Merge pull request #207 from tghoward/metadataForReviewedModels

Metadata for reviewed models

4c_additMetadComments_rubricUpdate.r

@@ -61,6 +61,15 @@ sql <- paste0("SELECT Reviewer.EGT_ID, Reviewer.response, Reviewer.date_complete
               FROM Reviewer
               WHERE (((Reviewer.EGT_ID)= ", ElementNames$EGT_ID, " ));")
 reviewerData <- dbGetQuery(cn, sql)
+
+sql <- paste0("SELECT FinalSppList.Scientific_Name, FinalSppList.Common_Name, FinalSppList.ELEMENT_GLOBAL_ID, ",
+        "ModelCycle.EGT_ID, ModelCycle.model_cycle, SpeciesWorkFlow.cutecode, SpeciesWorkFlow.model_type, ",
+        "SpeciesWorkFlow.modeled, SpeciesWorkFlow.alternate_method, SpeciesWorkFlow.existing_model ",
+        "FROM (FinalSppList INNER JOIN ModelCycle ON FinalSppList.ID = ModelCycle.final_spp_list_ID) ",
+        "INNER JOIN SpeciesWorkFlow ON ModelCycle.ID = SpeciesWorkFlow.model_cycle_ID ",
+        "WHERE (((FinalSppList.ELEMENT_GLOBAL_ID)= ", ElementNames$EGT_ID, "));")
+modelCycleData <- dbGetQuery(cn, sql)
+
 dbDisconnect(cn)
 rm(cn)
 
@@ -128,6 +137,27 @@ sql <- paste0("update lkpSpeciesRubric set process_review = '", revUpdate$rAttri
               "', process_reviewNotes = '", revUpdate$rComments, 
               "' where EGT_ID = ", ElementNames$EGT_ID, " ;")
 dbExecute(db, statement = sql)
+## iterative
+iterMatrix <- data.frame("iAttribute" = c("C","A"),
+                          "iComments" = c("Model not re-run with new or modified data.",
+                                          "Model was re-run with new or modified data."))
+nCycles <- nrow(modelCycleData)
+maxCycle <- max(modelCycleData$model_cycle)
+if(nCycles > 1){
+  if(nCycles == 2 & "Both" %in% modelCycleData$model_type){
+    iterAtt <- "C"
+  } else if(TRUE %in% modelCycleData[modelCycleData$model_cycle == maxCycle, c("alternate_method","existing_model")]){
+    iterAtt <- "C"
+  } else {
+    iterAtt <- "A"
+  }
+}
+
+iterUpdate <- iterMatrix[match(iterAtt, iterMatrix$iAttribute),]
+sql <- paste0("update lkpSpeciesRubric set interative = '", iterUpdate$iAttribute, 
+              "', interativeNotes = '", iterUpdate$iComments, 
+              "' where EGT_ID = ", ElementNames$EGT_ID, " ;")
+dbExecute(db, statement = sql)
 
 ## clean up ----
 dbDisconnect(db)

MetadataEval_knitr.rnw

@@ -331,6 +331,7 @@ Table 3. Thresholds {\protect\NoHyper\cite{LiuEtAl2005, LiuEtAl2015}\protect\end
 \textbf{Model Evaluation and Intended Use} \\\\
 All SDMs are sensitive to data inputs and methodological choices. Table 4 presents scoring of modeling factors based on the model evaluation rubric presented in Sofaer et al. 2019 {\protect\NoHyper\cite{SofaerEtAl2019}\protect\endNoHyper}. \Sexpr{as.character(project_blurb)}
 \\
+
 \smallskip
 \pagebreak
 
@@ -544,14 +545,14 @@ NatureServe and Heritage Network Partners. \Sexpr{format(Sys.Date(), "%Y")}. Spe
   \bibitem{LiuEtAl2015} Liu, C., G. Newell, and M. White. 2015. On the selection of 
     thresholds for predicting species occurrence with presence-only data. Ecology and 
     Evolution 6:337–348. 
-  \bibitem{SofaerEtAl2019} Sofaer, H. R., C. S. Jarnevich1, I. S. Pearse, R. L. Smyth, S. Auer, G. L. Cook, T. C. Edwards, Jr., G. F. Guala, T. G. Howard, J. T. Morisette, and H. Hamilton. (In press). The development and delivery of species distribution models to inform decision-making. BioScience.
+  \bibitem{SofaerEtAl2019} Sofaer, H. R., C. S. Jarnevich1, I. S. Pearse, R. L. Smyth, S. Auer, G. L. Cook, T. C. Edwards, Jr., G. F. Guala, T. G. Howard, J. T. Morisette, and H. Hamilton. 2019. The development and delivery of species distribution models to inform decision-making. BioScience 69:544-557.
 \end{thebibliography}
 
 \pagebreak
 \noindent
 
-\begin{table}
-\caption{Appendix 1. Descriptions for environmental variables included in model.}
+Appendix 1. Descriptions for environmental variables included in model.
+\begin{table}[H]
 \resizebox{\textwidth}{!}{
 <<tableFour, results="asis", echo = FALSE>>=
   # For variable descriptions, get variable name, source, description (3 columns)

postReview_0_user_run_SDM.R

@@ -0,0 +1,42 @@
+# File: postReview_0_user_run_SDM.r
+# Purpose: recreate metadata after model review and export 
+# in the Mobi project
+
+library(here)
+rm(list=ls())
+loc_scripts <- here()
+
+#######
+###  loop it
+######
+rootPath <- file.path("H:","spp_models", "_test")
+
+fldrs <- list.dirs(rootPath, recursive = FALSE)
+
+# if you want to run fewer than the full list of folders
+# subset here. 
+#fldrs <- fldrs[c(3,6)]
+#
+
+
+
+sppVec <- unlist(lapply(strsplit(fldrs, split = "/"), FUN = function(x) x[[4]]))
+sppVec
+
+for(sv in 1:length(sppVec)){
+
+  loc_model <- fldrs[[sv]]
+  model_species <- sppVec[[sv]]
+  load(file.path(loc_model, "outputs","rdata",paste0(model_species,"_runSDM_paths.Rdata")))
+  # the vars we need
+  fn_arg_vars <- c("project_overview","model_comments","metaData_comments","modeller","project_blurb","modelrun_meta_data")
+  for(arg in fn_arg_vars)
+    assign(arg, fn_args[[arg]])
+
+  nm_refBoundaries <- file.path(loc_scripts,"_data","other_spatial","feature", "US_States.shp")
+  nm_db_file <- file.path(loc_scripts,"_data", "databases", "SDM_lookupAndTracking.sqlite")
+
+  source(file.path(loc_scripts,"postReview_createMetadata.r"))
+
+}
+