Fixing docstring and NAMESPACE glitches

Author: davidorme

NAMESPACE

@@ -15,6 +15,7 @@ S3method(na.omit,comparative.data)
 S3method(nobs,pgls)
 S3method(plot,caic)
 S3method(plot,fusco)
+S3method(plot,pgls)
 S3method(plot,pgls.profile)
 S3method(plot,phylo.d)
 S3method(predict,caic)
@@ -43,14 +44,18 @@ export(caic.robust)
 export(caic.table)
 export(clade.matrix)
 export(clade.members)
+export(clade.members.list)
 export(comparative.data)
 export(crunch)
+export(ed.calc)
 export(fusco.test)
 export(growTree)
 export(macrocaic)
+export(pd.bootstrap)
 export(pd.calc)
 export(pgls)
 export(pgls.confint)
+export(pgls.profile)
 export(phylo.d)
 export(phylo.d.subset)
 importFrom(stats,na.omit)

R/clade.members.R

@@ -31,7 +31,10 @@
 #'
 #' data(perissodactyla)
 #' # use comparative.data to add node labels
-#' perisso <- comparative.data(perissodactyla.tree, perissodactyla.data, Binomial, na.omit = FALSE)
+#' perisso <- comparative.data(
+#'     perissodactyla.tree, perissodactyla.data, Binomial,
+#'     na.omit = FALSE
+#' )
 #' plot(perisso$phy, show.node.label = TRUE)
 #' clade.members(22, perisso$phy, tip.labels = TRUE)
 #' clade.members.list(perisso$phy, tip.labels = FALSE)
@@ -79,6 +82,8 @@ clade.members <- function(x, phy, tip.labels = FALSE,
     return(RET)
 }
 
+#' @describeIn clade.members Return clade members of all nodes in a phylogeny
+#' @export
 clade.members.list <- function(phy, tips = FALSE, tip.labels = FALSE,
                                include.nodes = FALSE) {
     # OLD2NEW CONVERTED

R/macrocaic.R

@@ -149,7 +149,7 @@ macrocaic <- function(formula, data, phy, names.col, macroMethod = "RRD",
 
     # Get the model frame including missing data
     # and check the number of complete cases in the model frame
-    initMf <- stats::model.frame(formula, data, na.action = "stats::na.pass")
+    initMf <- stats::model.frame(formula, data, na.action = stats::na.pass)
     initMfComplete <- stats::complete.cases(initMf)
     # TODO - think whether this check is always sufficient...
     if (sum(initMfComplete) < 2) {

R/pd.calc.R

@@ -197,7 +197,8 @@ pd.calc <- function(cm, tip.subset = NULL, method = "TBL", root.edge = FALSE) {
     return(RET)
 }
 
-
+#' @describeIn pd.calc Phylogenetic diversity of random subclades
+#' @export
 pd.bootstrap <- function(cm, ntips, reps = 1000, method = "TBL",
                          tip.weights = NULL) {
     # check we have a valid method
@@ -259,6 +260,8 @@ pd.bootstrap <- function(cm, ntips, reps = 1000, method = "TBL",
     return(structure(.Data = pd.store, pd.method = method))
 }
 
+#' @describeIn pd.calc Calculation of evolutionary distinctiveness scores
+#' @export
 ed.calc <- function(cm, polytomy.cf = c("isaac", "mooers", "none")) {
     # Nick Isaac, March 2009 + David Orme 2011 takes the phylogeny and returns a
     # list containing ED scores of a) species and b) branches the polytomy.cf

R/pgls-methods.R

@@ -25,6 +25,8 @@
 #' @param x An object of class 'pgls'.
 #' @param phylo Return phylogenetically corrected residuals or ordinary
 #' residuals (see details).
+#' @param REML Return the REML estimate of log likelihood - this is not
+#' implemented for PGLS models.
 #' @param newdata Alternative data for predicting from 'pgls' models.
 #' @param digits Number of digits to show in summary methods.
 #' @param ... Further arguments to methods.
@@ -202,7 +204,7 @@ coef.pgls <- function(object, ...) {
     return(cf)
 }
 
