Additional checks and outputs for LAWA data

seanlhodges · Jul 23, 2017 · 13f9db0 · 13f9db0
1 parent 89d71e5
commit 13f9db0
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Showing 4 changed files with 28 additions and 12 deletions.
diff --git a/PackageDataForDelivery - NAs added in for trend.R b/PackageDataForDelivery - NAs added in for trend.R
@@ -1,13 +1,22 @@
 #requestData(vendor[tss],tss_url,"service=Hilltop&request=Reset")
+ANALYSIS<-"DELIVERY"
+# Set working directory
+od<-getwd()
+setwd("//file/herman/r/oa/08/02/2017/Water Quality/R/lawa_state")
 
+#/* -===Include required function libraries===- */ 
+
+source("scripts/WQualityStateTrend/lawa_state_functions.R")
+
+wqparam <- c("BDISC","TURB","PH","NH4","TON","TN","DRP","TP","ECOLI") 
 # build template file of all possible results for Trend - Sites x Parameter x Five/Ten Yr
 
 # specify a matrix of appropriate size
 
 # building blank data file
 if(!exists("templateSeason")){
   library(readr)
-  seasons <- read_csv("//file/herman/R/OA/08/02/2016/Water Quality/R/lawa_state/seasons.csv")
+  seasons <- read_csv("//file/herman/R/OA/08/02/2017/Water Quality/R/lawa_state/seasons.csv")
 
 
   for(j in 1:nrow(l)){
@@ -35,7 +44,7 @@ if(!exists("templateSeason")){
 
 #build blank trend results file
 
-trend_fordelivery <- read.csv("//file/herman/R/OA/08/02/2016/Water Quality/ROutput/trend_fordelivery.csv")
+trend_fordelivery <- read.csv("//file/herman/R/OA/08/02/2017/Water Quality/ROutput/trend_fordelivery.csv")
 trend_fordelivery <- trend_fordelivery[,c(2:length(trend_fordelivery))]
 
 #/* -===Local variable/constant definitions===- */
@@ -44,21 +53,23 @@ l$SWQLanduse[l$SWQLanduse=="Native"|l$SWQLanduse=="Exotic"|l$SWQLanduse=="Natura
 
 wqparam  <- c("BDISC","TURB","NH4","TON","TN","DRP","TP","ECOLI") 
 
+landuse  <- unique(l$SWQLanduse)
+altitude <- unique(l$SWQAltitude)
 
 blank.trend.rows <- nrow(l)*length(wqparam)*2
 data.blank <- matrix(data=NA, nrow=blank.trend.rows, ncol=length(trend_fordelivery), byrow=TRUE)
 
 counter<-1
 for(i in 1:nrow(l)){
   for(j in 1:length(wqparam)){
-    for(k in 1:length(landuse)){
-      for(m in 1:length(altitude)){
+    #for(k in 1:length(landuse)){
+      #for(m in 1:length(altitude)){
       data.blank[counter,] <- c(l$LawaSiteID[i],wqparam[j],l$SWQLanduse[i],l$SWQAltitude[i],NA,l$SWQFrequencyLast5[i],l$Region[i],5)
       counter<-counter+1
       data.blank[counter,] <- c(l$LawaSiteID[i],wqparam[j],l$SWQLanduse[i],l$SWQAltitude[i],NA,l$SWQFrequencyAll[i],l$Region[i],10)
       counter<-counter+1
-      }
-    }
+      #}
+    #}
   }
 }
 
@@ -75,4 +86,4 @@ names(tmp) <- c("Location","Parameter","Altitude","Landuse","TrendScore","Freque
 tmp$TrendScore <- as.character(tmp$TrendScore)
 tmp$TrendScore[is.na(tmp$TrendScore)] <- "NA"
 
-trend_fordelivery <- write.csv(tmp, "//file/herman/R/OA/08/02/2016/Water Quality/ROutput/trend_fordelivery_with_NA.csv")
+trend_fordelivery <- write.csv(tmp, "//file/herman/R/OA/08/02/2017/Water Quality/ROutput/trend_fordelivery_with_NA.csv")
diff --git a/lawa_dataPrep_WFS.R b/lawa_dataPrep_WFS.R
@@ -24,7 +24,7 @@ logfolder <- "\\\\file\\herman\\R\\OA\\08\\02\\2017\\Water Quality\\ROutput\\"
 #/* -===Include required function libraries===- */ 
 
 
-source("lawa_state_functions.R")
+source("scripts/WQualityStateTrend/lawa_state_functions.R")
 
 ## Supplementary functions
 

diff --git a/lawa_load_swq.R b/lawa_load_swq.R
@@ -5,8 +5,13 @@
 message("Load Surface Water Quality data from Councils")
 message("-- A folder for todays date will be created and the imported files will be stashed there.")
 
-shell(paste('mkdir "R:/2017/Water Quality/1.Imported/"',format(Sys.Date(),"%Y-%m-%d"),sep=""), translate=TRUE)
-shell(paste('mkdir "R:/2017/Water Quality/4.Analysis/"',format(Sys.Date(),"%Y-%m-%d"),sep=""), translate=TRUE)
+# Encapsulating mkdir commands in the try() in order to suppress error messages on failure
+# Failure's can mean
+#               1. Directories already exist
+#               1. R:/ drive not mapped to \\file\herman\R\OA\08\02
+
+try(shell(paste('mkdir "R:/2017/Water Quality/1.Imported/"',format(Sys.Date(),"%Y-%m-%d"),sep=""), translate=TRUE),silent = TRUE)
+try(shell(paste('mkdir "R:/2017/Water Quality/4.Analysis/"',format(Sys.Date(),"%Y-%m-%d"),sep=""), translate=TRUE),silent = TRUE)
 
 
 ## ----------------------------------------------------------------------------,
@@ -41,7 +46,7 @@ source("//file/herman/r/oa/08/02/2017/Water Quality/R/lawa_state/loadTRC.R")
 rm("Data","df","df2","df2","sample","udf")
 
 #Hawkes Bay
-source("//file/herman/r/oa/08/02/2017/Water Quality/R/lawa_state/loadHBRC.R")
+source("//file/herman/r/oa/08/02/2017/Water Quality/R/lawa_state/loadHBRC_v2.R")
 rm("Data","df","df2","df2","sample","udf")
 
 #Horizons

diff --git a/main.R b/main.R
@@ -4,7 +4,7 @@ ANALYSIS<-"Main routine"
 od<-getwd()
 rm(list = ls())
 setwd("//file/herman/r/oa/08/02/2017/Water Quality/R/lawa_state")
-source("lawa_state_functions.R")
+source("scripts/WQualityStateTrend/lawa_state_functions.R")
 
 
 message("LAWA State and Trend analysis started")