lab}] a numerical vector of the form c(x, y, len). The values of x and y give the (approximate) number of tickmarks on the x and y axes. \item[\code{lab.z}] the same as \code{lab}, but for z axis. \item[\code{type}] character indicating the type of plot: "p" for points, "l" for lines, "h" for vertical lines to x-y-plane, etc. \item[\code{highlight.3d}] points will be drawn in different colors related to y coordinates (only if \code{type = "p"} or \code{type = "h"}, else \code{color} will be used).\\ On some devices not all colors can be displayed. In this case try the postscript device or use \code{highlight.3d = FALSE}. \item[\code{mar}] A numerical vector of the form c(bottom, left, top, right) which gives the lines of margin to be specified on the four sides of the plot. \item[\code{col.axis, col.grid, col.lab}] the color to be used for axis / grid / axis labels. \item[\code{cex.symbols, cex.axis, cex.lab}] the magnification to be used for point symbols, axis annotation, labels relative to the current. \item[\code{font.axis, font.lab}] the font to be used for axis annotation / labels. \item[\code{lty.axis, lty.grid}] the line type to be used for axis / grid. \item[\code{lty.hide}] line style used to plot \sQuote{non-visible} edges (defaults of the \code{lty.axis} style) \item[\code{log}] Not yet implemented! A character string which contains "x" (if the x axis is to be logarithmic), "y", "z", "xy", "xz", "yz", "xyz". \item[\code{...}] more graphical parameters can be given as arguments, \code{pch = 16} or \code{pch = 20} may be nice. \end{ldescription} \end{Arguments} \begin{Value} \begin{ldescription} \item[\code{xyz.convert}] function which converts coordinates from 3D (x, y, z) to 2D-projection (x, y) of \code{scatterplot3d}. Useful to plot objects into existing plot. \item[\code{points3d}] function which draws points or lines into the existing plot. \item[\code{plane3d}] function which draws a plane into the existing plot: \code{plane3d(Intercept, x.coef = NULL, y.coef = NULL, lty = "dashed", lty.box = NULL, ...)}. Instead of \code{Intercept} a vector containing 3 elements or an (g)lm object can be specified. The argument \code{lty.box} allows to set a different line style for the intersecting lines in the box's walls. \item[\code{box3d}] function which "refreshes" the box surrounding the plot. \end{ldescription} \end{Value} \begin{Note}\relax Some graphical parameters should only be set as arguments in \code{scatterplot3d} but not in a previous \code{\LinkA{par}{par}()} call. One of these is \code{mar}, which is also non-standard in another way: Users who want to extend an existing \code{scatterplot3d} graphic with another function than \code{points3d}, \code{plane3d} or \code{box3d}, should consider to set \code{par(mar = c(b, l, t, r))} to the value of \code{mar} used in \code{scatterplot3d}, which defaults to \code{c(5, 3, 4, 3) + 0.1}. Other \code{par} arguments may be split into several arguments in \code{scatterplot3d}, e.g., for specifying the line type. And finally some of \code{par} arguments do not apply here, e.g., many of those for axis calculation. So we recommend to try the specification of graphical parameters at first as arguments in \code{scatterplot3d} and only if needed as arguments in previous \code{par()} call. \end{Note} \begin{Author}\relax Uwe Ligges \email{ligges@statistik.tu-dortmund.de}; \url{http://www.statistik.tu-dortmund.de/~ligges}. \end{Author} \begin{References}\relax Ligges, U., and Maechler, M. (2003): Scatterplot3d -- an R Package for Visualizing Multivariate Data. \emph{Journal of Statistical Software} 8(11), 1--20. \url{http://www.jstatsoft.org/} \end{References} \begin{SeeAlso}\relax \code{\LinkA{persp}{persp}}, \code{\LinkA{plot}{plot}}, \code{\LinkA{par}{par}}. \end{SeeAlso} \begin{Examples} \begin{ExampleCode} ## On some devices not all colors can be displayed. ## Try the postscript device or use highlight.3d = FALSE. ## example 1 z <- seq(-10, 10, 0.01) x <- cos(z) y <- sin(z) scatterplot3d(x, y, z, highlight.3d=TRUE, col.axis="blue", col.grid="lightblue", main="scatterplot3d - 1", pch=20) ## example 2 temp <- seq(-pi, 0, length = 50) x <- c(rep(1, 50) %*% t(cos(temp))) y <- c(cos(temp) %*% t(sin(temp))) z <- c(sin(temp) %*% t(sin(temp))) scatterplot3d(x, y, z, highlight.3d=TRUE, col.axis="blue", col.grid="lightblue", main="scatterplot3d - 2", pch=20) ## example 3 temp <- seq(-pi, 0, length = 50) x <- c(rep(1, 50) %*% t(cos(temp))) y <- c(cos(temp) %*% t(sin(temp))) z <- 10 * c(sin(temp) %*% t(sin(temp))) color <- rep("green", length(x)) temp <- seq(-10, 10, 0.01) x <- c(x, cos(temp)) y <- c(y, sin(temp)) z <- c(z, temp) color <- c(color, rep("red", length(temp))) scatterplot3d(x, y, z, color, pch=20, zlim=c(-2, 10), main="scatterplot3d - 3") ## example 4 my.mat <- matrix(runif(25), nrow=5) dimnames(my.mat) <- list(LETTERS[1:5], letters[11:15]) my.mat # the matrix we want to plot ... s3d.dat <- data.frame(cols=as.vector(col(my.mat)), rows=as.vector(row(my.mat)), value=as.vector(my.mat)) scatterplot3d(s3d.dat, type="h", lwd=5, pch=" ", x.ticklabs=colnames(my.mat), y.ticklabs=rownames(my.mat), color=grey(25:1/40), main="scatterplot3d - 4") ## example 5 data(trees) s3d <- scatterplot3d(trees, type="h", highlight.3d=TRUE, angle=55, scale.y=0.7, pch=16, main="scatterplot3d - 5") # Now adding some points to the "scatterplot3d" s3d$points3d(seq(10,20,2), seq(85,60,-5), seq(60,10,-10), col="blue", type="h", pch=16) # Now adding a regression plane to the "scatterplot3d" attach(trees) my.lm <- lm(Volume ~ Girth + Height) s3d$plane3d(my.lm, lty.box = "solid") ## example 6; by Martin Maechler cubedraw <- function(res3d, min = 0, max = 255, cex = 2, text. = FALSE) { ## Purpose: Draw nice cube with corners cube01 <- rbind(c(0,0,1), 0, c(1,0,0), c(1,1,0), 1, c(0,1,1), # < 6 outer c(1,0,1), c(0,1,0)) # <- "inner": fore- & back-ground cub <- min + (max-min)* cube01 ## visibile corners + lines: res3d$points3d(cub[c(1:6,1,7,3,7,5) ,], cex = cex, type = 'b', lty = 1) ## hidden corner + lines res3d$points3d(cub[c(2,8,4,8,6), ], cex = cex, type = 'b', lty = 3) if(text.)## debug text(res3d$xyz.convert(cub), labels=1:nrow(cub), col='tomato', cex=2) } ## 6 a) The named colors in R, i.e. colors() cc <- colors() crgb <- t(col2rgb(cc)) par(xpd = TRUE) rr <- scatterplot3d(crgb, color = cc, box = FALSE, angle = 24, xlim = c(-50, 300), ylim = c(-50, 300), zlim = c(-50, 300)) cubedraw(rr) ## 6 b) The rainbow colors from rainbow(201) rbc <- rainbow(201) Rrb <- t(col2rgb(rbc)) rR <- scatterplot3d(Rrb, color = rbc, box = FALSE, angle = 24, xlim = c(-50, 300), ylim = c(-50, 300), zlim = c(-50, 300)) cubedraw(rR) rR$points3d(Rrb, col = rbc, pch = 16) \end{ExampleCode} \end{Examples} scatterplot3d/inst/doc/SFBs3d_Conclusion.tex0000744000175100001440000000237210175246655020567 0ustar hornikusers\section{Conclusion\label{conclusion}} In the design (Section \ref{design}) of the scatter plot function \sdd\ emphasis is placed on generality and extensibility (Section \ref{extend}). These two properties are demonstrated in Section \ref{examples}, as well as the high printout quality. A high printout quality and a homogeneous appearance with respect of any other \RR\ (2D) graphics is extremely important for publications and presentations. Thus we recommend to use \sdd\ particularly for these purposes. Other \RR\ related 3D ``tools'' (Section \ref{tools}) are focused on different properties, such as surface plotting (e.g. function {\tt persp}), interactivity and online analysis (e.g. \emph{ggobi} or \emph{RGL}). \section*{Acknowledgements} The financial support of the Deutsche Forschungsgemeinschaft (SFB 475, ``Reduction of complexity in multivariate data structures") is gratefully acknowledged. We express our sincere thanks to the following people (in alphabetical order) for their extensive comments on the features and bugs during the time of development, as well as for the discussion of the example data:\\ Ben Bolker, Anja Busse, Ursula Garczarek, Joachim Hartung, Guido Knapp, Winfried Theis, Brigitta Vo\ss, and Claus Weihs. scatterplot3d/inst/doc/SFBs3d_Def.tex0000744000175100001440000000363011544600204017130 0ustar hornikusers\NeedsTeXFormat{LaTeX2e} \documentclass[12pt,titlepage,oneside,a4paper]{article} \usepackage{verbatim} \usepackage{fancyvrb} \usepackage{array} \usepackage[active]{srcltx} \usepackage[intlimits]{amsmath} \usepackage{amsthm} \usepackage{amssymb} \usepackage[final]{graphicx} \usepackage{float} \usepackage{color} \usepackage{Rd} \usepackage{chicago} \usepackage{hyperref} \definecolor{Blue}{rgb}{0,0,0.8} \definecolor{Red}{rgb}{0.7,0,0} \hypersetup{% backref, hyperindex,% colorlinks,% pagebackref,% linktocpage,% plainpages=false,% linkcolor=Blue,% citecolor=Blue,% urlcolor=Red,% pdfstartview=Fit,% pdfview={XYZ null null null} } \setlength{\paperwidth}{21cm} \setlength{\paperheight}{29.7cm} \setlength{\oddsidemargin}{0.46cm} \setlength{\topmargin}{-0.5cm} \setlength{\headheight}{1cm} \setlength{\headsep}{0cm} \setlength{\footskip}{2cm} \setlength{\textwidth}{15cm} \setlength{\textheight}{22cm} \setlength{\tabcolsep}{3mm} \setlength{\doublerulesep}{0.2mm} \parindent = 0em \parskip = 2ex plus0.3ex minus0.3ex \renewcommand{\baselinestretch}{1.3} \sloppy \raggedbottom \setlength{\partopsep}{0mm} \setlength\topsep{0mm} \setlength\parsep{0mm} \renewcommand{\cite}[1]{\shortciteANP{#1}, \citeyearNP{#1}} \renewcommand{\citeN}[1]{\shortciteN{#1}} \newcommand{\bmath}{\begin{eqnarray}} \newcommand{\emath}{\end{eqnarray}} \newcommand{\bmathn}{\begin{eqnarray*}} \newcommand{\emathn}{\end{eqnarray*}} \newcommand{\RR}{{\normalfont\textsf{R}}{}} \newcommand{\sdd}{\emph{scatterplot3d}} \newcommand{\D}{\displaystyle} \renewcommand{\epsilon}{\varepsilon} \renewcommand{\R}{\mathbb{R}} \newcommand{\C}{\mathbb{C}} \newcommand{\N}{\mathbb{N}} \newcommand{\Z}{\mathbb{Z}} \newcommand{\Q}{\mathbb{Q}} \newcommand{\bi}{\begin{itemize} \setlength\itemsep{0.5ex plus0.2ex minus0.3ex}} \newcommand{\ei}{\end{itemize}} scatterplot3d/inst/doc/SFBs3d_Design.tex0000744000175100001440000001403310175240524017646 0ustar hornikusers\section{Design\label{design}} \emph{Scatterplot3d} is designed to plot three dimensional point clouds by exclusive usage of functions in the \RR\ base package. Advantages of this ``\emph{\RR\ code only}'' design are the well known generality and extensibility of the \RR\ graphics system, the similar behavior of arguments and the similar look and feel with respect to common \RR\ graphics, as well as the quality of the graphics, which is extremely important for publications. Drawbacks are the lack of interactivity, and the missing 3D support (2D design). While the function {\tt persp} for plotting surfaces (cf.