Merge pull request #101 from NOAA-EDAB/operation_phoenix

book enhancements
NOAA-EDAB · Feb 20, 2024 · c097f13 · c097f13
2 parents 83599bb + 52f3b53
commit c097f13
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diff --git a/.github/workflows/bookdown.yaml b/.github/workflows/bookdown.yaml
@@ -4,6 +4,7 @@ on:
   push:
     branches:
       - master
+      - operation_phoenix
   pull_request:
     branches:
       - master

diff --git a/.gitignore b/.gitignore
@@ -5,4 +5,5 @@
 
 # local files/folders
 _book
-_bookdown_files
+_bookdown_files
+docs
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -13,5 +13,5 @@ Depends:
 Suggests:
   downlit
 Remotes: 
-  NOAA-EDAB/ecodata
+  NOAA-EDAB/ecodata@dev
 
diff --git a/R/find_dataset_submissions.R b/R/find_dataset_submissions.R
@@ -4,6 +4,8 @@
 #'
 #' @return character vector
 
+source(here::here("R/parse_issue.r"))
+
 find_dataset_submissions <- function(){
 
   issueData <- readRDS(here::here("data-raw/submissionIssueNumbers.rds"))

diff --git a/R/find_rmds_not_in_book.r b/R/find_rmds_not_in_book.r
@@ -23,7 +23,7 @@ find_rmds_not_in_book <- function(){
   # find the rmdfiles not referenced in the yml
   missingrmds <- setdiff(rmdfiles,rmdrefs)
   message("The following rmds are not found in the _bookdown.yml")
-  print(missingrmds)
+  #print(missingrmds)
 
   return(missingrmds)
 

diff --git a/R/make_rmd.R b/R/make_rmd.R
@@ -21,6 +21,7 @@ make_rmd <- function(listobject){
   # start to create the Rmd
   #cat(paste0("# ",stringr::str_to_title(indicator_name)),append=T,fill=T,file=con)  
   ### DESCRIPTION, CONTRIBUTORS, AFFILIATION, FAMILY
+#  cat(paste0("# ",listobject$dataname," {#",listobject$indicatorname,"}"),append=T,fill=T,file=con)    
   cat(paste0("# ",listobject$dataname),append=T,fill=T,file=con)    
   cat("",append=T,fill=T,file=con) # add space
   cat(paste0("**Description**: ",listobject$description),append=T,fill=T,file=con)
@@ -59,7 +60,8 @@ make_rmd <- function(listobject){
     at <- attributes(eval(parse(text=paste0("ecodata::plot_",listobject$indicatorname))))
 
