From 96e54339157a0758726f5a6836dc394b73affefb Mon Sep 17 00:00:00 2001
From: "Matthew L. Fidler" <matthew.fidler@gmail.com>
Date: Tue, 28 Nov 2023 20:37:38 -0600
Subject: [PATCH] Grab missing 1.2.10 release and add 1.2.11 info & fix man

---
 DESCRIPTION              |  2 +-
 NEWS.md                  | 13 ++++--
 R/ggPMX-options.R        |  2 +-
 R/plot-density.R         | 24 +++++-----
 R/plot-distribution.R    | 22 ++++-----
 R/plot-eta-cov.R         |  6 +--
 R/plot-qq.R              | 12 ++---
 R/plot-residual.R        | 14 +++---
 R/plot-vpc.R             | 44 +++++++++---------
 R/pmx_read_nm_model.R    | 98 ++++++++++++++++++++--------------------
 R/read_extfile.R         | 74 ++++++++++++++----------------
 man/distrib.Rd           | 18 ++++----
 man/eta_cov.Rd           |  6 +--
 man/pmxOptions.Rd        |  2 +-
 man/pmx_dens.Rd          | 24 +++++-----
 man/pmx_qq.Rd            | 12 ++---
 man/pmx_read_nm_model.Rd | 18 ++++----
 man/pmx_vpc_ci.Rd        | 16 +++----
 man/pmx_vpc_pi.Rd        | 28 ++++++------
 man/read_extfile.Rd      |  6 +--
 man/residual.Rd          | 14 +++---
 21 files changed, 228 insertions(+), 227 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 52f8ff8e..629028f4 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -11,7 +11,7 @@ Description: At Novartis, we aimed at standardizing the set of diagnostic plots
     <https://monolix.lixoft.com/monolix-api/lixoftconnectors_installation/>.
     When 'lixoftConnectors' is available, 'R' can use 'Monolix' directly to create the required
     Chart Data instead of exporting it from the 'Monolix' gui.
-Version: 1.2.10
+Version: 1.2.11
 Authors@R: c(
               person("Amine", "Gassem", email="contact@ag-study.com", role=c("aut")),
               person("Bruno", "Bieth", email="biethb@hotmail.com", role="aut"),
diff --git a/NEWS.md b/NEWS.md
index 93e03c13..3fd82a4d 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,11 +1,16 @@
-# ggPMX 1.2.10
+# ggPMX 1.2.11
 
-- Fix bug so that reading monolix works on R devel (as requested by CRAN)
+* Fix bug so that reading monolix works on R devel (as requested by CRAN)
 
-- Change defaults so that scientific notation is not enabled by default
+* Change defaults so that scientific notation is not enabled by default
   and title is also not added by default
 
-- Monolix 2023 can now be read by ggPMX
+* Monolix 2023 can now be read by ggPMX
+
+# ggPMX 1.2.10
+
+* Skip draft parameter template creation test on CRAN, on some systems
+  it doesn't seem to work correctly.
 
