[Sciviews-commits] r251 - in pkg: . SciViews SciViews/R SciViews/inst SciViews/inst/doc SciViews/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Mar 18 16:05:26 CET 2010
Author: phgrosjean
Date: 2010-03-18 16:05:26 +0100 (Thu, 18 Mar 2010)
New Revision: 251
Added:
pkg/SciViews/
pkg/SciViews/COPYING
pkg/SciViews/DESCRIPTION
pkg/SciViews/NAMESPACE
pkg/SciViews/NEWS
pkg/SciViews/R/
pkg/SciViews/R/colors.R
pkg/SciViews/R/correlation.R
pkg/SciViews/R/ln.R
pkg/SciViews/R/panels.R
pkg/SciViews/R/panels.diag.R
pkg/SciViews/R/pcomp.R
pkg/SciViews/R/vectorplot.R
pkg/SciViews/TODO
pkg/SciViews/inst/
pkg/SciViews/inst/CITATION
pkg/SciViews/inst/doc/
pkg/SciViews/inst/doc/correlation.lyx
pkg/SciViews/inst/doc/pca.lyx
pkg/SciViews/man/
pkg/SciViews/man/SciViews-package.Rd
pkg/SciViews/man/colors.Rd
pkg/SciViews/man/correlation.Rd
pkg/SciViews/man/ln.Rd
pkg/SciViews/man/panels.Rd
pkg/SciViews/man/panels.diag.Rd
pkg/SciViews/man/pcomp.Rd
pkg/SciViews/man/snippets.Rd
pkg/SciViews/man/vectorplot.Rd
Log:
Create the SciViews package
Added: pkg/SciViews/COPYING
===================================================================
--- pkg/SciViews/COPYING (rev 0)
+++ pkg/SciViews/COPYING 2010-03-18 15:05:26 UTC (rev 251)
@@ -0,0 +1,340 @@
+ GNU GENERAL PUBLIC LICENSE
+ Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+ 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+ Preamble
+
+ The licenses for most software are designed to take away your
+freedom to share and change it. By contrast, the GNU General Public
+License is intended to guarantee your freedom to share and change free
+software--to make sure the software is free for all its users. This
+General Public License applies to most of the Free Software
+Foundation's software and to any other program whose authors commit to
+using it. (Some other Free Software Foundation software is covered by
+the GNU Library General Public License instead.) You can apply it to
+your programs, too.
+
+ When we speak of free software, we are referring to freedom, not
+price. Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+this service if you wish), that you receive source code or can get it
+if you want it, that you can change the software or use pieces of it
+in new free programs; and that you know you can do these things.
+
+ To protect your rights, we need to make restrictions that forbid
+anyone to deny you these rights or to ask you to surrender the rights.
+These restrictions translate to certain responsibilities for you if you
+distribute copies of the software, or if you modify it.
+
+ For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must give the recipients all the rights that
+you have. You must make sure that they, too, receive or can get the
+source code. And you must show them these terms so they know their
+rights.
+
+ We protect your rights with two steps: (1) copyright the software, and
+(2) offer you this license which gives you legal permission to copy,
+distribute and/or modify the software.
+
+ Also, for each author's protection and ours, we want to make certain
+that everyone understands that there is no warranty for this free
+software. If the software is modified by someone else and passed on, we
+want its recipients to know that what they have is not the original, so
+that any problems introduced by others will not reflect on the original
+authors' reputations.
+
+ Finally, any free program is threatened constantly by software
+patents. We wish to avoid the danger that redistributors of a free
+program will individually obtain patent licenses, in effect making the
+program proprietary. To prevent this, we have made it clear that any
+patent must be licensed for everyone's free use or not licensed at all.
+
+ The precise terms and conditions for copying, distribution and
+modification follow.
+
+ GNU GENERAL PUBLIC LICENSE
+ TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+ 0. This License applies to any program or other work which contains
+a notice placed by the copyright holder saying it may be distributed
+under the terms of this General Public License. The "Program", below,
+refers to any such program or work, and a "work based on the Program"
+means either the Program or any derivative work under copyright law:
+that is to say, a work containing the Program or a portion of it,
+either verbatim or with modifications and/or translated into another
+language. (Hereinafter, translation is included without limitation in
+the term "modification".) Each licensee is addressed as "you".
