## ----setup, echo=FALSE, message=FALSE, warning=FALSE--------------------------
require(phylter)
require(ape)

## ----eval = FALSE-------------------------------------------------------------
# install.packages("remotes")

## ----eval = FALSE-------------------------------------------------------------
# remotes::install_github("damiendevienne/phylter")

## ----eval = FALSE-------------------------------------------------------------
# library("phylter")

## ----eval = FALSE-------------------------------------------------------------
# if (!requireNamespace("ape", quietly = TRUE))
#    install.packages("ape")
# trees <- ape::read.tree("treefile.tre")

## ----eval = FALSE-------------------------------------------------------------
# results <- phylter(trees, gene.names = names)

## ----eval = FALSE-------------------------------------------------------------
# phylter(X, bvalue = 0, distance = "patristic", k = 3, k2 = k, Norm = "median",
#   Norm.cutoff = 0.001, gene.names = NULL, test.island = TRUE,
#   verbose = TRUE, stop.criteria = 1e-5, InitialOnly = FALSE,
#   normalizeby = "row", parallel = TRUE)

## ----eval = FALSE-------------------------------------------------------------
# results$Final$Outliers

## ----eval = FALSE-------------------------------------------------------------
# # Get a summary: nb of outliers, gain in concordance, etc.
# summary(results)
# 
# # Show the number of species in each gene, and how many per gene are outliers
# plot(results, "genes")
# 
# # Show the number of genes where each species is found, and how many are outliers
# plot(results, "species")
# 
# # Compare before and after genes $\times$ species matrices, highlighting missing data and outliers
# # identified (not efficient for large datasets)
# plot2WR(results)
# 
# # Plot the dispersion of data before and after outlier removal. One dot represents one
# # gene $\times$ species association
# plotDispersion(results)
# 
# # Plot the genes $\times$ genes matrix showing pairwise correlation between genes
# plotRV(results)
# 
# # Plot optimization scores during optimization
# plotopti(results)

## ----eval = FALSE-------------------------------------------------------------
# write.phylter(results, file = "phylter.out")

## ----results='hide'-----------------------------------------------------------
data(carnivora, package = "phylter")
results <- phylter(carnivora, parallel = FALSE) # for example

## -----------------------------------------------------------------------------
summary(results)

## -----------------------------------------------------------------------------
results$Initial
results$Final

## -----------------------------------------------------------------------------
results$Final$Outliers

## ----eval = FALSE-------------------------------------------------------------
# write.phylter(results)