Renamed xtra_report.R -> table.R

xtra_report.R → table.R

@@ -9,56 +9,56 @@
 
 library(icesTAF)
 
-mkdir("upload/report")
+mkdir("table")
 
 ## catage (plus group)
-catage <- read.taf("upload/input/catage.csv")
+catage <- read.taf("data/catage.csv")
 catage$"10" <- rowSums(catage[as.character(10:14)])
 catage <- catage[c("Year", as.character(2:10))]
 names(catage)[names(catage)=="10"] <- "10+"
-write.taf(catage, "upload/report/catage_rep.csv")
+write.taf(catage, "table/catage_rep.csv")
 
 ## smh (skip year)
-smh <- read.taf("upload/input/smh.csv")
+smh <- read.taf("data/smh.csv")
 smh <- na.omit(smh)
-write.taf(smh, "upload/report/smh_rep.csv")
+write.taf(smh, "table/smh_rep.csv")
 
 ## wstock (trim year and age)
-wstock <- read.taf("upload/input/wstock.csv")
+wstock <- read.taf("data/wstock.csv")
 wstock <- head(wstock, -1)[c("Year",as.character(1:10))]
-write.taf(wstock, "upload/report/wstock_rep.csv")
+write.taf(wstock, "table/wstock_rep.csv")
 
 ## wcatch (trim year and age)
-wcatch <- read.taf("upload/input/wcatch.csv")
+wcatch <- read.taf("data/wcatch.csv")
 wcatch <- head(wcatch, -2)[c("Year",as.character(2:10))]
-write.taf(wcatch, "upload/report/wcatch_rep.csv")
+write.taf(wcatch, "table/wcatch_rep.csv")
 
 ## maturity (trim year and age)
-maturity <- read.taf("upload/input/maturity.csv")
+maturity <- read.taf("data/maturity.csv")
 maturity <- head(maturity, -1)[c("Year",as.character(2:10))]
-write.taf(maturity, "upload/report/maturity_rep.csv")
+write.taf(maturity, "table/maturity_rep.csv")
 
 ## summary (trim year, insert NA, average, round)
-summary <- read.taf("upload/output/summary.csv")
+summary <- read.taf("output/summary.csv")
 summary <- head(summary, -4)
 summary$Fbar[nrow(summary)] <- NA
 avg <- as.data.frame(t(colMeans(head(summary,-1), na.rm=TRUE)))
 avg["Year"] <- paste0("Mean79-", summary$Year[nrow(summary)-1])
 summary <- rbind(summary, avg)
 summary[c("Rec","RefB","SSB","Landings")] <- round(summary[c("Rec","RefB","SSB","Landings")])
 summary[c("YoverSSB","Fbar")] <- round(summary[c("YoverSSB","Fbar")], 3)
-write.taf(summary, "upload/report/summary_rep.csv")
+write.taf(summary, "table/summary_rep.csv")
 
 ## natage (trim year and age, change units, round)
-natage <- read.taf("upload/output/natage.csv")
+natage <- read.taf("output/natage.csv")
 natage <- head(natage, -2)[c("Year", as.character(1:10))]
 natage <- natage / 1000
 natage[as.character(1:5)] <- round(natage[as.character(1:5)], 1)
 natage[as.character(6:10)] <- round(natage[as.character(6:10)], 2)
-write.taf(natage, "upload/report/natage_rep.csv")
+write.taf(natage, "table/natage_rep.csv")
 
 ## fatage (trim year and age)
-fatage <- read.taf("upload/output/fatage.csv")
+fatage <- read.taf("output/fatage.csv")
 fatage <- head(fatage, -2)[c("Year", as.character(2:10))]
 fatage <- round(fatage, 3)
-write.taf(fatage, "upload/report/fatage_rep.csv")
+write.taf(fatage, "table/fatage_rep.csv")