+
+Activities other than copying, distribution and modification are not
+covered by this License; they are outside its scope. The act of
+running the Program is not restricted, and the output from the Program
+is covered only if its contents constitute a work based on the
+Program (independent of having been made by running the Program).
+Whether that is true depends on what the Program does.
+
+ 1. You may copy and distribute verbatim copies of the Program's
+source code as you receive it, in any medium, provided that you
+conspicuously and appropriately publish on each copy an appropriate
+copyright notice and disclaimer of warranty; keep intact all the
+notices that refer to this License and to the absence of any warranty;
+and give any other recipients of the Program a copy of this License
+along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and
+you may at your option offer warranty protection in exchange for a fee.
+
+ 2. You may modify your copy or copies of the Program or any portion
+of it, thus forming a work based on the Program, and copy and
+distribute such modifications or work under the terms of Section 1
+above, provided that you also meet all of these conditions:
+
+ a) You must cause the modified files to carry prominent notices
+ stating that you changed the files and the date of any change.
+
+ b) You must cause any work that you distribute or publish, that in
+ whole or in part contains or is derived from the Program or any
+ part thereof, to be licensed as a whole at no charge to all third
+ parties under the terms of this License.
+
+ c) If the modified program normally reads commands interactively
+ when run, you must cause it, when started running for such
+ interactive use in the most ordinary way, to print or display an
+ announcement including an appropriate copyright notice and a
+ notice that there is no warranty (or else, saying that you provide
+ a warranty) and that users may redistribute the program under
+ these conditions, and telling the user how to view a copy of this
+ License. (Exception: if the Program itself is interactive but
+ does not normally print such an announcement, your work based on
+ the Program is not required to print an announcement.)
+
+These requirements apply to the modified work as a whole. If
+identifiable sections of that work are not derived from the Program,
+and can be reasonably considered independent and separate works in
+themselves, then this License, and its terms, do not apply to those
+sections when you distribute them as separate works. But when you
+distribute the same sections as part of a whole which is a work based
+on the Program, the distribution of the whole must be on the terms of
+this License, whose permissions for other licensees extend to the
+entire whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest
+your rights to work written entirely by you; rather, the intent is to
+exercise the right to control the distribution of derivative or
+collective works based on the Program.
+
+In addition, mere aggregation of another work not based on the Program
+with the Program (or with a work based on the Program) on a volume of
+a storage or distribution medium does not bring the other work under
+the scope of this License.
+
+ 3. You may copy and distribute the Program (or a work based on it,
+under Section 2) in object code or executable form under the terms of
+Sections 1 and 2 above provided that you also do one of the following:
+
+ a) Accompany it with the complete corresponding machine-readable
+ source code, which must be distributed under the terms of Sections
+ 1 and 2 above on a medium customarily used for software interchange; or,
+
+ b) Accompany it with a written offer, valid for at least three
+ years, to give any third party, for a charge no more than your
+ cost of physically performing source distribution, a complete
+ machine-readable copy of the corresponding source code, to be
+ distributed under the terms of Sections 1 and 2 above on a medium
+ customarily used for software interchange; or,
+
+ c) Accompany it with the information you received as to the offer
+ to distribute corresponding source code. (This alternative is
+ allowed only for noncommercial distribution and only if you
+ received the program in object code or executable form with such
+ an offer, in accord with Subsection b above.)
+
+The source code for a work means the preferred form of the work for
+making modifications to it. For an executable work, complete source
+code means all the source code for all modules it contains, plus any
+associated interface definition files, plus the scripts used to
+control compilation and installation of the executable. However, as a
+special exception, the source code distributed need not include
+anything that is normally distributed (in either source or binary
+form) with the major components (compiler, kernel, and so on) of the
+operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering
+access to copy from a designated place, then offering equivalent
+access to copy the source code from the same place counts as
+distribution of the source code, even though third parties are not
+compelled to copy the source along with the object code.
+
+ 4. You may not copy, modify, sublicense, or distribute the Program
+except as expressly provided under this License. Any attempt
+otherwise to copy, modify, sublicense or distribute the Program is
+void, and will automatically terminate your rights under this License.
+However, parties who have received copies, or rights, from you under
+this License will not have their licenses terminated so long as such
+parties remain in full compliance.
+
+ 5. You are not required to accept this License, since you have not
+signed it. However, nothing else grants you permission to modify or
+distribute the Program or its derivative works. These actions are
+prohibited by law if you do not accept this License. Therefore, by
+modifying or distributing the Program (or any work based on the
+Program), you indicate your acceptance of this License to do so, and
+all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+ 6. Each time you redistribute the Program (or any work based on the
+Program), the recipient automatically receives a license from the
+original licensor to copy, distribute or modify the Program subject to
+these terms and conditions. You may not impose any further
+restrictions on the recipients' exercise of the rights granted herein.
+You are not responsible for enforcing compliance by third parties to
+this License.
+
+ 7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues),
+conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License. If you cannot
+distribute so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you
+may not distribute the Program at all. For example, if a patent
+license would not permit royalty-free redistribution of the Program by
+all those who receive copies directly or indirectly through you, then
+the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under
+any particular circumstance, the balance of the section is intended to
+apply and the section as a whole is intended to apply in other
+circumstances.
+
+It is not the purpose of this section to induce you to infringe any
+patents or other property right claims or to contest validity of any
+such claims; this section has the sole purpose of protecting the
+integrity of the free software distribution system, which is
+implemented by public license practices. Many people have made
+generous contributions to the wide range of software distributed
+through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing
+to distribute software through any other system and a licensee cannot
+impose that choice.
+
+This section is intended to make thoroughly clear what is believed to
+be a consequence of the rest of this License.
+
+ 8. If the distribution and/or use of the Program is restricted in
+certain countries either by patents or by copyrighted interfaces, the
+original copyright holder who places the Program under this License
+may add an explicit geographical distribution limitation excluding
+those countries, so that distribution is permitted only in or among
+countries not thus excluded. In such case, this License incorporates
+the limitation as if written in the body of this License.
+
+ 9. The Free Software Foundation may publish revised and/or new versions
+of the General Public License from time to time. Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+Each version is given a distinguishing version number. If the Program
+specifies a version number of this License which applies to it and "any
+later version", you have the option of following the terms and conditions
+either of that version or of any later version published by the Free
+Software Foundation. If the Program does not specify a version number of
+this License, you may choose any version ever published by the Free Software
+Foundation.
+
+ 10. If you wish to incorporate parts of the Program into other free
+programs whose distribution conditions are different, write to the author
+to ask for permission. For software which is copyrighted by the Free
+Software Foundation, write to the Free Software Foundation; we sometimes
+make exceptions for this. Our decision will be guided by the two goals
+of preserving the free status of all derivatives of our free software and
+of promoting the sharing and reuse of software generally.
+
+ NO WARRANTY
+
+ 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
+OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
+PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
+OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS
+TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE
+PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
+REPAIR OR CORRECTION.
+
+ 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
+REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
+INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
+OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
+TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
+YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
+PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+convey the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program; if not, write to the Free Software
+ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this
+when it starts in an interactive mode:
+
+ Gnomovision version 69, Copyright (C) year name of author
+ Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use may
+be called something other than `show w' and `show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the program, if
+necessary. Here is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+ `Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ <signature of Ty Coon>, 1 April 1989
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Library General
+Public License instead of this License.
