added PVA chapter

Lab-fitting-multi-ss-models/multivariate-ss.Rmd

@@ -764,7 +764,7 @@ ggplot(pdat , aes(x = year , y = mean)) +
 For these questions, use the `harborSealWA` data set in **MARSS**.  The data are already logged, but you will need to remove the year column and have time going across the columns not down the rows.
 ```{r}
 require(MARSS)
-#Here is the dat to use for MARSS()
+data(harborSealWA, package="MARSS")
 dat <- t(harborSealWA[,2:6])
 ```
 The sites are San Juan de Fuca (SJF 3), San Juan Islands (SJI 4), Eastern Bays (EBays 5), Puget Sound (PSnd 6) and Hood Canal (HC 7).

datasets.Rmd

@@ -0,0 +1,5 @@
+# Datasets {-}
+
+Public Domain Datasets
+
+https://www.fisheries.noaa.gov/topic/recreational-fishing-data#using-the-data

rnw_to_rmd.R

@@ -0,0 +1,211 @@
+## script to convert a Rnw file to Rmd
+
+rnw.to.rmd <- function(file){
+  require(stringr)
+  content=readLines(file)
+  content=str_replace_all(content, "<<","```{r ")
+  content=str_replace_all(content, ">>=", "}")
+  chaplines=which(str_detect(content, "chapter[{]"))
+  for(i in chaplines){
+    content[i]=str_replace(content[i],"\\\\chapter[{]","# ")
+    content[i]=str_split(content[i],"[}]")[[1]][1]
+  }
+  for(rem in c("chaptermark[{]", "label[{]chap", "end[{]example", "SweaveOpts")){
+    removelines=which(str_detect(content, rem))
+    if(length(removelines)!=0) content=content[-1*removelines]
+  }
+
+  seclines=which(str_detect(content, "section[{]"))
+  for(i in seclines){
+    content[i]=str_replace(content[i],"\\\\section[{]","## ")
+    content[i]=str_split(content[i],"[}]")[[1]][1]
+  }
+  subseclines=which(str_detect(content, "subsection[{]"))
+  for(i in subseclines){
+    content[i]=str_replace(content[i],"\\\\subsection[{]","### ")
+    content[i]=str_split(content[i],"[}]")[[1]][1]
+  }
+  comments=which(str_detect(content, "%%%%%%%%%%") | str_detect(content, "%~~~~~~~~~"))
+  if(length(comments)!=0) content=content[-1*comments]
+  comments=which(str_detect(content, "%[/^]"))
+  if(length(comments)!=0) content=content[-1*comments]
+  for(i in c("clearpage","renewcommand","addcontentsline","newline","exend", "exbegin")){
+    removelines=which(str_detect(content, i))
+    if(length(removelines)!=0) content=content[-1*removelines]
+  }
+  endlines=which(str_detect(content, "<<reset"))
+  if(length(endlines)!=0) content=content[-1*(endlines:length(content))]
+  #homework
+  hwsec=which(str_detect(content, "section[*][{]Problems"))
+  content[hwsec]="## Problems"
+  enumstart=which(str_detect(content, "begin[{]hwenumerate"))
+  enumend=which(str_detect(content, "end[{]hwenumerate"))
+  items=which(str_detect(content, "\\item"))
+  items=items[items>enumstart & items<enumend]
+  for(i in 1:length(items)){
+    content[items[i]]=str_replace(content[items[i]],"\\\\item", paste(i,".",sep=""))
+  }
+  #enumerate
+  enumstart=which(str_detect(content, "begin[{]enumerate"))
+  enumend=which(str_detect(content, "end[{]enumerate"))
+  items=which(str_detect(content, "\\item"))
+  items=items[items>enumstart & items<enumend]
+  for(i in 1:length(items)){
