Possibility to fit without parameter transformation

6 files changed, 98 insertions, 35 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index 563431e2..f3482480 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,8 +2,8 @@ Package: mkin
 Type: Package
 Title: Routines for fitting kinetic models with one or more state
   variables to chemical degradation data
-Version: 0.9-25
-Date: 2014-03-24
+Version: 0.9-26
+Date: 2014-04-22
 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), 
                     email = "jranke@uni-bremen.de"),
              person("Katrin", "Lindenberger", role = "ctb"),
diff --git a/R/mkinfit.R b/R/mkinfit.R
index 326f4044..a623146e 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -30,6 +30,8 @@ mkinfit <- function(mkinmod, observed,
   method.ode = "lsoda",

   method.modFit = "Marq",

   control.modFit = list(),

+  transform_rates = TRUE,

+  transform_fractions = TRUE,

   plot = FALSE, quiet = FALSE,

   err = NULL, weight = "none", scaleVar = FALSE,

   atol = 1e-8, rtol = 1e-10, n.outtimes = 100,

@@ -83,7 +85,9 @@ mkinfit <- function(mkinmod, observed,
   if(is.null(names(state.ini))) names(state.ini) <- mod_vars

 

   # Transform initial parameter values for fitting

-  transparms.ini <- transform_odeparms(parms.ini, mod_vars)

+  transparms.ini <- transform_odeparms(parms.ini, mod_vars, 

+                                       transform_rates = transform_rates,

+                                       transform_fractions = transform_fractions)

 

   # Parameters to be optimised:

   # Kinetic parameters in parms.ini whose names are not in fixed_parms

@@ -156,7 +160,9 @@ mkinfit <- function(mkinmod, observed,
 

     odeparms <- c(P[(length(state.ini.optim) + 1):length(P)], parms.fixed)

 

-    parms <- backtransform_odeparms(odeparms, mod_vars)

+    parms <- backtransform_odeparms(odeparms, mod_vars,

+                                    transform_rates = transform_rates,

+                                    transform_fractions = transform_fractions)

 

     # Solve the system with current transformed parameter values

     out <- mkinpredict(mkinmod, parms, odeini, outtimes, 

@@ -241,6 +247,8 @@ mkinfit <- function(mkinmod, observed,
 

   # We need to return some more data for summary and plotting

   fit$solution_type <- solution_type

+  fit$transform_rates <- transform_rates

+  fit$transform_fractions <- transform_fractions

 

   # We also need the model for summary and plotting

   fit$mkinmod <- mkinmod

@@ -252,19 +260,27 @@ mkinfit <- function(mkinmod, observed,
 

   # Collect initial parameter values in two dataframes

   fit$start <- data.frame(value = c(state.ini.optim, 

-		  backtransform_odeparms(parms.optim, mod_vars)))

+		  backtransform_odeparms(parms.optim, mod_vars,

+                             transform_rates = transform_rates,

+                             transform_fractions = transform_fractions)))

   fit$start$type = c(rep("state", length(state.ini.optim)), 

                      rep("deparm", length(parms.optim)))

   fit$start$transformed = c(state.ini.optim, parms.optim)

 

   fit$fixed <- data.frame(value = c(state.ini.fixed, 

-      backtransform_odeparms(parms.fixed, mod_vars)))

+      backtransform_odeparms(parms.fixed, mod_vars,

+                             transform_rates = transform_rates,

+                             transform_fractions = transform_fractions)))

   fit$fixed$type = c(rep("state", length(state.ini.fixed)), 

                      rep("deparm", length(parms.fixed)))

 

-  bparms.optim = backtransform_odeparms(fit$par, mod_vars)

+  bparms.optim = backtransform_odeparms(fit$par, mod_vars,

+                                        transform_rates = transform_rates,

+                                        transform_fractions = transform_fractions)

   bparms.fixed = backtransform_odeparms(c(state.ini.fixed, parms.fixed), 

-                                        mod_vars)

+                                        mod_vars,

+                                        transform_rates = transform_rates,

+                                        transform_fractions = transform_fractions)

   bparms.all = c(bparms.optim, bparms.fixed)

 

   # Collect observed, predicted, residuals and weighting

@@ -328,8 +344,10 @@ summary.mkinfit <- function(object, data = TRUE, distimes = TRUE, alpha = 0.05,
     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)[pname]

-    buci[pname] <- backtransform_odeparms(par.upper, mod_vars)[pname]

