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updating function Fishtaxamaker
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@GabrielNakamura
GabrielNakamura committed Feb 17, 2023
1 parent ac3ab8d commit fb3441d
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3 changes: 1 addition & 2 deletions DESCRIPTION
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Expand Up @@ -21,7 +21,7 @@ License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
RoxygenNote: 7.2.3
Imports:
ape,
fishtree,
Expand All @@ -41,4 +41,3 @@ Suggests: markdown,
gh
Remotes:
ropensci/rfishbase

164 changes: 82 additions & 82 deletions R/tab_function.R
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Expand Up @@ -61,91 +61,91 @@
#'
FishTaxaMaker <-
function (data, allow.manual.insert = TRUE)
{
if (is.data.frame(data) == TRUE) {
names_data <- colnames(data)
names_data_rfishbase <- gsub("_", " ", names_data)
}
if (is.matrix(data) == TRUE) {
if (dim(data)[2] < 1) {
stop("\n More than one species must be supplied in occurence matrix \n")
{
if (is.data.frame(data) == TRUE) {
names_data <- colnames(data)
names_data_rfishbase <- gsub("_", " ", names_data)
}
names_data <- colnames(data)
names_data_rfishbase <- gsub("_", " ", names_data)
}
if (is.vector(data) == TRUE) {
if (length(data) == 1) {
stop("\n More than one species must be supplied \n")
}
names_data <- data
names_data_rfishbase <- gsub("_", " ", names_data)
}
df_taxon <- data.frame(user_spp = names_data, valid_names = rep(NA,
length(names_data)))
fishbasedata <- as.data.frame(data.frame(rfishbase::load_taxa()))
not_find <- names_data_rfishbase[which(is.na(match(names_data_rfishbase,
fishbasedata$Species)) == TRUE)]
found <- gsub("_", " ", names_data[which(!is.na(match(names_data_rfishbase,
fishbasedata$Species)) == TRUE)])
names_not_find <- rfishbase::synonyms(species_list = not_find)
names_not_find_valid <- names_not_find[which(names_not_find$Status ==
"synonym"), ]
df_taxon[match(found, gsub("_", " ", df_taxon$user_spp)),
"valid_names"] <- found
df_taxon[match(names_not_find_valid$synonym, gsub("_", " ",
df_taxon$user_spp)), "valid_names"] <- names_not_find_valid$Species
not_found_fishtree <- data.frame(names_not_find[match(gsub("_",
" ", df_taxon[which(is.na(df_taxon$valid_names) == TRUE),
"user_spp"]), names_not_find$synonym), ])$synonym
list_res <- vector(mode = "list", length = 3)
tax_hierarch <- fishbasedata[match(df_taxon$valid_names,
fishbasedata$Species), c("Subfamily", "Family", "Order",
"Class", "SuperClass")]
data_fishbase_complete <- cbind(df_taxon, tax_hierarch)
list_res[[1]] <- data_fishbase_complete
list_res[[2]] <- data_fishbase_complete[, c("valid_names",
"Family", "Order")]
colnames(list_res[[2]]) <- c("s", "f", "o")
list_res[[2]]$s <- gsub(" ", "_", list_res[[2]]$s)
list_res[[2]][match(gsub(" ", "_", na.omit(not_found_fishtree)),
list_res[[1]]$user_spp), "s"] <- na.omit(not_found_fishtree)
list_res[[2]][match(gsub(" ", "_", na.omit(not_found_fishtree)),
list_res[[1]]$user_spp), c("f", "o")] <- paste("not_found")
list_res[[2]]$s <- gsub(" ", "_", list_res[[2]]$s)
if (length(not_found_fishtree) >= 1) {
list_res[[3]] <- not_found_fishtree
}
else {
list_res[[3]] <- paste("All species were found in Fishtree")
}
names(list_res) <- c("All_info_fishbase", "Taxon_data_FishPhyloMaker",
"Species_not_in_Fishbase")
if (length(not_found_fishtree) >= 1) {
if (allow.manual.insert == TRUE) {
print_cat_Family <- function(not_found_fishtree) {
cat("tell the Family of ", not_found_fishtree)
cat("\n")
if (is.matrix(data) == TRUE) {
if (dim(data)[2] < 1) {
stop("\n More than one species must be supplied in occurence matrix \n")
}
print_cat_Order <- function(not_found_fishtree) {
cat("tell the Order of ", not_found_fishtree)
cat("\n")
names_data <- colnames(data)
names_data_rfishbase <- gsub("_", " ", names_data)
}
if (is.vector(data) == TRUE) {
if (length(data) == 1) {
stop("\n More than one species must be supplied \n")
