version 1.1.2

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: RRPP
 Title: Linear Model Evaluation with Randomized Residuals in a
         Permutation Procedure
-Version: 1.1.1
+Version: 1.1.2
 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: 2021-10-24 14:52:27 UTC; m.collyer
+Packaged: 2021-11-04 13:12:27 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: 2021-10-24 15:20:02 UTC
+Date/Publication: 2021-11-04 13:40:02 UTC
 Config/testthat/edition: 3

MD5

@@ -1,38 +1,38 @@
-6b4e52bf548d3d6c9b7908d361acf604 *DESCRIPTION
+dd99cf53c4134fa50296d92052cf5d69 *DESCRIPTION
 7775f8d88fc4d13226e08dac717796d5 *NAMESPACE
-67cbf66d430f7b07a181e18485208bc4 *NEWS.md
-2a9b99e0239c94e610fe8e92769ecfad *R/RRPP.support.code.r
+9f0fb73d78eb7e723e58da3dc041c0a4 *NEWS.md
+79d84a47a942264f08b516135c848ee5 *R/RRPP.support.code.r
 47d942cc496e7beea63647e26a8b2cff *R/RRPP.utils.r
 a110900330d278eba804f1e1cfb0d248 *R/add.tree.r
 10048c1ad554721bb868dade05b626e0 *R/anova.lm.rrpp.r
 12a242809b917dc77a5462854f008574 *R/coef.lm.rrpp.r
 da9ac26867f339e21cd86a2a31af1da1 *R/convert2ggplot.r
 48035d2216df49a6bdbcba7960714751 *R/deprecated.defunct.R
-4a20fd48c3671ac196f9c26044ed373f *R/lm.rrpp.r
+d145f6b185bc808f303903bcc7db488d *R/lm.rrpp.r
 11e059c8656b9d08df3506113278674b *R/looCV.r
 03bef75cc954f704fb47d205e96fddde *R/manova.update.r
 9398ce29d5275f8254ea23b272d8d276 *R/model.comparison.r
 442aa763236a98f4f1d35d3843f0ef23 *R/ordinate.r
-430ab5bc8f90f92448d7df04e843ad4c *R/pairwise.r
+11985790c9f850f7963a83918e1bf6dd *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
 987d403df491c09b6db91776c4443a53 *README.md
-cff046aaeef848aeefc6bf4a4d25ad06 *build/vignette.rds
+5ef4b2e3f4d328e2aadba44bc2cf96b6 *build/vignette.rds
 cc73a1467ca5f48d52a03686d50ca8d7 *data/PlethMorph.rda
 4b4ee52bfcac42caf2b6b3c506af6db0 *data/Pupfish.rda
 b7ceda4ee18eb3d0d3f966360dc02936 *data/PupfishHeads.rda
 0033a37910a893b33a05c44e405022e0 *data/motionpaths.rda
 4b9ec9953a6af5354c47d2f9c8ff5922 *inst/CITATION
 ffe064f8e355aeaa59384288e1fa49e2 *inst/doc/ANOVA.vs.MANOVA.R
 eb473a6d066dda15f7d3bb2d9a6789a8 *inst/doc/ANOVA.vs.MANOVA.Rmd
-9b79cefc6c071a71a7e3fe3174ec4b6b *inst/doc/ANOVA.vs.MANOVA.html
+387cc917a4d671e730bbe67d2076c0f8 *inst/doc/ANOVA.vs.MANOVA.html
 94a6a86ee9d0f970fbf911a228e5f4c4 *inst/doc/Using.RRPP.R
 2ff8ca8f06df21dbc14f676995a0faa4 *inst/doc/Using.RRPP.Rmd
-470afc16aa8a80f101e89add7348ec46 *inst/doc/Using.RRPP.html
-62000dade2dbf91cece8db6929c14228 *man/PlethMorph.Rd
+56f3b4dd831af095e18203457c182279 *inst/doc/Using.RRPP.html
+be7cd478ec8f194ca3bfb4ea80dc9aa4 *man/PlethMorph.Rd
 8dc1d16560450c0cfd709bed8c735f0d *man/Pupfish.Rd
 d764e38c7e273adb4a6a884f2a8d6f1d *man/PupfishHeads.Rd
 afa34f5180a71b5c2a7b8ef3b13cf87f *man/RRPP-package.Rd
@@ -77,7 +77,7 @@ dee2473a6f8021b7f361ddffbb69eed6 *man/print.summary.lm.rrpp.Rd
 a2c3a95f8bb4ccaea49707237ed41bee *man/print.trajectory.analysis.Rd
 e2f4d3ded41cac1f1baf52d5709ac5fc *man/residuals.lm.rrpp.Rd
 f6985949fae79d175333feb4a95b4396 *man/reveal.model.designs.Rd
-ce2357b32270e2b89ff1b91c543bfed9 *man/rrpp.data.frame.Rd
+42c50fd8280f6167e1e1440b92e0bee4 *man/rrpp.data.frame.Rd
 3feb50b2cd634fb9812fba13a02ff65d *man/summary.anova.lm.rrpp.Rd
 ad97e4ce6e14cb92ac228d0f798d7717 *man/summary.coef.lm.rrpp.Rd
 beb55085de49d23665272a0db65d1dff *man/summary.lm.rrpp.Rd

