diff --git a/R/process.data/process.fun.R b/R/process.data/process.fun.R index 740f44f2bbd931c5c99d8da923e7f12215e5e7c0..8a7485c289fbbbd1efba874d59f079e9ef285372 100644 --- a/R/process.data/process.fun.R +++ b/R/process.data/process.fun.R @@ -344,14 +344,10 @@ fun.data.per.ecoregion <- function(ecoregion, data.tot, weight.full.plot, site.n if (sum(!data.BA.sp[["obs.id"]] == data[["obs.id"]]) > 0) stop("competition index not in the same order than data") - ##### - data.traits = NA - ## ADD TRY DATA IF NEEDED + data.TRAITS.s <- NA if (is.data.frame(data.TRAITS)) - data.TRAITS.s <- subset(data.TRAITS, subset = data.TRAITS[[sp.code]] %in% - data[[sp.code2]]) else data.TRAITS.s <- NA - + data.TRAITS.s <- subset(data.TRAITS, subset = data.TRAITS[[sp.code]] %in% data[[sp.code2]]) write.csv(data, file = file.path(path, "data.tree.csv"), quote = FALSE, row.names = FALSE) write.csv(data.BA.sp, file = file.path(path, "data.BA.SP.csv"), quote = FALSE, @@ -363,10 +359,12 @@ fun.data.per.ecoregion <- function(ecoregion, data.tot, weight.full.plot, site.n ####### FUNCTION TO FORMAT DATA FOR BIG TROPICAL PLOT fun.data.per.bigplot <- function(data, site.name, data.TRAITS = NA, Rlim = 15, xy.name, - parallel = FALSE, rpuDist = FALSE, sp.code = "sp", sp.code2 = "sp") { + parallel = FALSE, rpuDist = FALSE, sp.code = "sp", sp.code2 = "sp", out.dir = "output/processed/") { require(data.table) - dir.create(paste("output/processed/", site.name, sep = ""), recursive = TRUE, - showWarnings = FALSE) + + path <- file.path(out.dir, site.name) + dir.create(path, recursive = TRUE, showWarnings = FALSE) + data$sp <- factor(data$sp) data.TRAITS$sp <- factor(data.TRAITS$sp) print(paste("plots :", unique(data[["plot"]]))) @@ -399,18 +397,19 @@ fun.data.per.bigplot <- function(data, site.name, data.TRAITS = NA, Rlim = 15, x if (sum(!as.character(data.BA.SP[["obs.id"]]) == as.character(data[["obs.id"]])) > 0) stop("competition index not in the same order than data") - ##### ADD TRY DATA OR TRAITS IF NEEDED - if (is.data.frame(data.TRAITS)) { - data.TRAITS.s <- subset(data.TRAITS, subset = data.TRAITS[[sp.code]] %in% - data[[sp.code2]]) - list.temp <- list(data.tree = data, data.BA.SP = data.BA.SP, data.traits = data.TRAITS.s) - saveRDS(list.temp, file = paste("output/processed/", site.name, "/list.rds", - sep = "")) - } else { - list.temp <- list(data.tree = data, data.BA.SP = data.BA.sp, data.traits = NA) - saveRDS(list.temp, file = paste("output/processed/", site.name, "/list.rds", - sep = "")) - } + + browser() + ## ADD TRY DATA IF NEEDED + data.TRAITS.s <- NA + if (is.data.frame(data.TRAITS)) + data.TRAITS.s <- subset(data.TRAITS, subset = data.TRAITS[[sp.code]] %in% data[[sp.code2]]) + + write.csv(data, file = file.path(path, "data.tree.csv"), quote = FALSE, row.names = FALSE) + write.csv(data.BA.sp, file = file.path(path, "data.BA.SP.csv"), quote = FALSE, + row.names = FALSE) + write.csv(data.TRAITS.s, file = file.path(path, "data.traits.csv"), quote = FALSE, + row.names = FALSE) + } process_inventory_dataset <- function(set, path.formatted = "output/formatted", path.processed = "output/processed"){