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PecanProject · Sep 21, 2024 · 76f2b72 · 76f2b72
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commit 76f2b72
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Showing 3 changed files with 1 addition and 5 deletions.
diff --git a/modules/assim.sequential/R/Multi_Site_Constructors.R b/modules/assim.sequential/R/Multi_Site_Constructors.R
@@ -32,7 +32,6 @@ Contruct.Pf <- function(site.ids, var.names, X, localization.FUN=NULL, t=1, bloc
   #I put this into a sperate loop so we can have more control over it
   site.cov.orders <- expand.grid(site.ids,site.ids) %>%
     dplyr::filter( .data$Var1 != .data$Var2)
-
   for (i in seq_len(nrow(site.cov.orders))){
     # first we need to find out where to put it in the big matrix
     rows.in.matrix <- which(attr(X,"Site") %in% site.cov.orders[i,1])
@@ -60,7 +59,6 @@ Contruct.Pf <- function(site.ids, var.names, X, localization.FUN=NULL, t=1, bloc
   rownames(pf.matrix.out ) <-labelss
 
   return(pf.matrix.out)
-
 }
 
 ##' @title Construct.R

diff --git a/modules/assim.sequential/R/Nimble_codes.R b/modules/assim.sequential/R/Nimble_codes.R
@@ -187,14 +187,12 @@ GEF.MultiSite.Nimble <-  nimbleCode({
       # Sorting out qs
       q[1:YN, 1:YN] ~ dwish(R = aq[1:YN, 1:YN], df = bq) ## aq and bq are estimated over time
     }
-
     for (i in 1:nH) {
       tmpX[i]  <- X.mod[H[i]]
       Xs[i] <- tmpX[i]
     }
     ## add process error to x model but just for the state variables that we have data and H knows who
     X[1:YN]  ~ dmnorm(Xs[1:YN], prec = q[1:YN, 1:YN])
-
     ## Likelihood
     y.censored[1:YN] ~ dmnorm(X[1:YN], prec = r[1:YN, 1:YN])
 

diff --git a/modules/assim.sequential/R/sda.batch.functions.R b/modules/assim.sequential/R/sda.batch.functions.R
@@ -209,4 +209,4 @@ qsub_analysis <- function(folder.path, cores) {
   parallel::stopCluster(cl)
   writeLines("finished",con = file.path(folder.path, "result.txt"))
   save(results, file = file.path(folder.path, "results.Rdata"))
-}
+}