     functionArgs <- names(formals(eval(parse(text=paste0("ecodata::plot_",listobject$indicatorname)))))
-    if (length(functionArgs) == 2) {
+
+    if (length(functionArgs) == 2 | ((length(functionArgs) == 3) & (any(c("year","scale") %in% functionArgs)))) {
       # this is standard shadedRegion and report
       # check to see how many EPUs are listed in data object and/or they are "All" (shelfwide)
       indicatorData <- eval(parse(text=paste0("ecodata::",listobject$indicatorname)))  
@@ -69,7 +71,7 @@ make_rmd <- function(listobject){
         cat(paste0("```{r plot_",listobject$indicatorname,"MAB}"),append=T,fill=T,file=con)
         cat("# Plot indicator",append=T,fill=T,file=con)
         cat(paste0("ggplotObject <- ecodata::plot_",listobject$indicatorname,"(report='MidAtlantic')"),append=T,fill=T,file=con)
-        cat("print(ggplotObject)",append=T,fill=T,file=con)
+        cat("ggplotObject",append=T,fill=T,file=con)
         cat("```",append=T,fill=T,file=con)
         cat("",append=T,fill=T,file=con) # add space
       } else {
@@ -81,7 +83,7 @@ make_rmd <- function(listobject){
           cat(paste0("```{r plot_",listobject$indicatorname,"MAB}"),append=T,fill=T,file=con)
           cat("# Plot indicator",append=T,fill=T,file=con)
           cat(paste0("ggplotObject <- ecodata::plot_",listobject$indicatorname,"(report='MidAtlantic')"),append=T,fill=T,file=con)
-          cat("print(ggplotObject)",append=T,fill=T,file=con)
+          cat("ggplotObject",append=T,fill=T,file=con)
           cat("```",append=T,fill=T,file=con)
           cat("",append=T,fill=T,file=con) # add space
         } 
@@ -92,7 +94,7 @@ make_rmd <- function(listobject){
           cat(paste0("```{r plot_",listobject$indicatorname,"NE}"),append=T,fill=T,file=con)
           cat("# Plot indicator",append=T,fill=T,file=con)
           cat(paste0("ggplotObject <- ecodata::plot_",listobject$indicatorname,"(report='NewEngland')"),append=T,fill=T,file=con)
-          cat("print(ggplotObject)",append=T,fill=T,file=con)
+          cat("ggplotObject",append=T,fill=T,file=con)
           cat("```",append=T,fill=T,file=con)
           cat("",append=T,fill=T,file=con) # add space
         }
@@ -105,7 +107,7 @@ make_rmd <- function(listobject){
       cat(paste0("```{r plot_",listobject$indicatorname,"MAB}"),append=T,fill=T,file=con)
       cat("# Plot indicator",append=T,fill=T,file=con)
       cat(paste0("ggplotObject <- ecodata::plot_",listobject$indicatorname,"(report='MidAtlantic')"),append=T,fill=T,file=con)
-      cat("print(ggplotObject)",append=T,fill=T,file=con)
+      cat("ggplotObject",append=T,fill=T,file=con)
       cat("```",append=T,fill=T,file=con)
       cat("",append=T,fill=T,file=con) # add space
 
@@ -115,7 +117,7 @@ make_rmd <- function(listobject){
       cat(paste0("```{r plot_",listobject$indicatorname,"NEGB}"),append=T,fill=T,file=con)
       cat("# Plot indicator",append=T,fill=T,file=con)
       cat(paste0("ggplotObject <- ecodata::plot_",listobject$indicatorname,"(report='NewEngland',EPU='GB')"),append=T,fill=T,file=con)
-      cat("print(ggplotObject)",append=T,fill=T,file=con)
+      cat("ggplotObject",append=T,fill=T,file=con)
       cat("```",append=T,fill=T,file=con)
       cat("",append=T,fill=T,file=con) # add space
 
@@ -125,7 +127,7 @@ make_rmd <- function(listobject){
       cat(paste0("```{r plot_",listobject$indicatorname,"NEGOM}"),append=T,fill=T,file=con)
       cat("# Plot indicator",append=T,fill=T,file=con)
       cat(paste0("ggplotObject <- ecodata::plot_",listobject$indicatorname,"(report='NewEngland',EPU='GOM')"),append=T,fill=T,file=con)
-      cat("print(ggplotObject)",append=T,fill=T,file=con)
+      cat("ggplotObject",append=T,fill=T,file=con)
       cat("```",append=T,fill=T,file=con)
       cat("",append=T,fill=T,file=con) # add space
 
@@ -143,7 +145,7 @@ make_rmd <- function(listobject){
           cat(paste0("```{r plot_",listobject$indicatorname,arep,avarws,"}"),append=T,fill=T,file=con)
           cat("# Plot indicator",append=T,fill=T,file=con)
           cat(paste0("ggplotObject <- ecodata::plot_",listobject$indicatorname,"(report= '",arep,"', varName= '",avar,"')"),append=T,fill=T,file=con)
-          cat("print(ggplotObject)",append=T,fill=T,file=con)
+          cat("ggplotObject",append=T,fill=T,file=con)
           cat("```",append=T,fill=T,file=con)
           cat("",append=T,fill=T,file=con) # add space
         }
@@ -162,7 +164,7 @@ make_rmd <- function(listobject){
           cat(paste0("```{r plot_",listobject$indicatorname,arep,avarws,"}"),append=T,fill=T,file=con)
           cat("# Plot indicator",append=T,fill=T,file=con)
           cat(paste0("ggplotObject <- ecodata::plot_",listobject$indicatorname,"(report= '",arep,"', plottype= '",avar,"')"),append=T,fill=T,file=con)
-          cat("print(ggplotObject)",append=T,fill=T,file=con)
+          cat("ggplotObject",append=T,fill=T,file=con)
           cat("```",append=T,fill=T,file=con)
           cat("",append=T,fill=T,file=con) # add space
 