 # ggPMX 1.2.9
 
diff --git a/R/ggPMX-options.R b/R/ggPMX-options.R
index c3e2eb89..5c561103 100755
--- a/R/ggPMX-options.R
+++ b/R/ggPMX-options.R
@@ -56,7 +56,7 @@ getPmxOption <- function(name, default = NULL) {
 #' @section Options used in ggPMX:
 #'
 #' \itemize{
-#' \item {\strong{template_dir:}} {path to template directory}
+#' \item \strong{template_dir:} path to template directory
 #' }
 #'
 #' @examples
diff --git a/R/plot-density.R b/R/plot-density.R
index a7a6fbc9..487305e8 100644
--- a/R/plot-density.R
+++ b/R/plot-density.R
@@ -19,30 +19,30 @@
 #'
 #' \strong{labels} is a list that contains:
 #' \itemize{
-#' \item {\strong{title:}} {plot title default  "IWRES density plot"}
-#' \item {\strong{x:}} {x axis label default to "Etas"}
-#' \item {\strong{y:}} {y axis label default to empty}
+#' \item \strong{title:} plot title default  "IWRES density plot"
+#' \item \strong{x:} x axis label default to "Etas"
+#' \item \strong{y:} y axis label default to empty
 #' }
 #'
 #' \strong{var_line} is a list that contains:
 #' \itemize{
-#' \item {\strong{linetype:}} {default to 1}
-#' \item {\strong{color:}} {default to black}
-#' \item {\strong{linewidth:}} {default to 1}
+#' \item \strong{linetype:} default to 1
+#' \item \strong{color:} default to black
+#' \item \strong{linewidth:} default to 1
 #' }
 #'
 #' \strong{snd_line} is a list that contains:
 #' \itemize{
-#' \item {\strong{linetype:}} {default to 2}
-#' \item {\strong{color:}} {default to black}
-#' \item {\strong{linewidth:}} {default to 1}
+#' \item \strong{linetype:} default to 2
+#' \item \strong{color:} default to black
+#' \item \strong{linewidth:} default to 1
 #' }
 #'
 #' \strong{vline} is a list that contains:
 #' \itemize{
-#' \item {\strong{linetype:}} {default to 3}
-#' \item {\strong{color:}} {default to black}
-#' \item {\strong{linewidth:}} {default to 1}
+#' \item \strong{linetype:} default to 3
+#' \item \strong{color:} default to black
+#' \item \strong{linewidth:} default to 1
 #' }
 #'
 pmx_dens <- function(
diff --git a/R/plot-distribution.R b/R/plot-distribution.R
index 51b2e7af..df2b40de 100755
--- a/R/plot-distribution.R
+++ b/R/plot-distribution.R
@@ -19,18 +19,18 @@
 #'
 #' \strong{labels} is a list that contains:
 #' \itemize{
-#' \item {\strong{title:}} {plot title default "EBE distribution"}
-#' \item {\strong{subtitle:}} {plot subtitle default empty}
-#' \item {\strong{x:}} {x axis label default to "Etas"}
-#' \item {\strong{y:}} {y axis label default to empty}
-#' \item {\strong{legend:}} {legend title default to "random Effect"}
+#' \item \strong{title:} plot title default "EBE distribution"
+#' \item \strong{subtitle:} plot subtitle default empty
+#' \item \strong{x:} x axis label default to "Etas"
+#' \item \strong{y:} y axis label default to empty
+#' \item \strong{legend:} legend title default to "random Effect"
 #' }
 #' \strong{shrink} is a list that contains:
 #' \itemize{
-#' \item {\strong{fun:}} {shrinkage function can be \code{sd} or \code{var}}
-#' \item {\strong{size:}} {shrinkage text size}
-#' \item {\strong{color:}} {shrinkage text color}
-#' \item {\strong{vjust:}} {shrinkage position vertical adjustment}
+#' \item \strong{fun:} shrinkage function can be \code{sd} or \code{var}
+#' \item \strong{size:} shrinkage text size
+#' \item \strong{color:} shrinkage text color
+#' \item \strong{vjust:} shrinkage position vertical adjustment
 #' }
 distrib <- function(
                     labels,
@@ -109,11 +109,11 @@ wrap_formula <- function(x, origin = "lfacet") {
 }
 
 jitter_layer <- function(jitter, strat.color) {
-  
+
   if (is.null(jitter)){
     stop("jitter cannot be null")
   }
-  
+