Property changes on: pkg/SciViews/COPYING
___________________________________________________________________
Name: svn:executable
+ *
Added: pkg/SciViews/DESCRIPTION
===================================================================
--- pkg/SciViews/DESCRIPTION (rev 0)
+++ pkg/SciViews/DESCRIPTION 2010-03-18 15:05:26 UTC (rev 251)
@@ -0,0 +1,13 @@
+Package: SciViews
+Type: Package
+Title: SciViews GUI API - Main package
+Imports: ellipse
+Depends: R (>= 2.6.0), stats, grDevices, graphics, MASS
+Description: Functions to install SciViews additions to R, and more (various) tools
+Version: 0.9-1
+Date: 2010-02-15
+Author: Philippe Grosjean
+Maintainer: Philippe Grosjean <phgrosjean at sciviews.org>
+License: GPL (>= 2)
+LazyLoad: yes
+URL: http://www.sciviews.org/SciViews-R
Property changes on: pkg/SciViews/DESCRIPTION
___________________________________________________________________
Name: svn:executable
+ *
Added: pkg/SciViews/NAMESPACE
===================================================================
--- pkg/SciViews/NAMESPACE (rev 0)
+++ pkg/SciViews/NAMESPACE 2010-03-18 15:05:26 UTC (rev 251)
@@ -0,0 +1,54 @@
+import(stats, grDevices, graphics, MASS, ellipse)
+
+export(correlation,
+ is.correlation,
+ as.correlation,
+ cwm.colors,
+ rwb.colors,
+ ryg.colors,
+ e,
+ ln,
+ ln1p,
+ lg,
+ lg1p,
+ panel.boxplot,
+ panel.density,
+ panel.hist,
+ panel.qqnorm,
+ panel.cor,
+ panel.ellipse,
+ panel.reg,
+ pcomp,
+ scores,
+ vectorplot)
+
+S3method(vectorplot, default)
+S3method(vectorplot, loadings)
+S3method(vectorplot, correlation)
+
+S3method(correlation, formula)
+S3method(correlation, default)
+
+S3method(print, correlation)
+S3method(summary, correlation)
+S3method(print, summary.correlation)
+S3method(plot, correlation)
+S3method(lines, correlation)
+
+S3method(pcomp, formula)
+S3method(pcomp, default)
+
+S3method(print, pcomp)
+S3method(summary, pcomp)
+S3method(print, summary.pcomp)
+S3method(plot, pcomp)
+S3method(points, pcomp)
+S3method(lines, pcomp)
+S3method(text, pcomp)
+S3method(screeplot, pcomp)
+S3method(biplot, pcomp)
+S3method(predict, pcomp)
+#S3method(loadings, pcomp) # This is NOT a generic function, but it works well on pcomp
+S3method(pairs, pcomp)
+S3method(scores, pcomp)
+S3method(correlation, pcomp)
Property changes on: pkg/SciViews/NAMESPACE
___________________________________________________________________
Name: svn:executable
+ *
Added: pkg/SciViews/NEWS
===================================================================
--- pkg/SciViews/NEWS (rev 0)
+++ pkg/SciViews/NEWS 2010-03-18 15:05:26 UTC (rev 251)
@@ -0,0 +1,19 @@
+= SciViews News
+
+== SciViews version 0.9-0
+
+This is the first version on R-forge. There used to ba a SciViews **bundle**
+that contained svMisc, svSocket, svIDE, svGUI, ..., but bundles are obsolete
+now. The new SciViews package plays a similar role as the bundle, i.e., it is
+a convenient way to install all SciViews-R packages with one instruction:
+
+> install.packages("SciViews", dependencies = TRUE).
+
+It now plays also other roles: (1) to load all SciViews requirements with a
+single instruction:
+
+> require(SciViews)
+
+(2) To make sure to reconfigure the socket server properly (that is, with the
+same configuration as latest one), (3) To provides a series of R functions that
+ease learning of R through the use of the R reference toolbox in Komodo Edit.
Property changes on: pkg/SciViews/NEWS
___________________________________________________________________
Name: svn:executable
+ *
Added: pkg/SciViews/R/colors.R
===================================================================
--- pkg/SciViews/R/colors.R (rev 0)
+++ pkg/SciViews/R/colors.R 2010-03-18 15:05:26 UTC (rev 251)
@@ -0,0 +1,33 @@
+# We often need a red-white-blue color ramp, or a red-yellow-green one
+# So, define rwb.colors() and ryg.colors()
+rwb.colors <- function (n, alpha = 1, gamma = 1, s = 0.9, v = 0.9)
+{
+ if ((n <- as.integer(n[1L])) <= 0) return(character(0L))
+ # Define the initial (red) and final (blue) colors with white in between
+ cols <- c(hsv(0, s, v, gamma, alpha), # Red
+ hsv(0, 0, v, gamma, alpha), # White
+ hsv(2/3, s, v, gamma, alpha)) # Blue
+ # Use a color ramp from red to white to blue
+ return(colorRampPalette(cols)(n))
+}
+
+# Red-yellow-green palette (take care for color-blind people here)!
