### 0. Print method for class: data.phy:-----------------------------------------
#' @importFrom utils str
#' @export
print.data.phy <- function(x, ...)
{
cat("Comparative dataset of", nrow(x$data), "taxa with",
ncol(x$data), "variables", "\n")
if (class(x$phy) == "phylo") {
cat("-Phylogeny:", "\n")
cat(" ", length(x$phy$tip.label), " tips, ", x$phy$Nnode,
" internal nodes\n ", sep = "")
utils::str(x$phy$tip.label)
}
if (class(x$phy) == "multiPhylo") {
cat("-Multiphylo: \n")
print(x$phy)
}
cat("-Dataset:", "\n")
str(x$data)
if (length(x$dropped) > 0) {
cat("Dropped taxa: \n")
cat(length(x$dropped), "taxa were dropped from phylogeny or datset \n")
}
}
### 1. PRINT FOR PGLS--------------------------------------------------------------
### sensiIntra:-----------------------------------------
#' @export
print.sensiIntra <- function(x, ...)
{
cat("Sensitivity analysis for intraspecific variation\n")
cat("Call:\n")
print(x$call)
cat("\n")
cat("Transformation: \n")
cat("X axis: ")
print(x$y.transf)
cat("Y axis: ")
print(x$x.transf)
cat("Number of observations: ", nrow(x$data), "\n")
cat("Number of simulations: ", nrow(x$model_results), "\n")
cat(message("use summary(x) and sensi_plot(x) to check results"))
}
### sensiSamp:----------------------------------------
#' @export
print.sensiSamp <- function(x, ...)
{
cat("Sensitivity analysis for sampling uncertainty\n")
cat("Call:\n")
print(x$call)
cat("\n")
cat("Breaks: ", x$sign.analysis$percent_sp_removed, "\n")
cat("Number of simulations: ", nrow(x$sensi.estimates), "\n")
cat(message("use summary(x) and sensi_plot(x) to check results"))
}
### sensiClade:----------------------------------------
#' @export
print.sensiClade <- function(x, ...)
{
cat("Sensitivity analysis of influential clades \n")
cat("Call:\n")
print(x$call)
cat("\n")
cat("Analyzed clades: ")
cat(x$sensi.estimates$clade, sep = "; ", "\n")
cat(message("use summary(x) and sensi_plot(x) to check results"))
}
### sensiTree:-----------------------------------------
#' @export
print.sensiTree <- function(x, ...)
{
cat("Sensitivity analysis for phylogenetic uncertainty \n")
cat("Call:\n")
print(x$call)
cat("\n")
cat("Number of observations: ", nrow(x$data), "\n")
cat("Number of simulations: ", nrow(x$model_results), "\n")
cat(message("use summary(x) and sensi_plot(x) to check results"))
}
### Print method for class: sensiInflu:-----------------------------------------
#' @export
print.sensiInflu <- function(x, ...)
{
cat("Sensitivity analysis for influential species \n")
cat("Call:\n")
print(x$call)
cat("\n")
cat("Number of simulations:", nrow(x$sensi.estimates), "\n")
cat(message("use summary(x) and sensi_plot(x) to check results"))
}
### 2. PRINT PHYLOGENETIC SIGNAL------------------------------------------
### clade.physig:---------------------------------------
#' @export
print.clade.physig <- function(x, ...)
{
cat("Sensitivity analysis of influential clades for Phylogenetic signal \n")
cat("\n")
cat("Call:\n")
print(x$call)
cat("\n")
cat("Number of randomizations: ")
cat(x$call$n.sim)
cat("\n")
cat("Clades analysed: ")
cat(x$sensi.estimates$clade)
cat(message("use summary(x) and sensi_plot(x) to check results"))
cat(message("use x$sensi.estimates to access sensitivity analysis data"))
}
### influ.physig:---------------------------------------
#' @export
print.influ.physig <- function(x, ...)
{
cat("Sensitivity analysis of influential species for Phylogenetic signal \n")
cat("\n")
cat("Call:\n")
print(x$call)
cat("\n")
cat("Number of species: ")
cat(nrow(x$data))
cat("\n")
cat(message("use summary(x) and sensi_plot(x) to check results"))
cat(message("use x$influ.physig.estimates to access sensitivity analysis data"))
}
### samp.physig:---------------------------------------
#' @export
print.samp.physig <- function(x, ...)
