From c97a47bcce5455478a18dcdcd71f4a2f2344bce0 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Sun, 23 Nov 2014 16:24:14 +0100
Subject: Avoid spurious warning in mkinparplot, bump version

---
 DESCRIPTION     |  4 ++--
 NEWS.md         |  6 ++++++
 R/mkinparplot.R | 14 ++++++++++----
 3 files changed, 18 insertions(+), 6 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index aa382e66..202251fb 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,8 +2,8 @@ Package: mkin
 Type: Package
 Title: Routines for Fitting Kinetic Models with One or More State
   Variables to Chemical Degradation Data
-Version: 0.9-34
-Date: 2014-11-21
+Version: 0.9-35
+Date: 2014-11-22
 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 5d51c6ed..fdd25051 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,9 @@
+# CHANGES in mkin VERSION 0.9-35
+
+## BUG FIXES
+
+- `mkinparplot()`: Avoid warnings that occurred when not all confidence intervals were available in the summary of the fit
+
 # CHANGES in mkin VERSION 0.9-34
 
 ## NEW FEATURES
diff --git a/R/mkinparplot.R b/R/mkinparplot.R
index 4abecab9..b2debe9d 100644
--- a/R/mkinparplot.R
+++ b/R/mkinparplot.R
@@ -39,6 +39,8 @@ mkinparplot <- function(object) {
   for (type in names(n.plot)) {
     parnames <- get(type)
     values <- bpar[parnames]
+    values_with_confints <- data.frame(t(subset(data.frame(t(values)), !is.na(Lower))))
+    parnames_with_confints <- names(values_with_confints)
     xlim = switch(type,
                   state.optim = range(c(0, unlist(values)), 
                                       na.rm = TRUE, finite = TRUE),
@@ -48,7 +50,10 @@ mkinparplot <- function(object) {
                                       na.rm = TRUE, finite = TRUE),
                   fractions.optim = range(c(0, 1, unlist(values)), 
                                           na.rm = TRUE, finite = TRUE))
-    stripchart(values["Estimate", ][length(parnames):1], 
+    parname_index <- length(parnames):1 # Reverse order for strip chart
+    names(parname_index) <- parnames
+    parnames_with_confints_index <- parname_index[parnames_with_confints]
+    stripchart(values["Estimate", ][parname_index], 
                xlim = xlim,
                ylim = c(0.5, length(get(type)) + 0.5),
                yaxt = "n")
@@ -58,9 +63,10 @@ mkinparplot <- function(object) {
     text(ifelse(position == "left", min(xlim), max(xlim)), 
          length(parnames):1, parnames, 
          pos = ifelse(position == "left", 4, 2))
-    values.upper.nonInf <- ifelse(values["Upper", ] == Inf, 1.5 * xlim[[2]], values["Upper", ])
-    arrows(as.numeric(values["Lower", ]), length(parnames):1, 
-           as.numeric(values.upper.nonInf), length(parnames):1, 
+
+    values_with_confints.upper.nonInf <- ifelse(values_with_confints["Upper", ] == Inf, 1.5 * xlim[[2]], values_with_confints["Upper", ])
+    arrows(as.numeric(values_with_confints["Lower", ]), parnames_with_confints_index, 
+           as.numeric(values_with_confints.upper.nonInf), parnames_with_confints_index, 
            code = 3, angle = 90, length = 0.05)
   }
   par(oldpars)
-- 
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