Fix R CMD check

7 files changed, 32 insertions, 17 deletions

diff --git a/NAMESPACE b/NAMESPACE
index 4755f631..877fc744 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -6,6 +6,7 @@ S3method(AIC,mhmkin)
 S3method(AIC,mmkin)
 S3method(BIC,mhmkin)
 S3method(BIC,mmkin)
+S3method(anova,mhmkin)
 S3method(anova,saem.mmkin)
 S3method(aw,mixed.mmkin)
 S3method(aw,mkinfit)
@@ -26,6 +27,7 @@ S3method(logLik,saem.mmkin)
 S3method(lrtest,mkinfit)
 S3method(lrtest,mmkin)
 S3method(mhmkin,list)
+S3method(mhmkin,mmkin)
 S3method(mixed,mmkin)
 S3method(mkinpredict,mkinfit)
 S3method(mkinpredict,mkinmod)
diff --git a/R/mhmkin.R b/R/mhmkin.R
index 2fb4d9bc..175d12ec 100644
--- a/R/mhmkin.R
+++ b/R/mhmkin.R
@@ -8,6 +8,8 @@
 #'
 #' @param objects A list of [mmkin] objects containing fits of the same
 #' degradation models to the same data, but using different error models.
+#' Alternatively, a single [mmkin] object containing fits of several
+#' degradation models to the same data
 #' @param backend The backend to be used for fitting. Currently, only saemix is
 #' supported
 #' @param algorithm The algorithm to be used for fitting (currently not used)
@@ -35,8 +37,8 @@ mhmkin <- function(objects, backend = "saemix", algorithm = "saem", ...) {
 
 #' @export
 #' @rdname mhmkin
-mhmkin.mmkin <- function(object, ...) {
-  mhmkin(list(object), ...)
+mhmkin.mmkin <- function(objects, ...) {
+  mhmkin(list(objects), ...)
 }
 
 #' @export
@@ -199,7 +201,7 @@ update.mhmkin <- function(object, ..., evaluate = TRUE) {
   else call
 }
 
-#' export
+#' @export
 anova.mhmkin <- function(object, ...,
   method = c("is", "lin", "gq"), test = FALSE, model.names = "auto") {
   if (identical(model.names, "auto")) {
diff --git a/log/check.log b/log/check.log
index c2b4aa50..36bd30ca 100644
--- a/log/check.log
+++ b/log/check.log
@@ -5,7 +5,7 @@
 * using options ‘--no-tests --as-cran’
 * checking for file ‘mkin/DESCRIPTION’ ... OK
 * checking extension type ... Package
-* this is package ‘mkin’ version ‘1.1.2’
+* this is package ‘mkin’ version ‘1.2.0’
 * package encoding: UTF-8
 * checking CRAN incoming feasibility ... NOTE
 Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’
diff --git a/log/test.log b/log/test.log
index b4298c40..bb81dd43 100644
--- a/log/test.log
+++ b/log/test.log
@@ -5,18 +5,18 @@
 ✔ |         5 | Calculation of Akaike weights
 ✔ |         3 | Export dataset for reading into CAKE
 ✔ |        12 | Confidence intervals and p-values [1.0s]
-✔ |     1  12 | Dimethenamid data from 2018 [31.7s]
+✔ |     1  12 | Dimethenamid data from 2018 [31.9s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip (test_dmta.R:98:3): Different backends get consistent results for SFO-SFO3+, dimethenamid data
 Reason: Fitting this ODE model with saemix takes about 15 minutes on my system
 ────────────────────────────────────────────────────────────────────────────────
-✔ |        14 | Error model fitting [5.0s]
+✔ |        14 | Error model fitting [4.9s]
 ✔ |         5 | Time step normalisation
 ✔ |         4 | Calculation of FOCUS chi2 error levels [0.6s]
 ✔ |        14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8s]
 ✔ |         4 | Test fitting the decline of metabolites from their maximum [0.3s]
 ✔ |         1 | Fitting the logistic model [0.2s]
-✔ |         7 | Batch fitting and diagnosing hierarchical kinetic models [14.4s]
+✔ |         7 | Batch fitting and diagnosing hierarchical kinetic models [15.8s]
 ✔ |     1  12 | Nonlinear mixed-effects models [0.3s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip (test_mixed.R:74:3): saemix results are reproducible for biphasic fits
@@ -27,12 +27,12 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve
 ✔ |         3 | mkinfit features [0.7s]
 ✔ |         8 | mkinmod model generation and printing [0.2s]
 ✔ |         3 | Model predictions with mkinpredict [0.3s]
-✔ |         7 | Multistart method for saem.mmkin models [38.1s]
+✔ |         7 | Multistart method for saem.mmkin models [36.3s]
 ✔ |        16 | Evaluations according to 2015 NAFTA guidance [2.4s]
-✔ |         9 | Nonlinear mixed-effects models with nlme [8.6s]
-✔ |        16 | Plotting [9.8s]
+✔ |         9 | Nonlinear mixed-effects models with nlme [8.9s]
+✔ |        16 | Plotting [9.9s]
 ✔ |         4 | Residuals extracted from mkinfit models
-✔ |     1  36 | saemix parent models [72.0s]
+✔ |     1  36 | saemix parent models [72.6s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip (test_saemix_parent.R:152:3): We can also use mkin solution methods for saem
 Reason: This still takes almost 2.5 minutes although we do not solve ODEs
@@ -43,11 +43,11 @@ Reason: This still takes almost 2.5 minutes although we do not solve ODEs
 ✔ |         1 | Summaries of old mkinfit objects
 ✔ |         5 | Summary [0.2s]
 ✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s]
-✔ |         9 | Hypothesis tests [8.3s]
-✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.1s]
+✔ |         9 | Hypothesis tests [8.1s]
+✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 208.6 s
+Duration: 209.2 s
 