NEWS.md

@@ -1,3 +1,8 @@
+# CHANGES IN RRPP 1.1.2
+
+### BUG FIXES
+* Fixed a few issues with dropped names when working with `data.frame` objects.
+
 # CHANGES IN RRPP 1.1.1
 
 ### BUG FIXES

R/RRPP.support.code.r

@@ -109,7 +109,8 @@ NULL
 #' (SVL) as species size, tail length, head length, snout to eye length, 
 #' body width, forelimb length,
 #' and hind limb length, all measured in mm.  A grouping variable is also 
-#' included for functional guild size.  
+#' included for functional guild size.  A variable for species names is also 
+#' included.
 #' The data set also includes a phylogenetic covariance matrix based on a 
 #' Brownian model of evolution, to assist in 
 #' generalized least squares (GLS) estimation.
@@ -159,7 +160,6 @@ NULL
 #' See \code{\link{lm.rrpp}} for examples.
 #'
 #' @param ... Components (objects) to combine in the data frame.
-#' @keywords utilities
 #' @export
 #' @author Michael Collyer
 #' @examples
@@ -183,7 +183,7 @@ NULL
 #' fit <- lm.rrpp(d ~ x, data = rdf)
 #' summary(fit)
 
-rrpp.data.frame<- function(...){
+rrpp.data.frame<- function(...) {
   dots <- list(...)
   if(length(dots) == 1 && is.data.frame(dots[[1]])) {
     dots <- dots[[1]]
@@ -233,20 +233,41 @@ rrpp.data.frame<- function(...){
       stop("Inputs have different numbers of observations")
     class(dots) <- c("rrpp.data.frame")
   }
+
   dots
 }
 
 #####--------------------------------------------------------------\
 
 # SUPPORT FUNCTIONS
 
-
 # lm.rrpp subfunctions
 # lm-like fit modified for all submodels
 # general workhorse for all 'lm.rrpp' functions
 # used in all 'lm.rrpp' functions
 
-makeDF <- function(form, data, n) {
+get.names <- function(Y) {
+  nms <- if(is.vector(Y)) names(Y) else if(inherits(Y, "dist")) attr(Y, "Labels") else
+    if(inherits(Y, "matrix")) rownames(Y) else dimnames(Y)[[3]]
+  nms
+}
+
+get.names.from.list <- function(L) {
+  temp <- lapply(L, get.names)
+  check <- which(!sapply(temp, is.null))
+  temp <- if(length(check) > 0) temp[check] else NULL
+  nms <- if(!is.null(temp)) temp[[1]] else NULL
+  nms
+}
+
+add.names <- function(Y, nms) {
+  if(is.vector(Y)) names(Y) <- nms
+  if(inherits(Y, "matrix")) rownames(Y) <- nms
+  if(inherits(Y, "dist")) attr(Y, "Labels") <- nms
+  Y
+}
+
+makeDF <- function(form, data, n, nms) {
 
   if(!is.list(data)) 
     stop("\nThe data frame provide is not class rrpp.data.frame, 
@@ -282,6 +303,8 @@ makeDF <- function(form, data, n) {
 
   dat <- if(length(dat) == 0)  NULL else as.data.frame(dat)
 
+  if(!is.null(dat)) rownames(dat) <- nms
+
   dat
 }
 
@@ -307,17 +330,14 @@ lm.args.from.formula <- function(cl){
   Dy <- NULL
   Y <- try(eval(lm.args$formula[[2]], lm.args$data, parent.frame()),
            silent = TRUE)
-
-  nms <- if(is.vector(Y)) names(Y) else if(inherits(Y, "dist")) attr(Y, "Labels") else
-      if(inherits(Y, "matrix")) rownames(Y) else dimnames(Y)[[3]]
+  nmsY <- get.names(Y)
 
   if(inherits(Y, "try-error"))
     stop("Data are missing from either the data frame or global environment.\n", 
          call. = FALSE)
 
   if(is.vector(Y)) {
     Y <- as.matrix(Y)
-    if(!is.null(nms)) rownames(Y) <- nms
     Dy <- NULL
   }
 
@@ -348,33 +368,37 @@ lm.args.from.formula <- function(cl){
   form <- update(form, Y ~.,)
   lm.args$formula <- form
 