\ Section \ref{tools}) applies a perspective projection, in \sdd\ a parallel projection for a better comparison of distances between different points is used. The final implementation of the function and the building of the package was done according to the ``\RR\ Language definition'' and ``Writing \RR\ Extensions'' manuals of the \shortciteANP{r-lang} (in short, `\emph{R core}'), \citeyearNP{r-lang} and \citeyearNP{r-ext}. \enlargethispage{10mm} \subsection{Arguments\label{arguments}} The \sdd\ function has been designed to accept as many common arguments to \RR\ graphics functions as possible, particularly those mentioned in the help pages of the function {\tt par} and {\tt plot.default} (R core, \citeyearNP{r-ref}). In principle, arguments of {\tt par} with a particular 2D design are replaced by new arguments in \sdd . % Regularly, values of the corresponding arguments in {\tt par} for the first two dimensions are read out, and \sdd\ either ``guesses'' the value for the third dimension or has an appropriate default. A few graphical parameters can only be set as arguments in \sdd\ but not in {\tt par}. For details on which arguments have got a non common default with respect to other \RR\ graphics functions see the ``Usage'' and ``Arguments'' sections of the help page in the Appendix. % Other arguments of {\tt par} may be split into several arguments in \sdd , e.g. for specification of the line type. Finally, some of the arguments in {\tt par} do not work, e.g. some of those for axis calculation. As common in \RR , additional arguments that are not mentioned on the help page can be passed through to underlying low level graphics functions by making use of the general `\texttt{...}' argument. \subsection{xyz.coords()\label{xyzcoords}} As well known from other \RR\ functions, vectors $x$, $y$ and $z$ (for the 3D case) are used to specify the locations of points. If $x$ has got an appropriate structure, it can be provided as a single argument. In this case, an attempt has to be made to interpret the argument in a way suitable for plotting. % For that purpose, we added the function {\tt xyz.coords} (R core, \citeyearNP{r-ref}) into the \RR\ base package that accept various combinations of $x$ and optionally $y$ and $z$ arguments. % It is a ``utility for obtaining consistent $x$, $y$ and $z$ coordinates and labels for three dimensional plots'' (R core, \citeyearNP{r-ref}). Many ideas used in this function are taken from the function {\tt xy.coords} already existing for the 2D case. % Even though {\tt xyz.coords} was introduced to support \sdd , it is designed to be used by \textsl{any} 3D plot functions making use of $(x_i, y_i, z_i)$ triples\footnote{The functions \code{persp}, \code{image} and \code{contour} are restricted to use a \emph{grid} of $x,y$ values and hence only need $n$ $x-$ and $m$ $y-$ values for $n \times m$ $z-$ values.}. If the argument is a formula of type \verb& zvar ~ xvar + yvar& (cf.\ R core \citeyear{r-lang} for details on formulas), {\tt xvar}, {\tt yvar} and {\tt zvar} are used as $x$, $y$ and $z$ variables. If the argument is a list with components $x$, $y$ and $z$, these are assumed to define plotting coordinates. If it is a matrix with three columns, the first is assumed to contain the $x$ values, etc. Alternatively, two arguments $x$ and $y$ can be be provided, one may be real, the other complex. In any other case, the arguments are coerced to vectors and the values plotted against their indices. If no axis labels are given explicitly, {\tt xyz.coords} attempts to extract appropriate axis labels {\tt xlab}, {\tt ylab} and {\tt zlab} from the above mentioned data structures. Additionally, color vectors contained in a matrix, data frame or list can be detected by \sdd\ internally. \subsection{Structure\label{structure}} The \RR\ code of \sdd\ is structured into a few parts:\\ A quite long list of arguments in the first part of the function is followed by some plausibility checks, extraction of characters, conversion of data structures (cf.\ Section \ref{xyzcoords}), basic calculations of the angle for displaying the cube, and calculations regarding the data region limits, as well as data sorting for an optional ``3D highlighting" feature. In order to optimize the fit of the data into the plotting region, the second part of the function deals with optimal scaling of the three axis. This yields a high printout quality as well known from regular \RR\ graphics, but unfortunately it results also in a static plot, i.e.~rotation is not possible. If \sdd s with different viewing angles are put together as a ``slide show" to imitate a rotation, each of these ``slides" is {\sl individually} optimally sized regarding the plotting region, so all in all such a ``slide show" will not work. After the graphics device is initialized in the third part, axis, tick marks, box, grid and labels are added to the plot, if it is required. In the last but one part, the data is plotted and overlayed by the front edges of the box. Besides the primarily expected result, a drawn plot, four functions are generated and invisibly returned as \emph{Values} in the last part of \sdd\ (cf. the Appendix). These functions, namely \code{xyz.convert}, \code{points3d}, \code{plane3d} and \code{box3d}, are required to provide extensibility of the three dimensional plot; details are described in Section~\ref{extend}. scatterplot3d/inst/doc/SFBs3d_Examples.tex0000744000175100001440000004750011042405611020212 0ustar hornikusers\section{Examples\label{examples}} \subsection{Feature demonstration\label{artificial}} In this section some of the features of \sdd\ will be demonstrated using artificially generated data, well known examples from other \RR\ functions and the (slightly modified) examples of \sdd 's help file (cf.\ the Appendix). The presentation starts with the latter, each example printed on an individual page to obtain lucidity. \vspace*{30mm} \begin{center}\sl\small this space intentionally left blank \end{center} \clearpage\subsubsection{Helix} In Figure \ref{helix} points of a helix are calculated and plotted using the 3D highlighting mode (% \verb|highlight.3d = TRUE|) in a blue box with a light blue grid. We produce the solid look with the point symbol, \texttt{pch = 20}. \vspace*{10mm} \begin{figure}[htb!] \small \begin{Verbatim}[frame=single] z <- seq(-10, 10, 0.01) x <- cos(z) y <- sin(z) scatterplot3d(x, y, z, highlight.3d = TRUE, col.axis = "blue", col.grid = "lightblue", main = "Helix", pch = 20) \end{Verbatim} \normalsize \begin{center} \includegraphics[width=13cm]{helix} \end{center} \vspace*{-10mm}\caption{Helix\label{helix}} \end{figure} \clearpage\subsubsection{Hemisphere} Figure \ref{hemisphere} shows points on a hemisphere. Except for angle and the size of axes annotation, this figure is generated analogously to Figure \ref{helix}. \vspace*{10mm} \begin{figure}[htb!] \small \begin{Verbatim}[frame=single] temp <- seq(-pi, 0, length = 50) x <- c(rep(1, 50) %*% t(cos(temp))) y <- c(cos(temp) %*% t(sin(temp))) z <- c(sin(temp) %*% t(sin(temp))) scatterplot3d(x, y, z, highlight.3d = TRUE, angle = 120, col.axis = "blue", col.grid = "lightblue", cex.axis = 1.3, cex.lab = 1.1, main = "Hemisphere", pch = 20) \end{Verbatim} \normalsize \begin{center} \includegraphics[width=13cm]{hemisphere} \end{center} \vspace*{-10mm}\caption{Hemisphere\label{hemisphere}} \end{figure} \clearpage\subsubsection{3D barplot} With some simple modifications, it is possible to generate a 3D barplot, as shown in this example. To make the plot look like a barplot, {\tt type = "h"} is set to draw vertical lines to the $x$--$y$ plane, {\tt pch = " "} to avoid plotting of point symbols and {\tt lwd = 5} to make the lines looking like bars. Furthermore, instead of three vectors a data frame is given as the first argument to \sdd . \enlargethispage{1cm} \vspace*{5mm} \begin{figure}[htb!] \small \begin{Verbatim}[frame=single] my.mat <- matrix(runif(25), nrow = 5) dimnames(my.mat) <- list(LETTERS[1:5], letters[11:15]) s3d.dat <- data.frame(columns = c(col(my.mat)), rows = c(row(my.mat)), value = c(my.mat)) scatterplot3d(s3d.dat, type = "h", lwd = 5, pch = " ", x.ticklabs = colnames(my.mat), y.ticklabs = rownames(my.mat), color = grey(25:1 / 40), main = "3D barplot") \end{Verbatim} \normalsize \begin{center} \includegraphics[width=12.5cm]{barplot} \end{center} \vspace*{-10mm}\caption{3D barplot\label{barplot}} \end{figure} \clearpage\subsubsection{Adding elements} The importance of \textsl{Lexical Scoping} to generate \textsl{function closures} to provide extensibility of \sdd\ was discussed in Section \ref{extend}. An example how to use the invisibly returned functions is given below on the famous (at least for \textsf{S} users) tree data. After the tree data is loaded, it is plotted by \sdd , and the (invisibly returned) result is assigned to the variable {\tt s3d}. The (blue colored) points are plotted using {\tt type = "h"}, so one can see the $x$--$y$ location of those points very clearly. In the next step, a linear model (assumption: volume depends on girth and height of the trees) is calculated. Furthermore, this \textsf{lm} object is plotted by the returned {\tt plane3d} function (was assigned to {\tt s3d} before), and it results in a regression plane. Just for demonstration purposes, in the last step some red colored points (on a imaginary line crossing the plot) are plotted with an asterisk as its point symbol. \vspace*{10mm} \small \begin{Verbatim}[frame=single] data(trees) s3d <- scatterplot3d(trees, type = "h", color = "blue", angle = 55, scale.y = 0.7, pch = 16, main = "Adding elements") my.lm <- lm(trees$Volume ~ trees$Girth + trees$Height) s3d$plane3d(my.lm) s3d$points3d(seq(10, 20, 2), seq(85, 60, -5), seq(60, 10, -10), col = "red", type = "h", pch = 8) \end{Verbatim} %$ \normalsize \clearpage \begin{figure}[htb!] \begin{center} \includegraphics[width=13cm]{elements} \end{center} \vspace*{-10mm}\caption{Adding elements\label{elements}} \end{figure} \subsubsection{Bivariate normal distribution} In Figure \ref{binorm} a surface of the density of a bivariate normal distribution is plotted. This example is a bit more sophisticated than the examples before and shows the extensibility of \sdd. Note that \sdd\ is designed to generate scatter plots, not to draw surfaces, is not really user friendly for this purpose, for which we'd typically rather use \RR's \code{persp} function. In a first step a matrix containing the density is calculated. The call of \sdd\ sets up the plot (axes, labels, etc.), but doesn't draw the surface itself which is accomplished by the two loops at the end of the code. Additionally, we give an example of quite sophisticated mathematical annotation. \clearpage \small \begin{Verbatim}[frame=single] library(mvtnorm) x1 <- x2 <- seq(-10, 10, length = 51) dens <- matrix(dmvnorm(expand.grid(x1, x2), sigma = rbind(c(3, 2), c(2, 3))), ncol = length(x1)) s3d <- scatterplot3d(x1, x2, seq(min(dens), max(dens), length = length(x1)), type = "n", grid = FALSE, angle = 70, zlab = expression(f(x[1], x[2])), xlab = expression(x[1]), ylab = expression(x[2]), main = "Bivariate normal distribution") text(s3d$xyz.convert(-1, 10, 0.07), labels = expression(f(x) == frac(1, sqrt((2 * pi)^n * phantom(".") * det(Sigma[X]))) * phantom(".") * exp{ bgroup("(", - scriptstyle(frac(1, 2) * phantom(".")) * (x - mu)^T * Sigma[X]^-1 * (x - mu), ")")})) text(s3d$xyz.convert(1.5, 10, 0.05), labels = expression("with" * phantom("m") * mu == bgroup("(", atop(0, 0), ")") * phantom(".") * "," * phantom(0) * Sigma[X] == bgroup("(", atop(3 * phantom(0) * 2, 2 * phantom(0) * 3), ")"))) for(i in length(x1):1) s3d$points3d(rep(x1[i], length(x2)), x2, dens[i,], type = "l") for(i in length(x2):1) s3d$points3d(x1, rep(x2[i], length(x1)), dens[,i], type = "l") \end{Verbatim} \normalsize \clearpage \begin{figure}[htb!] \begin{center} \includegraphics[width=13cm]{binorm} \end{center} \vspace*{-12mm}\caption{Density of a bivariate normal distribution\label{binorm}} \end{figure} \subsubsection{RGB color cube} In Figure \ref{colorcube}, we visualize the RGB (red--green--blue) color space which \RR{} and most computer screens use for color coding. First, we draw all the \emph{named} colors available in \RR{} via \texttt{colors()}. Note that it might be interesting to find a better background color here than white. Optimally it would correspond to an RGB location as far away as possible from all given colors. %%\enlargethispage{1cm}% Trick, damit es passt ... Second, we show the \texttt{rainbow()} colors in the RGB space. Here we redraw the points \emph{on top} of the cube, using the \texttt{points3d()} closure which is also the basis of our \texttt{cubedraw()} function. \begin{figure}[htb!] \small %% to save space, suppressed things like %% ## Purpose: Draw nice cube with corners %% par(mfrow = 1:2) \begin{Verbatim}[frame=single] cubedraw <- function(res3d, min = 0, max = 255, cex = 2) { cube01 <- rbind(0,c(1,0,0),c(1,1,0),1,c(0,1,1),c(0,0,1),c(1,0,1), c(1,0,0),c(1,0,1),1,c(1,1,0), c(0,1,0),c(0,1,1), c(0,1,0),0) cub <- min + (max-min)* cube01 res3d$points3d(cub[ 1:11,], cex = cex, type = 'b', lty = 1) res3d$points3d(cub[11:15,], cex = cex, type = 'b', lty = 3) } crgb <- t(col2rgb(cc <- colors())) rr <- scatterplot3d(crgb, color = cc, box = FALSE, angle = 24) cubedraw(rr) Rrb <- t(col2rgb(rbc <- rainbow(201))) rR <- scatterplot3d(Rrb, color = rbc, box = FALSE, angle = 24) cubedraw(rR) rR$points3d(Rrb, col = rbc, pch = 16) \end{Verbatim} \par\vspace*{-12mm}%$ \normalsize \centerline{\includegraphics[width=19cm]{colorcube}} \par\vspace*{-5mm} \caption{The RGB color cube. On the left, the named colors in \RR{}, i.e., \texttt{colors()}. Note the diagonal of gray tones. On the right, the locations and colors of \texttt{rainbow(201)}.\label{colorcube}} \end{figure} \clearpage \subsection{Real world examples\label{realworld}} Three real world examples are presented in this section. The data are from the following recent projects of the collaborative research centre 475 (Deutsche Forschungsgemeinschaft, SFB 475: ``Reduction of complexity in multivariate data structures''): \vspace{-5mm}\begin{description} \item[C3 \textmd{(Biometrics)}] Meta--Analysis in Biometry and Epidemiology, \item[B3 \textmd{(Econometrics)}] Multivariate Analysis of Business Cycles, and \item[C5 \textmd{(Technometrics)}] Analysis and Modelling of the Deephole--Drilling--Process with Methods of Statistics and Neuronal Networks. \end{description} \subsubsection{Meta--analysis of controlled clinical trials\label{meta}} In the first real world example the data from a project on ``Meta--Analysis in Biometry and Epidemiology'' is taken. The data set contains the results of 13 placebo--controlled clinical trials which evaluated the efficacy of the Bacillus Calmette--Gu\'{e}rin (BCG) vaccine for the prevention of tuberculosis (TB). % An important task in combining the results of clinical trials is to detect possible sources of heterogeneity which may influence the true treatment effect. % In the present example, a possible influential covariate is the distance of each trial from the equator, which may serve as a surrogate for the presence of environmental mycobacteria that provide a certain level of natural immunity against TB. % Other covariates may be the year the trial was carried out and the allocation scheme of the vaccination (A = alternate, R = random, S = systematic). %% For more details, especially on the choice of the trials and the meta--analytical methods of combining the results, we refer to \citeN{knapp02} and the references given therein. In Figure \ref{fig:meta} the estimated risks of TB disease are plotted for the vaccinated group and the non--vaccinated group, respectively, in the dependence of the year the trial was carried out, of the absolute distance from the equator and of the allocation scheme. The color represents the precisions of the estimated risks. Figure \ref{fig:meta} clearly reveals a spatio--temporal trend in the realization of the trials. The former trials were carried out far away from the equator, and in all these trials one can observe an evident superiority of the BCG vaccine for the prevention of TB. Except one trial all the other later trials were realized closer to the equator. In these trials, it is apparently that the estimated risks in the non--vaccinated groups are even rather low and, consequently, cannot graphically separated from the estimated risks in the vaccinated groups. Finally, it is worthwhile to note that the later trial which was carried out far away from the equator has a relative small estimated risk in the non--vaccinated group compared to the former trials and, hence, does not yield such an evident superiority of the BCG vaccine. \begin{figure}[b!] \small \begin{Verbatim}[frame=single] layout(cbind(1:2, 1:2), heights = c(7, 1)) prc <- hsv((prc <- 0.7 * Prec / diff(range(Prec))) - min(prc) + 0.3) s3d <- scatterplot3d(Year, Latitude, Risk, mar = c(5, 3, 4, 3), type = "h", pch = " ", main = "Estimated TB risks") s3d$points(Year, Latitude, Risk, pch = ifelse(vac, 22, 21), bg = prc, cex = ifelse(vac, 2, 1.5)) s3d.coords <- s3d$xyz.convert(Year, Latitude, Risk) al.char <- toupper(substr(as.character(Allocation), 