Add likelihood ratio test and other methods, fixes

The likelihood ratio test method is lrtest, in addition,
methods for update and residuals were added.

7 files changed, 122 insertions, 6 deletions

diff --git a/man/confint.mkinfit.Rd b/man/confint.mkinfit.Rd
index bad73407..ee07c9c1 100644
--- a/man/confint.mkinfit.Rd
+++ b/man/confint.mkinfit.Rd
@@ -71,7 +71,8 @@ system.time(ci_profile <- confint(f_d_1, cores = 1, quiet = TRUE))
 #   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_no_parent_0 <- confint(f_d_1, 
+#   c("k_parent_sink", "k_parent_m1", "k_m1_sink", "sigma"), cores = 4))
 ci_profile
 ci_quadratic_transformed <- confint(f_d_1, method = "quadratic")
 ci_quadratic_transformed
diff --git a/man/logLik.mkinfit.Rd b/man/logLik.mkinfit.Rd
index bb2c2957..502fb4d7 100644
--- a/man/logLik.mkinfit.Rd
+++ b/man/logLik.mkinfit.Rd
@@ -17,10 +17,11 @@ An object of class \code{\link{logLik}} with the number of estimated
   as attribute.
 }
 \description{
-This function simply calculates the product of the likelihood densities
-calculated using \code{\link{dnorm}}, i.e. assuming normal distribution,
-with of the mean predicted by the degradation model, and the standard
-deviation predicted by the error model.
+This function returns the product of the likelihood densities of each
+observed value, as calculated as part of the fitting procedure using
+\code{\link{dnorm}}, i.e. assuming normal distribution, and with the means
+predicted by the degradation model, and the standard deviations predicted by
+the error model.
 }
 \details{
 The total number of estimated parameters returned with the value of the
diff --git a/man/lrtest.mkinfit.Rd b/man/lrtest.mkinfit.Rd
new file mode 100644
index 00000000..b38732b4
--- /dev/null
+++ b/man/lrtest.mkinfit.Rd
@@ -0,0 +1,43 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/lrtest.mkinfit.R
+\name{lrtest.mkinfit}
+\alias{lrtest.mkinfit}
+\title{Likelihood ratio test for mkinfit models}
+\usage{
+\method{lrtest}{mkinfit}(object, object_2 = NULL, ...)
+}
+\arguments{
+\item{object}{An \code{\link{mkinfit}} object}
+
+\item{object_2}{Optionally, another mkinfit object fitted to the same data.}
+
+\item{\dots}{Argument to \code{\link{mkinfit}}, passed to
+\code{\link{update.mkinfit}} for creating the alternative fitted object.}
+}
+\description{
+Compare two mkinfit models based on their likelihood. If two fitted
+mkinfit objects are given as arguments, it is checked if they have been
+fitted to the same data. It is the responsibility of the user to make sure
+that the models are nested, i.e. one of them has less degrees of freedom
+and can be expressed by fixing the parameters of the other.
+}
+\details{
+Alternatively, an argument to mkinfit can be given which is then passed
+to \code{\link{update.mkinfit}} to obtain the alternative model.
+
+The comparison is then made by the \code{\link[lmtest]{lrtest.default}}
+method from the lmtest package. The model with the higher number of fitted
+parameters (alternative hypothesis) is listed first, then the model with the
+lower number of fitted parameters (null hypothesis).
+}
+\examples{
+\dontrun{
+test_data <- subset(synthetic_data_for_UBA_2014[[12]]$data, name == "parent")
+sfo_fit <- mkinfit("SFO", test_data, quiet = TRUE)
+dfop_fit <- mkinfit("DFOP", test_data, quiet = TRUE)
+lrtest(dfop_fit, sfo_fit)
+lrtest(sfo_fit, dfop_fit)
+lrtest(dfop_fit, error_model = "tc")
+lrtest(dfop_fit, fixed_parms = c(k2 = 0))
+}
+}
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
index d9afb753..e58e61e2 100644
--- a/man/mkinfit.Rd
+++ b/man/mkinfit.Rd
@@ -65,7 +65,9 @@ default values.  Otherwise, inital values for all error model parameters
 must be given.}
 
 \item{fixed_parms}{The names of parameters that should not be optimised but
-rather kept at the values specified in \code{parms.ini}.}
+rather kept at the values specified in \code{parms.ini}. Alternatively,
+a named numeric vector of parameters to be fixed, regardless of the values
+in parms.ini.}
 
 \item{fixed_initials}{The names of model variables for which the initial
 state at time 0 should be excluded from the optimisation. Defaults to all
diff --git a/man/reexports.Rd b/man/reexports.Rd
new file mode 100644
index 00000000..bb77acc5
--- /dev/null
+++ b/man/reexports.Rd
@@ -0,0 +1,16 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/lrtest.mkinfit.R
+\docType{import}
+\name{reexports}
+\alias{reexports}
+\alias{lrtest}
+\title{Objects exported from other packages}
+\keyword{internal}
+\description{
+These objects are imported from other packages. Follow the links
+below to see their documentation.
+
+\describe{
+  \item{lmtest}{\code{\link[lmtest]{lrtest}}}
+}}
+
diff --git a/man/residuals.mkinfit.Rd b/man/residuals.mkinfit.Rd
new file mode 100644
index 00000000..407b89b9
--- /dev/null
+++ b/man/residuals.mkinfit.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/residuals.mkinfit.R
+\name{residuals.mkinfit}
+\alias{residuals.mkinfit}
+\title{Extract residuals from an mkinfit model}
+\usage{
+\method{residuals}{mkinfit}(object, standardized = FALSE, ...)
+}
+\arguments{
+\item{object}{An \code{\link{mkinfit}} object}
+
+\item{standardized}{Should the residuals be standardized by dividing by the
+standard deviation obtained from the fitted error model?}
+
+\item{\dots}{Not used}
+}
+\description{
+Extract residuals from an mkinfit model
+}
+\examples{
+f <- mkinfit("DFOP", FOCUS_2006_C, quiet = TRUE)
+residuals(f)
+residuals(f, standardized = TRUE)
+}
diff --git a/man/update.mkinfit.Rd b/man/update.mkinfit.Rd
new file mode 100644
index 00000000..aae1fbb4
--- /dev/null
+++ b/man/update.mkinfit.Rd
@@ -0,0 +1,29 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/update.mkinfit.R
+\name{update.mkinfit}
+\alias{update.mkinfit}
+\title{Update an mkinfit model with different arguments}
+\usage{
+\method{update}{mkinfit}(object, ..., evaluate = TRUE)
+}
+\arguments{
+\item{object}{An mkinfit object to be updated}
+
+\item{\dots}{Arguments to \code{\link{mkinfit}} that should replace
+the arguments from the original call. Arguments set to NULL will
+remove arguments given in the original call}
+
+\item{evaluate}{Should the call be evaluated or returned as a call}
+}
+\description{
+This function will return an updated mkinfit object. The fitted degradation
+model parameters from the old fit are used as starting values for the
+updated fit. Values specified as 'parms.ini' and/or 'state.ini' will
+override these starting values.
+}
+\examples{
+\dontrun{
+fit <- mkinfit("DFOP", subset(FOCUS_2006_D, value != 0), quiet = TRUE)
+update(fit, error_model = "tc")
+}
+}