   if (is.null(strat.color)) {
     jitter$height <- 0 #no jitter in height (y-axis required)
     do.call(geom_jitter, jitter)
diff --git a/R/plot-eta-cov.R b/R/plot-eta-cov.R
index 9b006e80..8d8b3601 100644
--- a/R/plot-eta-cov.R
+++ b/R/plot-eta-cov.R
@@ -50,9 +50,9 @@ is_pmxcov <- function(x)
 #'
 #' \strong{labels} is a list that contains:
 #' \itemize{
-#' \item {\strong{title:}} {plot title default  "EBE vs. covariates"}
-#' \item {\strong{x:}} {x axis label default to "Etas"}
-#' \item {\strong{y:}} {y axis label default to empty}
+#' \item \strong{title:} plot title default  "EBE vs. covariates"
+#' \item \strong{x:} x axis label default to "Etas"
+#' \item \strong{y:} y axis label default to empty
 #' }
 eta_cov <- function(
                     labels,
diff --git a/R/plot-qq.R b/R/plot-qq.R
index 6e608247..516bc752 100644
--- a/R/plot-qq.R
+++ b/R/plot-qq.R
@@ -42,16 +42,16 @@ pmx_qq_stats <- function(points) {
 #'
 #' \strong{labels} is a list that contains:
 #' \itemize{
-#' \item {\strong{title:}} {plot title default  "EBE vs. covariates"}
-#' \item {\strong{x:}} {x axis label default to "Etas"}
-#' \item {\strong{y:}} {y axis label default to empty}
+#' \item \strong{title:} plot title default  "EBE vs. covariates"
+#' \item \strong{x:} x axis label default to "Etas"
+#' \item \strong{y:} y axis label default to empty
 #' }
 #'
 #' \strong{point} is a list that contains:
 #' \itemize{
-#' \item {\strong{shape:}} {default to 1}
-#' \item {\strong{color:}} {default to black}
-#' \item {\strong{size:}} {default to 1}
+#' \item \strong{shape:} default to 1
+#' \item \strong{color:} default to black
+#' \item \strong{size:} default to 1
 #' }
 #' @param is.hline logical if TRUE add horizontal line y=0 ( TRUE by default)
 #' @param hline geom hline graphical parameters
diff --git a/R/plot-residual.R b/R/plot-residual.R
index aa68c101..133f004e 100755
--- a/R/plot-residual.R
+++ b/R/plot-residual.R
@@ -20,17 +20,17 @@
 #'
 #' \strong{point} is a list that contains:
 #' \itemize{
-#' \item {\strong{shape:}} {default to 1}
-#' \item {\strong{color:}} {default to black}
-#' \item {\strong{size:}} {default to 1}
+#' \item \strong{shape:} default to 1
+#' \item \strong{color:} default to black
+#' \item \strong{size:} default to 1
 #' }
 #'
 #' \strong{labels} is a list that contains:
 #' \itemize{
-#' \item {\strong{title:}} {plot title default to AES_X versus AES_Y}
-#' \item {\strong{subtitle:}} {plot subtitle default empty}
-#' \item {\strong{x:}} {x axis label default to AES_X}
-#' \item {\strong{y:}} {y axis label default to AES_Y}
+#' \item \strong{title:} plot title default to AES_X versus AES_Y
+#' \item \strong{subtitle:} plot subtitle default empty
+#' \item \strong{x:} x axis label default to AES_X
+#' \item \strong{y:} y axis label default to AES_Y
 #' }
 residual <- function(x, y, labels = NULL, point = NULL, is.hline = FALSE,
                      hline = NULL, dname = NULL, facets = NULL, bloq = NULL,
diff --git a/R/plot-vpc.R b/R/plot-vpc.R
index 5dedbbfc..0c804771 100644
--- a/R/plot-vpc.R
+++ b/R/plot-vpc.R
@@ -65,10 +65,10 @@ pmx_vpc_obs <-
 #'
 #' @param show  \code{charcater} how lines are displayed:
 #' \itemize{
-#' \item {\strong{show=all}} {lines will be displayed for each of
-#' the 3 percentiles. with a shaded area.}
-#' \item {\strong{show=median}} {Show only median line.}
-#' \item {\strong{show=area}} {Show only median line and the shaded area}
+#' \item \strong{show=all} lines will be displayed for each of
+#' the 3 percentiles. with a shaded area.
+#' \item \strong{show=median} Show only median line.
+#' \item \strong{show=area} Show only median line and the shaded area
 