1, 1)) text(s3d.coords$x[!vac], s3d.coords$y[!vac], labels = al.char[!vac], pos = 2, offset = 0.5) legend(s3d$xyz.convert(80, 15, 0.21), pch = c("A", "R", "S"), yjust=0, legend = c("alternate", "random", "systematic"), cex = 1.1) legend(s3d$xyz.convert(47, 60, 0.24), pch = 22:21, yjust = 0, legend = c("vaccinated", "not vaccinated"), cex = 1.1) par(mar=c(5, 3, 0, 3)) plot(seq(min(Prec), max(Prec), length = 100), rep(0, 100), pch = 15, axes = FALSE, xlab = "color code of variable \"Precision\"", ylab = "", col = hsv(seq(0.3, 1, length = 100))) axis(1, at = 4:7, labels = expression(10^4, 10^5, 10^6, 10^7)) \end{Verbatim} \end{figure} \normalsize Three variables are represented by the three dimensions of the cube, while variable ``Precision'' is represented by color. To realize color representation for metric variables, some manual tuning is necessary, though. Two kinds of point symbols stand for the ``Vaccinated'' variable, and for a sixth variable, ``Allocation'', an appropriate letter is printed additionally close to the ``not vaccinated'' symbol. For each of the latter three variables a legend is desirable. Thus the smaller two legends are plotted into the \sdd , while the legend for the color coding gets a single plot. The function {\tt layout} arranges the two plots suitably on the same device. \begin{figure}[htb!] \begin{center}\includegraphics[width=13cm]{meta}\end{center} \caption{Estimated TB risks\label{fig:meta}} \end{figure} \clearpage \subsubsection{Business cycle data} The example in this section shows the plotting of data from a project on ``Multivariate Analysis of Business Cycles''. One of the main interests of the project is the prediction of business cycle phases. An extraction of available relevant (concerning the purposes of this section) variables and its abbreviations is given in Table \ref{StyFacts}. The abbreviation 'gr' stands for growth rates with respect to last year's corresponding quarter. \begin{table}[htb!] \centering \vspace{0.2cm} \begin{tabular}{|l|l|} \hline abbr & description \\ \hline IE & real investment in equipment (gr) \\ C & real private consumption (gr) \\ Y & real gross national product (gr) \\ L & wage and salary earners (gr) \\ \hline \end{tabular} \caption{Abbreviations\label{StyFacts}} \end{table} The experts' classification of the data into business cycle phases (``PH'') was done by \citeN{heilemann} using a 4-phase scheme. These phases are called {\sl lower turning points}, {\sl upswing}, {\sl upper turning points}, and {\sl downswing}. In Figure~\ref{business} the three variables C, Y, and L are represented by the three dimensions of the cube. The variable IE is represented by color, while four different point symbols stand for the four business cycle phases (PH). For each of the latter two variables, a legend is desirable. Thus the smaller one (for PH) is plotted into the \sdd , while the legend for the color coding of IE got a single plot, analogously to the example in Section~\ref{meta}. A regression plane is added to the plot to support the visual impression. Obviously all the plotted variables are highly correlated, with the exception of the class variable which does not appear to be well predictable by the other variables. Details are discussed in \citeN{theis99}. % In order to provide a correct impression of the fit, the residuals, i.e. the projection lines to the plane, are drawn in Figure~\ref{residuals} where different color and line types are used for positive and negative residuals respectively. \begin{figure}[H] \vspace*{-10mm} \footnotesize \begin{Verbatim}[frame=single] layout(cbind(1:2, 1:2), heights = c(7, 1)) temp <- hsv((temp <- 0.7 * IE / diff(range(IE))) - min(temp) + 0.3) s3d <- scatterplot3d(L, C, Y, pch = Phase, color = temp, mar = c(5, 3, 4, 3), main = "Business cycle phases") legend(s3d$xyz.convert(-2, 0, 16), pch = 1:4, yjust = 0, legend = c("upswing", "upper turning points", "downswing", "lower turning points")) s3d$plane3d(my.lm <- lm(Y ~ L + C), lty = "dotted") par(mar=c(5, 3, 0, 3)) plot(seq(min(IE), max(IE), length = 100), rep(0, 100), pch = 15, axes = FALSE, xlab = "color code of variable \"IE\"", ylab = "", col = hsv(seq(0.3, 1, length = 100))) axis(1, at = seq(-20, 25, 5)) \end{Verbatim} \normalsize \begin{center}\includegraphics[width=13cm]{business}\end{center} \vspace*{-5mm}\caption{Business cycle phases\label{business}} \end{figure} \begin{figure}[htb!] \small \begin{Verbatim}[frame=single] s3d <- scatterplot3d(L, C, Y, pch = 20, mar = c(5, 3, 4, 3), main = "Residuals") s3d$plane3d(my.lm, lty = "dotted") orig <- s3d$xyz.convert(L, C, Y) plane <- s3d$xyz.convert(L, C, fitted(my.lm)) i.negpos <- 1 + (resid(my.lm) > 0) segments(orig$x, orig$y, plane$x, plane$y, col = c("blue", "red")[i.negpos], lty = (2:1)[i.negpos]) \end{Verbatim} %%$ \normalsize \begin{center}\includegraphics[width=13cm]{residuals}\end{center} \vspace*{-5mm}\caption{Residuals (cf. Figure \ref{business})\label{residuals}} \end{figure} \clearpage \subsubsection{Deep hole drilling} Our last real world example shows phase spaces (\cite{tong93}) of the drilling torque of a deep hole drilling process. The data is taken from a project on "Analysis and Modelling of the Deephole--Drilling--Process with Methods of Statistics and Neuronal Networks". More detailed analysis on the data than provided in the following example was done by, e.g., \citeN{busse} and \citeN{weinert}. Figure \ref{drill1} visualizes the phase spaces of the drilling torques of two deep hole drilling processes, a regular and a chattering one. Obviously the points in the phase space of the chattering process are very systematically scattered, and the range of the data is very different for the two processes. The magnification of the regular process in Figure \ref{drill2} shows that the points of the regular process are scattered unsystematically. Note that other lags like 10, 20, 100 would produce a similar plot. This indicates a sine wave like relationship in the chattering case. \vspace{10mm} \small \begin{Verbatim}[frame=single] s3d <- scatterplot3d(drill1[1:400], drill1[7:406], drill1[32:431], color = "red", type = "l", angle = 120, xlab = "drilling torque", ylab = "drilling torque, lag 6", zlab = "drilling torque, lag 31", main = "Two deep hole drilling processes") s3d$points3d(drill2[1:400], drill2[7:406], drill2[32:431], col = "blue", type = "l") legend(s3d$xyz.convert(-400, 1000, 950), col= c("blue", "red"), legend = c("regular process", "chattering process"), lwd = 2, bg = "white") scatterplot3d(drill2[1:400], drill2[7:406], drill2[32:431], color = "blue", type = "l", angle = 120, xlab = "drilling torque", ylab = "drilling torque, lag 6", zlab = "drilling torque, lag 31", main = "Magnification of the regular process") \end{Verbatim} \normalsize \begin{figure}[htb!] \vspace*{-15mm} \begin{center}\includegraphics[width=11.5cm]{drill1} \vspace*{-10mm}\caption{Phase spaces of the drilling torques of two deep hole drilling processes\label{drill1}} \vspace*{10mm} \includegraphics[width=11.5cm]{drill2}\end{center} \vspace*{-10mm}\caption{Magnification of the regular process (Figure \ref{drill1})\label{drill2}} \end{figure} \clearpage scatterplot3d/inst/doc/SFBs3d_Extend.tex0000744000175100001440000001257410175240746017702 0ustar hornikusers\section{Extensibility\label{extend}} Two kinds of extensibilities will be described in this section. On one hand, regarding the \sdd\ design, the extensibility of the \RR\ graphics system will be discussed; it provides the tools and features enabling the programmer to write complex high level plot functions in a very general manner. On the other hand we describe the extensibility of \sdd\ itself. \subsection{Extensibility of \RR\ graphics\label{exR}} \RR\ provides a huge collection of low level graphic functions like those for adding elements to an existing plot or for computations related to plotting. % These functions are used to build very general high level functions, at least for the two dimensional case, and without them, the ``\RR\ code only'' design of \sdd\ would be impossible. A selection of these low level functions begins with the functions to obtain $x$, $y$ (and~$z$) coordinates for plotting, namely {\tt xy.coords} and {\tt xyz.coords} (for the 3D case, cf.\ Section \ref{xyzcoords}). Further on, the functions {\tt plot.new} and {\tt plot.window} can be used to set up the plotting region appropriately, {\tt pretty} to calculate pretty axis tick marks, {\tt segments} to draw line segments between pairs of points, and functions like {\tt title}, {\tt axis}, {\tt points}, {\tt lines}, {\tt text} etc.~are self-explanatory. A huge collection of graphical parameters for \RR\ is documented in the help pages for {\tt par} and {\tt plot.default} (cf.\ R core \citeyear{r-ref}). Almost all low level graphic functions make use of the argument `\code{...}' which allows specifying most of these parameters in a very general manner. If this argument, `\code{...