+    blci[pname] <- backtransform_odeparms(par.lower, mod_vars, 

+                                          object$transform_rates, object$transform_fractions)[pname]

+    buci[pname] <- backtransform_odeparms(par.upper, mod_vars,

+                                          object$transform_rates, object$transform_fractions)[pname]

   }

   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 f56478f1..31200c76 100644
--- a/R/transform_odeparms.R
+++ b/R/transform_odeparms.R
@@ -1,6 +1,4 @@
-# $Id$

-

-# Copyright (C) 2010-2013 Johannes Ranke

+# Copyright (C) 2010-2014 Johannes Ranke

 # Contact: jranke@uni-bremen.de

 

 # This file is part of the R package mkin

@@ -18,17 +16,21 @@
 # You should have received a copy of the GNU General Public License along with

 # this program. If not, see <http://www.gnu.org/licenses/>

 

-transform_odeparms <- function(parms, mod_vars) {

+transform_odeparms <- function(parms, mod_vars, 

+                               transform_rates = TRUE, 

+                               transform_fractions = TRUE) 

+{

   # Set up container for transformed parameters

   transparms <- parms

 

-  # Log transformation for rate constants

+  # Log transformation for rate constants if requested

   index_k <- grep("^k_", names(transparms))

   if (length(index_k) > 0) {

-    transparms[index_k] <- log(parms[index_k])

+    if(transform_rates) transparms[index_k] <- log(parms[index_k])

+    else transparms[index_k] <- parms[index_k]

   }

 

-  # Go through state variables and apply isotropic logratio transformation

+  # Go through state variables and apply isotropic 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)

@@ -37,32 +39,38 @@ transform_odeparms <- function(parms, mod_vars) {
       f <- parms[indices_f]

       trans_f <- ilr(c(f, 1 - sum(f)))

       names(trans_f) <- f_names

-      transparms[indices_f] <- trans_f

+      if(transform_fractions) transparms[indices_f] <- trans_f

+      else transparms[indices_f] <- f

     }

   }

 

-  # Transform parameters also for FOMC, DFOP and HS models

+  # Transform parameters also for FOMC, DFOP and HS models if requested

   for (pname in c("alpha", "beta", "k1", "k2", "tb")) {

     if (!is.na(parms[pname])) {

-      transparms[pname] <- log(parms[pname])

+      transparms[pname] <- ifelse(transform_rates, log(parms[pname]), parms[pname])

+      transparms[pname] <- ifelse(transform_rates, log(parms[pname]), parms[pname])

     } 

   }

   if (!is.na(parms["g"])) {

     g <- parms["g"]

-    transparms["g"] <- ilr(c(g, 1- g))

+    transparms["g"] <- ifelse(transform_fractions, ilr(c(g, 1 - g)), g)

   }

 

   return(transparms)

 }

 

-backtransform_odeparms <- function(transparms, mod_vars) {

+backtransform_odeparms <- function(transparms, mod_vars,

+                                   transform_rates = TRUE,

+                                   transform_fractions = TRUE)

+{

   # Set up container for backtransformed parameters

   parms <- transparms

 

   # Exponential transformation for rate constants

   index_k <- grep("^k_", names(parms))

   if (length(index_k) > 0) {

-    parms[index_k] <- exp(transparms[index_k])

+    if(transform_rates) parms[index_k] <- exp(transparms[index_k])

+    else parms[index_k] <- transparms[index_k]

   }

 

   # Go through state variables and apply inverse isotropic logratio transformation

@@ -73,19 +81,20 @@ backtransform_odeparms <- function(transparms, mod_vars) {
     if (n_paths > 0) {

       f <- invilr(transparms[indices_f])[1:n_paths] # We do not need the last component

       names(f) <- f_names

-      parms[indices_f] <- f

+      if(transform_fractions) parms[indices_f] <- f

+      else parms[indices_f] <- transparms[indices_f]

     }

   }

 

   # Transform parameters also for DFOP and HS models

   for (pname in c("alpha", "beta", "k1", "k2", "tb")) {

     if (!is.na(transparms[pname])) {

-      parms[pname] <- exp(transparms[pname])

+      parms[pname] <- ifelse(transform_rates, exp(transparms[pname]), transparms[pname])

     } 

   }

   if (!is.na(transparms["g"])) {

     g <- transparms["g"]

-    parms["g"] <- invilr(g)[1]

+    parms["g"] <- ifelse(transform_fractions, invilr(g)[1], g)