@@ -195,7 +197,7 @@ make_rmd <- function(listobject){
             cat(paste0("```{r plot_",listobject$indicatorname,arep,avarws,aval,"}"),append=T,fill=T,file=con)
             cat("# Plot indicator",append=T,fill=T,file=con)
             cat(paste0("ggplotObject <- ecodata::plot_",listobject$indicatorname,"(report= '",arep,"', varName= '",avar,"' ,",newV,"= '",aval,"')"),append=T,fill=T,file=con)
-            cat("print(ggplotObject)",append=T,fill=T,file=con)
+            cat("ggplotObject",append=T,fill=T,file=con)
             cat("```",append=T,fill=T,file=con)
             cat("",append=T,fill=T,file=con) # add space
 
@@ -216,7 +218,7 @@ make_rmd <- function(listobject){
               cat(paste0("```{r plot_",listobject$indicatorname,arep,avarws,atype,"}"),append=T,fill=T,file=con)
               cat("# Plot indicator",append=T,fill=T,file=con)
               cat(paste0("ggplotObject <- ecodata::plot_",listobject$indicatorname,"(report= '",arep,"', varName= '",avar,"', plottype = '",atype,"')"),append=T,fill=T,file=con)
-              cat("print(ggplotObject)",append=T,fill=T,file=con)
+              cat("ggplotObject",append=T,fill=T,file=con)
               cat("```",append=T,fill=T,file=con)
               cat("",append=T,fill=T,file=con) # add space
 
@@ -326,15 +328,19 @@ make_rmd <- function(listobject){
   cat("",append=T,fill=T,file=con) # add space
 
 
-  cat("**tech-doc link**",append=T,fill=T,file=con)
-
-  cat(paste0("<https://noaa-edab.github.io/tech-doc/",listobject$indicatorname,".html>"),append=T,fill=T,file=con)
-  cat("",append=T,fill=T,file=con) # add space
-
-
-  cat("## References",append=T,fill=T,file=con)
-  cat("",append=T,fill=T,file=con) # add space
+  # write catalog link if ecodata data is present
+  if (exists(paste0(listobject$indicatorname))) {
+    cat("**tech-doc link**",append=T,fill=T,file=con)
+
+    cat(paste0("<https://noaa-edab.github.io/tech-doc/",listobject$indicatorname,".html>"),append=T,fill=T,file=con)
+    cat("",append=T,fill=T,file=con) # add space
+
+  } else {
+    # No link since this is a synthesis type of page
+  }
 
+  # References are generated automatically  
+
 
   #close the connection
   close(con)

diff --git a/R/parse_issue.R b/R/parse_issue.R
@@ -18,22 +18,24 @@ parse_issue <- function(issueData,issueNum){
     body <- issueData$issues[id,]$body
   }
 
