documentation details

.Rbuildignore

@@ -52,6 +52,8 @@ LINK.LNK
 ^inst/examples/nonmem/.*\.msf
 ^inst/examples/simulations/.+
 ^inst/examples/R/NMexec_run_estimates.R
+;; so far, there is nothing of real value here
+^inst/examples/R/*
 ^vignettes$
 .*_dir.*
 ^R/NMwritePreamble.R

DESCRIPTION

@@ -12,7 +12,7 @@ Roxygen: list(roclets=c("collate", "namespace", "rd", "vignette"))
 Depends: R (>= 3.5.0)
 Imports:
   data.table,
-  NMdata (>= 0.1.5),
+  NMdata (>= 0.1.6),
   R.utils,
   MASS,
   fst,

NEWS.md

@@ -3,27 +3,29 @@
 ## New features
 
 * `NMsim()`
-- New simulation method `NMsim_NWPRI()` to simulate with parameter
+
+  - New simulation method `NMsim_NWPRI()` to simulate with parameter
   uncertainty. This automates simulation with parameter uncertainty
   using Nonmem's `NWPRI` subroutine for models with a successful
-  covariance step. For now this method only works for `THETA` since 
-  we have found that the parameter distributions sampled for 
-  `OMEGA` and `SIGMA` do not always match the model estimates and 
-  therefore cannot be trusted. To ensure that only `THETA` are 
-  sampled and simulated, this method should only be run using the
-  `typical=TRUE` argument. This method is much faster
-  than the existing methods in NMsim for simulation with parameter
-  uncertainty (`NMsim_VarCov()`). This method depends on `NMdata` 
-  version 0.1.7 or greater. Big thanks to Brian Reilly for his
-  excellent work on this important contribution.
-
-* The `add()` function to be used in `NMsim()`'s `modify.model`
+  covariance step. For now this method only works for `THETA` since we
+  have found that the parameter distributions sampled for `OMEGA` and
+  `SIGMA` do not always match the model estimates and therefore cannot
+  be trusted. To ensure that only `THETA` are sampled and simulated,
+  this method should only be run using the `typical=TRUE`
+  argument. This method is much faster than the existing methods in
+  NMsim for simulation with parameter uncertainty
+  (`NMsim_VarCov()`). This method depends on `NMdata` version 0.1.7 or
+  greater. Big thanks to Brian Reilly for his excellent work on this
+  important contribution.
+
+  - The `add()` function to be used in `NMsim()`'s `modify.model`
   argument now supports prepending and appending of text lines to
   control stream sections. The default is still to append and
   `add("text",.pos="top")` will now prepend "text".
 
 * `NMexec()` 
-- A "cleaning" feature has been added to `NMexec()`, removing some of
+
+  - A "cleaning" feature has been added to `NMexec()`, removing some of
   the temporary files generated by Nonmem after ended execution. The
   interface is inspired by PSN's `clean` argument supporting values 0
   (no cleaning), 1-4 (quite some cleaning - so far no difference
@@ -32,13 +34,13 @@
   execute passing on the `clean` value.
 
 
-- Default number of cores to be used by `NMexec()` can be controlled
+  - Default number of cores to be used by `NMexec()` can be controlled
   using `NMdataConf(nc=N)` where `N` is the desired default. Notice,
   `NMsim()` will not use this default. This is because
   parallellization is not as commonly used in simulation as in
   estimation.
 
-- A useful backup feature has been added. Before execution, any
+  - A useful backup feature has been added. Before execution, any
   existing results files related to a model are by default moved to a
   backup folder. The backup files are not