+  Y <- add.names(Y, nmsY)
   n <- NROW(Y)
 
   if(!is.null(lm.args$data)) {
-    lm.args$data <- makeDF(form, lm.args$data, n)
+    nmsDF <- if(inherits(lm.args$data, "data.frame"))  
+      attr(lm.args$data, "row.names") else 
+        get.names.from.list(lm.args$data)
+
+    lm.args$data <- makeDF(form, lm.args$data, n, nmsDF)
   }
 
   if(is.null(lm.args$data)) {
     lm.args$data <- data.frame(Int = rep(1, n))
     lm.args$data$Y <- as.matrix(Y)
     lm.args$data <- lm.args$data[-1]
+    rownames(lm.args$data) <-nmsY
   }
 
   lm.args$data$Y <- Y
 
   dfmat <- try(as.matrix(lm.args$data), silent = TRUE)
   if(!inherits(dfmat, "try-error"))
-    rownames(lm.args$data) <- nms
-
-  f <- try(do.call(lm, lm.args), silent = TRUE)
+    f <- try(do.call(lm, lm.args), silent = TRUE)
 
   if(inherits(f, "try-error")) 
-    stop("Variables or data are missing from either the data frame or 
-           global environment\n", 
+    stop("Variables or data might be missing from either the data frame or 
+           global environment, or a linear model fit just does not work...\n", 
          call. = FALSE)
 
-  Y = as.matrix(f$y)
-  rownames(Y) <- nms
+  Y <- as.matrix(f$y)
+  Y <- add.names(Y, rownames(f$model))
   out <- list(Terms = f$terms, model = f$model, Y = Y)
   if(!is.null(Dy)) {
     d <- as.matrix(Dy)

R/lm.rrpp.r

@@ -488,13 +488,13 @@ lm.rrpp <- function(f1, iter = 999, turbo = FALSE, seed = NULL, int.first = FALS
   mods <- getTerms(Terms, SS.type)
   exchange.args$mods <- mods
 
-  id <- rownames(Y)
+  id <- get.names(Y)
   dims <- dim(Y)
   n <- dims[1]
   p <- dims[2]
   if(is.null(id)) {
     id <- 1:n
-    rownames(Y) <- id
+    Y <- add.names(Y, id)
   }
 
   if(!is.null(w)) {
@@ -504,8 +504,10 @@ lm.rrpp <- function(f1, iter = 999, turbo = FALSE, seed = NULL, int.first = FALS
   }
 
   if(!is.null(Cov)) {
-    if(!is.null(rownames(Y)) && !is.null(rownames(Cov)))
-      Cov <- Cov[rownames(Y), rownames(Y)]
+    if(!is.null(id) && !is.null(rownames(Cov)))
+      if(length(setdiff(id, rownames(Cov))) > 0)
+        stop("Data names and coavriance matrix names do not match.\n", call. = FALSE)
+      Cov <- Cov[id, id]
     Pcov <- Cov.proj(Cov)
   } else Pcov <- NULL
 

R/pairwise.r

@@ -249,6 +249,11 @@ pairwise <- function(fit, fit.null = NULL, groups, covariate = NULL,
   n <- fitf$LM$n
   p <- fitf$LM$p
   k <- length(fitf$LM$term.labels)
+  kk <- length(fitf$Models$full)
+  if(k != kk) {
+    cat("Because the linear model design matrix is not full rank, there might be an issue.\n")
+    cat("If there is a subsequent error, this is probably why.\n\n")
+  }
 
   Y <- fitf$LM$Y
   if(gls) {

inst/doc/ANOVA.vs.MANOVA.html

@@ -12,7 +12,7 @@
 
 <meta name="author" content="Michael L. Collyer" />
 
-<meta name="date" content="2021-10-24" />
+<meta name="date" content="2021-11-04" />
 
 <title>ANOVA versus MANOVA in RRPP</title>
 
@@ -141,7 +141,7 @@
 
 <h1 class="title toc-ignore">ANOVA versus MANOVA in RRPP</h1>
 <h4 class="author">Michael L. Collyer</h4>
-<h4 class="date">2021-10-24</h4>
+<h4 class="date">2021-11-04</h4>
 
 
 

inst/doc/Using.RRPP.html

@@ -11,7 +11,7 @@
 <meta name="viewport" content="width=device-width, initial-scale=1" />
 
 
-<meta name="date" content="2021-10-24" />
+<meta name="date" content="2021-11-04" />
 
 <title>Using RRPP</title>
 
@@ -139,7 +139,7 @@
 
 
 <h1 class="title toc-ignore">Using RRPP</h1>
-<h4 class="date">2021-10-24</h4>
+<h4 class="date">2021-11-04</h4>