Step one to start organizgin working examples

R/readData.R

@@ -74,7 +74,7 @@ dat2list <- function(fn) {
 #' @param stock Name of the stock, defaults to "BSAI Atka mackerel".
 #' @return HTML tables for the specified Tier 3 data.
 #' @export
-#' @importFrom xtable xtable
+#' @importFrom xtable
 #' @importFrom dplyr select, group_by, summarise, spread
 #' @examples
 #' # Example usage:
@@ -87,48 +87,48 @@ print_Tier3_tables <- function(df, modname="base", stock="BSAI Atka mackerel") {
   tabcap[4]=paste0("Tier 3 projections of ",stock," spawning biomass for the 7 scenarios.")
 
   # Stock Alt Sim Yr  SSB Rec Tot_biom SPR_Implied F Ntot Catch ABC OFL AvgAge AvgAgeTot SexRatio FABC FOFL
-  bfsum <- df %>% select(Alt,Yr,SSB,F,ABC ,Catch) %>% group_by(Alt,Yr) %>% summarise(Catch=mean(Catch),SSB=mean(SSB),F=mean(F),ABC=mean(ABC))
+  bfsum <- df %>% select(Alternative,Yr,SSB,F,ABC ,Catch) %>% group_by(Alternative,Yr) %>% summarise(Catch=mean(Catch),SSB=mean(SSB),F=mean(F),ABC=mean(ABC))
 
-  tC <- bfsum %>% select(Alt,Yr,Catch) %>% spread(Alt,Catch)
+  tC <- bfsum %>% select(Alternative,Yr,Catch) %>% spread(Alternative,Catch)
   names(tC) <- c("Catch","Scenario 1","Scenario 2","Scenario 3","Scenario 4","Scenario 5","Scenario 6","Scenario 7")
 
-  tB <- bfsum %>% select(Alt,Yr,SSB) %>% spread(Alt,SSB)
+  tB <- bfsum %>% select(Alternative,Yr,SSB) %>% spread(Alternative,SSB)
   names(tB) <- c("SSB","Scenario 1","Scenario 2","Scenario 3","Scenario 4","Scenario 5","Scenario 6","Scenario 7")
 
-  tF <- bfsum %>% select(Alt,Yr,F) %>% spread(Alt,F)
+  tF <- bfsum %>% select(Alternative,Yr,F) %>% spread(Alternative,F)
   names(tF) <- c("F","Scenario 1","Scenario 2","Scenario 3","Scenario 4","Scenario 5","Scenario 6","Scenario 7")
 
-  tA <- bfsum %>% select(Alt,Yr,ABC) %>% spread(Alt,ABC)
+  tA <- bfsum %>% select(Alternative,Yr,ABC) %>% spread(Alternative,ABC)
   names(tA) <- c("ABC","Scenario 1","Scenario 2","Scenario 3","Scenario 4","Scenario 5","Scenario 6","Scenario 7")
 
   tab <- (data.frame(tC))
   rownames(tab)<-c()
   cap <- tabcap[1]
   for (i in 2:length(tab[1,]) )
     tab[,i] <- formatC((tab[,i]), format="d", big.mark=",")
-  tab <- xtable(tab, caption = cap, label=paste0("tab:",tablab[1]),
+  tab <- xtable::xtable(tab, caption = cap, label=paste0("tab:",tablab[1]),
                 digits=0, auto=TRUE, align=rep("r",(length(tab[1,])+1)) )
   print(tab, "html", caption.placement = "top",include.rownames = FALSE, sanitize.text.function = function(x){x}, scalebox=.85)
 
   tab <- (data.frame(tB))
   cap <- tabcap[2]
   for (i in 2:length(tab[1,]) )
     tab[,i] <- formatC(as.numeric(tab[,i]), format="d", big.mark=",")
-  tab <- xtable(tab, caption = cap, label=paste0("tab:",tablab[2]),digits=0, auto=TRUE, align=rep("r",(length(tab[1,])+1)) )
+  tab <- xtable::xtable(tab, caption = cap, label=paste0("tab:",tablab[2]),digits=0, auto=TRUE, align=rep("r",(length(tab[1,])+1)) )
   print(tab, "html", caption.placement = "top",include.rownames = FALSE, sanitize.text.function = function(x){x}, scalebox=.85)
 
   tab <- (data.frame(tF))
   cap <- tabcap[3]
   for (i in 2:length(tab[1,]) )
     tab[,i] <- formatC(as.numeric(tab[,i]), format="f",digits=3)
-  tab <- xtable(tab, caption = cap, label=paste0("tab:",tablab[3]), digits=3, align=rep("r",(length(tab[1,])+1)) )
+  tab <- xtable::xtable(tab, caption = cap, label=paste0("tab:",tablab[3]), digits=3, align=rep("r",(length(tab[1,])+1)) )
   print(tab, "html", caption.placement = "top",include.rownames = FALSE, sanitize.text.function = function(x){x}, scalebox=.85)
 
   tab <- (data.frame(tA))
   cap <- tabcap[4]
   for (i in 2:length(tab[1,]) )
     tab[,i] <- formatC(as.numeric(tab[,i]), format="d", big.mark=",")
-  tab <- xtable(tab, caption = cap, label=paste0("tab:",tablab[4]),digits=0, auto=TRUE, align=rep("r",(length(tab[1,])+1)) )
+  tab <- xtable::xtable(tab, caption = cap, label=paste0("tab:",tablab[4]),digits=0, auto=TRUE, align=rep("r",(length(tab[1,])+1)) )
   print(tab, "html", caption.placement = "top",include.rownames = FALSE, sanitize.text.function = function(x){x}, scalebox=.85)
   return(tab)
 #