}', is also used in a high level function, arguments which are not \textsl{explicitly} introduced in the arguments list, can be passed through to lower level graphic functions as well; this is a powerful feature of the \textsf{S} language. \enlargethispage{5mm} Since the \RR\ graphics system is designed for two dimensional graphics, it lacks of some features for the three dimensional case. %% Unfortunately, the {\tt axis} function works only for 2D graphics. Consequently a large amount of code was required to enable oblique axes for displaying the 3D scatter plot in an arbitrary angle. Locations in \RR\ graphics devices can be addressed with 2D coordinates, Thus the information on the projection has to be calculated by the 3D graphic functions internally. As described in Section \ref{design}, \sdd\ uses a parallel projection. Since the \RR\ graphics device does not know anything about the projection, without any appropriate additional tools it is not possible to add elements into an existing \sdd . \subsection{Extensibility of \sdd\label{exsdd}} In Sections \ref{introduction} and \ref{design} it was emphasized that the \sdd\ design was intended to be as general as possible. Some attempts to obtain this generality are described in Section \ref{design} and its subsections. %% Because of the missing projection information, the ability of adding elements to an already existing \sdd\ would be restricted, if only the already defined (and for the 2D case general) \RR\ functions could be used (cf.\ Section \ref{exR}). For this reason, \sdd\ (invisibly) returns a list of \textsl{function closures} (cf.\ Section~\ref{structure}). A \textsl{function closure} is a function together with an \textsl{environment}, and an \textsl{environment} is a collection of symbols and associated values (i.e. \RR\ variables). Thus these properties of \RR's scoping rules, called \textsl{Lexical Scoping} (\cite{gentleman}), are extensively used in \sdd. % Notice that \textsl{Lexical Scoping} is a feature of \RR, not defined as such in the \textsf{S} language. In other words, the values returned by \sdd\ are functions together with the environment in which they (and the scatter plot) were created. The benefit of returning function closures is, that the function somehow ``knows'' the values of variables (in the environment) that were assigned to those variables at the time when the function was created. All in all, we made those functions know details about the axis scaling and the projection information that are required to add elements to an existing plot appropriately. The following functions are returned by \sdd , for details see the Appendix:\\ \vspace{-11mm} \begin{description} \setlength\itemsep{0.5ex plus0.2ex minus0.3ex} \item[{\tt xyz.convert}:] A function which converts 3D coordinates to the 2D parallel projection of the existing \sdd . It is useful to add arbitrary elements into the plot. \item[{\tt points3d}:] A function which draws points or lines into the existing plot. \item[{\tt plane3d}:] A function which draws a plane into the existing plot:\\ \verb+plane3d(Intercept, x.coef=NULL, y.coef=NULL, lty="dashed", ...)+. Instead of an intercept, a vector containing three elements or an \textsf{(g)lm} object can be specified. \item[{\tt box3d}:] This function draws a box (or ``refreshes'' an existing one) around the plot. \end{description} {\tt xyz.convert} is the most important function, because it does the parallel projection by converting the given 3D coordinates into the 2D coordinates needed for the \RR\ graphics devices. Examples how to use the mentioned function closures are given in Section \ref{examples}. scatterplot3d/inst/doc/SFBs3d_Intro.tex0000744000175100001440000000424310175246731017540 0ustar hornikusers\section{Introduction\label{introduction}} \emph{Scatterplot3d} is an \RR\ package for the visualization of multivariate data in a three dimensional space. \RR\ itself is ``A Language and Environment for Statistical Computing'' (\cite{r-ref}) and a freely available statistical software package implementing that language, see \url{http://www.R-project.org/}. Basically \sdd\ generates a scatter plot in the 3D space using a parallel projection. Higher dimensions (fourth, fifth, etc.) of the data can be visualized to some extent using, e.g. different colors, symbol types or symbol sizes. The following properties of \sdd\ will be further described and discussed in the present paper: % A plot is generated entirely by using interpreted \RR\ graphics functions, so the appearance of the plot is consistent with other \RR\ graphics. Such a behavior is % extremely important for publications. Most features of the \RR\ graphics system can be applied in \sdd , among them are vectorizing of colors or plotting symbols and mathematical annotation (\cite{murrell00}). The latter means whole formulas with e.g.\ greek letters and mathematical symbols inside can be added into plots using a \LaTeX\ like syntax. % \emph{Scatterplot3d} can be easily extended e.g., by adding additional points or drawing regression lines or planes into an already generated plot (via function closures, see below). The package is platform independent and can easily be installed, because it only requires an installed version of \RR. This paper is structured as follows: % In Section \ref{design} the design of \sdd\ will be described, followed by remarks on the extensibility of the function in Section \ref{extend}. % Some examples (including code and results) on generated and real world data are provided in Section \ref{examples}. % We present other \RR\ related 3D ``tools'' in Section \ref{tools}, followed by the conclusion in Section \ref{conclusion}. % In the Appendix the source code as well as the help page of \sdd\ are printed. \RR\ and \sdd\ are available from \emph{CRAN} (Common \RR\ Archive Network), i.e. \url{http://CRAN.R-Project.org } or one of its mirrors. scatterplot3d/inst/doc/SFBs3d_Related.tex0000744000175100001440000000473110175243373020026 0ustar hornikusers\section{Other 3D tools in \RR\label{tools}} At the time of writing \sdd , the function \code{persp()} in the base package of \RR\ for three dimensional surface plots was available, but there was no way to generate 3D scatter plots in \RR\ itself. The data visualization system \emph{xgobi} (\cite{swayne98}) provides interactive visualization of multidimensional data, e.g. brush and spin, higher-dimensional rotation, grand tour, etc. The \RR\ package \emph{xgobi} (\cite{swayne91}; we have to distinguish the visualization system and the package) provides an Interface to \emph{xgobi} and launches a \emph{xgobi} process appropriately. %% \emph{ggobi}\footnote{\url{http://www.ggobi.org}} (\cite{swayne02}) is the next edition of \emph{xgobi}. Analogously to \emph{xgobi} a \RR\ package \emph{Rggobi} (\cite{temple01}) exists in the \emph{Omegahat} project\footnote{\url{http://www.omegahat.org}} (\cite{temple00}) that allows one to embed \emph{ggobi} within \RR\ and to both set and query the \emph{ggobi} contents. All in all, \emph{ggobi} can be loaded dynamically into \RR\ (as well as into other software products, in principle), and \RR\ into \emph{ggobi}. This provides interactive, direct manipulation, linked, high-dimensional graphics within \RR . The package \emph{rgl}\footnote{\url{http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler/rgl/}} by \cite{AdlerNenadic2003} is a portable \RR\ programing interface to \emph{OpenGL}. Its features include, e.g., interactive viewpoint navigation, automatic data focus, up to 8 light sources, alpha-blending (transparency), and environmental effects like fogging. The package \emph{djmrgl}\footnote{This package was formerly called \emph{rgl}, similar to the other mentioned package by Daniel Adler and Oleg Nenadi\'{c}. \emph{djmrgl} is only available for the Windows operating system.} (\cite{murdoch}) also provides an \RR\ interface to \emph{OpenGL}. A huge collection of useful functions to generate, manipulate and interactively rotate 3D objects is available. Efforts are under way to merge these two packages. The function \code{cloud} in the lattice package is a 3D scatter plot function that works in the \emph{lattice} (\cite{sarkar02}) (and \emph{grid} (\cite{murrell01})) environment of \RR . \emph{Lattice} is an implementation of \emph{Trellis Graphics}, which is a framework for data visualization developed at the Bell Labs by \citeN{becker96}, extending ideas presented in \citeN{cleveland}. scatterplot3d/inst/doc/srcltx.sty0000744000175100001440000001047510055435142016674 0ustar hornikusers%% %% This is file `srcltx.sty', %% generated with the docstrip utility. %% %% The original source files were: %% %% srcltx.dtx (with options: `package,latex') %% %% This package is in the public domain. It comes with no guarantees %% and no reserved rights. You can use or modify this package at your %% own risk. %% Originally written by: Aleksander Simonic %% Current maintainer: Stefan Ulrich %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \NeedsTeXFormat{LaTeX2e} \ProvidesPackage{srcltx}[2004/05/15 v1.4 Source specials for inverse search in DVI files] \newif\ifSRCOK \SRCOKtrue \newif\ifsrc@debug@ \newif\ifsrc@dviwin@ \newif\ifsrc@winedt@\src@winedt@true \newif\ifsrc@everypar@\src@everypar@true \newif\ifsrc@everymath@\src@everymath@true \DeclareOption{active}{\SRCOKtrue} \DeclareOption{inactive}{\SRCOKfalse} \DeclareOption{nowinedt}{\src@winedt@false} \DeclareOption{debug}{\src@debug@true} \DeclareOption{nopar}{\global\src@everypar@false} \DeclareOption{nomath}{\global\src@everymath@false} \newcommand*\src@maybe@space{} \let\src@maybe@space\space \DeclareOption{dviwin}{\let\src@maybe@space\relax} \ExecuteOptions{active} \ProcessOptions \newcount\src@lastline \global\src@lastline=-1 \newcommand*\src@debug{} \def\src@debug#1{\ifsrc@debug@\typeout{DBG: |#1|}\fi} \newcommand*\MainFile{} \def\MainFile{\jobname.tex} \newcommand*\CurrentInput{} \gdef\CurrentInput{\MainFile} \newcommand*\WinEdt{} \def\WinEdt#1{\ifsrc@winedt@\typeout{:#1}\fi} \newcommand\src@AfterFi{} \def\src@AfterFi#1\fi{\fi#1} \AtBeginDocument{% \@ifpackageloaded{soul}{% \let\src@SOUL@\SOUL@ \def\SOUL@#1{% \ifSRCOK \SRCOKfalse\src@SOUL@{#1}\SRCOKtrue \else \src@AfterFi\src@SOUL@{#1}% \fi }% }{}% } \newcommand*\src@spec{} \def\src@spec{% \ifSRCOK \ifnum\inputlineno>\src@lastline \global\src@lastline=\inputlineno \src@debug{% src:\the\inputlineno\src@maybe@space\CurrentInput}% \special{src:\the\inputlineno\src@maybe@space\CurrentInput}% \fi \fi } \newcommand\src@before@file@hook{} \newcommand\src@after@file@hook{} \def\src@before@file@hook#1{% \protected@xdef\CurrentInput{#1}% \WinEdt{<+ \CurrentInput}% \global\src@lastline=0 \ifSRCOK\special{src:1\CurrentInput}\fi } \def\src@after@file@hook#1{% \WinEdt{<-}% \global\src@lastline=\inputlineno \global\advance\src@lastline by -1% \gdef\CurrentInput{#1}% \src@spec } \newcommand*\src@include{} \newcommand*\src@@include{} \let\src@include\include \def\include#1{% \src@spec \clearpage \expandafter\src@@include\expandafter{\CurrentInput}{#1}% }% \def\src@@include#1#2{% \src@before@file@hook{#2.tex}% \src@include{#2}% \src@after@file@hook{#1}% } \newcommand*\src@input{} \newcommand*\src@@input{} \newcommand*\src@@@input{} \let\src@input\input \def\input{\src@spec\@ifnextchar\bgroup\src@@input\@@input}% \def\src@@input#1{% \expandafter\src@@@input\expandafter{\CurrentInput}{#1}% } \def\src@@@input#1#2{% \src@before@file@hook{#2}% \src@input{#2}% \src@after@file@hook{#1}% } \newcommand\Input{} \let\Input\input \ifsrc@everypar@ \newcommand*\src@old@everypar{} \let\src@old@everypar\everypar \newtoks\src@new@everypar \let\everypar\src@new@everypar \everypar\expandafter{\the\src@old@everypar} \src@old@everypar{\the\src@new@everypar\src@spec} \fi \ifsrc@everymath@ \def\@tempa#1\the\everymath#2\delimiter{{#1\src@spec\the\everymath#2}} \frozen@everymath=\expandafter\@tempa\the\frozen@everymath\delimiter \fi \newcommand*\src@bibliography{} \newcommand*\src@@bibliography{} \let\src@bibliography\bibliography \def\bibliography#1{% \expandafter\src@@bibliography\expandafter{\CurrentInput}{#1}% } \def\src@@bibliography#1#2{% \src@before@file@hook{\jobname.bbl}% \src@bibliography{#2}% \src@after@file@hook{#1}% } \newcommand*\src@old@output{} \let\src@old@output\output \newtoks\src@new@output \let\output\src@new@output \output\expandafter{\the\src@old@output} \src@old@output{\SRCOKfalse\the\src@new@output} \endinput %% %% End of file `srcltx.sty'. scatterplot3d/inst/po/0000755000175100001440000000000011544601042014453 5ustar hornikusersscatterplot3d/inst/po/de/0000755000175100001440000000000011544601042015043 5ustar hornikusersscatterplot3d/inst/po/de/LC_MESSAGES/0000755000175100001440000000000011544601042016630 5ustar hornikusersscatterplot3d/inst/po/de/LC_MESSAGES/R-scatterplot3d.mo0000744000175100001440000000153410201432007022153 0ustar hornikusersL |)  ).  ! 0+color is ignored when highlight.3d = TRUElength(color)length(pch)must be equal length(x) or 1no data left within (x|y|z)limProject-Id-Version: R 2.1.0 Report-Msgid-Bugs-To: bugs@r-project.org POT-Creation-Date: 2005-02-06 15:50 PO-Revision-Date: 2005-02-06 16:13+0100 Last-Translator: Uwe Ligges Language-Team: MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Poedit-Language: German X-Poedit-Country: GERMANY X-Poedit-SourceCharset: iso-8859-1 color wird ignoriert falls highlight.3d = TRUElength(color)length(pch)muss gleich length(x) oder 1 seinkeine Daten innerhalb von der Grenzen (x|y|z)limscatterplot3d/inst/po/en/0000755000175100001440000000000011544601042015055 5ustar hornikusersscatterplot3d/inst/po/en/LC_MESSAGES/0000755000175100001440000000000011544601042016642 5ustar hornikusersscatterplot3d/inst/po/en/LC_MESSAGES/R-scatterplot3d.mo0000744000175100001440000000072010201433065022166 0ustar hornikusers$,89Project-Id-Version: R 2.1.0 Report-Msgid-Bugs-To: bugs@r-project.org POT-Creation-Date: 2005-02-06 15:50 PO-Revision-Date: 2005-02-06 16:22+0100 Last-Translator: Uwe Ligges Language-Team: MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Poedit-Language: German X-Poedit-Country: GERMANY X-Poedit-SourceCharset: iso-8859-1 scatterplot3d/man/0000755000175100001440000000000011544601042013633 5ustar hornikusersscatterplot3d/man/scatterplot3d.Rd0000744000175100001440000002263111325304473016727 0ustar hornikusers\name{scatterplot3d} \alias{scatterplot3d} \title{3D Scatter Plot} \description{ Plots a three dimensional (3D) point cloud. } \usage{ scatterplot3d(x, y=NULL, z=NULL, color=par("col"), pch=NULL, main=NULL, sub=NULL, xlim=NULL, ylim=NULL, zlim=NULL, xlab=NULL, ylab=NULL, zlab=NULL, scale.y=1, angle=40, axis=TRUE, tick.marks=TRUE, label.tick.marks=TRUE, x.ticklabs=NULL, y.ticklabs=NULL, z.ticklabs=NULL, y.margin.add=0, grid=TRUE, box=TRUE, lab=par("lab"), lab.z=mean(lab[1:2]), type="p", highlight.3d=FALSE, mar=c(5,3,4,3)+0.1, col.axis=par("col.axis"), col.grid="grey", col.lab=par("col.lab"), cex.symbols=par("cex"), cex.axis=0.8 * par("cex.axis"), cex.lab=par("cex.lab"), font.axis=par("font.axis"), font.lab=par("font.lab"), lty.axis=par("lty"), lty.grid=par("lty"), lty.hide=NULL, lty.hplot=par("lty"), log="", ...) } \arguments{ \item{x}{the coordinates of points in the plot.} \item{y}{the y coordinates of points in the plot, optional if \code{x} is an appropriate structure.} \item{z}{the z coordinates of points in the plot, optional if \code{x} is an appropriate structure.} \item{color}{colors of points in the plot, optional if \code{x} is an appropriate structure. Will be ignored if \code{highlight.3d = TRUE}.} \item{pch}{plotting "character", i.e. symbol to use.} \item{main}{an overall title for the plot.} \item{sub}{sub-title.} \item{xlim, ylim, zlim}{the x, y and z limits (min, max) of the plot. Note that setting enlarged limits may not work as exactly as expected (a known but unfixed bug).} \item{xlab, ylab, zlab}{titles for the x, y and z axis.} \item{scale.y}{scale of y axis related to x- and z axis.} \item{angle}{angle between x and y axis (Attention: result depends on scaling).} \item{axis}{a logical value indicating whether axes should be drawn on the plot.} \item{tick.marks}{a logical value indicating whether tick marks should be drawn on the plot (only if \code{axis = TRUE}).} \item{label.tick.marks}{a logical value indicating whether tick marks should be labeled on the plot (only if \code{axis = TRUE} and \code{tick.marks = TRUE}).} \item{x.ticklabs, y.ticklabs, z.ticklabs}{vector of tick mark labels.} \item{y.margin.add}{add additional space between tick mark labels and axis label of the y axis} \item{grid}{a logical value indicating whether a grid should be drawn on the plot.} \item{box}{a logical value indicating whether a box should be drawn around the plot.} \item{lab}{a numerical vector of the form c(x, y, len). The values of x and y give the (approximate) number of tickmarks on the x and y axes.} \item{lab.z}{the same as \code{lab}, but for z axis.} \item{type}{character indicating the type of plot: "p" for points, "l" for lines, "h" for vertical lines to x-y-plane, etc.} \item{highlight.3d}{points will be drawn in different colors related to y coordinates (only if \code{type = "p"} or \code{type = "h"}, else \code{color} will be used).\cr On some devices not all colors can be displayed. In this case try the postscript device or use \code{highlight.3d = FALSE}.} \item{mar}{A numerical vector of the form c(bottom, left, top, right) which gives the lines of margin to be specified on the four sides of the plot.} \item{col.axis, col.grid, col.lab}{the color to be used for axis / grid / axis labels.} \item{cex.symbols, cex.axis, cex.lab}{the magnification to be used for point symbols, axis annotation, labels relative to the current.} \item{font.axis, font.lab}{the font to be used for axis annotation / labels.} \item{lty.axis, lty.grid}{the line type to be used for axis / grid.} \item{lty.hide}{line style used to plot \sQuote{non-visible} edges (defaults of the \code{lty.axis} style)} \item{lty.hplot}{the line type to be used for vertical segments with \code{type = "h"}.} \item{log}{Not yet implemented! A character string which contains "x" (if the x axis is to be logarithmic), "y", "z", "xy", "xz", "yz", "xyz".} \item{\dots}{more graphical parameters can be given as arguments, \code{pch = 16} or \code{pch = 20} may be nice.} } \value{ \item{xyz.convert}{function which converts coordinates from 3D (x, y, z) to 2D-projection (x, y) of \code{scatterplot3d}. Useful to plot objects into existing plot.} \item{points3d}{function which draws points or lines into the existing plot.} \item{plane3d}{function which draws a plane into the existing plot: \code{plane3d(Intercept, x.coef = NULL, y.coef = NULL, lty = "dashed", lty.box = NULL, ...)}. Instead of \code{Intercept} a vector containing 3 elements or an (g)lm object can be specified. The argument \code{lty.box} allows to set a different line style for the intersecting lines in the box's walls.