Remove trailing whitespace, clean headers

Also ignore test.R in the top level directory, as it is not meant to
be public

1 files changed, 10 insertions, 10 deletions

diff --git a/R/mkinmod.R b/R/mkinmod.R
index 5ec62bbe..7f7f8587 100644
--- a/R/mkinmod.R
+++ b/R/mkinmod.R
@@ -44,7 +44,7 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verb
 

   # Do not return a coefficient matrix mat when FOMC, IORE, DFOP or HS is used for the parent {{{

   if(spec[[1]]$type %in% c("FOMC", "IORE", "DFOP", "HS")) {

-    mat = FALSE 

+    mat = FALSE

   } else mat = TRUE

   #}}}

 

@@ -60,7 +60,7 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verb
     if(!spec[[varname]]$type %in% c("SFO", "FOMC", "IORE", "DFOP", "HS", "SFORB")) stop(

       "Available types are SFO, FOMC, IORE, DFOP, HS and SFORB only")

     if(spec[[varname]]$type %in% c("FOMC", "DFOP", "HS") & match(varname, obs_vars) != 1) {

-        stop(paste("Types FOMC, DFOP and HS are only implemented for the first compartment,", 

+        stop(paste("Types FOMC, DFOP and HS are only implemented for the first compartment,",

                    "which is assumed to be the source compartment"))

     }

     #}}}

@@ -109,7 +109,7 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verb
             decline_term <- paste0(decline_term, "^", N)

           }

         } else { # otherwise no decline term needed here

-          decline_term = "0" 

+          decline_term = "0"

         }

       } else {

         k_compound <- paste("k", box_1, sep = "_")

@@ -156,7 +156,7 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verb
       } else { # Use formation fractions also for the free compartment

         stop("The maximum use of formation fractions is not supported for SFORB models")

         # The problems were: Calculation of dissipation times did not work in this case

-        # and the coefficient matrix is not generated correctly by the code present 

+        # and the coefficient matrix is not generated correctly by the code present

         # in this file in this case

         f_free_bound <- paste("f", varname, "free", "bound", sep = "_")

         k_bound_free <- paste("k", varname, "bound", "free", sep = "_")

@@ -189,9 +189,9 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verb
         {

           k_from_to <- paste("k", origin_box, target_box, sep = "_")

           parms <- c(parms, k_from_to)

-          diffs[[origin_box]] <- paste(diffs[[origin_box]], "-", 

+          diffs[[origin_box]] <- paste(diffs[[origin_box]], "-",

             k_from_to, "*", origin_box)

-          diffs[[target_box]] <- paste(diffs[[target_box]], "+", 

+          diffs[[target_box]] <- paste(diffs[[target_box]], "+",

             k_from_to, "*", origin_box)

         } else {

           # Do not introduce a formation fraction if this is the only target

@@ -201,7 +201,7 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verb
           } else {

             fraction_to_target = paste("f", origin_box, "to", target, sep = "_")

             parms <- c(parms, fraction_to_target)

-            diffs[[target_box]] <- paste(diffs[[target_box]], "+", 

+            diffs[[target_box]] <- paste(diffs[[target_box]], "+",

                 fraction_to_target, "*", decline_term)

           }

         }

@@ -261,7 +261,7 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verb
             k.candidate = paste("k", from, to, sep = "_")

             # SFORB with maximum use of formation fractions not implemented, see above

             m[to, from] = ifelse(f.candidate %in% model$parms,

-              paste(f.candidate, " * k_", from, sep = ""), 

+              paste(f.candidate, " * k_", from, sep = ""),

               ifelse(k.candidate %in% model$parms, k.candidate, "0"))

             # Special case: singular pathway and no sink

             if (spec[[from]]$sink == FALSE && length(spec[[from]]$to) == 1 && to %in% spec[[from]]$to) {

@@ -317,7 +317,7 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verb
 

       derivs_sig <- signature(n = "integer", t = "numeric", y = "numeric",

                               f = "numeric", rpar = "numeric", ipar = "integer")

-      

+

       # Declare the time variable in the body of the function if it is used

       derivs_code <- if (spec[[1]]$type %in% c("FOMC", "DFOP", "HS")) {

         paste0("double time = *t;\n", diffs.C)

@@ -369,6 +369,6 @@ print.mkinmod <- function(x, ...) {
     cat("\n")

   }

   if (is.matrix(x$coefmat)) cat("Coefficient matrix $coefmat available\n")

-  if (!is.null(x$cf)) cat("Compiled model $cf available\n")  

+  if (!is.null(x$cf)) cat("Compiled model $cf available\n")

 }

 # vim: set foldmethod=marker ts=2 sw=2 expandtab: