version 1.2.1

cran · Mar 1, 2022 · 893e8f8 · 893e8f8
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: RRPP
 Title: Linear Model Evaluation with Randomized Residuals in a
         Permutation Procedure
-Version: 1.1.2
+Version: 1.2.1
 Authors@R: c(
     person("Michael", "Collyer", , "mlcollyer@gmail.com", c("aut", "cre"), 
     comment = c(ORCID = "0000-0003-0238-2201")),
@@ -26,10 +26,10 @@ Imports: parallel, ape, ggplot2, Matrix
 Suggests: knitr, rmarkdown, testthat (>= 3.0.0), dplyr, tibble
 VignetteBuilder: knitr
 NeedsCompilation: no
-Packaged: 2021-11-04 13:12:27 UTC; m.collyer
+Packaged: 2022-02-28 14:29:53 UTC; m.collyer
 Author: Michael Collyer [aut, cre] (<https://orcid.org/0000-0003-0238-2201>),
   Dean Adams [aut] (<https://orcid.org/0000-0001-9172-7894>)
 Maintainer: Michael Collyer <mlcollyer@gmail.com>
 Repository: CRAN
-Date/Publication: 2021-11-04 13:40:02 UTC
+Date/Publication: 2022-03-01 17:30:14 UTC
 Config/testthat/edition: 3
diff --git a/MD5 b/MD5
@@ -1,24 +1,24 @@
-dd99cf53c4134fa50296d92052cf5d69 *DESCRIPTION
-7775f8d88fc4d13226e08dac717796d5 *NAMESPACE
-9f0fb73d78eb7e723e58da3dc041c0a4 *NEWS.md
-79d84a47a942264f08b516135c848ee5 *R/RRPP.support.code.r
-47d942cc496e7beea63647e26a8b2cff *R/RRPP.utils.r
+421d66ad132418ec09dcc809027b6690 *DESCRIPTION
+af12c8f8ca9fc63073480cdaba995a56 *NAMESPACE
+52e687fb7de941e18acb4bc367c667d1 *NEWS.md
+4c5a86dee8726748a063a00cd63f303c *R/RRPP.support.code.r
+349a0e95cade8cb350992364ec5f84d9 *R/RRPP.utils.r
 a110900330d278eba804f1e1cfb0d248 *R/add.tree.r
-10048c1ad554721bb868dade05b626e0 *R/anova.lm.rrpp.r
+f32134cc27403cea765bc84785d571a3 *R/anova.lm.rrpp.r
 12a242809b917dc77a5462854f008574 *R/coef.lm.rrpp.r
 da9ac26867f339e21cd86a2a31af1da1 *R/convert2ggplot.r
 48035d2216df49a6bdbcba7960714751 *R/deprecated.defunct.R
-d145f6b185bc808f303903bcc7db488d *R/lm.rrpp.r
+28138b036a756fd9d50efbe52ee86ff6 *R/lm.rrpp.r
 11e059c8656b9d08df3506113278674b *R/looCV.r
-03bef75cc954f704fb47d205e96fddde *R/manova.update.r
+5c80a00dcd6e5109d4216b75d8a4a9da *R/manova.update.r
 9398ce29d5275f8254ea23b272d8d276 *R/model.comparison.r
-442aa763236a98f4f1d35d3843f0ef23 *R/ordinate.r
-11985790c9f850f7963a83918e1bf6dd *R/pairwise.r
+b0e5e2f0758f8c6ceb0c05c75f0ff9ce *R/ordinate.r
+3fd497d23c462d21f678cdf5601bad81 *R/pairwise.r
 c5b3c55cdaf9e5c50e741bbb367527cb *R/predict.lm.rrpp.r
 b53b46f8f101da913f49472e1a42c291 *R/prep.lda.r
-b22d16f04ed8861ecf31a8d637e492be *R/reveal.model.designs.r
-e48904181f297c96e03addf040955322 *R/shared.support.code.r
-2adaacf7f3f4f11c001cb2449b93958e *R/trajectory.analysis.r
+b31047f3feb173e1f2de50976c52e55a *R/reveal.model.designs.r
+7e4808bceeec6a971521f3a90f2db9a6 *R/shared.support.code.r
+846b10b5a8bd58c47e72666815dd306c *R/trajectory.analysis.r
 987d403df491c09b6db91776c4443a53 *README.md
 5ef4b2e3f4d328e2aadba44bc2cf96b6 *build/vignette.rds
 cc73a1467ca5f48d52a03686d50ca8d7 *data/PlethMorph.rda
@@ -28,17 +28,17 @@ b7ceda4ee18eb3d0d3f966360dc02936 *data/PupfishHeads.rda