{
cat("Sensitivity analysis of sampling uncertainty for Phylogenetic Signal \n")
cat("\n")
cat("Call:\n")
print(x$call)
cat("\n")
cat("Number of randomizations: ")
cat(x$call$nsim)
cat("\n")
cat(message("use summary(x) and sensi_plot(x) to check results"))
cat(message("use x$influ.physig.estimates to access sensitivity analysis data"))
}
### tree.physig:---------------------------------------
#' @export
print.tree.physig <- function(x, ...)
{
cat("Sensitivity analysis of phylogenetic uncertainty for Phylogenetic signal \n")
cat("\n")
cat("Call:\n")
print(x$call)
cat("\n")
cat("Number of trees evaluated: ")
cat(nrow(x$tree.physig.estimates))
cat("\n")
cat(message("use summary(x) and sensi_plot(x) to check results"))
cat(message("use x$tree.physig.estimates to access sensitivity analysis data"))
}
### intra.physig:---------------------------------------
#' @export
print.intra.physig <- function(x, ...)
{
cat("Sensitivity analysis of intraspecific variability for Phylogenetic signal \n")
cat("\n")
cat("Call:\n")
print(x$call)
cat("\n")
cat("Number of simulations: ")
cat(nrow(x$intra.physig.estimates))
cat("\n")
cat(message("use summary(x) and sensi_plot(x) to check results"))
cat(message("use x$tree.intra.estimates to access sensitivity analysis data"))
}
### 3. PRINT interaction PGLS------------------------------------------
#' @export
print.sensiTree_Clade <- function(x, ...)
{
cat("Sensitivity analysis for interaction between tree:clade \n")
cat("Call:\n")
print(x$call)
cat("\n")
cat("Analyzed clades: ")
cat(unique(x$sensi.estimates$clade), sep = "; ", "\n")
cat(message("use summary(x) and sensi_plot(x) to check results"))
}
#' @export
print.sensiIntra_Clade <- function(x, ...)
{
cat("Sensitivity analysis for interaction between intra:clade \n")
cat("Call:\n")
print(x$call)
cat("\n")
cat("Analyzed clades: ")
cat(unique(x$sensi.estimates$clade), sep = "; ", "\n")
cat(message("use summary(x) and sensi_plot(x) to check results"))
}
#' @export
print.sensiTree_Influ <- function(x, ...)
{
cat("Sensitivity analysis for interaction between tree:influ \n")
cat("Call:\n")
print(x$call)
cat("\n")
cat(message("use summary(x) and sensi_plot(x) to check results"))
}
#' @export
print.sensiIntra_Influ <- function(x, ...)
{
cat("Sensitivity analysis for interaction between intra:influ \n")
cat("Call:\n")
print(x$call)
cat("\n")
cat(message("use summary(x) and sensi_plot(x) to check results"))
}
#' @export
print.sensiTree_Samp <- function(x, ...)
{
cat("Sensitivity analysis for interaction between tree:influ \n")
cat("Call:\n")
print(x$call)
cat("\n")
cat(message("use summary(x) and sensi_plot(x) to check results"))
}
#' @export
print.sensiTree_SampL <- function(x, ...)
{
cat("Sensitivity analysis for interaction between tree:samp \n")
cat("Call:\n")
print(x$call)
cat("\n")
cat(message("use summary(x) and sensi_plot(x) to check results"))
}
#' @export
print.sensiIntra_Samp <- function(x, ...)
{
cat("Sensitivity analysis for interaction between intra:samp \n")
cat("Call:\n")
print(x$call)
cat("\n")
cat(message("use summary(x) and sensi_plot(x) to check results"))
}
#' @export
print.sensiIntra_SampL <- function(x, ...)
{
cat("Sensitivity analysis for interaction between intra:samp \n")
cat("Call:\n")
print(x$call)
cat("\n")
cat(message("use summary(x) and sensi_plot(x) to check results"))
}
### 4. PRINT diversification ------------------------------------------
### tree.physig:---------------------------------------
#' @export
print.tree.bd <- function(x, ...)
{
cat("Sensitivity analysis of net diversification rate \n")
cat("\n")
cat("Call:\n")
print(x$call)
cat("\n")
cat("Number of trees evaluated: ")
cat(nrow(x$tree.bd.estimates))
cat("\n")
cat(message("use summary(x) and sensi_plot(x) to check results"))
cat(message("use x$tree.bd.estimates to access sensitivity analysis data"))
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.