Tweak files for running jags locally

.gitignore

@@ -14,3 +14,4 @@ figs
 *.rds
 docs/metadata/sites
 .Rproj.user
+GROWTH.MODEL.*

R/analysis/fun.analysis.R → R/analysis/JAGS.fun.R

 ###########################
 ###########################
 ##### FUNCTIONS USED IN FORMATTING DATA FOR JAGS AND RUN ANALYSIS
-
+source("R/packages.R")
+check_packages(c("rjags", "R2jags"))
 
 ######
 ######
@@ -165,7 +166,8 @@ return(jags.data)
 
 #########################################
 ### WRITE JAGS MODELS
-
+write.jags.model.HD <- function(file =  "GROWTH.MODEL.LOGLIN.HD"){
+  
 ### LOG LIN HD
 GROWTH.MODEL.LOGLIN.HD <-
  "################################################################################
@@ -233,7 +235,10 @@ sigma.alpha ~ dunif(0.000001,5)
 } # End of the jags model
  "
 
-cat(GROWTH.MODEL.LOGLIN.HD , file = "GROWTH.MODEL.LOGLIN.HD", sep=" ", fill = FALSE, labels = NULL, append = FALSE)
+cat(GROWTH.MODEL.LOGLIN.HD , file = file, sep=" ", fill = FALSE, labels = NULL, append = FALSE)
+}
+
+write.jags.model.AD <- function(file =  "GROWTH.MODEL.LOGLIN.AD"){
 
 ### LOG LIN HD
 GROWTH.MODEL.LOGLIN.AD <-
@@ -302,8 +307,8 @@ sigma.alpha ~ dunif(0.000001,5)
 } # End of the jags model
  "
 
-cat(GROWTH.MODEL.LOGLIN.AD , file = "GROWTH.MODEL.LOGLIN.AD", sep=" ", fill = FALSE, labels = NULL, append = FALSE)
-
+cat(GROWTH.MODEL.LOGLIN.AD , file = file, sep=" ", fill = FALSE, labels = NULL, append = FALSE)
+}
 
 ################################################
 ###########################
@@ -455,3 +460,22 @@ n.chain <- dim(jags.output$BUGSoutput$sims.array)[2]
 length.chain <- dim(jags.output$BUGSoutput$sims.array)[1]
 plot(x,y,col=rep(1:n.chain,each=length.chain),xlab=param.name.1,ylab=param.name.2)
 }
+
+
+get.ecoregions <- function(site){
+  sub(paste("./output/processed/",site,"/",sep=""),"",list.dirs(paste("./output/processed/",site,sep="")))[-1]
+}
+
+run.jags.for.trait <- function(site, trait, A1, A2, ecoregions = get.ecoregions(site)){
+  for (e in ecoregions)
+  try(fun.run.4models.jags(site=site,ecoregion.name=e,min.obs=10, 
+                      name.trait=trait, 
+                      A1=A1, 
+                      A2=A2, 
+                      n.chains=3, 
+                      n.iter=3000, 
+                      n.burnin=1000, 
+                      n.thin=1,
+                      sample.size=2000,
+                      na.action.traits="fill with global mean"))
+}

R/analysis/run.local.R

 #####
-## run jags code
-
-source("./R/analysis/fun.analysis.R")
-site <- "NVS"
-
-ecoregion.code <- sub(paste("./output/processed/",site,"/",sep=""),"",list.dirs(paste("./output/processed/",site,sep="")))[-1]
-
-for (i in ecoregion.code[1]){
-fun.run.4models.jags(site=site,ecoregion.name=i,min.obs=10, 
-                      name.trait="SLA", 
-                      A1="MAT", 
-                      A2="MAP", 
-                      n.chains=3, 
-                      n.iter=3000, 
-                      n.burnin=1000, 
-                      n.thin=1,
-                      sample.size=NA,
-                      na.action.traits="fill with global mean")
-}
+
+source("R/analysis/JAGS.fun.R")
+
+write.jags.model.HD()
+write.jags.model.AD()
+
+traits <- c("SLA", "Leaf.N","Seed.mass","SLA","Wood.density","Max.height")
+
+for(this.trait in traits)
+	run.jags.for.trait("France", trait = this.trait, A1 = "sgdd", A2 = "WB.s")
+
+for(this.trait in traits)
+	run.jags.for.trait("NVS", trait = this.trait, A1 = "MAT", A2 = "MAP")
+
+for(this.trait in traits)
+	run.jags.for.trait("US", trait = this.trait, A1 = "MAT", A2 = "MAP")
+
+for(this.trait in traits)
+	run.jags.for.trait("Spain", trait = this.trait, A1 = "MAT", A2 = "PP")
+
+for(this.trait in traits)
+	run.jags.for.trait("Canada", trait = this.trait, A1 = "MAT", A2 = "MAP")
+

readme.md

@@ -33,6 +33,7 @@ We are making use of the following tools:
 - [*markdown*](http://daringfireball.net/projects/markdown/)
 - The [*knitr*](http://cran.r-project.org/web/packages/knitr/index.html) package in R, for generating documents with R and markdown. For a n intro see [here](http://nicercode.github.io/guides/reports/)
 - version control via git (see next section)
+- JAGS - Just another Gibbs Sampler. Install [here](http://sourceforge.net/projects/mcmc-jags/files/)
 
 ### Git