} \item{box3d}{function which "refreshes" the box surrounding the plot.} } \references{ Ligges, U., and Maechler, M. (2003): Scatterplot3d -- an R Package for Visualizing Multivariate Data. \emph{Journal of Statistical Software} 8(11), 1--20. \url{http://www.jstatsoft.org/} } \note{ Some graphical parameters should only be set as arguments in \code{scatterplot3d} but not in a previous \code{\link[graphics]{par}()} call. One of these is \code{mar}, which is also non-standard in another way: Users who want to extend an existing \code{scatterplot3d} graphic with another function than \code{points3d}, \code{plane3d} or \code{box3d}, should consider to set \code{par(mar = c(b, l, t, r))} to the value of \code{mar} used in \code{scatterplot3d}, which defaults to \code{c(5, 3, 4, 3) + 0.1}. Other \code{par} arguments may be split into several arguments in \code{scatterplot3d}, e.g., for specifying the line type. And finally some of \code{par} arguments do not apply here, e.g., many of those for axis calculation. So we recommend to try the specification of graphical parameters at first as arguments in \code{scatterplot3d} and only if needed as arguments in previous \code{par()} call. } \author{ Uwe Ligges \email{ligges@statistik.tu-dortmund.de}; \url{http://www.statistik.tu-dortmund.de/~ligges}. } \seealso{ \code{\link[graphics]{persp}}, \code{\link[graphics]{plot}}, \code{\link[graphics]{par}}. } \examples{ ## On some devices not all colors can be displayed. ## Try the postscript device or use highlight.3d = FALSE. ## example 1 z <- seq(-10, 10, 0.01) x <- cos(z) y <- sin(z) scatterplot3d(x, y, z, highlight.3d=TRUE, col.axis="blue", col.grid="lightblue", main="scatterplot3d - 1", pch=20) ## example 2 temp <- seq(-pi, 0, length = 50) x <- c(rep(1, 50) \%*\% t(cos(temp))) y <- c(cos(temp) \%*\% t(sin(temp))) z <- c(sin(temp) \%*\% t(sin(temp))) scatterplot3d(x, y, z, highlight.3d=TRUE, col.axis="blue", col.grid="lightblue", main="scatterplot3d - 2", pch=20) ## example 3 temp <- seq(-pi, 0, length = 50) x <- c(rep(1, 50) \%*\% t(cos(temp))) y <- c(cos(temp) \%*\% t(sin(temp))) z <- 10 * c(sin(temp) \%*\% t(sin(temp))) color <- rep("green", length(x)) temp <- seq(-10, 10, 0.01) x <- c(x, cos(temp)) y <- c(y, sin(temp)) z <- c(z, temp) color <- c(color, rep("red", length(temp))) scatterplot3d(x, y, z, color, pch=20, zlim=c(-2, 10), main="scatterplot3d - 3") ## example 4 my.mat <- matrix(runif(25), nrow=5) dimnames(my.mat) <- list(LETTERS[1:5], letters[11:15]) my.mat # the matrix we want to plot ... s3d.dat <- data.frame(cols=as.vector(col(my.mat)), rows=as.vector(row(my.mat)), value=as.vector(my.mat)) scatterplot3d(s3d.dat, type="h", lwd=5, pch=" ", x.ticklabs=colnames(my.mat), y.ticklabs=rownames(my.mat), color=grey(25:1/40), main="scatterplot3d - 4") ## example 5 data(trees) s3d <- scatterplot3d(trees, type="h", highlight.3d=TRUE, angle=55, scale.y=0.7, pch=16, main="scatterplot3d - 5") # Now adding some points to the "scatterplot3d" s3d$points3d(seq(10,20,2), seq(85,60,-5), seq(60,10,-10), col="blue", type="h", pch=16) # Now adding a regression plane to the "scatterplot3d" attach(trees) my.lm <- lm(Volume ~ Girth + Height) s3d$plane3d(my.lm, lty.box = "solid") ## example 6; by Martin Maechler cubedraw <- function(res3d, min = 0, max = 255, cex = 2, text. = FALSE) { ## Purpose: Draw nice cube with corners cube01 <- rbind(c(0,0,1), 0, c(1,0,0), c(1,1,0), 1, c(0,1,1), # < 6 outer c(1,0,1), c(0,1,0)) # <- "inner": fore- & back-ground cub <- min + (max-min)* cube01 ## visibile corners + lines: res3d$points3d(cub[c(1:6,1,7,3,7,5) ,], cex = cex, type = 'b', lty = 1) ## hidden corner + lines res3d$points3d(cub[c(2,8,4,8,6), ], cex = cex, type = 'b', lty = 3) if(text.)## debug text(res3d$xyz.convert(cub), labels=1:nrow(cub), col='tomato', cex=2) } ## 6 a) The named colors in R, i.e. colors() cc <- colors() crgb <- t(col2rgb(cc)) par(xpd = TRUE) rr <- scatterplot3d(crgb, color = cc, box = FALSE, angle = 24, xlim = c(-50, 300), ylim = c(-50, 300), zlim = c(-50, 300)) cubedraw(rr) ## 6 b) The rainbow colors from rainbow(201) rbc <- rainbow(201) Rrb <- t(col2rgb(rbc)) rR <- scatterplot3d(Rrb, color = rbc, box = FALSE, angle = 24, xlim = c(-50, 300), ylim = c(-50, 300), zlim = c(-50, 300)) cubedraw(rR) rR$points3d(Rrb, col = rbc, pch = 16) } \keyword{hplot} scatterplot3d/NAMESPACE0000744000175100001440000000002710201466316014301 0ustar hornikusersexport(scatterplot3d) scatterplot3d/po/0000755000175100001440000000000011544601042013476 5ustar hornikusersscatterplot3d/po/R-de.po0000744000175100001440000000151710743375422014644 0ustar hornikusersmsgid "" msgstr "" "Project-Id-Version: R 2.1.0\n" "Report-Msgid-Bugs-To: bugs@r-project.org\n" "POT-Creation-Date: 2005-02-06 15:50\n" "PO-Revision-Date: 2005-02-06 16:13+0100\n" "Last-Translator: Uwe Ligges \n" "Language-Team: \n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=iso-8859-1\n" "Content-Transfer-Encoding: 8bit\n" "X-Poedit-Language: German\n" "X-Poedit-Country: GERMANY\n" "X-Poedit-SourceCharset: iso-8859-1\n" msgid "color is ignored when highlight.3d = TRUE" msgstr "color wird ignoriert falls highlight.3d = TRUE" msgid "length(color)" msgstr "length(color)" msgid "must be equal length(x) or 1" msgstr "muss gleich length(x) oder 1 sein" msgid "no data left within (x|y|z)lim" msgstr "keine Daten innerhalb von der Grenzen (x|y|z)lim" msgid "length(pch)" msgstr "length(pch)" scatterplot3d/po/R-en.po0000744000175100001440000000112510743375440014651 0ustar hornikusersmsgid "" msgstr "" "Project-Id-Version: R 2.1.0\n" "Report-Msgid-Bugs-To: bugs@r-project.org\n" "POT-Creation-Date: 2005-02-06 15:50\n" "PO-Revision-Date: 2005-02-06 16:22+0100\n" "Last-Translator: Uwe Ligges \n" "Language-Team: \n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=iso-8859-1\n" "Content-Transfer-Encoding: 8bit\n" msgid "color is ignored when highlight.3d = TRUE" msgstr "" msgid "length(color)" msgstr "" msgid "must be equal length(x) or 1" msgstr "" msgid "no data left within (x|y|z)lim" msgstr "" msgid "length(pch)" msgstr "" scatterplot3d/po/R-scatterplot3d.pot0000744000175100001440000000115410201427252017214 0ustar hornikusersmsgid "" msgstr "" "Project-Id-Version: R 2.1.0\n" "Report-Msgid-Bugs-To: bugs@r-project.org\n" "POT-Creation-Date: 2005-02-06 15:50\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME \n" "Language-Team: LANGUAGE \n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=ASCII\n" "Content-Transfer-Encoding: 8bit\n" msgid "color is ignored when highlight.3d = TRUE" msgstr "" msgid "length(color)" msgstr "" msgid "must be equal length(x) or 1" msgstr "" msgid "no data left within (x|y|z)lim" msgstr "" msgid "length(pch)" msgstr "" scatterplot3d/R/0000755000175100001440000000000011544601042013261 5ustar hornikusersscatterplot3d/R/scatterplot3d.R0000744000175100001440000003531411462573567016231 0ustar hornikusersscatterplot3d <- function(x, y = NULL, z = NULL, color = par("col"), pch = NULL, main = NULL, sub = NULL, xlim = NULL, ylim = NULL, zlim = NULL, xlab = NULL, ylab = NULL, zlab = NULL, scale.y = 1, angle = 40, axis = TRUE, tick.marks = TRUE, label.tick.marks = TRUE, x.ticklabs = NULL, y.ticklabs = NULL, z.ticklabs = NULL, y.margin.add = 0, grid = TRUE, box = TRUE, lab = par("lab"), lab.z = mean(lab[1:2]), type = "p", highlight.3d = FALSE, mar = c(5, 3, 4, 3) + 0.1, col.axis = par("col.axis"), col.grid = "grey", col.lab = par("col.lab"), cex.symbols = par("cex"), cex.axis = 0.8 * par("cex.axis"), cex.lab = par("cex.lab"), font.axis = par("font.axis"), font.lab = par("font.lab"), lty.axis = par("lty"), lty.grid = par("lty"), lty.hide=NULL, lty.hplot = par("lty"), log = "", ...) # log not yet implemented { ## Uwe Ligges , ## http://www.statistik.tu-dortmund.de/~ligges ## ## For MANY ideas and improvements thanks to Martin Maechler!!! ## Parts of the help files are stolen from the standard plotting functions in R. mem.par <- par(mar = mar) x.scal <- y.scal <- z.scal <- 1 xlabel <- if (!missing(x)) deparse(substitute(x)) ylabel <- if (!missing(y)) deparse(substitute(y)) zlabel <- if (!missing(z)) deparse(substitute(z)) ## verification, init, ... if(highlight.3d && !missing(color)) warning("color is ignored when highlight.3d = TRUE") ## color as part of `x' (data.frame or list): if(!is.null(d <- dim(x)) && (length(d) == 2) && (d[2] >= 4)) color <- x[,4] else if(is.list(x) && !is.null(x$color)) color <- x$color ## convert 'anything' -> vector xyz <- xyz.coords(x=x, y=y, z=z, xlab=xlabel, ylab=ylabel, zlab=zlabel, log=log) if(is.null(xlab)) { xlab <- xyz$xlab; if(is.null(xlab)) xlab <- "" } if(is.null(ylab)) { ylab <- xyz$ylab; if(is.null(ylab)) ylab <- "" } if(is.null(zlab)) { zlab <- xyz$zlab; if(is.null(zlab)) zlab <- "" } if(length(color) == 1) color <- rep(color, length(xyz$x)) else if(length(color) != length(xyz$x)) stop("length(color) ", "must be equal length(x) or 1") angle <- (angle %% 360) / 90 yz.f <- scale.y * abs(if(angle < 1) angle else if(angle > 3) angle - 4 else 2 - angle) yx.f <- scale.y * (if(angle < 2) 1 - angle else angle - 3) if(angle > 2) { ## switch y and x axis to ensure righthand oriented coord. temp <- xyz$x; xyz$x <- xyz$y; xyz$y <- temp temp <- xlab; xlab <- ylab; ylab <- temp temp <- xlim; xlim <- ylim; ylim <- temp } angle.1 <- (1 < angle && angle < 2) || angle > 3 angle.2 <- 1 <= angle && angle <= 3 dat <- cbind(as.data.frame(xyz[c("x","y","z")]), col = color) ## xlim, ylim, zlim -- select the points inside the limits if(!is.null(xlim)) { xlim <- range(xlim) dat <- dat[ xlim[1] <= dat$x & dat$x <= xlim[2] , , drop = FALSE] } if(!is.null(ylim)) { ylim <- range(ylim) dat <- dat[ ylim[1] <= dat$y & dat$y <= ylim[2] , , drop = FALSE] } if(!is.null(zlim)) { zlim <- range(zlim) dat <- dat[ zlim[1] <= dat$z & dat$z <= zlim[2] , , drop = FALSE] } n <- nrow(dat) if(n < 1) stop("no data left within (x|y|z)lim") y.range <- range(dat$y[is.finite(dat$y)]) ### 3D-highlighting / colors / sort by y if(type == "p" || type == "h") { y.ord <- rev(order(dat$y)) dat <- dat[y.ord, ] if(length(pch) > 1) if(length(pch) != length(y.ord)) stop("length(pch) ", "must be equal length(x) or 1") else pch <- pch[y.ord] if(length(cex.symbols) > 1) if(length(cex.symbols) != length(y.ord)) stop("length(cex.symbols) ", "must be equal length(x) or 1") else cex.symbols <- cex.symbols[y.ord] daty <- dat$y daty[!is.finite(daty)] <- mean(daty[is.finite(daty)]) if(highlight.3d && !