-  headings <- unlist(stringr::str_extract_all(body,"###\\s+[a-zA-Z (.)\"\\?,]+"))
+  headings <- unlist(stringr::str_extract_all(body,"\n###\\s+[a-zA-Z (.)\"\\?,]+"))
+
   for (ahead in headings) {
     modifiedHead <- gsub("\\","",ahead,fixed=T)
     modifiedHead <- gsub("(","\\(",modifiedHead,fixed=T)
     modifiedHead <- gsub(")","\\)",modifiedHead,fixed=T)
     modifiedHead <- gsub("?","\\?",modifiedHead,fixed=T)
     byhead <- unlist(strsplit(body,modifiedHead))[2]
-    res <- unlist(strsplit(byhead,"###"))[1]
+    res <- unlist(strsplit(byhead,"\n### "))[1]
     # remove beginning and trailing \n (line feed) and \r (carriage return)
     modifiedRes <- trimws(res)
     # modifiedRes <- sub("\\n+$","",modifiedRes)
     # modifiedRes <- sub("^\\r\\n+","",modifiedRes)
     # modifiedRes <- sub("\\r\\n+$","",modifiedRes)
+    ahead <- trimws(ahead)
     objectList[ahead] <- modifiedRes
   }
-  
+
   return(objectList)
 
 }
diff --git a/README.md b/README.md
@@ -1,12 +1,8 @@
----
-editor_options: 
-  markdown: 
-    wrap: 72
----
 
 # [Synthetic Indicator Catalog](https://noaa-edab.github.io/catalog/)
 
-![gitleaks](https://github.com/NOAA-EDAB/catalog/workflows/gitleaks/badge.svg)
+[![build-book](https://github.com/NOAA-EDAB/catalog/actions/workflows/bookdown.yaml/badge.svg)](https://github.com/NOAA-EDAB/catalog/actions/workflows/bookdown.yaml)
+[![gitleaks](https://github.com/NOAA-EDAB/catalog/actions/workflows/secretScan.yml/badge.svg)](https://github.com/NOAA-EDAB/catalog/actions/workflows/secretScan.yml)
 
 Catalog of indicators used in the State of the Ecosystem reports and
 other ecosystem assessment products.

diff --git a/_bookdown.yml b/_bookdown.yml
@@ -1,51 +1,59 @@
 book_filename: "catalog"
 rmd_files: 
     -   "index.Rmd"
+    #-   "chapters/introduction.rmd"
 