 ── Skipped tests  ──────────────────────────────────────────────────────────────
 • Fitting this ODE model with saemix takes about 15 minutes on my system (1)
diff --git a/man/anova.saem.mmkin.Rd b/man/anova.saem.mmkin.Rd
index ab6022bc..34711c41 100644
--- a/man/anova.saem.mmkin.Rd
+++ b/man/anova.saem.mmkin.Rd
@@ -31,6 +31,8 @@ only be done for nested models.}
 an "anova" data frame; the traditional (S3) result of anova()
 }
 \description{
-Generate an anova object. The method to calculate the BIC is that from
-the saemix package. As in other prominent anova methods, models are sorted
+Generate an anova object. The method to calculate the BIC is that from the
+saemix package. As in other prominent anova methods, models are sorted by
+number of parameters, and the tests (if requested) are always relative to
+the model on the previous line.
 }
diff --git a/man/mhmkin.Rd b/man/mhmkin.Rd
index 0ef1599e..1a6e3869 100644
--- a/man/mhmkin.Rd
+++ b/man/mhmkin.Rd
@@ -2,6 +2,7 @@
 % Please edit documentation in R/mhmkin.R
 \name{mhmkin}
 \alias{mhmkin}
+\alias{mhmkin.mmkin}
 \alias{mhmkin.list}
 \alias{[.mhmkin}
 \alias{print.mhmkin}
@@ -10,6 +11,8 @@ degradation models and one or more error models}
 \usage{
 mhmkin(objects, backend = "saemix", algorithm = "saem", ...)
 
+\method{mhmkin}{mmkin}(objects, ...)
+
 \method{mhmkin}{list}(
   objects,
   backend = "saemix",
@@ -24,7 +27,9 @@ mhmkin(objects, backend = "saemix", algorithm = "saem", ...)
 }
 \arguments{
 \item{objects}{A list of \link{mmkin} objects containing fits of the same
-degradation models to the same data, but using different error models.}
+degradation models to the same data, but using different error models.
+Alternatively, a single \link{mmkin} object containing fits of several
+degradation models to the same data}
 
 \item{backend}{The backend to be used for fitting. Currently, only saemix is
 supported}
diff --git a/man/saem.Rd b/man/saem.Rd
index d7b04691..9167b51f 100644
--- a/man/saem.Rd
+++ b/man/saem.Rd
@@ -14,6 +14,7 @@ saem(object, ...)
 \method{saem}{mmkin}(
   object,
   transformations = c("mkin", "saemix"),
+  error_model = "auto",
   degparms_start = numeric(),
   test_log_parms = TRUE,
   conf.level = 0.6,
@@ -37,6 +38,7 @@ saemix_model(
   object,
   solution_type = "auto",
   transformations = c("mkin", "saemix"),
+  error_model = "auto",
   degparms_start = numeric(),
   covariance.model = "auto",
   no_random_effect = NULL,
@@ -64,6 +66,8 @@ are done in 'saemix' for the supported cases, i.e. (as of version 1.1.2)
 SFO, FOMC, DFOP and HS without fixing \code{parent_0}, and SFO or DFOP with
 one SFO metabolite.}
 
+\item{error_model}{Possibility to override the error model used in the mmkin object}
+
 \item{degparms_start}{Parameter values given as a named numeric vector will
 be used to override the starting values obtained from the 'mmkin' object.}