CVS commit: pkgsrc/math/R-compositions

["Makoto Fujiwara" <mef%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   mef
Date:           Sat Aug 28 05:30:45 UTC 2021

Modified Files:
        pkgsrc/math/R-compositions: Makefile distinfo

Log Message:
(math/R-compositions) Updated 1.40.2 to 2.0.2

Version 2.0-1.9001

Minor changes / Bugfixes:
  * functions that do not work with sticky classes are now wrapped
  (e.g. `anova()`)

Version 2.0-1.9000

Major change: sticky classes!
  Now objects of compositional classes do not miss their class
  when subsetting. For example, if `x` is an "acomp" object,
  x[1:2,] will also be an "acomp" object. Selection of columns work
  as well, but it is a bit more tricky. Check ?`[.acomp` for
  details. You can get skip this behaviour by setting
  setStickyClassOption(FALSE). The dollar notation `$` also works!

Added:
  * Limited support for using compositions classes as formal S4
  classes, for instance in slots of S4 classes expecting a
  "data.frame" or a "structure" (matrix or array).
  * self-invertibility: now "rmult" objects created by any
  transformation (cdt, clr, cpt, idt, ilr, ipt, iit, ilt, alr,
  apt) remember the original data and the transformation between
  them, and can be back-transformed with `backtransform`.
  * added cdt and idt methods for objects of class "factor" (returning
  the contrasts and their ipt transformation), and for "data.frame"
  objects (exploiting the attribute "origClass" if they have it).
  * `pwlr()`: pairwise logratio transformation (and inverse: `pwlrInv()`)
  * `pwlrPlot()`: pairwise logratio plots vs covariables, both as explained
   and as explanatory variables. This makes use of the ability of plot(x~y)
  to react to the nature of `x` and `y` to create scatterplots, boxplots
  and spineplots.
  * transformation functions between variation and clrvar: variation2clrvar
  and clrvar2variation
  * `split()` methods for compositional classes
  * new panels for filling `pairs()` plots with boxplots, densities,
  kde2d-densities, etc...: check ?vp.kde2dplot

Minor Changes:
  * the function to fit linear models of coregionalisation is now called
  `fit.lmc()`; use full name specification with it! `compositions::fit.lmc()`

Bugfixes:
  * bug in subsetting of one-column rmult object corected


To generate a diff of this commit:
cvs rdiff -u -r1.1 -r1.2 pkgsrc/math/R-compositions/Makefile \
    pkgsrc/math/R-compositions/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/math/R-compositions/Makefile
diff -u pkgsrc/math/R-compositions/Makefile:1.1 pkgsrc/math/R-compositions/Makefile:1.2
--- pkgsrc/math/R-compositions/Makefile:1.1     Fri Aug  9 15:50:05 2019
+++ pkgsrc/math/R-compositions/Makefile Sat Aug 28 05:30:45 2021
@@ -1,8 +1,7 @@
-# $NetBSD: Makefile,v 1.1 2019/08/09 15:50:05 brook Exp $
+# $NetBSD: Makefile,v 1.2 2021/08/28 05:30:45 mef Exp $
 
 R_PKGNAME=     compositions
-R_PKGVER=      1.40-2
-CATEGORIES=    math
+R_PKGVER=      2.0-2
 
 MAINTAINER=    pkgsrc-users%NetBSD.org@localhost
 COMMENT=       Compositional data analysis
@@ -13,6 +12,10 @@ DEPENDS+=    R-energy>=1.7.6:../../math/R-e
 DEPENDS+=      R-robustbase>=0.93.5:../../math/R-robustbase
 DEPENDS+=      R-tensorA>=0.36.1:../../math/R-tensorA
 
+# Packages suggested but not available: 'rgl', 'combinat'
+#TEST_DEPENDS+=        R-rgl-[0-9]*:../..
+#TEST_DEPENDS+=        R-combinat-[0-9]*:../..
+
 USE_LANGUAGES= c fortran
 
 .include "../../math/R/Makefile.extension"
Index: pkgsrc/math/R-compositions/distinfo
diff -u pkgsrc/math/R-compositions/distinfo:1.1 pkgsrc/math/R-compositions/distinfo:1.2
--- pkgsrc/math/R-compositions/distinfo:1.1     Fri Aug  9 15:50:05 2019
+++ pkgsrc/math/R-compositions/distinfo Sat Aug 28 05:30:45 2021
@@ -1,6 +1,6 @@
-$NetBSD: distinfo,v 1.1 2019/08/09 15:50:05 brook Exp $
+$NetBSD: distinfo,v 1.2 2021/08/28 05:30:45 mef Exp $
 
-SHA1 (R/compositions_1.40-2.tar.gz) = 8fe5f70401f4a4daf44c649e210f5f9bd663c270
-RMD160 (R/compositions_1.40-2.tar.gz) = dff95b6b41104b17a9f50b9fbf6c9b3482e8b324
-SHA512 (R/compositions_1.40-2.tar.gz) = c5b39eb71dbfadae3a4dccb9f19309ccc3297be39a5ab1ce63e50317a64b0beb7e62d3e1edaf9cb2cf33b0cd00ef27fadb5c442d62eb24eaf04cc304265bec12
-Size (R/compositions_1.40-2.tar.gz) = 792954 bytes
+SHA1 (R/compositions_2.0-2.tar.gz) = 07aef5c2a57d7728870fe5a266090cbe8c7c31d8
+RMD160 (R/compositions_2.0-2.tar.gz) = deae014cd47a693ce9d42c3e769916c8bcbfb524
+SHA512 (R/compositions_2.0-2.tar.gz) = f3484aeba165891a39cec95d5eb700d475e71f7bde063bc223fb88642b582897599a4480c75cbc43722437fd907a6565f1a58694f4b99a37d676d4cda5a5c867
+Size (R/compositions_2.0-2.tar.gz) = 1168643 bytes