+ryg.colors <- function (n, alpha = 1, gamma = 1, s = 0.9, v = 0.9)
+{
+ # This is essentially rainbow(), but going from 0 (red) to 2/6 (green)
+ return(rainbow(n, s = s, v = v, start = 0, end = 2/6, gamma = gamma,
+ alpha = alpha))
+}
+
+# Slighly different than cm.colors(), allowing for s, v and gamma!
+# Produce probably better results on a CMYK device (color printer)?
+cwm.colors <- function (n, alpha = 1, gamma = 1, s = 0.9, v = 0.9)
+{
+ if ((n <- as.integer(n[1L])) <= 0) return(character(0L))
+ # Define the initial (red) and final (blue) colors with white in between
+ cols <- c(hsv(1/2, s, v, gamma, alpha), # Cyan
+ hsv(0, 0, v, gamma, alpha), # White
+ hsv(5/6, s, v, gamma, alpha)) # Magenta
+ # Use a color ramp from red to white to blue
+ return(colorRampPalette(cols)(n))
+}
Property changes on: pkg/SciViews/R/colors.R
___________________________________________________________________
Name: svn:executable
+ *
Added: pkg/SciViews/R/correlation.R
===================================================================
--- pkg/SciViews/R/correlation.R (rev 0)
+++ pkg/SciViews/R/correlation.R 2010-03-18 15:05:26 UTC (rev 251)
@@ -0,0 +1,280 @@
+# A wrapper around cor() and the like, building a "correlation" S3 object
+# TODO: cov.wt(), cov2correlation(), and perhaps, functions cov.XXX() from MASS
+# TODO: max, min, range, which.max, which.min for 'correlation' objects that do
+# not consider elements on the diagonal... or put something else to avoid it is
+# extracted for max, or which.max??? + something like 'highest' which considers
+# the absolute value??? How to deal with that?
+
+# A generic function to calculate correlation from an object
+correlation <- function (x, ...)
+ UseMethod("correlation")
+
+correlation.formula <- function (formula, data = NULL, subset, na.action, ...)
+{
+ mt <- terms(formula, data = data)
+ if (attr(mt, "response") > 0L)
+ stop("response not allowed in formula")
+ cl <- match.call()
+ mf <- match.call(expand.dots = FALSE)
+ mf$... <- NULL
+ mf[[1L]] <- as.name("model.frame")
+ mf <- eval.parent(mf)
+ if (stats:::.check_vars_numeric(mf))
+ stop("Correlation applies only to numerical variables")
+ mt <- attr(mf, "terms")
+ attr(mt, "intercept") <- 0L
+ x <- model.matrix(mt, mf)
+ res <- correlation.default(x, ...)
+ cl[[1L]] <- as.name("correlation")
+ attr(res, "call") <- cl
+ attr(res, "na.method") <- NULL
+ if (!is.null(na.action))
+ attr(res, "na.action") <- as.character(na.action)
+ res
+}
+
+# Create the 'correlation' object (same arguments as cor() in stats package)
+correlation.default <- function (x, y = NULL, use = "everything",
+method = c("pearson", "kendall", "spearman"), ...)
+{
+ Call <- match.call()
+ x <- as.matrix(x)
+ na.methods <- c("all.obs", "complete.obs", "pairwise.complete.obs",
+ "everything", "na.or.complete")
+ na.method <- pmatch(use, na.methods)
+ method <- match.arg(method)
+
+ # Just call cor in stats package
+ res <- stats:::cor(x = x, y = y, use = use, method = method)
+
+ # We want to return a correlation matrix, even if there is one correlation
+ if (length(res) == 1) {
+ # Create a simple correlation matrix using 'x' and 'y' as labels
+ res <- matrix(c(1, res, res, 1), ncol = 2,
+ dimnames = list(c("x", "y"), c("x", "y")))
+ }
+
+ # Same strings as for cor.test()
+ attr(res, "method") <- switch(method,
+ pearson = "Pearson's product-moment correlation",
+ kendall = "Kendall's rank correlation tau",
+ spearman = "Spearman's rank correlation rho",
+ method)
+ attr(res, "na.method") <- na.methods[na.method]
+ attr(res, "call") <- Call
+ class(res) <- c("correlation", "matrix")
+
+ return(res)
+}
+
+# Check if an object is a correlation matrix
+is.correlation <- function (x)
+ return(inherits(x, "correlation"))
+
+# Transform a square matrix or a data.frame with values between -1 and 1
+# in a 'correlation' object
+# TODO: should we keep more attributes, in order to document other correlation
+# calculations?
