Add a simple anova method for model comparison

Update docs

4 files changed, 57 insertions, 1 deletions

diff --git a/man/anova.saem.mmkin.Rd b/man/anova.saem.mmkin.Rd
new file mode 100644
index 00000000..8f9cb241
--- /dev/null
+++ b/man/anova.saem.mmkin.Rd
@@ -0,0 +1,35 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/anova.saem.mmkin.R
+\name{anova.saem.mmkin}
+\alias{anova.saem.mmkin}
+\title{Anova method for saem.mmkin objects}
+\usage{
+\method{anova}{saem.mmkin}(
+  object,
+  ...,
+  method = c("is", "lin", "gq"),
+  test = FALSE,
+  model.names = NULL
+)
+}
+\arguments{
+\item{object}{An \link{saem.mmkin} object}
+
+\item{...}{further such objects}
+
+\item{method}{Method for likelihood calculation: "is" (importance sampling),
+"lin" (linear approximation), or "gq" (Gaussian quadrature). Passed
+to \link[saemix:logLik]{saemix::logLik.SaemixObject}}
+
+\item{test}{Should a likelihood ratio test be performed? If TRUE,
+the alternative models are tested against the first model. Should
+only be done for nested models.}
+
+\item{model.names}{Optional character vector of model names}
+}
+\value{
+an "anova" data frame; the traditional (S3) result of anova()
+}
+\description{
+Anova method for saem.mmkin objects
+}
diff --git a/man/logLik.saem.mmkin.Rd b/man/logLik.saem.mmkin.Rd
new file mode 100644
index 00000000..8ea3426f
--- /dev/null
+++ b/man/logLik.saem.mmkin.Rd
@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/saem.R
+\name{logLik.saem.mmkin}
+\alias{logLik.saem.mmkin}
+\title{logLik method for saem.mmkin objects}
+\usage{
+\method{logLik}{saem.mmkin}(object, ..., method = c("lin", "is", "gq"))
+}
+\arguments{
+\item{method}{Passed to \link[saemix:logLik]{saemix::logLik.SaemixObject}}
+}
+\description{
+logLik method for saem.mmkin objects
+}
diff --git a/man/parhist.Rd b/man/parhist.Rd
index 67bbadad..f86ff734 100644
--- a/man/parhist.Rd
+++ b/man/parhist.Rd
@@ -6,6 +6,7 @@
 \usage{
 parhist(
   object,
+  llmin = -Inf,
   scale = c("best", "median"),
   lpos = "bottomleft",
   main = "",
@@ -15,6 +16,8 @@ parhist(
 \arguments{
 \item{object}{The \link{multistart} object}
 
+\item{llmin}{The minimum likelihood of objects to be shown}
+
 \item{scale}{By default, scale parameters using the best available fit.
 If 'median', parameters are scaled using the median parameters from all fits.}
 
diff --git a/man/saem.Rd b/man/saem.Rd
index a9c4a1bb..2b9199dd 100644
--- a/man/saem.Rd
+++ b/man/saem.Rd
@@ -19,6 +19,8 @@ saem(object, ...)
   conf.level = 0.6,
   solution_type = "auto",
   covariance.model = "auto",
+  covariates = NULL,
+  covariate_models = NULL,
   no_random_effect = NULL,
   nbiter.saemix = c(300, 100),
   control = list(displayProgress = FALSE, print = FALSE, nbiter.saemix = nbiter.saemix,
@@ -38,13 +40,15 @@ saemix_model(
   degparms_start = numeric(),
   covariance.model = "auto",
   no_random_effect = NULL,
+  covariates = NULL,
+  covariate_models = NULL,
   test_log_parms = FALSE,
   conf.level = 0.6,
   verbose = FALSE,
   ...
 )
 
-saemix_data(object, verbose = FALSE, ...)
+saemix_data(object, covariates = NULL, verbose = FALSE, ...)
 
 \method{parms}{saem.mmkin}(object, ci = FALSE, ...)
 }