pass threshold into workflow PecanProject#18

mchenry · Jan 14, 2015 · 062c4b5 · 062c4b5
1 parent 855cfe7
commit 062c4b5
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Showing 11 changed files with 17 additions and 13 deletions.
diff --git a/all/tests/testthat/test.workflow.R b/all/tests/testthat/test.workflow.R
@@ -15,7 +15,7 @@
 #settings <- read.settings(settings.file)
 
 # settings$pfts <- get.trait.data(settings$pfts, settings$model$type, settings$run$dbfiles, settings$database$bety, settings$meta.analysis$update)
-# run.meta.analysis(settings$pfts, settings$meta.analysis$iter, settings$meta.analysis$random.effects, settings$run$dbfiles, settings$database$bety)
+# run.meta.analysis(settings$pfts, settings$meta.analysis$iter, settings$meta.analysis$random.effects, settings$meta.analysis$threshold, settings$run$dbfiles, settings$database$bety)
 # run.write.configs("ED2")
 # clear.scratch(settings)
 # start.model.runs("ED2")

diff --git a/models/biocro/BioCro_demo.Rmd b/models/biocro/BioCro_demo.Rmd
@@ -11,7 +11,7 @@ model <- settings$model$type
 settings$pfts <- get.trait.data(settings$pfts, settings$model$type, settings$run$dbfiles, settings$database$bety, settings$meta.analysis$update)
 
 # Run the PEcAn meta.analysis
-run.meta.analysis(settings$pfts, settings$meta.analysis$iter, settings$run$dbfiles, settings$database$bety)
+run.meta.analysis(settings$pfts, settings$meta.analysis$iter, settings$meta.analysis$threshold, settings$run$dbfiles, settings$database$bety)
 
 run.write.configs(model)        # Calls model specific write.configs e.g. write.config.ed.R
 ## load met data

diff --git a/models/biocro/inst/workflow.R b/models/biocro/inst/workflow.R
@@ -24,7 +24,7 @@ settings$meta.analysis$update <- TRUE
 settings$pfts <- get.trait.data(settings$pfts, settings$model$type, settings$run$dbfiles, settings$database$bety, settings$meta.analysis$update)
 
 # Run the PEcAn meta.analysis
-run.meta.analysis(settings$pfts, settings$meta.analysis$iter, settings$meta.analysis$random.effects, settings$run$dbfiles, settings$database$bety)
+run.meta.analysis(settings$pfts, settings$meta.analysis$iter, settings$meta.analysis$random.effects, settings$meta.analysis$threshold, settings$run$dbfiles, settings$database$bety)
 
 run.write.configs(model)        # Calls model specific write.configs e.g. write.config.ed.R
 ## load met data

diff --git a/models/biocro/vignettes/workflow.R b/models/biocro/vignettes/workflow.R
@@ -20,7 +20,7 @@ model <- settings$model$type
 settings$pfts <- get.trait.data(settings$pfts, settings$model$type, settings$run$dbfiles, settings$database$bety, settings$meta.analysis$update)
 
 # Run the PEcAn meta.analysis
-run.meta.analysis(settings$pfts, settings$meta.analysis$iter, settings$meta.analysis$random.effects, settings$run$dbfiles, settings$database$bety)
+run.meta.analysis(settings$pfts, settings$meta.analysis$iter, settings$meta.analysis$random.effects, settings$meta.analysis$threshold, settings$run$dbfiles, settings$database$bety)
 
 ## @knitr , echo=FALSE,warning=FALSE,cache=TRUE
 run.write.configs(model)        # Calls model specific write.configs e.g. write.config.ed.R

diff --git a/models/biocro/vignettes/workflow.Rmd b/models/biocro/vignettes/workflow.Rmd
@@ -25,7 +25,7 @@ settings$pfts <- get.trait.data(settings$pfts, settings$model$type, settings$run
 
 ### Run Meta-analysis
 ```{r, echo=FALSE,warning=FALSE,cache=TRUE}
-run.meta.analysis(settings$pfts, settings$meta.analysis$iter, settings$run$dbfiles, settings$database$bety)
+run.meta.analysis(settings$pfts, settings$meta.analysis$iter, settings$meta.analysis$random.effects, settings$meta.analysis$threshold, settings$run$dbfiles, settings$database$bety)
 ```
 
 

diff --git a/modules/meta.analysis/R/run.meta.analysis.R b/modules/meta.analysis/R/run.meta.analysis.R
@@ -6,7 +6,7 @@
 # which accompanies this distribution, and is available at
 # http://opensource.ncsa.illinois.edu/license.html
 #-------------------------------------------------------------------------------
-run.meta.analysis.pft <- function(pft, iterations, random, dbfiles, dbcon) {
+run.meta.analysis.pft <- function(pft, iterations, random, threshold, dbfiles, dbcon) {
   # check to see if get.trait was executed
   if (!file.exists(file.path(pft$outdir, 'trait.data.Rdata')) || !file.exists(file.path(pft$outdir, 'prior.distns.Rdata'))) {
     logger.severe("Could not find output from get.trait for", pft$name)
@@ -101,7 +101,7 @@ run.meta.analysis.pft <- function(pft, iterations, random, dbfiles, dbcon) {
   }
 