 #' }
 
@@ -76,23 +76,23 @@ pmx_vpc_obs <-
 #' to \code{c(.05,.95)}
 #' @param median \code{list} containing: \cr
 #' \itemize{
-#' \item {\strong{color}} {\code{charcater}  Color of the median percentile line. Default: "#000000". }
-#' \item {\strong{linewidth}} {\code{numeric}  Thickness of the median percentile line. Default: 1.}
-#' \item {\strong{alpha}} {\code{numeric} Transparency of the median percentile line. Default: 0.7.}
-#' \item {\strong{linetype}} {\code{charcater} Linetype of the median percentile line. Default: "solid".}
+#' \item \strong{color} \code{charcater}  Color of the median percentile line. Default: "#000000".
+#' \item \strong{linewidth} \code{numeric}  Thickness of the median percentile line. Default: 1.
+#' \item \strong{alpha} \code{numeric} Transparency of the median percentile line. Default: 0.7.
+#' \item \strong{linetype} \code{charcater} Linetype of the median percentile line. Default: "solid".
 #' }
 
 #' @param extreme \code{list} containing: \cr
 #' \itemize{
-#' \item {\strong{color}} {\code{charcater} Color of the median percentile line. Default: "#000000". }
-#' \item {\strong{linewidth}} {\code{numeric} Thickness of the median percentile line. Default: 1.}
-#' \item {\strong{alpha}} {\code{numeric} Transparency of the median percentile line. Default: 0.7.}
-#' \item {\strong{linetype}} {\code{charcater} Linetype of the median percentile line. Default: "solid"}
+#' \item \strong{color} \code{charcater} Color of the median percentile line. Default: "#000000".
+#' \item \strong{linewidth} \code{numeric} Thickness of the median percentile line. Default: 1.
+#' \item \strong{alpha} \code{numeric} Transparency of the median percentile line. Default: 0.7.
+#' \item \strong{linetype} \code{charcater} Linetype of the median percentile line. Default: "solid"
 #' }
 #' @param area \code{list} containing: \cr
 #' \itemize{
-#' \item {\strong{fill}} {\code{charcater}  Color of the shaded area. Default: "blue". }
-#' \item {\strong{alpha}} {\code{numeric} Transparency of the sahded area. Default: 0.1.}
+#' \item \strong{fill} \code{charcater}  Color of the shaded area. Default: "blue".
+#' \item \strong{alpha} \code{numeric} Transparency of the sahded area. Default: 0.1.
 #' }
 #'
 #' @family vpc
@@ -142,27 +142,27 @@ pmx_vpc_pi <-
 
