/
tree_intra_phylm.R
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tree_intra_phylm.R
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#' Interaction between phylogenetic uncertainty and intraspecific variability - Phylogenetic Linear Regression
#'
#' Performs Phylogenetic linear regression evaluating
#' intraspecific variability in response and/or predictor variables
#' and uncertainty in trees topology.
#'
#' @param formula The model formula: \code{response~predictor}.
#' @param data Data frame containing species traits and species names as row names.
#' @param phy A phylogeny (class 'phylo', see ?\code{ape}).
#' @param Vy Name of the column containing the standard deviation or the standard error of the response
#' variable. When information is not available for one taxon, the value can be 0 or \code{NA}.
#' @param Vx Name of the column containing the standard deviation or the standard error of the predictor
#' variable. When information is not available for one taxon, the value can be 0 or \code{NA}
#' @param y.transf Transformation for the response variable (e.g. \code{log} or \code{sqrt}). Please use this
#' argument instead of transforming data in the formula directly (see also details below).
#' @param x.transf Transformation for the predictor variable (e.g. \code{log} or \code{sqrt}). Please use this
#' argument instead of transforming data in the formula directly (see also details below).
#' @param n.intra Number of times to repeat the analysis generating a random value for response and/or predictor variables.
#' If NULL, \code{n.intra} = 30
#' @param n.tree Number of times to repeat the analysis with n different trees picked
#' randomly in the multiPhylo file.
#' If NULL, \code{n.tree} = 2
#' @param distrib A character string indicating which distribution to use to generate a random value for the response
#' and/or predictor variables. Default is normal distribution: "normal" (function \code{\link{rnorm}}).
#' Uniform distribution: "uniform" (\code{\link{runif}})
#' Warning: we recommend to use normal distribution with Vx or Vy = standard deviation of the mean.
#' @param model The phylogenetic model to use (see Details). Default is \code{lambda}.
#' @param track Print a report tracking function progress (default = TRUE)
#' @param ... Further arguments to be passed to \code{phylolm}
#' @details
#' This function fits a phylogenetic linear regression model using \code{\link[phylolm]{phylolm}} to n trees (\code{n.tree}),
#' randomly picked in a multiPhylo file. The regression is also repeated \code{n.intra} times.
#' At each iteration the function generates a random value for each row in the dataset using the standard deviation
#' or errors supplied and assuming a normal or uniform distribution. To calculate means and se for your raw data,
#' you can use the \code{summarySE} function from the package \code{Rmisc}.
#'
#' #' All phylogenetic models from \code{phylolm} can be used, i.e. \code{BM},
#' \code{OUfixedRoot}, \code{OUrandomRoot}, \code{lambda}, \code{kappa},
#' \code{delta}, \code{EB} and \code{trend}. See ?\code{phylolm} for details.
#'
#' Currently, this function can only implement simple linear models (i.e. \eqn{trait~
#' predictor}). In the future we will implement more complex models.
#'
#' Output can be visualised using \code{sensi_plot}.
#'
#' @section Warning:
#' When Vy or Vx exceed Y or X, respectively, negative (or null) values can be generated, this might cause problems
#' for data transformation (e.g. log-transformation). In these cases, the function will skip the simulation. This problem can
#' be solved by increasing \code{times}, changing the transformation type and/or checking the target species in output$sp.pb.
#'
#' @return The function \code{tree_intra_phylm} returns a list with the following
#' components:
#' @return \code{formula}: The formula
#' @return \code{data}: Original full dataset
#' @return \code{sensi.estimates}: Coefficients, aic and the optimised value of the phylogenetic
#' parameter (e.g. \code{lambda}) for each regression using a value in the interval of variation and
#' a different phylogenetic tree.
#' @return \code{N.obs}: Size of the dataset after matching it with tree tips and removing NA's.
#' @return \code{stats}: Main statistics for model parameters.\code{CI_low} and \code{CI_high} are the lower
#' and upper limits of the 95% confidence interval.
#' @return \code{all.stats}: Complete statistics for model parameters.
#' Fields coded using \code{all} describe statistics due to both intraspecific variation and phylogenetic uncertainty.
