remove option for progress file in ebase, can crash jags unexpectedly

R/ebase.R

@@ -18,7 +18,6 @@
 #' @param n.burnin number of MCMC chains to delete, passed to \code{\link[R2jags]{jags}}
 #' @param n.chains number of MCMC chains to run, passed to \code{\link[R2jags]{jags}}
 #' @param n.thin number of nth iterations to save for each chain, passed to \code{\link[R2jags]{jags}}
-#' @param progress character string of path where progress is saved to as 'log.txt', use \code{NULL} to suppress (default)
 #' @param model_file \code{NULL} to use the model file included with the package or a path to a model text file can be used
 #' 
 #' @export
@@ -71,7 +70,7 @@
 #' # run ebase, use more chains and iterations for a better fit, update.chains as T
 #' ebase(dat, interval = 900, Z = 1.85, n.chains = 2, n.iter = 50, 
 #'  update.chains = FALSE)
-ebase <- function(dat, Z, interval, ndays = 1, aprior = c(4, 2), rprior = c(300, 150), bprior = c(0.251, 0.125), bmax = 0.502, nogas = FALSE, doave = TRUE, maxinterp = 43200 / interval,  n.iter = 10000, update.chains = TRUE, n.burnin = n.iter*0.5, n.chains = 3, n.thin = 10, progress = NULL, model_file = NULL){
+ebase <- function(dat, Z, interval, ndays = 1, aprior = c(4, 2), rprior = c(300, 150), bprior = c(0.251, 0.125), bmax = 0.502, nogas = FALSE, doave = TRUE, maxinterp = 43200 / interval,  n.iter = 10000, update.chains = TRUE, n.burnin = n.iter*0.5, n.chains = 3, n.thin = 10, model_file = NULL){
 
   # prep data
   dat <- ebase_prep(dat, Z = Z, interval = interval, ndays = ndays)
@@ -94,23 +93,12 @@ ebase <- function(dat, Z, interval, ndays = 1, aprior = c(4, 2), rprior = c(300,
   if(nogas)
     bprior <- c(0, 1e-8)
 
-  # setup log file
-  strt <- Sys.time()
-
   # iterate through each date to estimate metabolism ------------------------
 
   # process
   output <- foreach(i = grps, .packages = c('R2jags', 'rjags', 'dplyr'), .export = c('nstepd', 'metab_update', 'interval', 'aprior', 'rprior', 'bprior', 'bmax')
                                                                          ) %dopar% {
 
-    if(!is.null(progress)){
-      sink(file.path(progress, 'log.txt'))
-      cat('Log entry time', as.character(Sys.time()), '\n')
-      cat('Group ', which(i == grps), ' of ', length(grps), '\n')
-      print(Sys.time() - strt)
-      sink()
-    }
-
     dat.sub <- dat[dat$grp == i,]
 
     # Define vectors for JAGS

tests/testthat/test-ebase.R

@@ -1,11 +1,8 @@
 test_that("Checking ebase output, doave as F", {
 
-  # temp dir for log
-  tmpdir <- tempdir()
-
   # check format
   result <- EBASE::ebase(dat, interval = 900, Z = 1.85, n.chains = 2, doave = F, 
-                         n.iter = 100, progress = tmpdir,
+                         n.iter = 100,
                       model_file = system.file("ebase_model.txt", package = "EBASE")) 
 
   expect_s3_class(result, 'data.frame')
@@ -16,9 +13,6 @@ test_that("Checking ebase output, doave as F", {
                          "DO_modhi", "dDO", "converge", "rsq", "a", "alo", "ahi", "b", "blo", 
                          "bhi", "P", "Plo", "Phi", "R", "Rlo", "Rhi", "D", "Dlo", "Dhi"))
 
-  # check log location
-  expect_true(file.exists(file.path(tmpdir, "log.txt")))
-
 })
 
 test_that("Checking ebase output, no gas exchange", {

vignettes/EBASE.Rmd

@@ -72,7 +72,7 @@ head(dat)
 Also note that any "dangling" observations at the start or end of the time series that do not include an entire day are removed from the input data prior to estimating metabolism.  A warning is returned if these observations are found and removed.  
 
 ```{r}
-res <- ebase(dat, interval = 900, Z = 1.85, n.chains = 2, nogas = T)
+res <- ebase(dat, interval = 900, Z = 1.85, n.chains = 2)
 head(res)
 ```