- Document endpoints() function

- Fix unit tests that were broken by introduction of 
  the endpoints function
- Small documentation fixes
- Format output of backtransformed parameters
- Integrate snippet for making static documentation
  using staticdocs by Hadley Wickham



git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@41 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

1 files changed, 16 insertions, 12 deletions

diff --git a/R/mkinfit.R b/R/mkinfit.R
index d3ee5e7b..3100b30f 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -228,21 +228,25 @@ summary.mkinfit <- function(object, data = TRUE, distimes = TRUE, ...) {
   param <- cbind(param, se)

   dimnames(param) <- list(pnames, c("Estimate", "Std. Error"))

 

+  bparam <- as.matrix(object$parms.all)

+  dimnames(bparam) <- list(pnames, c("Estimate"))

+

   ans <- list(

-          version = as.character(packageVersion("mkin")),

-          Rversion = paste(R.version$major, R.version$minor, sep="."),

+    version = as.character(packageVersion("mkin")),

+    Rversion = paste(R.version$major, R.version$minor, sep="."),

 	  date.fit = object$date,

 	  date.summary = date(),

 	  use_of_ff = object$mkinmod$use_of_ff,

-          residuals = object$residuals,

-          residualVariance = resvar,

-          sigma = sqrt(resvar),

-          modVariance = modVariance,

-          df = c(p, rdf), cov.unscaled = covar,

-          cov.scaled = covar * resvar,

-          info = object$info, niter = object$iterations,

-          stopmess = message,

-          par = param)

+    residuals = object$residuals,

+    residualVariance = resvar,

+    sigma = sqrt(resvar),

+    modVariance = modVariance,

+    df = c(p, rdf), cov.unscaled = covar,

+    cov.scaled = covar * resvar,

+    info = object$info, niter = object$iterations,

+    stopmess = message,

+    par = param,

+    bpar = bparam)

 

   ans$diffs <- object$mkinmod$diffs

   if(data) ans$data <- object$data

@@ -285,7 +289,7 @@ print.summary.mkinfit <- function(x, digits = max(3, getOption("digits") - 3), .
   printCoefmat(x$par, digits = digits, ...)

 

   cat("\nBacktransformed parameters:\n")

-  print(as.data.frame(list(Estimate = x$parms.all)))

+  printCoefmat(x$bpar, digits = digits, ...)

 

   cat("\nResidual standard error:",

       format(signif(x$sigma, digits)), "on", rdf, "degrees of freedom\n")