inst/utils/00_evaluate_funs.R

In franciscolobo/TaxonSampling: Hierarchical Taxonomic Sampling for Maximized Diversity at All Levels

# evaluate_TS <- function(x) {
#   # Collect metrics about the taxon diversity of a sample (outputIDs).
#   #
#   # Args:
#   #   taxlist: _taxonsampling_ list object returned by [run_TS()]
#   # Returns:
#   #   listTaxon: (char) children taxa selected at least once per level.
#   ow <- options("warn")
#   options(warn = -1)
#   selectedIDs <-  get_taxonomy_counts(ids_df = data.frame(taxID = x$outputIDs,
#                                                           seqID = NA),
#                                       nodes = x$nodes, verbose = FALSE)
#   options(ow)
#   listTaxon   <- list()
#   listBias    <- list()
#
#   # Find the sub-taxa (children nodes) of the current taxon
#   children <- 1
#   while (length(children) > 0) {
#     taxon    <- as.integer(children)
#     children <- selectedIDs$nodes$id[(selectedIDs$nodes$parent %in% taxon) & !(selectedIDs$nodes$id %in% taxon)]
#     children <- intersect(children, names(selectedIDs$countIDs))
#
#     selectedChildren <- intersect(children, names(selectedIDs$countIDs))
#     listTaxon        <- c(listTaxon, list(selectedChildren))
#   }
#
#   return(listTaxon)
# }
#
#
# library(pbmcapply)
# library(dplyr)
#
# #Number of reps
# n <- 10
#
# # preprocess stuff:
# taxlist <- get_taxonomy_counts(taxonomy_path = "data_files/taxdump/",
#                                ids_file      = "data_files/metadata/TaxID2SeqID.txt") %>%
#   get_species_counts(spp_file = "data_files/metadata/TaxID2sppCounts.tsv")
#
# # Test parameters
# rand <- c("yes", "no", "after_first_round")
# meth <- c("diversity", "balanced")
# samp <- c("agnostic", "known_species")
# repl <- c(TRUE, FALSE)
# m    <- 50 * (1:8)
# pars <- expand.grid(rand=rand, meth=meth, samp=samp, repl=repl, m = m,
#                     stringsAsFactors = FALSE)
# pars <- pars[-which(pars$meth == "balanced" & pars$rand == "after_first_round"), ]
#
# output <- vector("list", nrow(pars))
# for (k in 1:nrow(pars)){
#   cat(sprintf("\nTrying %02d/%02d: [%s]", k, nrow(pars), paste(pars[k, ], collapse = ",")))
#   output[[k]] <- list(pars = pars[k, ])
#
#   out <- vector("list", n)
#   names(out) <- paste0("Rep", 1:n)
#   for (i in 1:n){
#     out[[i]]$tl <- run_TS(taxlist          = taxlist,
#                           taxon            = 40674,
#                           m                = pars$m[k],
#                           seq_file         = NULL,
#                           out_file         = NULL,
#                           method           = pars$meth[k],
#                           randomize        = pars$rand[k],
#                           replacement      = pars$repl[k],
#                           ignoreIDs        = 9598,
#                           requireIDs       = 9606,
#                           ignoreNonLeafIDs = NULL,
#                           sampling         = pars$samp[k],
#                           verbose          = FALSE)
#
#     out[[i]]$perf <- evaluate_TS(out[[i]]$tl)
#     out[[i]]$tl$nodes  <- NULL
#     out[[i]]$tl$spp_df <- NULL
#   }
#
#   output[[k]]$out <- out
# }
#
# saveRDS(output, "./results/test.rds")
#
#
#