From 5c554944feec54d322f95835618b3cbff0caff81 Mon Sep 17 00:00:00 2001
From: Philip Delff <philip@delff.dk>
Date: Mon, 26 Aug 2024 11:35:24 -0400
Subject: [PATCH] documentation details

---
 .Rbuildignore         |  2 ++
 DESCRIPTION           |  2 +-
 NEWS.md               | 34 ++++++++++++++++++----------------
 man/prettyMatLines.Rd | 24 ++++++++++++++++++++++++
 4 files changed, 45 insertions(+), 17 deletions(-)
 create mode 100644 man/prettyMatLines.Rd

diff --git a/.Rbuildignore b/.Rbuildignore
index 35b2666a..601b31ae 100644
--- a/.Rbuildignore
+++ b/.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
diff --git a/DESCRIPTION b/DESCRIPTION
index c2e121f0..00664c97 100644
--- a/DESCRIPTION
+++ b/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,
diff --git a/NEWS.md b/NEWS.md
index 9f9f673a..e5d54d8c 100644
--- a/NEWS.md
+++ b/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 
 
diff --git a/man/prettyMatLines.Rd b/man/prettyMatLines.Rd
new file mode 100644
index 00000000..1e87950e
--- /dev/null
+++ b/man/prettyMatLines.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prettyMatLines.R
+\name{prettyMatLines}
+\alias{prettyMatLines}
+\title{Print OMEGA and SIGMA matrices for NONMEM sections in block format.
+Note: This function currently only works with fixed blocks as in 
+      the NMsim_NWPRI functionality for printing $THETAPV.}
+\usage{
+prettyMatLines(block_mat_string)
+}
+\arguments{
+\item{block_mat_string}{Output of NMsim::NMcreateMatLines. This is a string of
+OMEGA/SIGMA estimates that will be wrapped onto multiple lines for ease of
+reading in NONMEM control streams.}
+}
+\value{
+Character vector
+}
+\description{
+Print OMEGA and SIGMA matrices for NONMEM sections in block format.
+Note: This function currently only works with fixed blocks as in 
+      the NMsim_NWPRI functionality for printing $THETAPV.
+}
+\keyword{internal}