 4b9ec9953a6af5354c47d2f9c8ff5922 *inst/CITATION
 ffe064f8e355aeaa59384288e1fa49e2 *inst/doc/ANOVA.vs.MANOVA.R
 eb473a6d066dda15f7d3bb2d9a6789a8 *inst/doc/ANOVA.vs.MANOVA.Rmd
-387cc917a4d671e730bbe67d2076c0f8 *inst/doc/ANOVA.vs.MANOVA.html
+0592e8842525fb23d9a3495ce1d8d2a0 *inst/doc/ANOVA.vs.MANOVA.html
 94a6a86ee9d0f970fbf911a228e5f4c4 *inst/doc/Using.RRPP.R
-2ff8ca8f06df21dbc14f676995a0faa4 *inst/doc/Using.RRPP.Rmd
-56f3b4dd831af095e18203457c182279 *inst/doc/Using.RRPP.html
+ac68aad9cea609ec475b58ab6334adf0 *inst/doc/Using.RRPP.Rmd
+012ad98defc5c96688920bab1715d538 *inst/doc/Using.RRPP.html
 be7cd478ec8f194ca3bfb4ea80dc9aa4 *man/PlethMorph.Rd
 8dc1d16560450c0cfd709bed8c735f0d *man/Pupfish.Rd
 d764e38c7e273adb4a6a884f2a8d6f1d *man/PupfishHeads.Rd
 afa34f5180a71b5c2a7b8ef3b13cf87f *man/RRPP-package.Rd
 900a0d327b1a7ce565521a2fe92bbf78 *man/add.trajectories.Rd
 16069c5b9771b2daa94872dbc5f20b74 *man/add.tree.Rd
-f116620cabddf5e09ea327d314b8f56d *man/anova.lm.rrpp.Rd
+78396282d43399ec6e9c78890c0f89e4 *man/anova.lm.rrpp.Rd
 eee872a66eb743a1df7e8551bc54ce73 *man/classify.Rd
 969243a0a9e512eb12d2355f219c29ab *man/coef.lm.rrpp.Rd
 bdd5b8886e2de73ec61122394dc9ef16 *man/convert2ggplot.Rd
@@ -52,7 +52,7 @@ e8b89a5346e67e7f8ca498aa683980fe *man/model.comparison.Rd
 0e726f552fbf03e943ad5cebcc3fc09d *man/motionpaths.Rd
 2d4e482f72e3883ab05852e215e58acd *man/na.omit.rrpp.data.frame.Rd
 519cee3a198c5adc1ba8ad24511e1235 *man/ordinate.Rd
-2dfd2acc0cc9a36545e39f06847bafd7 *man/pairwise.Rd
+c5f05ab01012cce415088c47df14e621 *man/pairwise.Rd
 06bed2fd6a0565a41616bb737a3016c7 *man/plot.lm.rrpp.Rd
 33c3529beda41e33f92cb446d4567764 *man/plot.looCV.Rd
 f8ce4b58b48b33ae16ba5f0986d12781 *man/plot.model.comparison.Rd
@@ -94,4 +94,4 @@ e52a8af2dc8b337878160602b227ab75 *man/vec.cor.matrix.Rd
 d631691a132b8995618e408c3c67a193 *tests/testthat.R
 f3de6473ea0407d6d28818dbfb320fd2 *tests/testthat/test-RRPP.R
 eb473a6d066dda15f7d3bb2d9a6789a8 *vignettes/ANOVA.vs.MANOVA.Rmd
-2ff8ca8f06df21dbc14f676995a0faa4 *vignettes/Using.RRPP.Rmd
+ac68aad9cea609ec475b58ab6334adf0 *vignettes/Using.RRPP.Rmd
diff --git a/NAMESPACE b/NAMESPACE
@@ -77,5 +77,6 @@ import(graphics)
 import(parallel)
 import(stats)
 import(Matrix)
+importFrom(ape,collapse.singles)
 importFrom(ape,multi2di.phylo)
 importFrom(ape,root.phylo)
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,15 @@
+# CHANGES IN RRPP 1.2.1
+
+### NEW FEATURES
+* Updated many functions to be able to use `Matrix` class matrices for more efficient computation, when needed.
+* Updated `checkers` function to use better algorithms to switch among different class matrices, to better save memory and increase computation time efficiency.
+
+### BUG FIXES
+*  Added catch to `anc.BM` for singleton nodes.
+
+### OTHER CHANGES
+* Updated `lm.rrpp` to have less detritus during use.  Also adjusted/updated supprot functions to work wth updates.
+
 # CHANGES IN RRPP 1.1.2
 
 ### BUG FIXES