-#' @describeIn pgls Extract residuals from a pgls model
+#' @describeIn pgls-methods Extract residuals from a pgls model
 #' @export
 residuals.pgls <- function(object, phylo = FALSE, ...) {
     ret <- NULL
@@ -244,6 +246,9 @@ predict.pgls <- function(object, newdata = NULL, ...) {
 #' @describeIn pgls-methods Extract the log likelihood from a pgls model
 #' @export
 logLik.pgls <- function(object, REML = FALSE, ...) {
+    if (isTRUE(REML)) {
+        stop("Calculation of REML estimates of logLik not supported for pgls")
+    }
     val <- object$model$log.lik
 
     attr(val, "nall") <- object$n
@@ -283,7 +288,7 @@ nobs.pgls <- function(object, ...) length(stats::resid(object))
 #' mod1 <- pgls(log(Egg.Mass) ~ log(M.Mass) * log(F.Mass), shorebird)
 #' graphics::par(mfrow = c(2, 2))
 #' plot(mod1)
-#'
+#' @export
 plot.pgls <- function(x, ...) {
     res <- stats::residuals(x, phylo = TRUE)
     res <- res / sqrt(stats::var(res))[1]

R/pgls.R

@@ -111,6 +111,7 @@
 #' should be reduced to only those variables used in the maximal model in order
 #' to avoid prevent redundant variables causing rows to be dropped
 #' unnecessarily.
+#'
 #' @author Rob Freckleton; David Orme
 #' @seealso \code{\link{pgls.profile}}, \code{\link{anova.pgls}},
 #' \code{\link{summary.pgls}}
@@ -416,7 +417,7 @@ pgls <- function(formula, data, lambda = 1.0, kappa = 1.0, delta = 1.0,
 }
 
 
-
+#' @describeIn pgls Calcualate the log likelihood of a pgls model
 pgls.likelihood <- function(optimPar, fixedPar, y, x, V,
                             optim.output = TRUE, names.optim = NULL) {
     # Full ML estimation for given x and V: modified to also act as an engine
@@ -474,6 +475,7 @@ pgls.likelihood <- function(optimPar, fixedPar, y, x, V,
     }
 }
 
+#' @describeIn pgls Apply branch length transformations to a VCV matrix
 pgls.blenTransform <- function(V, fixedPar) {
     ## applies the three branch length transformations to a VCV matrix
 

R/pgls.profile.R

@@ -67,7 +67,7 @@
 #' mod.l <- pgls.profile(mod, "lambda")
 #' plot(mod.l)
 #' pgls.confint(mod, "lambda")
-#'
+#' @export
 pgls.profile <- function(pgls, which = c("lambda", "kappa", "delta"),
                          N = 50, param.CI = NULL) {
     ## takes a pgls model and profiles one of the branch length transformations

R/phylo.d.R

@@ -47,11 +47,11 @@
 #' @param permut Number of permutations to be used in the randomisation test.
 #' @param rnd.bias An optional name of a variable in \code{data} holding
 #' probability weights to bias the generation of the random distribution. See
-#' 'destails'
+#' 'details'
 #' @param x An object of class 'phylo.d'
 #' @param object An object of class 'phylo.d'
 #' @param bw The bandwidth to be used for the density plots
-#' @param list() Further arguments to print and summary methods
+#' @param ... Further arguments to print and summary methods
 #' @return Returns an object of class 'phylo.d', which is a list of the
 #' following:
 #'

R/phylo.d.subset.R

@@ -37,9 +37,8 @@
 #' @param max.nodes The maximum number of nodes a clade should have for it to
 #' have a D value calculated. Defaults to the number of nodes in the whole
 #' phylogeny (i.e. no limit).
-#' @param x An object of class 'phylo.d.subset'
 #' @param object An object of class 'phylo.d.subset'
-#' @param list() Further arguments to print and summary methods
+#' @param ... Further arguments to print and summary methods
 #' @return Returns an object of class 'phylo.d.subset', which is a list of the
 #' following:
 #'