(all(diff(daty) == 0))) dat$col <- rgb(seq(0, 1, length = n) * (y.range[2] - daty) / diff(y.range), g=0, b=0) } ### optim. axis scaling p.lab <- par("lab") ## Y y.range <- range(dat$y[is.finite(dat$y)], ylim) y.prty <- pretty(y.range, n = lab[2], min.n = max(1, min(.5 * lab[2], p.lab[2]))) y.scal <- round(diff(y.prty[1:2]), digits = 12) y.add <- min(y.prty) dat$y <- (dat$y - y.add) / y.scal y.max <- (max(y.prty) - y.add) / y.scal if(!is.null(ylim)) y.max <- max(y.max, ceiling((ylim[2] - y.add) / y.scal)) # if(angle > 2) dat$y <- y.max - dat$y ## turn y-values around ## X x.range <- range(dat$x[is.finite(dat$x)], xlim) x.prty <- pretty(x.range, n = lab[1], min.n = max(1, min(.5 * lab[1], p.lab[1]))) x.scal <- round(diff(x.prty[1:2]), digits = 12) dat$x <- dat$x / x.scal x.range <- range(x.prty) / x.scal x.max <- ceiling(x.range[2]) x.min <- floor(x.range[1]) if(!is.null(xlim)) { x.max <- max(x.max, ceiling(xlim[2] / x.scal)) x.min <- min(x.min, floor(xlim[1] / x.scal)) } x.range <- range(x.min, x.max) ## Z z.range <- range(dat$z[is.finite(dat$z)], zlim) z.prty <- pretty(z.range, n = lab.z, min.n = max(1, min(.5 * lab.z, p.lab[2]))) z.scal <- round(diff(z.prty[1:2]), digits = 12) dat$z <- dat$z / z.scal z.range <- range(z.prty) / z.scal z.max <- ceiling(z.range[2]) z.min <- floor(z.range[1]) if(!is.null(zlim)) { z.max <- max(z.max, ceiling(zlim[2] / z.scal)) z.min <- min(z.min, floor(zlim[1] / z.scal)) } z.range <- range(z.min, z.max) ### init graphics plot.new() if(angle.2) {x1 <- x.min + yx.f * y.max; x2 <- x.max} else {x1 <- x.min; x2 <- x.max + yx.f * y.max} plot.window(c(x1, x2), c(z.min, z.max + yz.f * y.max)) temp <- strwidth(format(rev(y.prty))[1], cex = cex.axis/par("cex")) if(angle.2) x1 <- x1 - temp - y.margin.add else x2 <- x2 + temp + y.margin.add plot.window(c(x1, x2), c(z.min, z.max + yz.f * y.max)) if(angle > 2) par("usr" = par("usr")[c(2, 1, 3:4)]) usr <- par("usr") # we have to remind it for use in closures title(main, sub, ...) ### draw axis, tick marks, labels, grid, ... if(grid) { ## X i <- x.min:x.max segments(i, z.min, i + (yx.f * y.max), yz.f * y.max + z.min, col = col.grid, lty = lty.grid) ## Y i <- 0:y.max segments(x.min + (i * yx.f), i * yz.f + z.min, x.max + (i * yx.f), i * yz.f + z.min, col = col.grid, lty = lty.grid) } if(axis) { xx <- if(angle.2) c(x.min, x.max) else c(x.max, x.min) if(tick.marks) { ## tick marks xtl <- (z.max - z.min) * (tcl <- -par("tcl")) / 50 ztl <- (x.max - x.min) * tcl / 50 mysegs <- function(x0,y0, x1,y1) segments(x0,y0, x1,y1, col=col.axis, lty=lty.axis) ## Y i.y <- 0:y.max mysegs(yx.f * i.y - ztl + xx[1], yz.f * i.y + z.min, yx.f * i.y + ztl + xx[1], yz.f * i.y + z.min) ## X i.x <- x.min:x.max mysegs(i.x, -xtl + z.min, i.x, xtl + z.min) ## Z i.z <- z.min:z.max mysegs(-ztl + xx[2], i.z, ztl + xx[2], i.z) if(label.tick.marks) { ## label tick marks las <- par("las") mytext <- function(labels, side, at, ...) mtext(text = labels, side = side, at = at, line = -.5, col=col.lab, cex=cex.axis, font=font.lab, ...) ## X if(is.null(x.ticklabs)) x.ticklabs <- format(i.x * x.scal) mytext(x.ticklabs, side = 1, at = i.x) ## Z if(is.null(z.ticklabs)) z.ticklabs <- format(i.z * z.scal) mytext(z.ticklabs, side = if(angle.1) 4 else 2, at = i.z, adj = if(0 < las && las < 3) 1 else NA) ## Y temp <- if(angle > 2) rev(i.y) else i.y ## turn y-labels around if(is.null(y.ticklabs)) y.ticklabs <- format(y.prty) else if (angle > 2) y.ticklabs <- rev(y.ticklabs) text(i.y * yx.f + xx[1], i.y * yz.f + z.min, y.ticklabs, pos=if(angle.1) 2 else 4, offset=1, col=col.lab, cex=cex.axis/par("cex"), font=font.lab) } } ## axis and labels mytext2 <- function(lab, side, line, at) mtext(lab, side = side, line = line, at = at, col = col.lab, cex = cex.lab, font = font.axis, las = 0) ## X lines(c(x.min, x.max), c(z.min, z.min), col = col.axis, lty = lty.axis) mytext2(xlab, 1, line = 1.5, at = mean(x.range)) ## Y lines(xx[1] + c(0, y.max * yx.f), c(z.min, y.max * yz.f + z.min), col = col.axis, lty = lty.axis) mytext2(ylab, if(angle.1) 2 else 4, line= 0.5, at = z.min + y.max * yz.f) ## Z lines(xx[c(2,2)], c(z.min, z.max), col = col.axis, lty = lty.axis) mytext2(zlab, if(angle.1) 4 else 2, line= 1.5, at = mean(z.range)) if(box) { if(is.null(lty.hide)) lty.hide <- lty.axis ## X temp <- yx.f * y.max temp1 <- yz.f * y.max lines(c(x.min + temp, x.max + temp), c(z.min + temp1, z.min + temp1), col = col.axis, lty = lty.hide) lines(c(x.min + temp, x.max + temp), c(temp1 + z.max, temp1 + z.max), col = col.axis, lty = lty.axis) ## Y temp <- c(0, y.max * yx.f) temp1 <- c(0, y.max * yz.f) lines(temp + xx[2], temp1 + z.min, col = col.axis, lty = lty.hide) lines(temp + x.min, temp1 + z.max, col = col.axis, lty = lty.axis) ## Z temp <- yx.f * y.max temp1 <- yz.f * y.max lines(c(temp + x.min, temp + x.min), c(z.min + temp1, z.max + temp1), col = col.axis, lty = if(!angle.2) lty.hide else lty.axis) lines(c(x.max + temp, x.max + temp), c(z.min + temp1, z.max + temp1), col = col.axis, lty = if(angle.2) lty.hide else lty.axis) } } ### plot points x <- dat$x + (dat$y * yx.f) z <- dat$z + (dat$y * yz.f) col <- as.character(dat$col) if(type == "h") { z2 <- dat$y * yz.f + z.min segments(x, z, x, z2, col = col, cex = cex.symbols, lty = lty.hplot, ...) points(x, z, type = "p", col = col, pch = pch, cex = cex.symbols, ...) } else points(x, z, type = type, col = col, pch = pch, cex = cex.symbols, ...) ### box-lines in front of points (overlay) if(axis && box) { lines(c(x.min, x.max), c(z.max, z.max), col = col.axis, lty = lty.axis) lines(c(0, y.max * yx.f) + x.max, c(0, y.max * yz.f) + z.max, col = col.axis, lty = lty.axis) lines(xx[c(1,1)], c(z.min, z.max), col = col.axis, lty = lty.axis) } # par(mem.par) # we MUST NOT set the margins back ### Return Function Object ob <- ls() ## remove all unused objects from the result's enviroment: rm(list = ob[!ob %in% c("angle", "mar", "usr", "x.scal", "y.scal", "z.scal", "yx.f", "yz.f", "y.add", "z.min", "z.max", "x.min", "x.max", "y.max", "x.prty", "y.prty", "z.prty")]) rm(ob) invisible(list( xyz.convert = function(x, y=NULL, z=NULL) { xyz <- xyz.coords(x, y, z) if(angle > 2) { ## switch y and x axis to ensure righthand oriented coord. temp <- xyz$x; xyz$x <- xyz$y; xyz$y <- temp } y <- (xyz$y - y.add) / y.scal return(list(x = xyz$x / x.scal + yx.f * y, y = xyz$z / z.scal + yz.f * y)) }, points3d = function(x, y = NULL, z = NULL, type = "p", ...) { xyz <- xyz.coords(x, y, z) if(angle > 2) { ## switch y and x axis to ensure righthand oriented coord. temp <- xyz$x; xyz$x <- xyz$y; xyz$y <- temp } y2 <- (xyz$y - y.add) / y.scal x <- xyz$x / x.scal + yx.f * y2 y <- xyz$z / z.scal + yz.f * y2 mem.par <- par(mar = mar, usr = usr) on.exit(par(mem.par)) if(type == "h") { y2 <- z.min + yz.f * y2 segments(x, y, x, y2, ...) points(x, y, type = "p", ...) } else points(x, y, type = type, ...) }, plane3d = function(Intercept, x.coef = NULL, y.coef = NULL, lty = "dashed", lty.box = NULL, ...){ if(!is.atomic(Intercept) && !is.null(coef(Intercept))) Intercept <- coef(Intercept) if(is.null(lty.box)) lty.box <- lty if(is.null(x.coef) && length(Intercept) == 3){ x.coef <- Intercept[if(angle > 2) 3 else 2] y.coef <- Intercept[if(angle > 2) 2 else 3] Intercept <- Intercept[1] } mem.par <- par(mar = mar, usr = usr) on.exit(par(mem.par)) x <- x.min:x.max ltya <- c(lty.box, rep(lty, length(x)-2), lty.box) x.coef <- x.coef * x.scal z1 <- (Intercept + x * x.coef + y.add * y.coef) / z.scal z2 <- (Intercept + x * x.coef + (y.max * y.scal + y.add) * y.coef) / z.scal segments(x, z1, x + y.max * yx.f, z2 + yz.f * y.max, lty = ltya, ...) y <- 0:y.max ltya <- c(lty.box, rep(lty, length(y)-2), lty.box) y.coef <- (y * y.scal + y.add) * y.coef z1 <- (Intercept + x.min * x.coef + y.coef) / z.scal z2 <- (Intercept + x.max * x.coef + y.coef) / z.scal segments(x.min + y * yx.f, z1 + y * yz.f, x.max + y * yx.f, z2 + y * yz.f, lty = ltya, ...) }, box3d = function(...){ mem.par <- par(mar = mar, usr = usr) on.exit(par(mem.par)) lines(c(x.min, x.max), c(z.max, z.max), ...) lines(c(0, y.max * yx.f) + x.max, c(0, y.max * yz.f) + z.max, ...) lines(c(0, y.max * yx.f) + x.min, c(0, y.max * yz.f) + z.max, ...) lines(c(x.max, x.max), c(z.min, z.max), ...) lines(c(x.min, x.min), c(z.min, z.max), ...) lines(c(x.min, x.max), c(z.min, z.min), ...) } )) }