 #' @param show  \code{charcater} how areas are displayed:
 #' \itemize{
-#' \item {\strong{show="all"}} {areas will be displayed for each of the 3 percentiles. }
-#' \item {\strong{show="median"}} {Show only median area.}
+#' \item \strong{show="all"} areas will be displayed for each of the 3 percentiles.
+#' \item \strong{show="median"} Show only median area.
 #' }
 
 #' @param interval \code{numeric} quantiles values default to \code{c(.05,.95)}
 #' @param method \code{charcater} which areas are displayed:
 #' \itemize{
-#' \item {\strong{method="ribbon"}} {areas are ribbons.}
-#' \item {\strong{method="rectangle"}} {ares are horizontal rectangles.}
+#' \item \strong{method="ribbon"} areas are ribbons.
+#' \item \strong{method="rectangle"} areas are horizontal rectangles.
 #' }
 
 #' @param median \code{list} containing: \cr
 #' \itemize{
-#' \item {\strong{fill}} { \code{character} Color of the area representing the CI for the median. Default: "#3388cc".}
-#' \item {\strong{alpha}} {\code{numeric} Transparency of the area representing the PI for the median. Default=0.3.}
+#' \item \strong{fill}  \code{character} Color of the area representing the CI for the median. Default: "#3388cc".
+#' \item \strong{alpha} \code{numeric} Transparency of the area representing the PI for the median. Default=0.3.
 #' }
 
 #' @param extreme \code{list} containing: \cr
 #' \itemize{
-#' \item {\strong{fill}} {\code{character} Color of the area representing the CI for the extreme percentiles. Default: "#3388cc".}
-#' \item {\strong{alpha}} {\code{numeric} Transparency of the area representing the PI for the extreme percentiles. Default=0.3.}
+#' \item \strong{fill} \code{character} Color of the area representing the CI for the extreme percentiles. Default: "#3388cc".
+#' \item \strong{alpha} \code{numeric} Transparency of the area representing the PI for the extreme percentiles. Default=0.3.
 #' }
 #'
 #' @export
diff --git a/R/pmx_read_nm_model.R b/R/pmx_read_nm_model.R
index bd1d3b8b..0e182535 100644
--- a/R/pmx_read_nm_model.R
+++ b/R/pmx_read_nm_model.R
@@ -2,48 +2,48 @@
 #' NONMEM model file parser
 #'
 #' @description Parse NONMEM model files in R format
-#' 
+#'
 #' @seealso \code{\link{pmx_read_nm_tables}}
-#' @return A \code{\link[dplyr]{tibble}} of class \code{model} containing the following columns: 
+#' @return A \code{\link[dplyr]{tibble}} of class \code{model} containing the following columns:
 #' \itemize{
-#'  \item{\strong{problem}}{: a numeric identifier for the $PROBLEM associated with the code.}
-#'  \item{\strong{level}}{: a unique numeric identifier to each subroutine block associated with the code.}
-#'  \item{\strong{subroutine}}{: a character identifier named after the 3 first letters of the subroutine name e.g. '$THETA' and 
-#'  '$TABLE' will become 'the' and 'tab' respectively. In addition all output from the .lst is labeled 'lst', the general nonmem 
-#'  output e.g. NM-TRAN messages are labelled 'oth'. With priors thp, tpv, omp, opd, sip, spd abbreviations are given to the THETAP, 
-#'  THETAPV, OMEGAP, etc.}
-#'  \item{\strong{code}}{: the code without comments or subroutine names e.g. '$THETA 0.5 ; TVCL' will return '0.5'.}
-#'  \item{\strong{comment}}{: the last comment of a record e.g. '0.5 ; Clearance (L/h) ; TVCL' will return 'TVCL'.}
+#'  \item \strong{problem}: a numeric identifier for the $PROBLEM associated with the code.
+#'  \item \strong{level}: a unique numeric identifier to each subroutine block associated with the code.
+#'  \item \strong{subroutine}: a character identifier named after the 3 first letters of the subroutine name e.g. '$THETA' and
+#'  '$TABLE' will become 'the' and 'tab' respectively. In addition all output from the .lst is labeled 'lst', the general nonmem
+#'  output e.g. NM-TRAN messages are labelled 'oth'. With priors thp, tpv, omp, opd, sip, spd abbreviations are given to the THETAP,
+#'  THETAPV, OMEGAP, etc.
+#'  \item \strong{code}: the code without comments or subroutine names e.g. '$THETA 0.5 ; TVCL' will return '0.5'.
+#'  \item \strong{comment}: the last comment of a record e.g. '0.5 ; Clearance (L/h) ; TVCL' will return 'TVCL'.
 #' }
-#' 
+#'
 #' @param runno run number which is used for generating the model file name
 #' @param prefix Prefix to be used to generate model file name. Used in combination with \code{runno} and \code{ext}.
 #' @param ext Extension to be used to generate model file name. Should be one of'.lst' (default), '.out', '.res', '.mod' or '.ctl' for NONMEM.
 #' @param file A character vector of path to the files or a \code{nm_table_list} object created with \code{list_nm_tables}.
 #' @param dir directory of the model files.
-#' 
+#'
 #' @examples
 #' \dontrun{
 #' # Using the `file` argument to import a model file:
 #' nm_model <- pmx_read_nm_model(file = 'run001.lst', dir = 'models')
-#' 
+#'
 #' # Using the `runno` argument to import a model file:
 #' nm_model <- pmx_read_nm_model(runno = '001', ext = '.lst', dir = 'models')
 #' }
-#' 
+#'
 
