From 76f2b7252dec013f0145eeaa387ebc5766469c88 Mon Sep 17 00:00:00 2001
From: Chris Black <chris@ckblack.org>
Date: Sat, 21 Sep 2024 01:29:21 -0700
Subject: [PATCH] whitespace

---
 modules/assim.sequential/R/Multi_Site_Constructors.R | 2 --
 modules/assim.sequential/R/Nimble_codes.R            | 2 --
 modules/assim.sequential/R/sda.batch.functions.R     | 2 +-
 3 files changed, 1 insertion(+), 5 deletions(-)

diff --git a/modules/assim.sequential/R/Multi_Site_Constructors.R b/modules/assim.sequential/R/Multi_Site_Constructors.R
index 290202d305..750ac4f43d 100755
--- 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
index 5ade894e09..90ca65c71e 100644
--- 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
index 4d6d984cf5..4b9de45cd3 100644
--- 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"))
-}
\ No newline at end of file
+}