+    content[items[i]]=str_replace(content[items[i]],"\\\\item", paste(i,". ",sep=""))
+  }
+  #itemize
+  enumstart=which(str_detect(content, "begin[{]itemize"))
+  enumend=which(str_detect(content, "end[{]itemize"))
+  items=which(str_detect(content, "\\item"))
+  items=items[items>enumstart & items<enumend]
+  for(i in 1:length(items)){
+    content[items[i]]=str_replace(content[items[i]],"\\\\item", "* ")
+  }
+
+  #change equation labels to bookdown format
+  eqnlabs=which(str_detect(content,"\\\\label[{]eqn:"))
+  for(i in eqnlabs){
+    locs=str_locate(content[i],"\\\\label[{]eqn:")
+    locsend=str_locate_all(content[i],"[}]")[[1]]
+    thisend=locsend[locsend[,1]>locs[1,2]][1]
+    str_sub(content[i],thisend,thisend)<-")"
+    str_sub(content[i],locs[1,1],locs[1,2])<-"(\\#eq:"
+  }
+
+  #change equation refs to bookdown format
+  eqnrefs=which(str_detect(content, "\\\\ref[{]eqn:"))
+  for(i in eqnrefs){
+    locs=str_locate_all(content[i],"\\\\ref[{]eqn:")[[1]]
+    locsend=str_locate_all(content[i],"[}]")[[1]]
+    for(j in 1:dim(locs)[1]){
+      thisend=locsend[locsend[,1]>locs[j,2]][1]
+      str_sub(content[i],thisend,thisend)<-")"
+      str_sub(content[i],locs[j,1],locs[j,2])<-"\\@ref(eq:"
+    }
+  }
+  #change section labels to bookdown format
+  seclabs=which(str_detect(content,"\\\\label[{]sec:"))
+  for(i in seclabs){
+    locs=str_locate(content[i],"\\\\label[{]sec:")
+    str_sub(content[i],locs[1,1],locs[1,2])<-"{#sec-"
+  }
+  val1 = "\\\\ref[{]sec:"; val2="[}]"
+  valr1 = "\\@ref(sec-"; valr2 =")" 
+  vals=which(str_detect(content, val1))
+  for(i in vals){
+    locs=str_locate_all(content[i],val1)[[1]]
+    while(nrow(locs)>0){
+      locsend=str_locate_all(content[i],val2)[[1]]
+      j=1
+      thisend=locsend[locsend[,1]>locs[j,2]][1]
+      str_sub(content[i],thisend,thisend)<-valr2
+      locs=str_locate_all(content[i],val1)[[1]] #REDO SINCE VALR2 IS LONGER
+      str_sub(content[i],locs[j,1],locs[j,2])<-valr1
+      locs=str_locate_all(content[i],val1)[[1]]
+    }
+  }
+  #change any leftoever refs to bookdown format
+  val1 = "\\\\ref[{]"; val2="[}]"
+  valr1 = "\\@ref("; valr2 =")" 
+  vals=which(str_detect(content, val1))
+  for(i in vals){
+    locs=str_locate_all(content[i],val1)[[1]]
+    while(nrow(locs)>0){
+      locsend=str_locate_all(content[i],val2)[[1]]
+      j=1
+      thisend=locsend[locsend[,1]>locs[j,2]][1]
+      str_sub(content[i],thisend,thisend)<-valr2
+      locs=str_locate_all(content[i],val1)[[1]] #REDO SINCE VALR2 IS LONGER
+      str_sub(content[i],locs[j,1],locs[j,2])<-valr1
+      locs=str_locate_all(content[i],val1)[[1]]
+    }
+  }
+  val1 = "\\\\textbf[{]"; val2="[}]"
+  valr1 = "**"; valr2 ="**" #valr2 must be same length as val2 part in []
+  vals=which(str_detect(content, val1))
+  for(i in vals){
+    locs=str_locate_all(content[i],val1)[[1]]
+    while(nrow(locs)>0){
+      locsend=str_locate_all(content[i],val2)[[1]]
+      j=1
+      thisend=locsend[locsend[,1]>locs[j,2]][1]
+      str_sub(content[i],thisend,thisend)<-valr2
+      locs=str_locate_all(content[i],val1)[[1]] #REDO SINCE VALR2 IS LONGER
