version 2.0.0

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: RRPP
 Title: Linear Model Evaluation with Randomized Residuals in a
         Permutation Procedure
-Version: 1.4.0
+Version: 2.0.0
 Authors@R: c(
     person("Michael", "Collyer", , "mlcollyer@gmail.com", c("aut", "cre"), 
     comment = c(ORCID = "0000-0003-0238-2201")),
@@ -21,15 +21,15 @@ License: GPL (>= 3)
 URL: https://github.com/mlcollyer/RRPP
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Imports: parallel, ape, ggplot2, Matrix
-Suggests: knitr, rmarkdown, testthat (>= 3.0.0), dplyr, tibble
+Suggests: knitr, rmarkdown, testthat (>= 3.2.0), dplyr, tibble
 VignetteBuilder: knitr
 NeedsCompilation: no
-Packaged: 2023-08-15 18:27:10 UTC; m.collyer
+Packaged: 2024-02-06 13:54:34 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: 2023-08-15 19:00:02 UTC
+Date/Publication: 2024-02-06 14:30:03 UTC
 Config/testthat/edition: 3

MD5

@@ -1,89 +1,102 @@
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 b4fe07260befe0f1b01a557cbbd3dd9e *man/predict.lm.rrpp.Rd
 6f4b53f12982cc54f3058d989e3893d9 *man/prep.lda.Rd
+f6f7682b9ccee0365c560b67e2d92b3f *man/print.ICCstats.Rd
 b1b2bc86ef6ed57ab44badf084182779 *man/print.anova.lm.rrpp.Rd
 1354129612f4c784fabcfb8a081e11d5 *man/print.coef.lm.rrpp.Rd
 3aff928928deb0f0d62d68d0f262a44b *man/print.lm.rrpp.Rd
 78865c8e99ad5252121285c557a3949c *man/print.looCV.Rd
-cffabf885b11d7769b7850cf906c57b5 *man/print.measurement.error.Rd
+8c1c4b5449f66a42afde037b52d17fd7 *man/print.lr_test.Rd
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 63fe7c719bd8f43d7700eb630d08c01b *man/print.model.comparison.Rd
 44daf8758d830b2ea00445b05e42ab00 *man/print.ordinate.Rd
 0e7d801ef41e4b8d359ce692294fd418 *man/print.pairwise.Rd
@@ -94,25 +107,28 @@ dee2473a6f8021b7f361ddffbb69eed6 *man/print.summary.lm.rrpp.Rd
 9ae760a71c70574a33826296fe5f95fb *man/print.summary.pairwise.Rd
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 a2c3a95f8bb4ccaea49707237ed41bee *man/print.trajectory.analysis.Rd
+f1d2b1710a92ae4fe0e74570d9d667ea *man/pval.Rd
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 e52a8af2dc8b337878160602b227ab75 *man/vec.cor.matrix.Rd
 d631691a132b8995618e408c3c67a193 *tests/testthat.R
-7afa9f64f831ffb4fd681eab67e14e81 *tests/testthat/test-RRPP.R
+c99589eeb1879a23893e15e7abc5f054 *tests/testthat/test-RRPP.R
 0635eca5f6d8a463b61c35f9596ee0f7 *vignettes/ANOVA.vs.MANOVA.Rmd
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NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 S3method(anova,lm.rrpp)
+S3method(anova,measurement.error)
 S3method(coef,lm.rrpp)
 S3method(fitted,lm.rrpp)
 S3method(logLik,lm.rrpp)
@@ -15,10 +16,12 @@ S3method(plot,ordinate)
 S3method(plot,predict.lm.rrpp)
 S3method(plot,trajectory.analysis)
 S3method(predict,lm.rrpp)
+S3method(print,ICCstats)
 S3method(print,anova.lm.rrpp)
 S3method(print,coef.lm.rrpp)
 S3method(print,lm.rrpp)
 S3method(print,looCV)
+S3method(print,lr_test)
 S3method(print,measurement.error)
 S3method(print,model.comparison)
 S3method(print,ordinate)
@@ -31,10 +34,12 @@ S3method(print,summary.pairwise)
 S3method(print,summary.trajectory.analysis)
 S3method(print,trajectory.analysis)
 S3method(residuals,lm.rrpp)
+S3method(summary,ICCstats)
 S3method(summary,anova.lm.rrpp)
 S3method(summary,coef.lm.rrpp)
 S3method(summary,lm.rrpp)
 S3method(summary,looCV)
+S3method(summary,lr_test)
 S3method(summary,manova.lm.rrpp)
 S3method(summary,measurement.error)
 S3method(summary,model.comparison)
@@ -43,11 +48,14 @@ S3method(summary,pairwise)
 S3method(summary,predict.lm.rrpp)
 S3method(summary,trajectory.analysis)
 S3method(terms,lm.rrpp)
+export(ICCstats)
 export(add.trajectories)
 export(add.tree)
 export(anova.lm.rrpp)
+export(anova.measurement.error)
 export(classify)
 export(convert2ggplot)
+export(effect.size)
 export(focusMEonSubjects)
 export(getANOVAStats)
 export(getModelCov)
@@ -59,6 +67,7 @@ export(interSubVar)
 export(lm.rrpp)
 export(lm.rrpp.ws)
 export(looCV)
+export(lr_test)
 export(manova.update)
 export(measurement.error)
 export(model.comparison)
@@ -76,6 +85,7 @@ export(print.summary.lm.rrpp)
 export(print.summary.pairwise)
 export(print.summary.trajectory.analysis)
 export(print.trajectory.analysis)
+export(pval)
 export(reveal.model.designs)
 export(rrpp.data.frame)
 export(scaleCov)