#' Fields coded using \code{intra} describe statistics due to intraspecific variation only.
#' Fields coded using \code{tree} describe statistics due to phylogenetic uncertainty only.
#' \code{sd} is the standard deviation. \code{CI_low} and \code{CI_high} are the lower and upper limits
#' of the 95% confidence interval.
#' @return \code{sp.pb}: Species that caused problems with data transformation (see details above).
#'
#' @author Caterina Penone & Pablo Ariel Martinez
#' @seealso \code{\link[phylolm]{phylolm}}, \code{\link{tree_phylm}}, \code{\link{intra_phylm}},
#' \code{\link{tree_intra_phyglm}}, \code{\link{sensi_plot}}
#' @references
#'
#' Paterno, G. B., Penone, C. Werner, G. D. A.
#' \href{http://doi.wiley.com/10.1111/2041-210X.12990}{sensiPhy:
#' An r-package for sensitivity analysis in phylogenetic
#' comparative methods.} Methods in Ecology and Evolution
#' 2018, 9(6):1461-1467
#'
#' Martinez, P. a., Zurano, J.P., Amado, T.F., Penone, C., Betancur-R, R.,
#' Bidau, C.J. & Jacobina, U.P. (2015). Chromosomal diversity in tropical reef
#' fishes is related to body size and depth range. Molecular Phylogenetics and
#' Evolution, 93, 1-4
#'
#' Ho, L. S. T. and Ane, C. 2014. "A linear-time algorithm for
#' Gaussian and non-Gaussian trait evolution models". Systematic Biology 63(3):397-408.
#' @examples
#'# Load data:
#'data(alien)
#'# run PGLS accounting for intraspecific and phylogenetic variation:
#'intra.tree <- tree_intra_phylm(gestaLen ~ adultMass, data = alien$data, phy = alien$phy,
#'Vy = "SD_gesta", n.intra = 3, n.tree = 3, y.transf = log, x.transf = log)
#'# To check summary results:
#'summary(intra.tree)
#'# Visual diagnostics
#'sensi_plot(intra.tree, uncer.type = "all") #or uncer.type = "tree", uncer.type = "intra"
#' @export
tree_intra_phylm <- function(formula,
data,
phy,
Vy = NULL,
Vx = NULL,
y.transf = NULL,
x.transf = NULL,
n.intra = 10,
n.tree = 2,
distrib = "normal",
model = "lambda",
track = TRUE,
...) {
#Error check
if (is.null(Vx) & is.null(Vy))
stop("Vx or Vy must be defined")
if (!inherits(formula, "formula"))
stop("formula must be class 'formula'")
if (!inherits(data, "data.frame"))
stop("data must be class 'data.frame'")
if (!inherits(phy, "multiPhylo"))
stop("phy must be class 'multiPhylo'")
if (formula[[2]] != all.vars(formula)[1] ||
formula[[3]] != all.vars(formula)[2])
stop("Please use arguments y.transf or x.transf for data transformation")
if (length(phy) < n.tree)
stop("'n.tree' must be smaller (or equal) than the number of trees in the 'multiPhylo' object")
if (distrib == "normal")
warning ("distrib = normal: make sure that standard deviation is provided for Vx and/or Vy")
if ((model == "trend") && (sum(ape::is.ultrametric(phy)) > 1))
stop("Trend is unidentifiable for ultrametric trees., see ?phylolm for details")
else
#Matching tree and phylogeny using utils.R
datphy <- match_dataphy(formula, data, phy, ...)
