fix bug bash inputs

euroargodev · Aug 18, 2020 · 6d00fe4 · 6d00fe4
1 parent 63851b9
commit 6d00fe4
Show file tree

Hide file tree

Showing 5 changed files with 24 additions and 19 deletions.
diff --git a/v1_paper/R/CANYON-MED_codes/CANYON_MED_AT.R b/v1_paper/R/CANYON-MED_codes/CANYON_MED_AT.R
@@ -22,14 +22,15 @@ CANYON_MED_AT<- function(date,lat,lon,pres,temp,psal,doxy) {
   #
   #
   # Marine Fourrier, LOV
-  # 10.06.2020
+  # 17.08.2020
 
   # No input checks! Assumes informed use, e.g., same dimensions for all
   # inputs, ...
   require(fields)
+  require(matrixStats)
 
 
-  basedir <- "C:/Users/nouno/OneDrive/Documents/GitHub/CANYON-MED/R/" # relative or absolute path to CANYON-MED folder
+  basedir <- "D:/Documents/Thèse/Docs/science/PAPIER_CANYON_MED/CODES/CANYON-MED/v1_paper/R/" # relative or absolute path to CANYON-MED folder
 
   # input preparation
   date <- as.POSIXct(date)
@@ -76,7 +77,7 @@ CANYON_MED_AT<- function(date,lat,lon,pres,temp,psal,doxy) {
   #
   n_list=10
 
-  AT_outputs_s=rep(0,n_list)
+  AT_outputs_s=data.frame(matrix(NA, nrow = nrow(data), ncol = 10))
 
   rx <-dim(data_N)[1]
   for(i in 1:n_list) {
@@ -100,7 +101,7 @@ CANYON_MED_AT<- function(date,lat,lon,pres,temp,psal,doxy) {
     AT_outputs_s[i]=AT_outputs
   }
 
-  AT_out=mean(AT_outputs_s);
+  AT_out<-rowMeans(AT_outputs_s,na.rm = TRUE)
 
   out=AT_out;
   return(out)

diff --git a/v1_paper/R/CANYON-MED_codes/CANYON_MED_CT.R b/v1_paper/R/CANYON-MED_codes/CANYON_MED_CT.R
@@ -22,14 +22,15 @@ CANYON_MED_CT<- function(date,lat,lon,pres,temp,psal,doxy) {
   #
   #
   # Marine Fourrier, LOV
-  # 10.06.2020
+  # 17.08.2020
 
   # No input checks! Assumes informed use, e.g., same dimensions for all
   # inputs, ...
   require(fields)
+  require(matrixStats)
 
 
-  basedir <- "C:/Users/nouno/OneDrive/Documents/GitHub/CANYON-MED/R/" # relative or absolute path to CANYON-MED folder
+  basedir <- "D:/Documents/Thèse/Docs/science/PAPIER_CANYON_MED/CODES/CANYON-MED/v1_paper/R/" # relative or absolute path to CANYON-MED folder
 
   # input preparation
   date <- as.POSIXct(date)
@@ -76,7 +77,7 @@ CANYON_MED_CT<- function(date,lat,lon,pres,temp,psal,doxy) {
   #
   n_list=10
 
-  CT_outputs_s=rep(0,n_list)
+  CT_outputs_s=data.frame(matrix(NA, nrow = nrow(data), ncol = 10))
 
   rx <-dim(data_N)[1]
   for(i in 1:n_list) {
@@ -100,7 +101,7 @@ CANYON_MED_CT<- function(date,lat,lon,pres,temp,psal,doxy) {
     CT_outputs_s[i]=CT_outputs
   }
 
-  CT_out=mean(CT_outputs_s);
+  CT_out<-rowMeans(CT_outputs_s,na.rm = TRUE)
 
   out=CT_out;
   return(out)

diff --git a/v1_paper/R/CANYON-MED_codes/CANYON_MED_PO4.R b/v1_paper/R/CANYON-MED_codes/CANYON_MED_PO4.R
@@ -22,14 +22,15 @@ CANYON_MED_PO4<- function(date,lat,lon,pres,temp,psal,doxy) {
   #
   #
   # Marine Fourrier, LOV
-  # 10.06.2020
+  # 17.08.2020
 
   # No input checks! Assumes informed use, e.g., same dimensions for all
   # inputs, ...
   require(fields)
+  require(matrixStats)
 
