From 4110808d1953b8704ef48d0dc5b5e445cbde9af0 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Tue, 20 May 2014 08:36:42 +0200
Subject: Step back regarding confidence intervals of formation fractions

- Don't give confidence intervals for formation fractions that belong
  to a set, only for single formation fractions
- Update the vignette with history and background
- Correct 'isotropic' into 'isometric' in the ilr documentation, the
  README and the comments in transform_odeparms
- Candidate for release to CRAN
---
 R/mkinfit.R            | 18 +++++++++++++++---
 R/transform_odeparms.R |  4 ++--
 2 files changed, 17 insertions(+), 5 deletions(-)

(limited to 'R')

diff --git a/R/mkinfit.R b/R/mkinfit.R
index ab1977d1..612e43d2 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -364,15 +364,27 @@ summary.mkinfit <- function(object, data = TRUE, distimes = TRUE, alpha = 0.05,
                                     "t value", "Pr(>|t|)", "Pr(>t)"))
 
   blci <- buci <- numeric()
-  # Only transform boundaries of CI for one parameter at a time
+  # Transform boundaries of CI for one parameter at a time,
+  # with the exception of sets of formation fractions (single fractions are OK).
+  f_names_skip <- character(0)
+  for (box in mod_vars) { # Figure out sets of fractions to skip
+    f_names <- grep(paste("^f", box, sep = "_"), pnames, value = TRUE)
+    n_paths <- length(f_names)
+    if (n_paths > 1) f_names_skip <- c(f_names_skip, f_names)
+  }
+
   for (pname in pnames) {
     par.lower <- par.upper <- object$par
     par.lower[pname] <- param[pname, "Lower"]
     par.upper[pname] <- param[pname, "Upper"]
-    blci[pname] <- backtransform_odeparms(par.lower, mod_vars, 
+    if (!pname %in% f_names_skip) {
+      blci[pname] <- backtransform_odeparms(par.lower, mod_vars, 
                                           object$transform_rates, object$transform_fractions)[pname]
-    buci[pname] <- backtransform_odeparms(par.upper, mod_vars,
+      buci[pname] <- backtransform_odeparms(par.upper, mod_vars,
                                           object$transform_rates, object$transform_fractions)[pname]
+    } else {
+      blci[pname] <- buci[pname] <- NA
+    }
   }
   bparam <- cbind(object$bparms.optim, blci, buci)
   dimnames(bparam) <- list(pnames, c("Estimate", "Lower", "Upper"))
diff --git a/R/transform_odeparms.R b/R/transform_odeparms.R
index a0c302f5..2438151b 100644
--- a/R/transform_odeparms.R
+++ b/R/transform_odeparms.R
@@ -30,7 +30,7 @@ transform_odeparms <- function(parms, mod_vars,
     else transparms[index_k] <- parms[index_k]
   }
 
-  # Go through state variables and apply isotropic logratio transformation if requested
+  # Go through state variables and apply isometric logratio transformation if requested
   for (box in mod_vars) {
     indices_f <- grep(paste("^f", box, sep = "_"), names(parms))
     f_names <- grep(paste("^f", box, sep = "_"), names(parms), value = TRUE)
@@ -73,7 +73,7 @@ backtransform_odeparms <- function(transparms, mod_vars,
     else parms[index_k] <- transparms[index_k]
   }
 
-  # Go through state variables and apply inverse isotropic logratio transformation
+  # Go through state variables and apply inverse isometric logratio transformation
   for (box in mod_vars) {
     indices_f <- grep(paste("^f", box, sep = "_"), names(transparms))
     f_names <- grep(paste("^f", box, sep = "_"), names(transparms), value = TRUE)
-- 
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