 pmx_read_nm_model <- function(runno   = NULL,
                           prefix  = 'run',
                           ext     = '.lst',
                           file    = NULL,
                           dir     = NULL) {
-  
+
   . <- NULL
-  
+
   if (is.null(runno) && is.null(file)) {
     stop('Argument `runno` or `file` required.', call. = FALSE)
   }
-  
+
   if (!is.null(runno)) {
     ext       <- pmx_make_extension(ext)
     full_path <- pmx_file_path(dir, stringr::str_c(prefix, runno, ext))
@@ -51,92 +51,92 @@ pmx_read_nm_model <- function(runno   = NULL,
     ext       <- pmx_get_extension(file)
     full_path <- pmx_file_path(dir, file)
   }
-  
+
   if (!ext %in% c('.lst', '.out', '.res', '.mod', '.ctl')) {
-    stop('NONMEM model file extension should be one lst, out, res, mod or ctl.', call. = FALSE) 
+    stop('NONMEM model file extension should be one lst, out, res, mod or ctl.', call. = FALSE)
   }
-  
-  if (!file.exists(full_path)) { 
-    stop('Model file ', basename(full_path), ' not found.', call. = FALSE) 
+
+  if (!file.exists(full_path)) {
+    stop('Model file ', basename(full_path), ' not found.', call. = FALSE)
   }
-  
+
   model <- readr::read_lines(full_path)
-  
+
   if (!any(stringr::str_detect(model, '^\\s*\\$PROB.+')) && ext %in% c('.lst', '.out', '.res')) {
     # Attempts to recover the model code from model file rather than in the nonmem output file
     full_path <- pmx_update_extension(full_path, c('.mod', '.ctl'))
     full_path <- full_path[file.exists(full_path)]
-    
+
     if (any(file.exists(full_path))) {
-      warning(c('No model code found in `', ext, '` NONMEM output file importing `', 
+      warning(c('No model code found in `', ext, '` NONMEM output file importing `',
                 pmx_get_extension(full_path)[1], '` instead.'), call. = FALSE)
       model <- readr::read_lines(full_path[1])
     }
   }
-  
+
   # Return error if input is bad
   if (!any(stringr::str_detect(model, '^\\s*\\$PROB.+'))) {
     stop(basename(full_path), ' is not a NONMEM model.', call. = FALSE)
   }
-  
-  model <- dplyr::tibble(code = model) %>% 
-    dplyr::filter(!stringr::str_detect(.$code, '^;[^;]*$|^$')) %>% 
-    dplyr::mutate(code = stringr::str_replace_all(.$code, '\\t+|\\s{2,}', ' ')) %>% 
+
+  model <- dplyr::tibble(code = model) %>%
+    dplyr::filter(!stringr::str_detect(.$code, '^;[^;]*$|^$')) %>%
+    dplyr::mutate(code = stringr::str_replace_all(.$code, '\\t+|\\s{2,}', ' ')) %>%
     dplyr::mutate(
       problem     = findInterval(seq_along(.$code), which(stringr::str_detect(.$code, '^\\s*\\$PROB.+'))),
       level       = findInterval(seq_along(.$code), which(stringr::str_detect(.$code, '^\\s*\\$.+'))),
-      subroutine  = stringr::str_match(.$code, '^\\s*\\$(\\w+)')[, 2]) %>% 
+      subroutine  = stringr::str_match(.$code, '^\\s*\\$(\\w+)')[, 2]) %>%
     tidyr::fill(dplyr::one_of('subroutine'))
-  
+
   # Generate abbreviated subroutine names
   special <- c('THETAI', 'THETAR', 'THETAP', 'THETAPV', 'OMEGAP', 'OMEGAPD', 'SIGMAP', 'SIGMAPD')
   match_special <- match(model$subroutine[model$subroutine %in% special], special)
-  model$subroutine[model$subroutine %in% special] <- c('thi', 'thr', 'thp', 'tpv', 
+  model$subroutine[model$subroutine %in% special] <- c('thi', 'thr', 'thp', 'tpv',
                                                        'omp', 'opd', 'sip', 'spd')[match_special]
   model$subroutine <- stringr::str_extract(tolower(model$subroutine), '[a-z]{1,3}')
-  
+
   # Format lst part
   if (any(stringr::str_detect(model$code, 'NM-TRAN MESSAGES'))) {
     lst_rows <- which(stringr::str_detect(model$code, 'NM-TRAN MESSAGES')):nrow(model)
-    model[lst_rows,] <- model %>% 
-      dplyr::slice(lst_rows) %>% 
-      dplyr::mutate(problem = findInterval(seq_along(.$problem), 
-                                           which(stringr::str_detect(.$code, '^\\s*PROBLEM NO\\.:\\s*\\d+$')))) %>% 
+    model[lst_rows,] <- model %>%
+      dplyr::slice(lst_rows) %>%
+      dplyr::mutate(problem = findInterval(seq_along(.$problem),
+                                           which(stringr::str_detect(.$code, '^\\s*PROBLEM NO\\.:\\s*\\d+$')))) %>%
       dplyr::mutate(level = 1 + .$level[1] + .$problem,
                     subroutine = 'lst')
   }
-  
+
   # Handle other special cases
   if (any(stringr::str_detect(model$code, '#CPUT'))) {
     cput_row <- which(stringr::str_detect(model$code, '#CPUT'))
     model[cput_row, 'problem'] <- 0
     model[cput_row:nrow(model), 'level'] <- model[cput_row:nrow(model), ]$level + 1
   }
-  
+
   if (any(stringr::str_detect(model$code, 'Stop Time'))) {
     end_rows <- which(stringr::str_detect(model$code, 'Stop Time')):nrow(model)
     model[end_rows, 'problem'] <- 0
     model[end_rows, 'level'] <- model[end_rows[1], ]$level + 1
   }
-  
+
   model[is.na(model$subroutine) | (model$problem == 0 & model$subroutine == 'lst'), 'subroutine'] <- 'oth'
-  
+
   # Remove subroutine names from the code
   model$code <- stringr::str_replace(model$code, '^\\s*\\$\\w+\\s*', '')
-  
+
   # Remove empty rows but $PROBLEM
   model <- model[!stringr::str_detect(model$code, '^(\\s|\\t)*$') | model$subroutine == 'pro', ]
-  
+
   # Create comment column
   code_rows <- !model$subroutine %in% c('lst', 'oth') | model$level == 0
   model[code_rows, 'comment'] <- stringr::str_match(model[code_rows, ]$code, ';\\s*(.*)\\s*$')[, 2]
   model[code_rows, 'code'] <- stringr::str_replace(model[code_rows, ]$code, '\\s*;.*$', '')
-  
+
   # Remove na values and output
-  tidyr::replace_na(model, replace = list(code = '', comment = '')) %>% 
-    dplyr::select(dplyr::one_of(c('problem', 'level', 'subroutine', 'code', 'comment'))) %>% 
+  tidyr::replace_na(model, replace = list(code = '', comment = '')) %>%
+    dplyr::select(dplyr::one_of(c('problem', 'level', 'subroutine', 'code', 'comment'))) %>%
     dplyr::mutate(problem = as.integer(.$problem),
-                  level   = as.integer(.$level)) %>% 
+                  level   = as.integer(.$level)) %>%
     structure(file     = basename(full_path),
               dir      = dirname(full_path),
               software = 'nonmem',
diff --git a/R/read_extfile.R b/R/read_extfile.R
index adcbf59e..88e15e2d 100755
--- a/R/read_extfile.R
+++ b/R/read_extfile.R
@@ -1,4 +1,3 @@
-# This code is strongly based on the read_nmext function of mrgsolve (nmxml.R) (Thanks to Kyle T Baron)
 
