Make the 'quadratic' the default for 'confint'

Also the documentation was improved here and there

1 files changed, 36 insertions, 30 deletions

diff --git a/man/confint.mkinfit.Rd b/man/confint.mkinfit.Rd
index ee07c9c1..e4a60556 100644
--- a/man/confint.mkinfit.Rd
+++ b/man/confint.mkinfit.Rd
@@ -5,7 +5,7 @@
 \title{Confidence intervals for parameters of mkinfit objects}
 \usage{
 \method{confint}{mkinfit}(object, parm, level = 0.95, alpha = 1 -
-  level, cutoff, method = c("profile", "quadratic"),
+  level, cutoff, method = c("quadratic", "profile"),
   transformed = TRUE, backtransform = TRUE,
   cores = round(detectCores()/2), quiet = FALSE, ...)
 }
@@ -23,11 +23,11 @@ confidence intervals. If missing, all parameters are considered.}
 in the log-likelihoods at the confidence boundary. Specifying an explicit
 cutoff value overrides arguments 'level' and 'alpha'}
 
-\item{method}{The 'profile' method searches the parameter space for the
-cutoff of the confidence intervals by means of a likelihood ratio test.
-The 'quadratic' method approximates the likelihood function at the
-optimised parameters using the second term of the Taylor expansion, using
-a second derivative (hessian) contained in the object.}
+\item{method}{The 'quadratic' method approximates the likelihood function at
+the optimised parameters using the second term of the Taylor expansion,
+using a second derivative (hessian) contained in the object.
+The 'profile' method searches the parameter space for the
+cutoff of the confidence intervals by means of a likelihood ratio test.}
 
 \item{transformed}{If the quadratic approximation is used, should it be
 applied to the likelihood based on the transformed parameters?}
@@ -49,9 +49,14 @@ A matrix with columns giving lower and upper confidence limits for
   each parameter.
 }
 \description{
-The default method 'profile' is based on the profile likelihood for each
-parameter. The method uses two nested optimisations. The speed of the method
-could likely be improved by using the method of Venzon and Moolgavkar (1988).
+The default method 'quadratic' is based on the quadratic approximation of
+the curvature of the likelihood function at the maximum likelihood parameter
+estimates.
+The alternative method 'profile' is based on the profile likelihood for each
+parameter. The method uses two nested optimisations and can take a very long
+time, even if parallelized by specifying 'cores' on unixoid platforms. The
+speed of the method could likely be improved by using the method of Venzon
+and Moolgavkar (1988).
 }
 \examples{
 f <- mkinfit("SFO", FOCUS_2006_C, quiet = TRUE)
@@ -60,19 +65,26 @@ confint(f, method = "quadratic")
 \dontrun{
 confint(f, method = "profile")
 
+# Set the number of cores for the profiling method for further examples
+if (identical(Sys.getenv("NOT_CRAN"), "true")) {
+  n_cores <- parallel::detectCores() - 1
+} else {
+ n_cores <- 1
+}
+if (Sys.getenv("TRAVIS") != "") n_cores = 1
+if (Sys.info()["sysname"] == "Windows") n_cores = 1
+
 SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"), quiet = TRUE)
 SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"),
   use_of_ff = "max", quiet = TRUE)
 f_d_1 <- mkinfit(SFO_SFO, subset(FOCUS_2006_D, value != 0), quiet = TRUE)
-system.time(ci_profile <- confint(f_d_1, cores = 1, quiet = TRUE))
-# The following does not save much time, as parent_0 takes up most of the time
-# system.time(ci_profile <- confint(f_d_1, cores = 5))
-# system.time(ci_profile <- confint(f_d_1,
-#   c("k_parent_sink", "k_parent_m1", "k_m1_sink", "sigma"), cores = 1))
-# If we exclude parent_0 (the confidence of which is often of minor interest), we get a nice
-# performance improvement from about 30 seconds to about 12 seconds
-# system.time(ci_profile_no_parent_0 <- confint(f_d_1, 
-#   c("k_parent_sink", "k_parent_m1", "k_m1_sink", "sigma"), cores = 4))
+system.time(ci_profile <- confint(f_d_1, method = "profile", cores = 1, quiet = TRUE))
+# Using more cores does not save much time here, as parent_0 takes up most of the time
+# If we additionally exclude parent_0 (the confidence of which is often of
+# minor interest), we get a nice performance improvement from about 50
+# seconds to about 12 seconds if we use at least four cores
+system.time(ci_profile_no_parent_0 <- confint(f_d_1, method = "profile",
+  c("k_parent_sink", "k_parent_m1", "k_m1_sink", "sigma"), cores = n_cores))
 ci_profile
 ci_quadratic_transformed <- confint(f_d_1, method = "quadratic")
 ci_quadratic_transformed
@@ -84,21 +96,14 @@ ci_quadratic_untransformed
 # interval based on the untransformed fit for k_m1_sink
 rel_diffs_transformed <- abs((ci_quadratic_transformed - ci_profile)/ci_profile)
 rel_diffs_untransformed <- abs((ci_quadratic_untransformed - ci_profile)/ci_profile)
-rel_diffs_transformed
-rel_diffs_untransformed
+rel_diffs_transformed < rel_diffs_untransformed
+signif(rel_diffs_transformed, 3)
+signif(rel_diffs_untransformed, 3)
 
-# Set the number of cores for further examples
-if (identical(Sys.getenv("NOT_CRAN"), "true")) {
-  n_cores <- parallel::detectCores() - 1
-} else {
- n_cores <- 1
-}
-if (Sys.getenv("TRAVIS") != "") n_cores = 1
-if (Sys.info()["sysname"] == "Windows") n_cores = 1
 
 # Investigate a case with formation fractions
 f_d_2 <- mkinfit(SFO_SFO.ff, subset(FOCUS_2006_D, value != 0), quiet = TRUE)
-ci_profile_ff <- confint(f_d_2, cores = n_cores)
+ci_profile_ff <- confint(f_d_2, method = "profile", cores = n_cores)
 ci_profile_ff
 ci_quadratic_transformed_ff <- confint(f_d_2, method = "quadratic")
 ci_quadratic_transformed_ff
@@ -108,8 +113,9 @@ rel_diffs_transformed_ff <- abs((ci_quadratic_transformed_ff - ci_profile_ff)/ci
 rel_diffs_untransformed_ff <- abs((ci_quadratic_untransformed_ff - ci_profile_ff)/ci_profile_ff)
 # While the confidence interval for the parent rate constant is closer to
 # the profile based interval when using the internal parameter
-# transformation, the intervals for the other parameters are 'better
+# transformation, the interval for the metabolite rate constant is 'better
 # without internal parameter transformation.
+rel_diffs_transformed_ff < rel_diffs_untransformed_ff
 rel_diffs_transformed_ff
 rel_diffs_untransformed_ff