Rudimentary support for setting up nlmixr models

- All degradation models are specified as ODE models. This appears to be
fast enough
- Error models are being translated to nlmixr as close to the mkin error
model as possible. When using the 'saem' backend, it appears not to be
possible to use the same error model for more than one observed variable
- No support yet for models with parallel formation of metabolites, where
the ilr transformation is used in mkin per default
- There is a bug in nlmixr which appears to be triggered if the data are
not balanced, see nlmixrdevelopment/nlmixr#530
- There is a print and a plot method, the summary method is not finished

1 files changed, 54 insertions, 14 deletions

diff --git a/check.log b/check.log
index 7de944a5..f6ee39db 100644
--- a/check.log
+++ b/check.log
@@ -1,19 +1,14 @@
 * using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’
-* using R version 4.0.5 (2021-03-31)
+* using R version 4.1.0 (2021-05-18)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * using session charset: UTF-8
 * using options ‘--no-tests --as-cran’
 * checking for file ‘mkin/DESCRIPTION’ ... OK
 * checking extension type ... Package
-* this is package ‘mkin’ version ‘1.0.4.9000’
+* this is package ‘mkin’ version ‘1.0.5’
 * package encoding: UTF-8
-* checking CRAN incoming feasibility ... NOTE
+* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
 Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
-
-Version contains large components (1.0.4.9000)
-
-Unknown, possibly mis-spelled, fields in DESCRIPTION:
-  ‘Remotes’
 * checking package namespace information ... OK
 * checking package dependencies ... OK
 * checking if this is a source package ... OK
@@ -46,22 +41,68 @@ Unknown, possibly mis-spelled, fields in DESCRIPTION:
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
 * checking foreign function calls ... OK
-* checking R code for possible problems ... OK
+* checking R code for possible problems ... NOTE
+saemix_model: no visible global function definition for
+  ‘packageVersion’
+Undefined global functions or variables:
+  packageVersion
+Consider adding
+  importFrom("utils", "packageVersion")
+to your NAMESPACE file.
 * checking Rd files ... OK
 * checking Rd metadata ... OK
 * checking Rd line widths ... OK
-* checking Rd cross-references ... OK
+* checking Rd cross-references ... WARNING
+Missing link or links in documentation object 'nlmixr.mmkin.Rd':
+  ‘nlmix_model’ ‘summary.nlmixr.mmkin’
+
+See section 'Cross-references' in the 'Writing R Extensions' manual.
 * checking for missing documentation entries ... OK
 * checking for code/documentation mismatches ... OK
-* checking Rd \usage sections ... OK
+* checking Rd \usage sections ... WARNING
+Undocumented arguments in documentation object 'mean_degparms'
+  ‘object’
+
+Undocumented arguments in documentation object 'nlmixr.mmkin'
+  ‘data’ ‘table’ ‘error_model’ ‘save’ ‘envir’
+Documented arguments not in \usage in documentation object 'nlmixr.mmkin':
+  ‘solution_type’
+
+Functions with \usage entries need to have the appropriate \alias
+entries, and all their arguments documented.
+The \usage entries must correspond to syntactically valid R code.
+See chapter ‘Writing R documentation files’ in the ‘Writing R
+Extensions’ manual.
 * checking Rd contents ... OK
 * checking for unstated dependencies in examples ... OK
 * checking contents of ‘data’ directory ... OK
 * checking data for non-ASCII characters ... OK
+* checking LazyData ... OK
 * checking data for ASCII and uncompressed saves ... OK
 * checking installed files from ‘inst/doc’ ... OK
 * checking files in ‘vignettes’ ... OK
-* checking examples ... OK
+* checking examples ... ERROR
+Running examples in ‘mkin-Ex.R’ failed
+The error most likely occurred in:
+
+> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
+> ### Name: nlmixr.mmkin
+> ### Title: Fit nonlinear mixed models using nlmixr
+> ### Aliases: nlmixr.mmkin print.nlmixr.mmkin nlmixr_model nlmixr_data
+> 
+> ### ** Examples
+> 
+> ds <- lapply(experimental_data_for_UBA_2019[6:10],
++  function(x) subset(x$data[c("name", "time", "value")]))
+> names(ds) <- paste("Dataset", 6:10)
+> f_mmkin_parent <- mmkin(c("SFO", "FOMC", "DFOP", "HS"), ds, quiet = TRUE, cores = 1)
+> f_mmkin_parent_tc <- mmkin(c("SFO", "FOMC", "DFOP"), ds, error_model = "tc", 
++   cores = 1, quiet = TRUE)
+> 
+> f_nlmixr_sfo_saem <- nlmixr(f_mmkin_parent["SFO", ], est = "saem")
+Error in nlmixr(f_mmkin_parent["SFO", ], est = "saem") : 
+  could not find function "nlmixr"
+Execution halted
 * checking for unstated dependencies in ‘tests’ ... OK
 * checking tests ... SKIPPED
 * checking for unstated dependencies in vignettes ... OK
@@ -72,9 +113,8 @@ Unknown, possibly mis-spelled, fields in DESCRIPTION:
 * checking for detritus in the temp directory ... OK
 * DONE
 
-Status: 1 NOTE
+Status: 1 ERROR, 2 WARNINGs, 1 NOTE
 See
   ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’
 for details.
 
-