}
for (i in 1:length(not_found_fishtree)) {
spp_family <- readline(prompt = print_cat_Family(not_found_fishtree = not_found_fishtree[i]))
list_res[[2]][which(list_res[[1]]$user_spp ==
gsub(" ", "_", not_found_fishtree[i])), c("s",
"f")] <- c(not_found_fishtree[i], spp_family)
spp_order <- unique(fishbasedata[which(fishbasedata$Family ==
spp_family), "Order"])
if (length(spp_order) == 0) {
warning("\n Please, check if the family name typed is valid \n")
spp_order <- readline(prompt = print_cat_Order(not_found_fishtree = not_found_fishtree[i]))
names_data <- data
names_data_rfishbase <- gsub("_", " ", names_data)
}
df_taxon <- data.frame(user_spp = names_data, valid_names = rep(NA,
length(names_data)))
fishbasedata <- as.data.frame(data.frame(rfishbase::load_taxa()))
not_find <- names_data_rfishbase[which(is.na(match(names_data_rfishbase,
fishbasedata$Species)) == TRUE)]
found <- gsub("_", " ", names_data[which(!is.na(match(names_data_rfishbase,
fishbasedata$Species)) == TRUE)])
names_not_find <- rfishbase::synonyms(species_list = not_find)
names_not_find_valid <- names_not_find[which(names_not_find$Status ==
"synonym"), ]
df_taxon[match(found, gsub("_", " ", df_taxon$user_spp)),
"valid_names"] <- found
df_taxon[match(names_not_find_valid$synonym, gsub("_", " ",
df_taxon$user_spp)), "valid_names"] <- names_not_find_valid$Species
not_found_fishtree <- data.frame(names_not_find[match(gsub("_",
" ", df_taxon[which(is.na(df_taxon$valid_names) == TRUE),
"user_spp"]), names_not_find$synonym), ])$synonym
list_res <- vector(mode = "list", length = 3)
tax_hierarch <- fishbasedata[match(df_taxon$valid_names,
fishbasedata$Species), c("Subfamily", "Family", "Order",
"Class", "SuperClass")]
data_fishbase_complete <- cbind(df_taxon, tax_hierarch)
list_res[[1]] <- data_fishbase_complete
list_res[[2]] <- data_fishbase_complete[, c("valid_names",
"Family", "Order")]
colnames(list_res[[2]]) <- c("s", "f", "o")
list_res[[2]]$s <- gsub(" ", "_", list_res[[2]]$s)
list_res[[2]][match(gsub(" ", "_", na.omit(not_found_fishtree)),
list_res[[1]]$user_spp), "s"] <- na.omit(not_found_fishtree)
list_res[[2]][match(gsub(" ", "_", na.omit(not_found_fishtree)),
list_res[[1]]$user_spp), c("f", "o")] <- paste("not_found")
list_res[[2]]$s <- gsub(" ", "_", list_res[[2]]$s)
if (length(not_found_fishtree) >= 1) {
list_res[[3]] <- not_found_fishtree
}
else {
list_res[[3]] <- paste("All species were found in Fishtree")
}
names(list_res) <- c("All_info_fishbase", "Taxon_data_FishPhyloMaker",
"Species_not_in_Fishbase")
if (length(not_found_fishtree) >= 1) {
if (allow.manual.insert == TRUE) {
print_cat_Family <- function(not_found_fishtree) {
cat("tell the Family of ", not_found_fishtree)
cat("\n")
}
print_cat_Order <- function(not_found_fishtree) {
cat("tell the Order of ", not_found_fishtree)
cat("\n")
}
for (i in 1:length(not_found_fishtree)) {
spp_family <- readline(prompt = print_cat_Family(not_found_fishtree = not_found_fishtree[i]))
list_res[[2]][which(list_res[[1]]$user_spp ==
gsub(" ", "_", not_found_fishtree[i])), c("s",
"f")] <- c(not_found_fishtree[i], spp_family)
spp_order <- unique(fishbasedata[which(fishbasedata$Family ==
spp_family), "Order"])
if (length(spp_order) == 0) {
warning("\n Please, check if the family name typed is valid \n")
spp_order <- readline(prompt = print_cat_Order(not_found_fishtree = not_found_fishtree[i]))
}
list_res[[2]][which(list_res[[2]]$s == not_found_fishtree[i]),
"o"] <- spp_order
}
list_res[[2]][which(list_res[[2]]$s == not_found_fishtree[i]),
"o"] <- spp_order
list_res[[2]]$s <- gsub(" ", "_", list_res[[2]]$s)
}
list_res[[2]]$s <- gsub(" ", "_", list_res[[2]]$s)
}
}
return(list_res)
}
return(list_res)
}
6 changes: 4 additions & 2 deletions man/FishTaxaMaker.Rd
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7 changes: 6 additions & 1 deletion man/PD_deficit.Rd
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