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

2 files changed, 17 insertions, 5 deletions

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)