NEWS.md

@@ -1,21 +1,25 @@
-# CHANGES IN RRPP 1.4.0
+# CHANGES IN RRPP 2.0.0
 
 ### NEW FEATURES
-*  Added arguments for restricted resampling to `lm.rrpp` and `predict.lm.rrpp`, and permutation of full model residuals (with restrictions) to lm.rrpp
+* Added arguments for restricted resampling to `lm.rrpp` and `predict.lm.rrpp`, and permutation of full model residuals (with restrictions) to `lm.rrpp`.
 * Added new function, `measurement.error`.
 * Added new function, `lm.rrpp.ws`.
 * Added `verbose` arguments to most analytical functions to reduce dense results.
 * Added utility functions (`getANOVAStats`, `getPermInfo`, `getTerms`, and `getModels`) to accommodate `verbose` function choices, plus allow users to easily extract objects as output.
+* Added new function, `ICCstats`, for calculating ICC statistics for `lm.rrpp` fits.
 * Added S3 generic functions for `measurement.error`, but also added a plot utility function, `focusMEonSubjects`, which builds off of `plot.measurement.error`, to focus attention on specific plot details.
+* Added function, `interSubVar`, a utility function to use along with `measurement.error`,
+to visualize how variation between replicate measures, within subjects, can affect inter-subject variation.
 
 ### BUG FIXES
 *  Fixed SSCP issue in `summary.lm.rrpp` that produces matrices of 0s.  The issue was inherent to `lm.rrpp`, from erroneous assignment of models, only for output (not for mechanics).
-*  Attempted fix of `predict.lm.rrpp` for QR-truncated design matrices. 
+* Attempted fix of `predict.lm.rrpp` for QR-truncated design matrices. 
 * Fixed illogical `print.progess` conditions in `pairwise`.
 * Fixed potential problem with reliance on `Matrix::qrQ`, using rather, `Matrix::qr.Q`.
 * Fixed GLS estimation issue with `pairwise`.
 
 ### OTHER CHANGES
+* argument `SE` added to `coef.lm.rrpp` for calculating bootstrap standard error.
 
 # CHANGES IN RRPP 1.3.1