+      str_sub(content[i],locs[j,1],locs[j,2])<-valr1
+      locs=str_locate_all(content[i],val1)[[1]]
+    }
+  }
+  val1 = "\\\\citet[{]"; val2="[}]"
+  valr1 = "@"; valr2 ="" 
+  vals=which(str_detect(content, val1))
+  for(i in vals){
+    locs=str_locate_all(content[i],val1)[[1]]
+    while(nrow(locs)>0){
+      locsend=str_locate_all(content[i],val2)[[1]]
+      j=1
+      thisend=locsend[locsend[,1]>locs[j,2]][1]
+      str_sub(content[i],thisend,thisend)<-valr2
+      locs=str_locate_all(content[i],val1)[[1]]
+      str_sub(content[i],locs[j,1],locs[j,2])<-valr1
+      locs=str_locate_all(content[i],val1)[[1]]
+    }
+  }
+  val1 = "\\\\citep[{]"; val2="[}]"
+  valr1 = "@["; valr2 ="]"
+  vals=which(str_detect(content, val1))
+  for(i in vals){
+    locs=str_locate_all(content[i],val1)[[1]]
+    while(nrow(locs)>0){
+      locsend=str_locate_all(content[i],val2)[[1]]
+      j=1
+      thisend=locsend[locsend[,1]>locs[j,2]][1]
+      str_sub(content[i],thisend,thisend)<-valr2
+      locs=str_locate_all(content[i],val1)[[1]]
+      str_sub(content[i],locs[j,1],locs[j,2])<-valr1
+      locs=str_locate_all(content[i],val1)[[1]]
+    }
+  }
+  val1 = "\\\\verb@"; val2="@"
+  valr1 = "`"; valr2 ="`" #valr2 must be same length as val2 part in []
+  vals=which(str_detect(content, val1))
+  for(i in vals){
+    locs=str_locate_all(content[i],val1)[[1]]
+    while(nrow(locs)>0){
+      locsend=str_locate_all(content[i],val2)[[1]]
+      j=1
+      thisend=locsend[locsend[,1]>locs[j,2]][1]
+      str_sub(content[i],thisend,thisend)<-valr2
+      locs=str_locate_all(content[i],val1)[[1]]
+      str_sub(content[i],locs[j,1],locs[j,2])<-valr1
+      locs=str_locate_all(content[i],val1)[[1]]
+    }
+  }
+  val1 = "\\\\texttt[{]"; val2="[}]"
+  valr1 = "`"; valr2 ="`" #valr2 must be same length as val2 part in []
+  vals=which(str_detect(content, val1))
+  for(i in vals){
+    locs=str_locate_all(content[i],val1)[[1]]
+    while(nrow(locs)>0){
+      locsend=str_locate_all(content[i],val2)[[1]]
+      j=1
+      thisend=locsend[locsend[,1]>locs[j,2]][1]
+      str_sub(content[i],thisend,thisend)<-valr2
+      locs=str_locate_all(content[i],val1)[[1]]
+      str_sub(content[i],locs[j,1],locs[j,2])<-valr1
+      locs=str_locate_all(content[i],val1)[[1]]
+    }
+  }
+  content[content=="@"]="```"
+  content=str_replace_all(content, "label=", "")
+  content=str_replace_all(content, ", keep[.]source=TRUE", "")
+  content=str_replace_all(content, ",keep[.]source=TRUE", "")
+  content=str_replace_all(content, ", include[.]source=TRUE", "")
+  content=str_replace_all(content, ",include[.]source=TRUE", "")
+  content=str_replace_all(content, ", keep[.]source=FALSE", "")
+  content=str_replace_all(content, ",keep[.]source=FALSE", "")
+  content=str_replace_all(content, ", include[.]source=FALSE", "")
+  content=str_replace_all(content, ",include[.]source=FALSE", "")
+  content=str_replace_all(content, "=hide", "='hide'")
+  outfile = paste0(str_split(file,"[.]")[[1]][1],".Rmd")
+  cat(content, file=outfile, sep="\n")
+}