Modified pda.mcmc to be part of package export and to only be called …

…if in settings
PecanProject · May 8, 2015 · bc6951e · bc6951e
1 parent 8557497
commit bc6951e
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Showing 4 changed files with 15 additions and 11 deletions.
diff --git a/modules/assim.batch/NAMESPACE b/modules/assim.batch/NAMESPACE
@@ -0,0 +1 @@
+export(pda.mcmc)
diff --git a/modules/assim.batch/R/pda.mcmc.R b/modules/assim.batch/R/pda.mcmc.R
@@ -10,6 +10,7 @@
 ##'
 ##' @author Mike Dietze
 ##' @author Ryan Kelly
+##' @export
 pda.mcmc <- function(settings, params=NULL, jvar=NULL, var.names=NULL, prior=NULL, chain=NULL,
                      adapt=NULL, adj.min=NULL, ar.target=NULL){
   # Quit if pda not requested in settings

diff --git a/modules/assim.batch/man/pda.mcmc.Rd b/modules/assim.batch/man/pda.mcmc.Rd
@@ -1,17 +1,17 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/pda.mcmc.R
 \name{pda.mcmc}
 \alias{pda.mcmc}
 \title{Paramater Data Assimilation using MCMC}
 \usage{
-pda.mcmc(settings)
+pda.mcmc(settings, params = NULL, jvar = NULL, var.names = NULL,
+  prior = NULL, chain = NULL, adapt = NULL, adj.min = NULL,
+  ar.target = NULL)
 }
 \arguments{
-\item{settings}{= a pecan settings list}
+  \item{settings}{= a pecan settings list}
 }
 \value{
-nothing. Diagnostic plots, MCMC samples, and posterior distributions
- are saved as files and db records.
+nothing. Diagnostic plots, MCMC samples, and posterior
+distributions are saved as files and db records.
 }
 \description{
 Paramater Data Assimilation using MCMC

diff --git a/web/workflow.R b/web/workflow.R
@@ -141,11 +141,13 @@ run.sensitivity.analysis()
 status.end()
 
 # Run parameter data assimilation
-status.start("PDA")
-settings$assim.batch <- pda.mcmc(settings)
-saveXML(listToXml(settings, "pecan"), file=file.path(settings$outdir, 'pecan.pda.xml'))
-status.end()
-
+if(('assim.batch' %in% names(settings))) {
+  status.start("PDA")
+  settings$assim.batch <- pda.mcmc(settings)
+  saveXML(listToXml(settings, "pecan"), file=file.path(settings$outdir, 'pecan.pda.xml'))
+  status.end()
+}
+
 # all done
 status.start("FINISHED")
 db.query(paste("UPDATE workflows SET finished_at=NOW() WHERE id=", settings$workflow$id, "AND finished_at IS NULL"), params=settings$database$bety)