+as.correlation <- function (x) {
+ if (is.correlation(x)) return(x)
+
+ # Make sure we have a matrix with numeric data, dimnames and nothing else
+ # (drop all other arguments, except 'comment', perhaps)
+ res <- structure(as.numeric(x), dim = dim(x), dimnames = dimnames(x))
+
+ # Check that it is a square (2D) matrix, or an atomic number
+ d <- dim(x)
+ if (is.null(d)) {
+ # Is this an atomic number?
+ if (length(x) == 1) {
+ # Create the simplest correlation matrix using generic 'x' and 'y' labels
+ res <- matrix(c(1, res, res, 1), ncol = 2,
+ dimnames = list(c("x", "y"), c("x", "y")))
+ }
+ } else { # Check that it is a square matrix
+ if (length(d) != 2 || d[1] != d[2])
+ stop("x must be a square matrix")
+ }
+
+ # Check the range that must be between -1 and 1
+ rg <- range(res, na.rm = TRUE)
+ if (rg[1] < -1 || rg[2] > 1)
+ stop("A correlation matrix cannot have values lower than -1 or larger than 1")
+
+ # Reinject comment, if it exists
+ comment(res) <- comment(x)
+
+ # Look for a "method" attribute
+ attr(res, "method") <- attr(x, "method")
+ # and a na.method, or na.action attribute
+ attr(res, "na.action") <- attr(x, "na.action")
+ attr(res, "na.method") <- attr(x, "na.method")
+
+ # Set this as both a 'correlation' and 'matrix' S3 object
+ class(res) <- c("correlation", "matrix")
+
+ return(res)
+}
+
+# Print a 'correlation' object
+print.correlation <- function (x, digits = 3, cutoff = 0, ...)
+{
+ if (!is.correlation(x))
+ stop("x must be a 'correlation' object (correlation matrix)")
+
+ method <- attr(x, "method")
+ if (is.null(method)) {
+ cat("Correlation matrix:\n")
+ } else {
+ cat("Matrix of ", method, ":\n", sep = "")
+ }
+
+ na.method <- attr(x, "na.method")
+ if (!is.null(na.method)) {
+ cat("(calculation uses ", na.method, ")\n", sep = "")
+ } else {
+ na.action <- attr(x, "na.action")
+ if (!is.null(na.action))
+ cat("(missing values are managed with ", na.action, ")\n", sep = "")
+ }
+ cform <- format(round(x, digits = digits))
+ nc <- nchar(cform[1L], type = "c")
+ cform[abs(x) < cutoff] <- paste(rep(" ", nc), collapse = "")
+ print(cform, quote = FALSE, ...)
+
+ return(invisible(x))
+}
+
+# Summary of a 'correlation' object
+summary.correlation <- function (object, cutpoints = c(0.3, 0.6, 0.8, 0.9, 0.95),
+symbols = c(" ", ".", ",", "+", "*", "B"), ...)
+{
+ # Replace the correlation matrix by symbols using symnum()
+ res <- symnum(unclass(object), cutpoints = cutpoints, symbols = symbols,
+ corr = TRUE, ...)
+
+ # Reinject comment, if it exists
+ comment(res) <- comment(object)
+
+ # Look for a "method" attribute
+ attr(res, "method") <- attr(object, "method")
+ # and na.action/na.method attributes
+ attr(res, "na.action") <- attr(object, "na.action")
+ attr(res, "na.method") <- attr(object, "na.method")
+
+ # Set this as 'summary.correlation' object
+ class(res) <- c("summary.correlation", "noquote")
+
+ return(res)
+}
+
+# And printing method for the 'summary.correlation' object
+print.summary.correlation <- function (x, ...)
