From fff1fc581da5b4ff935ebd4d7ded02f750472fdc Mon Sep 17 00:00:00 2001
From: jranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>
Date: Tue, 27 Mar 2012 01:03:18 +0000
Subject: Start of the transition to fitting transformed parameters. Many
 things are broken now (see TODO list)

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@20 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
---
 man/ilr.Rd             | 62 ++++++++++++++++++++++++++++++++++++++++++++++++++
 man/mkinfit.Rd         | 13 +----------
 man/mkinstart.Rd       | 38 -------------------------------
 man/summary.mkinfit.Rd |  5 +---
 4 files changed, 64 insertions(+), 54 deletions(-)
 create mode 100644 man/ilr.Rd
 delete mode 100644 man/mkinstart.Rd

(limited to 'man')

diff --git a/man/ilr.Rd b/man/ilr.Rd
new file mode 100644
index 0000000..fef0d29
--- /dev/null
+++ b/man/ilr.Rd
@@ -0,0 +1,62 @@
+\name{ilr}
+\alias{ilr}
+\alias{invilr}
+\title{
+  Function to perform isotropic log-ratio transformation
+}
+\description{
+  This implementation is a special case of the class of isotropic log-ratio transformations.
+}
+\usage{
+  ilr(x)
+  invilr(x)
+}
+\arguments{
+  \item{x}{
+    A numeric vector. Naturally, the forward transformation is only sensible for
+    vectors with all elements being greater than zero.
+  }
+}
+\details{
+}
+\value{
+  The result of the forward or backward transformation. The returned components always 
+  sum to 1 for the case of the inverse log-ratio transformation.
+}
+\references{
+%% ~put references to the literature/web site here ~
+}
+\author{
+  René Lehmann and Johannes Ranke
+}
+\note{
+%%  ~~further notes~~
+}
+
+\seealso{
+  Other implementations are in R packages \code{compositions} and \code{robCompositions}.
+}
+\examples{
+# Order matters
+ilr(c(0.1, 1, 10))
+ilr(c(10, 1, 0.1))
+# Equal entries give ilr transformations with zeros as elements
+ilr(c(3, 3, 3))
+# Almost equal entries give small numbers
+ilr(c(0.3, 0.4, 0.3))
+# Only the ration between the numbers counts, not their sum
+invilr(ilr(c(0.7, 0.29, 0.01)))
+invilr(ilr(2.1 * c(0.7, 0.29, 0.01)))
+# Inverse transformation of larger numbers gives unequal elements
+invilr(-10)
+invilr(c(-10, 0))
+# The sum of the elements of the inverse ilr is 1
+sum(invilr(c(-10, 0)))
+# This is why we do not need all elements of the inverse transformation to go back:
+a <- c(0.1, 0.3, 0.5)
+b <- invilr(a)
+length(b) # Four elements
+ilr(c(b[1:3], 1 - sum(b[1:3]))) # Gives c(0.1, 0.3, 0.5)
+}
+
+\keyword{ manip }
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
index d4139eb..24dcb83 100644
--- a/man/mkinfit.Rd
+++ b/man/mkinfit.Rd
@@ -11,9 +11,8 @@
 }
 \usage{
 mkinfit(mkinmod, observed, 
-  parms.ini = rep(0.1, length(mkinmod$parms)), 
+  parms.ini = "auto",
   state.ini = c(100, rep(0, length(mkinmod$diffs) - 1)), 
-  lower = 0, upper = Inf, 
   fixed_parms = NULL, fixed_initials = names(mkinmod$diffs)[-1], 
   eigen = FALSE,
   plot = FALSE, quiet = FALSE, err = NULL, weight = "none", 
@@ -48,16 +47,6 @@ mkinfit(mkinmod, observed,
     \code{\link{mkinmod}}). The default is to set the initial value of the first model
     variable to 100 and all others to 0.
   }
-  \item{lower}{
-    Lower bounds for the parameters, passed to \code{\link{modFit}}. Defaults to 0 because
-    negative values to not make sense for the models currently created by \code{\link{mkinmod}}.
-  }
-  \item{upper}{
-    Upper bounds for the parameters, passed to \code{\link{modFit}}. Defaults to \code{Inf} 
-    except for formation fraction parameters. Setting non-infinite upper bounds has a strong 
-    impact on performance, and using a method like "L-BFGS-B" (by specifying an additional 
-    \code{method} argument) is recommended.
-  }
   \item{fixed_parms}{
     The names of parameters that should not be optimised but rather kept at the values
     specified in \code{parms.ini}.
diff --git a/man/mkinstart.Rd b/man/mkinstart.Rd
deleted file mode 100644
index ec1204f..0000000
--- a/man/mkinstart.Rd
+++ /dev/null
@@ -1,38 +0,0 @@
-\name{mkinstart}
-\alias{mkinstart}
-\title{
-  Generate starting parameters for optimisations
-}
-\description{
-  This function is supposed to analyse a kinetic model and kinetic data in
-  order to generate suitable starting parameters for fitting the model.
-  It does not do anything really useful at the moment.
-}
-\usage{
-mkinstart(model, data, mode = "auto")
-}
-\arguments{
-  \item{model}{
-    A kinetic model of class \code{\link{mkinmod}}.
-}
-  \item{data}{
-    Kinetic data in wide format suitable for fitting with \code{\link{mkinfit}}.
-}
-  \item{mode}{
-    How the starting parameters should be generated. At the moment, only 
-    "auto" is supported, which internally uses \code{\link{kinfit}}. 
-}
-}
-\details{
-%%  ~~ If necessary, more details than the description above ~~
-}
-\value{
-  A named vector of starting parameters.
-}
-\author{
-  Johannes Ranke
-}
-\examples{
-   
-}
-\keyword{ manip }
diff --git a/man/summary.mkinfit.Rd b/man/summary.mkinfit.Rd
index 8a8c6ab..b3e7862 100644
--- a/man/summary.mkinfit.Rd
+++ b/man/summary.mkinfit.Rd
@@ -11,7 +11,7 @@
   and residual values.
 }
 \usage{
-\method{summary}{mkinfit}(object, data = TRUE, distimes = TRUE, ff = TRUE, cov = FALSE, ...)
+\method{summary}{mkinfit}(object, data = TRUE, distimes = TRUE, ff = TRUE, ...)
 \method{print}{summary.mkinfit}(x, digits = max(3, getOption("digits") - 3), tval = TRUE, ...)
 }
 
@@ -31,9 +31,6 @@
   \item{ff}{
   logical, indicating whether formation fractions should be included.
 }
-  \item{cov}{
-  logical, indicating whether parameter covariances should be calculated.
-Passed to \code{\link{summary.modFit}}.  }
   \item{digits}{
   Number of digits to use for printing
 }
-- 
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