From 34772a6a95a3009225153494e77b61b8054d151f Mon Sep 17 00:00:00 2001
From: nperez <nperez@bscearth372.int.bsc.es>
Date: Thu, 11 Jul 2019 17:39:10 +0200
Subject: [PATCH 1/2] Threshold function works with NA values

---
 R/Threshold.R | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/R/Threshold.R b/R/Threshold.R
index aa43b3a..2ba75e6 100644
--- a/R/Threshold.R
+++ b/R/Threshold.R
@@ -29,7 +29,7 @@
 #'a <- Threshold(data, dates = NULL, base.range = NULL, qtiles = 0.9, ncores = NULL)
 #'str(a)
 #'@export
-Threshold <- function(data, dates = NULL, calendar = NULL, base.range = NULL, qtiles = 0.9, ncores = NULL) {
+Threshold <- function(data, dates = NULL, calendar = NULL, base.range = NULL, qtiles = 0.9, ncores = NULL, na.rm = FALSE) {
   if (is.null(data)) {
     stop("Parameter 'data' cannot be NULL.")
   }
@@ -93,6 +93,14 @@ Threshold <- function(data, dates = NULL, calendar = NULL, base.range = NULL, qt
   if (stop_error) {
     stop("Parameter 'dates' must be of the same length as the 'time' dimension of the parameter 'data'.")
   }
+  if (!is.logical(na.rm)) {
+    stop("Parameter 'na.rm' must be logical.")
+  }
+  if (length(na.rm) > 1) {
+    na.rm <- na.rm[1]
+    warning("Parameter 'na.rm' has length > 1 and only the first ",
+            "element will be used.")
+  }
   dates <- as.PCICt(dates, cal = calendar)
   dates = as.character(dates)
   jdays <- as.numeric(strftime(dates, format = "%j"))
@@ -170,7 +178,7 @@ Threshold <- function(data, dates = NULL, calendar = NULL, base.range = NULL, qt
   if (length(dim(data)) > 1) {
     result <- Apply(data = data, margins = margins, 
                     fun = .Threshold, indices = jdays, qtiles = qtiles, 
-                    ncores = ncores)
+                    ncores = ncores, na.rm = na.rm)
     names(dim(result$output1)) <- c("jdays", dim_names[-time_dim])
   } else {
     result <- list() 
@@ -179,6 +187,6 @@ Threshold <- function(data, dates = NULL, calendar = NULL, base.range = NULL, qt
   }
   return(result$output1)
 }
-.Threshold <- function(data, indices,  qtiles) {
-  tapply(X = data, INDEX = indices, FUN = quantile, probs = qtiles)
+.Threshold <- function(data, indices,  qtiles, na.rm) {
+  tapply(X = data, INDEX = indices, FUN = quantile, probs = qtiles, na.rm = na.rm)
 } 
-- 
GitLab


From a2001677c4293c36acedbe0c53f3c6114dcbd00a Mon Sep 17 00:00:00 2001
From: nperez <nperez@bscearth372.int.bsc.es>
Date: Fri, 12 Jul 2019 10:11:31 +0200
Subject: [PATCH 2/2] na.rm set default

---
 R/Threshold.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/Threshold.R b/R/Threshold.R
index 2ba75e6..7b94021 100644
--- a/R/Threshold.R
+++ b/R/Threshold.R
@@ -187,6 +187,6 @@ Threshold <- function(data, dates = NULL, calendar = NULL, base.range = NULL, qt
   }
   return(result$output1)
 }
-.Threshold <- function(data, indices,  qtiles, na.rm) {
+.Threshold <- function(data, indices,  qtiles, na.rm = FALSE) {
   tapply(X = data, INDEX = indices, FUN = quantile, probs = qtiles, na.rm = na.rm)
 } 
-- 
GitLab