 
 #################### LOWER TROPHIC ##################
     -   "chapters/sectionHeaders/ltl.rmd" 
-    -   "chapters/ches_bay_wq.rmd" 
-    -   "chapters/chl_pp.rmd" 
+    -   "chapters/ches_bay_wq.rmd"
+    -   "chapters/chl_pp.rmd"
+    -   "chapters/phyto_size.rmd"
     #-   "chapters/annual_chl_pp.rmd"
-    -   "chapters/habs.rmd" 
-    -   "chapters/SAV.rmd" 
-    -   "chapters/calanus_variation.rmd" 
-    -   "chapters/wbts_mesozooplankton.rmd" 
-
-
-#################### MEGAFAUNA ##################
-    -   "chapters/sectionHeaders/megafauna.rmd" 
-    -   "chapters/aggregate_biomass.rmd" 
-    -   "chapters/mab_inshore_survey.rmd" 
-    -   "chapters/condition.rmd" 
-    -   "chapters/energy_density.rmd" 
+    -   "chapters/habs.rmd"
+    -   "chapters/SAV.rmd"
+    -   "chapters/calanus_variation.rmd"
+    -   "chapters/wbts_mesozooplankton.rmd"
+    -   "chapters/zoo_abundance_anom.rmd"
+    -   "chapters/zoo_diversity.rmd"
+#
+#
+# #################### MEGAFAUNA ##################
+    -   "chapters/sectionHeaders/megafauna.rmd"
+    -   "chapters/aggregate_biomass.rmd"
+    -   "chapters/mab_inshore_survey.rmd"
+    -   "chapters/mass_inshore_survey.rmd"
+    -   "chapters/ne_inshore_survey.rmd"
+    -   "chapters/osw_survey_impact.rmd"
+    -   "chapters/condition.rmd"
+    -   "chapters/habitat_diversity.rmd"
+    -   "chapters/species_dist.rmd"
+    -   "chapters/energy_density.rmd"
     -   "chapters/spawn_timing.rmd"
-    -   "chapters/exp_n.rmd" 
-    -   "chapters/forage_index.rmd" 
-    -   "chapters/harborporpoise.rmd" 
-    -   "chapters/hms_cpue.rmd" 
-    -   "chapters/hms_landings.rmd" 
-    -   "chapters/hms_stock_status.rmd" 
-    -   "chapters/HMS_species_distribution.rmd" 
-    -   "chapters/narw.rmd" 
-    -   "chapters/productivity_anomaly.rmd" 
-    -   "chapters/seal_pups.rmd" 
-    -   "chapters/gom_salmon.rmd" 
-    -   "chapters/grayseal.rmd" 
-    -   "chapters/seabird_ne.rmd" 
-    -   "chapters/species_groupings.rmd" 
-
-
-#################### OCEANOGRAPHIC ##################
+    -   "chapters/exp_n.rmd"
+    -   "chapters/forage_index.rmd"
+    -   "chapters/harborporpoise.rmd"
+    -   "chapters/hms_cpue.rmd"
+    -   "chapters/hms_landings.rmd"
+    -   "chapters/hms_stock_status.rmd"
+    -   "chapters/HMS_species_distribution.rmd"
+    -   "chapters/narw.rmd"
+    -   "chapters/productivity_anomaly.rmd"
+    -   "chapters/seal_pups.rmd"
+    -   "chapters/gom_salmon.rmd"
+    -   "chapters/grayseal.rmd"
+    -   "chapters/seabird_ne.rmd"
+    -   "chapters/species_groupings.rmd"
+#
+#
+# #################### OCEANOGRAPHIC ##################
     -   "chapters/sectionHeaders/oceanographic.rmd"
-    -   "chapters/bottom_temp.rmd" 
+    -   "chapters/bottom_temp.rmd"
     -   "chapters/bottom_temp_comp.rmd"
-    #-   "chapters/bottom_temp_glorys.rmd" 
-    -   "chapters/bottom_temp_seasonal_gridded.rmd" 
+    -   "chapters/bottom_temp_seasonal_gridded.rmd"
     -   "chapters/seasonal_sst_anomaly_gridded.rmd"
     -   "chapters/seasonal_oisst_anom.rmd"
-    -   "chapters/trans_dates.rmd" 
+    -   "chapters/trans_dates.rmd"
     -   "chapters/long_term_sst.rmd"
     -   "chapters/cold_pool.rmd"
     -   "chapters/gsi.rmd"
@@ -54,18 +62,20 @@ rmd_files:
     -   "chapters/wcr.rmd"
     -   "chapters/thermal_habitat_area.rmd"
     -   "chapters/thermal_habitat_persistence.rmd"
-    -   "chapters/ch_bay_sal.rmd" 
-    -   "chapters/ch_bay_temp.rmd" 
-    -   "chapters/ches_bay_sst.rmd" 
-    -   "chapters/ches_bay_synthesis.rmd" 
-    -   "chapters/heatwave.rmd" 
-    -   "chapters/heatwave_year.rmd" 
+    -   "chapters/ch_bay_sal.rmd"
+    -   "chapters/ch_bay_temp.rmd"
+    -   "chapters/ches_bay_sst.rmd"
+    -   "chapters/ches_bay_synthesis.rmd"
+    -   "chapters/heatwave.rmd"
+    -   "chapters/heatwave_year.rmd"
+    -   "chapters/timing_shifts.rmd"
+    -   "chapters/observation_synthesis.rmd"
     -   "chapters/ocean_acidification.rmd"
-
-
-######################## ECONOMIC ##################
+#
+#
+# ######################## ECONOMIC ##################
     -   "chapters/sectionHeaders/economic.rmd"
-    -   "chapters/comdat.rmd" 
+    -   "chapters/comdat.rmd"
     -   "chapters/commercial_div.rmd"
     -   "chapters/ppr.rmd"
     -   "chapters/recdat.rmd"

diff --git a/_output.yml b/_output.yml
@@ -1,4 +1,5 @@
 bookdown::bs4_book:
+  split_bib: true
   css: style.css
   theme:
     primary: "#4D6F8D"