Fix a bug in the listing of formation fractions

The bug could only occur if a parent compound with a metabolite would
end in the letter 'f' and was therefore not noticed earlier

3 files changed, 9 insertions, 5 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index 2b027c58..2cdf3d1a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -3,7 +3,7 @@ Type: Package
 Title: Routines for Fitting Kinetic Models with One or More State
   Variables to Chemical Degradation Data
 Version: 0.9.42.9000
-Date: 2016-04-21
+Date: 2016-06-06
 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), 
                     email = "jranke@uni-bremen.de"),
              person("Katrin", "Lindenberger", role = "ctb"),
diff --git a/NEWS.md b/NEWS.md
index 4c3bf690..9b0181ed 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -14,6 +14,10 @@
 
 - Remove an outdated reference to the inline package in the `compiled_models` vignette
 
+### Bug fixes
+
+- `endpoints`: When the name of a substance degrading to a metabolite (e.g. a parent compound) used in the model formulation ended in the letter `f`, some rate parameters could be listed as formation fractions with mixed up names. These would also appear in the summary.
+
 ## mkin 0.9.42 (2016-03-25)
 
 ### Major changes
diff --git a/R/endpoints.R b/R/endpoints.R
index 95966cf7..03c38ee0 100644
--- a/R/endpoints.R
+++ b/R/endpoints.R
@@ -15,7 +15,7 @@ endpoints <- function(fit) {
     type = names(fit$mkinmod$map[[obs_var]])[1]  

 

     # Get formation fractions if directly fitted, and calculate remaining fraction to sink

-    f_names = grep(paste("f", obs_var, sep = "_"), names(parms.all), value=TRUE)

+    f_names = grep(paste("^f", obs_var, sep = "_"), names(parms.all), value=TRUE)

     if (length(f_names) > 0) {

       f_values = parms.all[f_names]

       f_to_sink = 1 - sum(f_values)

@@ -30,7 +30,7 @@ endpoints <- function(fit) {
 

     # Get the rest

     if (type == "SFO") {

-      k_names = grep(paste("k", obs_var, sep="_"), names(parms.all), value=TRUE)

+      k_names = grep(paste("^k", obs_var, sep="_"), names(parms.all), value=TRUE)

       k_tot = sum(parms.all[k_names])

       DT50 = log(2)/k_tot

       DT90 = log(10)/k_tot

@@ -50,7 +50,7 @@ endpoints <- function(fit) {
       ep$distimes[obs_var, c("DT50back")] = DT50_back

     }

     if (type == "IORE") {

-      k_names = grep(paste("k__iore", obs_var, sep="_"), names(parms.all), value=TRUE)

+      k_names = grep(paste("^k__iore", obs_var, sep="_"), names(parms.all), value=TRUE)

       k_tot = sum(parms.all[k_names])

       # From the NAFTA kinetics guidance, p. 5

       n = parms.all[paste("N", obs_var, sep = "_")]

@@ -115,7 +115,7 @@ endpoints <- function(fit) {
     }

     if (type == "SFORB") {

       # FOCUS kinetics (2006), p. 60 f

-      k_out_names = grep(paste("k", obs_var, "free", sep="_"), names(parms.all), value=TRUE)

+      k_out_names = grep(paste("^k", obs_var, "free", sep="_"), names(parms.all), value=TRUE)

       k_out_names = setdiff(k_out_names, paste("k", obs_var, "free", "bound", sep="_"))

       k_1output = sum(parms.all[k_out_names])

       k_12 = parms.all[paste("k", obs_var, "free", "bound", sep="_")]