 
-  basedir <- "C:/Users/nouno/OneDrive/Documents/GitHub/CANYON-MED/R/" # relative or absolute path to CANYON-MED folder
+  basedir <- "D:/Documents/Thèse/Docs/science/PAPIER_CANYON_MED/CODES/CANYON-MED/v1_paper/R/" # relative or absolute path to CANYON-MED folder
 
   # input preparation
   date <- as.POSIXct(date)
@@ -76,7 +77,7 @@ CANYON_MED_PO4<- function(date,lat,lon,pres,temp,psal,doxy) {
   #
   n_list=10
 
-  phos_outputs_s=rep(0,n_list)
+  phos_outputs_s=data.frame(matrix(NA, nrow = nrow(data), ncol = 10))
 
   rx <-dim(data_N)[1]
   for(i in 1:n_list) {
@@ -100,7 +101,7 @@ CANYON_MED_PO4<- function(date,lat,lon,pres,temp,psal,doxy) {
     phos_outputs_s[i]=phos_outputs
   }
 
-  phos_out=mean(phos_outputs_s);
+  phos_out<-rowMeans(phos_outputs_s,na.rm = TRUE)
 
   out=phos_out;
   return(out)

diff --git a/v1_paper/R/CANYON-MED_codes/CANYON_MED_SiOH4.R b/v1_paper/R/CANYON-MED_codes/CANYON_MED_SiOH4.R
@@ -27,9 +27,10 @@ CANYON_MED_SiOH4<- function(date,lat,lon,pres,temp,psal,doxy) {
   # No input checks! Assumes informed use, e.g., same dimensions for all
   # inputs, ...
   require(fields)
+  require(matrixStats)
 
 
-  basedir <- "C:/Users/nouno/OneDrive/Documents/GitHub/CANYON-MED/R/" # relative or absolute path to CANYON-MED folder
+  basedir <- "D:/Documents/Thèse/Docs/science/PAPIER_CANYON_MED/CODES/CANYON-MED/v1_paper/R/" # relative or absolute path to CANYON-MED folder
 
   # input preparation
   date <- as.POSIXct(date)
@@ -76,7 +77,7 @@ CANYON_MED_SiOH4<- function(date,lat,lon,pres,temp,psal,doxy) {
   #
   n_list=10
 
-  sil_outputs_s=rep(0,n_list)
+  sil_outputs_s=data.frame(matrix(NA, nrow = nrow(data), ncol = 10))
 
   rx <-dim(data_N)[1]
   for(i in 1:n_list) {
@@ -100,7 +101,7 @@ CANYON_MED_SiOH4<- function(date,lat,lon,pres,temp,psal,doxy) {
     sil_outputs_s[i]=sil_outputs
   }
 
-  sil_out=mean(sil_outputs_s);
+  sil_out<-rowMeans(sil_outputs_s,na.rm = TRUE)
 
   out=sil_out;
   return(out)

diff --git a/v1_paper/R/CANYON-MED_codes/CANYON_MED_pHT.R b/v1_paper/R/CANYON-MED_codes/CANYON_MED_pHT.R
@@ -22,14 +22,15 @@ CANYON_MED_pHT<- function(date,lat,lon,pres,temp,psal,doxy) {
   #
   #
   # Marine Fourrier, LOV
-  # 10.06.2020
+  # 17.08.2020
 
   # No input checks! Assumes informed use, e.g., same dimensions for all
   # inputs, ...
   require(fields)
+  require(matrixStats)
 
 
-  basedir <- "C:/Users/nouno/OneDrive/Documents/GitHub/CANYON-MED/R/" # relative or absolute path to CANYON-MED folder
+  basedir <- "D:/Documents/Thèse/Docs/science/PAPIER_CANYON_MED/CODES/CANYON-MED/v1_paper/R/" # relative or absolute path to CANYON-MED folder
 
   # input preparation
   date <- as.POSIXct(date)
@@ -76,7 +77,7 @@ CANYON_MED_pHT<- function(date,lat,lon,pres,temp,psal,doxy) {
   #
   n_list=10
 
-  ph_outputs_s=rep(0,n_list)
+  ph_outputs_s=data.frame(matrix(NA, nrow = nrow(data), ncol = 10))
 
   rx <-dim(data_N)[1]
   for(i in 1:n_list) {
@@ -100,7 +101,7 @@ CANYON_MED_pHT<- function(date,lat,lon,pres,temp,psal,doxy) {
     ph_outputs_s[i]=ph_outputs
   }
 
-  ph_out=mean(ph_outputs_s);
+  ph_out<-rowMeans(ph_outputs_s,na.rm = TRUE)
 
   out=ph_out;
   return(out)