+{
+ method <- attr(x, "method")
+ if (is.null(method)) {
+ cat("Correlation matrix:\n")
+ } else {
+ cat("Matrix of ", method, ":\n", sep = "")
+ }
+
+ na.method <- attr(x, "na.method")
+ if (!is.null(na.method)) {
+ cat("(calculation uses ", na.method, ")\n", sep = "")
+ } else {
+ na.action <- attr(x, "na.action")
+ if (!is.null(na.action))
+ cat("(missing values are managed with ", na.action, ")\n", sep = "")
+ }
+
+ print(structure(as.character(x), dim = dim(x), dimnames = dimnames(x),
+ legend = attr(x, "legend"), class = "noquote"), ...)
+
+ return(invisible(x))
+}
+
+# Plot a 'correlation' object (basically the ellipse's plotcorr() function, but
+# as plot() method for 'corr' object and with different default values
+# Also, numbers are printed inside the ellipses with numbers = TRUE
+# TODO: change the way labels are plotted
+# TODO: a comparison plot, when y is not NULL
+plot.correlation <- function (x, y = NULL, outline = TRUE,
+cutpoints = c(0.3, 0.6, 0.8, 0.9, 0.95), palette = rwb.colors, col = NULL,
+numbers = TRUE, digits = 2, type = c("full", "lower", "upper"),
+diag = (type == "full"), cex.lab = par("cex.lab"), cex = 0.75 * par("cex"), ...)
+{
+ if (!is.correlation(x))
+ stop("x must be a 'correlation' object")
+
+ type <- match.arg(type)
+ diag <- as.logical(diag[1])
+ # Compute colors from cutpoints and palette
+ if (is.null(col)) {
+ # -1.1 to include -1 - intervals are (,]
+ # cutpoints - 0.0001 for positive values to include lower limits instead
+ br <- c(-1.1, rev(-cutpoints), cutpoints - 0.0001, 1)
+ ct <- cut(x, breaks = br)
+ col <- palette(length(levels(ct)))[as.numeric(ct)]
+ }
+
+ # Call the plotcorr() function from ellipse package
+ plotcorr(x, outline = outline, col = col, numbers = FALSE, type = type,
+ diag = diag, cex.lab = cex.lab, cex = cex, ...)
+ # Do we print the numbers inside the ellipses?
+ if (isTRUE(numbers)) {
+ coords <- expand.grid(1:nrow(x), nrow(x):1)
+ labels <- format(round(x, digits = digits), digits = digits)
+ # Do we plotted only upper or lower triangle and diagonal?
+ # Note: we need to invert y-coordinates!
+ yinv <- max(coords) + 1 - coords[, 2]
+ if (diag) {
+ if (type == "lower") {
+ # Keep only lower triangle + diagonal
+ coords <- coords[coords[, 1] <= yinv, ]
+ coords <- coords[order(coords[, 1]), ]
+ labels <- labels[lower.tri(labels, diag = TRUE)]
+ } else if (type == "upper") {
+ # Keep only upper triangle
+ coords <- coords[coords[, 1] >= yinv, ]
+ coords <- coords[order(coords[, 1]), ]
+ labels <- labels[upper.tri(labels, diag = TRUE)]
+ }
+ } else { # No diagonals
+ if (type == "lower") {
+ # Keep only lower triangle
+ coords <- coords[coords[, 1] < yinv, ]
+ coords <- coords[order(coords[, 1]), ]
+ labels <- labels[lower.tri(labels)]
+ } else if (type == "upper") {
+ # Keep only upper triangle
+ coords <- coords[coords[, 1] > yinv - 1, ]
+ coords <- coords[order(coords[, 1]), ]
+ coords[, 2] <- coords[, 2] - 1
+ labels <- labels[upper.tri(labels)]
+ } else {
+ # Plot everything, except diagonal => put test to "" there
+ diag(labels) <- ""
+ }
+ }
+ text(coords, labels = labels, cex = cex, ...)
+ }
+ return(invisible())
+}
+
+# Add vectors for supplementary variables in a PCA correlation plot
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/sciviews -r 251
More information about the Sciviews-commits
mailing list