 
 #' Reads .ext files generated by NONMEM
@@ -9,7 +8,7 @@
 #' @param path path full path and file name for `ext` file
 #' @param read_fun read_fun function to read the `ext` file
 #' @param quiet Logical, if \code{FALSE} messages are printed to the console.
-#' 
+#'
 #' @author This function is based on read_nmext from mrgsolve, Original Author: Kyle T Baron.
 #' This function has some changes to the original code:
 #'Addition of param, "quiet", (option of pmx_msg function, from xpose package) (Line: 27)
@@ -17,41 +16,41 @@
 #'The output was also slightly adjusted to fit ggPMX output (df and df2) (Line: 105,106)
 #'as_bmat was replaced by bmat_like to create the diagonal matrix (Line 116:142)
 #'
-#' @return A list with param, omega, and sigma in a format 
-#' ready to be used. 
+#' @return A list with param, omega, and sigma in a format
+#' ready to be used.
 
 #' @export
 #'
 #' @examples
-#' #project <- system.file("nonmem", package = "mrgsolve") 
-#' #est <- read_nmext(1005, project = project) 
+#' #project <- system.file("nonmem", package = "mrgsolve")
+#' #est <- read_nmext(1005, project = project)
 
-read_extfile <- function(run=NA_real_, project = getwd(), file=paste0(run,".ext"), 
+read_extfile <- function(run=NA_real_, project = getwd(), file=paste0(run,".ext"),
                        path=NULL, read_fun = c("data.table","read.table"),quiet) {
-  
+
   if(is.character(path)) {
-    extfile <- path  
+    extfile <- path
   } else {
     extfile <- file.path(project,run,file)
   }
-  
+
   if(!file.exists(extfile)) {
-    stop("[read_nmext] could not find the requested 'ext' file ", 
+    stop("[read_nmext] could not find the requested 'ext' file ",
          shQuote(basename(extfile)))
   }
-  
+
   read_fun <- match.arg(read_fun)
-  
+
   use_dt <- requireNamespace("data.table",quietly=TRUE) & read_fun=="data.table"
-  
+
   ## Check for multiple tables/problems
-  
+
   ext_tmp <- readLines(extfile)
   inds  <- grep("TABLE",ext_tmp)
   last_table <- 0
 
   ## Check if multiple Problems are found in .ext file
-  
+
   if (length(inds)!=1){
     last_table <- inds[length(inds)]
     colon <- regexpr(":",ext_tmp[last_table])[1]
@@ -59,13 +58,13 @@ read_extfile <- function(run=NA_real_, project = getwd(), file=paste0(run,".ext"
     last_table <- last_table-1
     pmx_msg(paste("Multiple Problems found in",file,"only using",last_table_name,"\n"),quiet) #multiple problems not currently supported, only using last table
   }
-  
+
   ## Read .ext file
-  
+
   if(use_dt) {
     df <- data.table::fread(
-      file=extfile, 
-      na.strings = '.', 
+      file=extfile,
+      na.strings = '.',
       data.table=FALSE,
       skip=last_table+1
     )
@@ -74,25 +73,25 @@ read_extfile <- function(run=NA_real_, project = getwd(), file=paste0(run,".ext"
       file=extfile,
       na.strings='.',
       stringsAsFactors=FALSE,
-      skip=last_table+1, 
+      skip=last_table+1,
       header=TRUE
     )
   }
-  
+
   ## Get parameters and standard errors
-  
+
   #get parameters
   ans <- ""
   ans <- df[df[["ITERATION"]] == -1E9,]
   bmat_ans <- ans #in order to use bmat_like function
   df_ans <- ans
-  
-  
+
+
   #get standard erros
   ans_se <- ""
   ans_se <- df[df[["ITERATION"]] == -1000000001,]
   df_ans_se <- ans_se
-  
+
   if(nrow(ans)==0) {
     stop(
       "[read_nmext] could not find final estimates",
@@ -102,18 +101,18 @@ read_extfile <- function(run=NA_real_, project = getwd(), file=paste0(run,".ext"
 