   ### Generate summaries and diagnostics
-  pecan.ma.summary(trait.mcmc, pft$name, pft$outdir)
+  pecan.ma.summary(trait.mcmc, pft$name, pft$outdir, threshold)
 
   ### Save the meta.analysis output
   save(trait.mcmc, file = file.path(pft$outdir, 'trait.mcmc.Rdata'))
@@ -142,10 +142,10 @@ run.meta.analysis.pft <- function(pft, iterations, random, dbfiles, dbcon) {
 ##' and post.distns.Rdata, respectively
 ##' @export
 ##' @author Shawn Serbin, David LeBauer
-run.meta.analysis <- function(pfts, iterations, random, dbfiles, database) {
+run.meta.analysis <- function(pfts, iterations, random, threshold, dbfiles, database) {
   # process all pfts
   dbcon <- db.open(database)
-  result <- lapply(pfts, run.meta.analysis.pft, iterations, random, dbfiles, dbcon)
+  result <- lapply(pfts, run.meta.analysis.pft, iterations, random, threshold, dbfiles, dbcon)
   db.close(dbcon)
 } ### End of function: run.meta.analysis.R
 ##==================================================================================================#

diff --git a/scripts/workflow.R b/scripts/workflow.R
@@ -49,7 +49,7 @@ status.end()
 # Run the PEcAn meta.analysis
 status.start("META")
 if('meta.analysis' %in% names(settings)) {
-  run.meta.analysis(settings$pfts, settings$meta.analysis$iter, settings$meta.analysis$random.effects, settings$run$dbfiles, settings$database$bety)
+  run.meta.analysis(settings$pfts, settings$meta.analysis$iter, settings$meta.analysis$random.effects, settings$meta.analysis$threshold, settings$run$dbfiles, settings$database$bety)
 }
 status.end()
 

diff --git a/settings/R/read.settings.R b/settings/R/read.settings.R
@@ -408,6 +408,10 @@ check.settings <- function(settings) {
     settings$meta.analysis$random.effects <- FALSE
     logger.info("Setting meta.analysis random effects to ", settings$meta.analysis$random.effects)
   }
+  if (is.null(settings$meta.analysis$threshold)) {
+    settings$meta.analysis$threshold <- 1.2
+    logger.info("Setting meta.analysis threshold to ", settings$meta.analysis$threshold)
+  }
   if (is.null(settings$meta.analysis$update)) {
     settings$meta.analysis$update <- 'AUTO'
     logger.info("Setting meta.analysis update to only update if no previous meta analysis was found")

diff --git a/tests/testpfts.R b/tests/testpfts.R
@@ -11,7 +11,7 @@ runmeta <- function(pftid, pftname, model, dbparam) {
   cat(paste0("TESTING [id=", pftid, " pft='", pftname, "' model='",  model, "'] : get.traits\n"), file=stderr())
   pfts <- get.trait.data(list(pft), model, dbparam$dbfiles, dbparam, TRUE)
   cat(paste0("TESTING [id=", pftid, " pft='", pftname, "' model='",  model, "'] : meta.analysis\n"), file=stderr())
-  run.meta.analysis(pfts, 3000, FALSE, dbparam$dbfiles, dbparam)
+  run.meta.analysis(pfts, 3000, FALSE, 1.2, dbparam$dbfiles, dbparam)
   cat(paste0("TESTING [id=", pftid, " pft='", pftname, "' model='",  model, "'] : OK\n"), file=stderr())
 }
 

diff --git a/tests/workflow.R b/tests/workflow.R
@@ -51,7 +51,7 @@ status.end()
 # run meta-analysis
 status.start("META")
 if('meta.analysis' %in% names(settings)) {
-  run.meta.analysis(settings$pfts, settings$meta.analysis$iter, settings$meta.analysis$random.effects, settings$run$dbfiles, settings$database$bety)
+  run.meta.analysis(settings$pfts, settings$meta.analysis$iter, settings$meta.analysis$random.effects, settings$meta.analysis$threshold, settings$run$dbfiles, settings$database$bety)
 }
 status.end()
 

diff --git a/web/workflow.R b/web/workflow.R
@@ -66,7 +66,7 @@ if (length(which(commandArgs() == "--continue")) == 0) {
 
   # run meta-analysis
   status.start("META")
-  run.meta.analysis(settings$pfts, settings$meta.analysis$iter, settings$meta.analysis$random.effects, settings$run$dbfiles, settings$database$bety)
+  run.meta.analysis(settings$pfts, settings$meta.analysis$iter, settings$meta.analysis$random.effects, settings$meta.analysis$threshold, settings$run$dbfiles, settings$database$bety)
   status.end()
 
   # do conversions