full.data <- datphy[[1]]
phy <- datphy[[2]]
# If the class of tree is multiphylo pick n=n.tree random trees
trees <- sample(length(phy), n.tree, replace = F)
#Model calculation
tree.intra <- list()
if (track == TRUE)
pb <- utils::txtProgressBar(min = 0, max = n.tree, style = 3)
counter = 1
for (j in trees) {
#Match data order to tip order
full.data <- full.data[phy[[j]]$tip.label, ]
#Select tree
tree <- phy[[j]]
#model (remove warnings about standard deviation in intra)
withCallingHandlers(
tree.intra[[counter]] <-
intra_phylm(
formula = formula,
data = full.data,
phy = tree,
Vx,
Vy,
y.transf,
x.transf,
n.intra = n.intra,
distrib,
model,
track = F,
verbose = F
),
warning = function(w) {
if (grepl("make sure that standard deviation", w$message))
invokeRestart("muffleWarning")
}
)
if (track == TRUE)
utils::setTxtProgressBar(pb, counter)
counter = counter + 1
}
if (track == TRUE)
close(pb)
names(tree.intra) <- trees
mod_results <- recombine(tree.intra, slot1 = 6)
mod_results$info <- NULL
names(mod_results)[1] <- "n.tree"
mod_results$n.tree <- as.numeric(mod_results$n.tree)
#calculate mean and sd for each parameter
#variation due to intraspecific variability
mean_by_randomval <-
stats::aggregate(. ~ n.intra, data = mod_results, mean)
#variation due to tree choice
mean_by_tree <- stats::aggregate(. ~ n.tree, data = mod_results, mean)
statresults <- data.frame(
min.all = apply(mod_results, 2, min),
max.all = apply(mod_results, 2, max),
mean.all = apply(mod_results, 2, mean),
sd_all = apply(mod_results, 2, stats::sd),
min.intra = apply(mean_by_randomval, 2, min),
max.intra = apply(mean_by_randomval, 2, max),
mean.intra = apply(mean_by_randomval, 2, mean),
sd_intra = apply(mean_by_randomval, 2, stats::sd),
min.tree = apply(mean_by_tree, 2, min),
max.tree = apply(mean_by_tree, 2, max),
mean.tree = apply(mean_by_tree, 2, mean),
sd_tree = apply(mean_by_tree, 2, stats::sd)
)[-(1:2),]
statresults$CI_low_all <-
statresults$mean.all - stats::qt(0.975, df = n.intra * n.tree - 1) * statresults$sd_all / sqrt(n.intra *
n.tree)
statresults$CI_low_intra <-
statresults$mean.intra - stats::qt(0.975, df = n.intra - 1) * statresults$sd_intra / sqrt(n.intra)
statresults$CI_low_tree <-
statresults$mean.tree - stats::qt(0.975, df = n.tree - 1) * statresults$sd_intra / sqrt(n.tree)
statresults$CI_high_all <-
statresults$mean.all + stats::qt(0.975, df = n.intra * n.tree - 1) * statresults$sd_all / sqrt(n.intra *
n.tree)
statresults$CI_high_intra <-
statresults$mean.intra + stats::qt(0.975, df = n.intra - 1) * statresults$sd_intra / sqrt(n.intra)
statresults$CI_high_tree <-
statresults$mean.tree + stats::qt(0.975, df = n.tree - 1) * statresults$sd_intra / sqrt(n.tree)
#reoder to later match sensi_plot for the single functions
statresults <-
statresults[, c(
"min.all",
"max.all",
"mean.all",
"sd_all",
"CI_low_all",
"CI_high_all",
"min.intra",
"max.intra",
"mean.intra",
"sd_intra",
"CI_low_intra",
"CI_high_intra",
"min.tree",
"max.tree",
"mean.tree",
"sd_tree",
"CI_low_tree",
"CI_high_tree"
)]
#species with transformation problems
nr <- n.tree * n.intra - nrow(mod_results)
sp.pb <- unique(unlist(lapply(tree.intra, function(x)
x$sp.pb)))
if (length(sp.pb) > 0)
warning (
paste(
"in",
nr,
"simulations, data transformations generated NAs, please consider using another function
for x.transf or y.transf and check output$sp.pb",
sep = " "
)
)
res <- list(
call = match.call(),
formula = formula,
y.transf = y.transf,
x.transf = x.transf,
data = full.data,
sensi.estimates = mod_results,
N.obs = tree.intra[[1]]$N.obs,
stats = round(statresults[c(1:6), c(
"mean.all",
"CI_low_all",
"CI_high_all",
"mean.intra",
"CI_low_intra",
"CI_high_intra",
"mean.tree",
"CI_low_tree",
"CI_high_tree"
)], digits = 3),
all.stats = statresults,
sp.pb = sp.pb
)
class(res) <- "sensiTree_Intra"
return(res)
}