   }

 

   return(parms)

diff --git a/TODO b/TODO
index affc5874..944ad57d 100644
--- a/TODO
+++ b/TODO
@@ -3,6 +3,7 @@ TODO for version 1.0
 - Support model definitions without pathway to sink in combination with formation fractions
 - Complete the main package vignette named mkin to include a method description
 - Calculate pseudoDT50 values as recommended by FOCUS
+- Improve formatting of differential equations in the summary
 
 Nice to have:
 - Calculate confidence intervals for DT50 and DT90 values when only one parameter is involved
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
index 0c5d76a9..839580a1 100644
--- a/man/mkinfit.Rd
+++ b/man/mkinfit.Rd
@@ -23,6 +23,8 @@ mkinfit(mkinmod, observed,
   method.ode = "lsoda",
   method.modFit = "Marq",
   control.modFit = list(),
+  transform_rates = TRUE,
+  transform_fractions = TRUE,
   plot = FALSE, quiet = FALSE, err = NULL, weight = "none", 
   scaleVar = FALSE, 
   atol = 1e-8, rtol = 1e-10, n.outtimes = 100, 
@@ -102,6 +104,22 @@ mkinfit(mkinmod, observed,
     Additional arguments passed to the optimisation method used by
     \code{\link{modFit}}.
   }
+  \item{transform_rates}{
+    Boolean specifying if kinetic rate constants should be transformed in the
+    model specification used in the fitting for better compliance with the
+    assumption of normal distribution of the estimator. If TRUE, also 
+    alpha and beta parameters of the FOMC model are log-transformed, as well 
+    as k1 and k2 rate constants for the DFOP and HS models.
+  }
+  \item{transform_fractions}{
+    Boolean specifying if formation fractions constants should be transformed in the
+    model specification used in the fitting for better compliance with the
+    assumption of normal distribution of the estimator. The default (TRUE) is 
+    to do transformations. The g parameter of the DFOP and HS models are also 
+    transformed, as they can also be seen as compositional data. The
+    transformation used for these transformations is the \code{\link{ilr}}
+    transformation.
+  }
   \item{plot}{
     Should the observed values and the numerical solutions be plotted at each
     stage of the optimisation?
diff --git a/man/transform_odeparms.Rd b/man/transform_odeparms.Rd
index 999beaaf..e251cf62 100644
--- a/man/transform_odeparms.Rd
+++ b/man/transform_odeparms.Rd
@@ -13,20 +13,37 @@
   negative, the \code{\link{ilr}} transformation is used.
 }
 \usage{
-transform_odeparms(parms, mod_vars)
-backtransform_odeparms(transparms, mod_vars)
+transform_odeparms(parms, mod_vars, transform_rates = TRUE, transform_fractions = TRUE)
+backtransform_odeparms(transparms, mod_vars, 
+                       transform_rates = TRUE, transform_fractions = TRUE)
 }
 \arguments{
   \item{parms}{
-  Parameters of kinetic models as used in the differential equations.
-}
+    Parameters of kinetic models as used in the differential equations.
+  }
   \item{transparms}{
-  Transformed parameters of kinetic models as used in the fitting procedure.
-}
+    Transformed parameters of kinetic models as used in the fitting procedure.
+  }
   \item{mod_vars}{
-  Names of the state variables in the kinetic model. These are used for 
-  grouping the formation fractions before \code{\link{ilr}} transformation.  
-}
+    Names of the state variables in the kinetic model. These are used for 
+    grouping the formation fractions before \code{\link{ilr}} transformation.  
+  }
+  \item{transform_rates}{
+    Boolean specifying if kinetic rate constants should be transformed in the
+    model specification used in the fitting for better compliance with the
+    assumption of normal distribution of the estimator. If TRUE, also 
+    alpha and beta parameters of the FOMC model are log-transformed, as well 
+    as k1 and k2 rate constants for the DFOP and HS models.
+  }
+  \item{transform_fractions}{
+    Boolean specifying if formation fractions constants should be transformed in the
+    model specification used in the fitting for better compliance with the
+    assumption of normal distribution of the estimator. The default (TRUE) is 
+    to do transformations. The g parameter of the DFOP and HS models are also 
+    transformed, as they can also be seen as compositional data. The
+    transformation used for these transformations is the \code{\link{ilr}}
+    transformation.
+  }
 }
 \value{
   A vector of transformed or backtransformed parameters with the same names