   #get numbers of "OMEGA" or "SIGMA" used in bmat_like
   get_num <- function(x,string){ #last_om = x
-    
+
     nums <- gsub(paste0(".*",string,"|[()]"), "", x)
-    
+
     num1 <- as.numeric(gsub(",.*", "", nums))
     num2 <- as.numeric(gsub(".*,", "", nums))
-    
+
     num_vec <- c(num1,num2)
-    
+
     return(num_vec)
-    
+
   }
-  
+
   #uses bmat_ans as an input and gives out diagonal matrix
   bmat_like <- function(x,string) {
     y <- x[grep(string,names(x))]
@@ -124,7 +123,7 @@ read_extfile <- function(run=NA_real_, project = getwd(), file=paste0(run,".ext"
     pre_mat <- matrix(nrow = num, ncol = num)
     mat <- pre_mat
     mat[] <- 0
-    
+
     i <- 1
     for (i in i:len_y) {
       om <- y[i]
@@ -132,15 +131,15 @@ read_extfile <- function(run=NA_real_, project = getwd(), file=paste0(run,".ext"
       pos <- get_num(nam_om,string)
       mat[pos[1],pos[2]] <- om[[1]]
     }
-    
+
     return(mat)
   }
-  
+
   ans <- as.list(ans)
   names(ans) <- gsub("[[:punct:]]", "", names(ans))
   ans <- list(
     param = ans[grepl("THETA", names(ans))],
-    omega = bmat_like(bmat_ans, "OMEGA"), 
+    omega = bmat_like(bmat_ans, "OMEGA"),
     sigma = bmat_like(bmat_ans, "SIGMA"),
     raw = ans,
     df = df_ans,
@@ -148,6 +147,3 @@ read_extfile <- function(run=NA_real_, project = getwd(), file=paste0(run,".ext"
   )
   return(ans)
 }
-
-
-
diff --git a/man/distrib.Rd b/man/distrib.Rd
index 5f171aa9..38bdd3e3 100644
--- a/man/distrib.Rd
+++ b/man/distrib.Rd
@@ -48,18 +48,18 @@ creates a graphic distribution object
 \details{
 \strong{labels} is a list that contains:
 \itemize{
-\item {\strong{title:}} {plot title default "EBE distribution"}
-\item {\strong{subtitle:}} {plot subtitle default empty}
-\item {\strong{x:}} {x axis label default to "Etas"}
-\item {\strong{y:}} {y axis label default to empty}
-\item {\strong{legend:}} {legend title default to "random Effect"}
+\item \strong{title:} plot title default "EBE distribution"
+\item \strong{subtitle:} plot subtitle default empty
+\item \strong{x:} x axis label default to "Etas"
+\item \strong{y:} y axis label default to empty
+\item \strong{legend:} legend title default to "random Effect"
 }
 \strong{shrink} is a list that contains:
 \itemize{
-\item {\strong{fun:}} {shrinkage function can be \code{sd} or \code{var}}
-\item {\strong{size:}} {shrinkage text size}
-\item {\strong{color:}} {shrinkage text color}
-\item {\strong{vjust:}} {shrinkage position vertical adjustment}
+\item \strong{fun:} shrinkage function can be \code{sd} or \code{var}
+\item \strong{size:} shrinkage text size
+\item \strong{color:} shrinkage text color
+\item \strong{vjust:} shrinkage position vertical adjustment
 }
 }
 \seealso{
diff --git a/man/eta_cov.Rd b/man/eta_cov.Rd
index eb32306f..c737262d 100644
--- a/man/eta_cov.Rd
+++ b/man/eta_cov.Rd
@@ -49,9 +49,9 @@ its shrinkage..
 \details{
 \strong{labels} is a list that contains:
 \itemize{
-\item {\strong{title:}} {plot title default  "EBE vs. covariates"}
-\item {\strong{x:}} {x axis label default to "Etas"}
-\item {\strong{y:}} {y axis label default to empty}
+\item \strong{title:} plot title default  "EBE vs. covariates"
+\item \strong{x:} x axis label default to "Etas"
+\item \strong{y:} y axis label default to empty
 }
 }
 \seealso{
diff --git a/man/pmxOptions.Rd b/man/pmxOptions.Rd
index 6b25af91..874d91de 100644
--- a/man/pmxOptions.Rd
+++ b/man/pmxOptions.Rd
@@ -21,7 +21,7 @@ There is a global option set, which is available by default.
 
 
 \itemize{
-\item {\strong{template_dir:}} {path to template directory}
+\item \strong{template_dir:} path to template directory
 }
 }
 
diff --git a/man/pmx_dens.Rd b/man/pmx_dens.Rd
index cb955ba5..844c3b1b 100644
--- a/man/pmx_dens.Rd
+++ b/man/pmx_dens.Rd
@@ -41,29 +41,29 @@ Creates a density plot object
 \details{
 \strong{labels} is a list that contains:
 \itemize{
-\item {\strong{title:}} {plot title default  "IWRES density plot"}
-\item {\strong{x:}} {x axis label default to "Etas"}
-\item {\strong{y:}} {y axis label default to empty}
+\item \strong{title:} plot title default  "IWRES density plot"
+\item \strong{x:} x axis label default to "Etas"
+\item \strong{y:} y axis label default to empty
 }
 
 \strong{var_line} is a list that contains:
 \itemize{
-\item {\strong{linetype:}} {default to 1}
-\item {\strong{color:}} {default to black}
-\item {\strong{linewidth:}} {default to 1}
+\item \strong{linetype:} default to 1
+\item \strong{color:} default to black
+\item \strong{linewidth:} default to 1
 }
 
 \strong{snd_line} is a list that contains:
 \itemize{
-\item {\strong{linetype:}} {default to 2}
-\item {\strong{color:}} {default to black}
-\item {\strong{linewidth:}} {default to 1}
+\item \strong{linetype:} default to 2
+\item \strong{color:} default to black
+\item \strong{linewidth:} default to 1
 }
 
 \strong{vline} is a list that contains:
 \itemize{
-\item {\strong{linetype:}} {default to 3}
-\item {\strong{color:}} {default to black}
-\item {\strong{linewidth:}} {default to 1}
+\item \strong{linetype:} default to 3
+\item \strong{color:} default to black
+\item \strong{linewidth:} default to 1
 }
 }
diff --git a/man/pmx_qq.Rd b/man/pmx_qq.Rd
index c4804b26..32464803 100644
--- a/man/pmx_qq.Rd
+++ b/man/pmx_qq.Rd
@@ -63,16 +63,16 @@ This function creates a qq plot object
 \details{
 \strong{labels} is a list that contains:
 \itemize{
-\item {\strong{title:}} {plot title default  "EBE vs. covariates"}
-\item {\strong{x:}} {x axis label default to "Etas"}
-\item {\strong{y:}} {y axis label default to empty}
+\item \strong{title:} plot title default  "EBE vs. covariates"
+\item \strong{x:} x axis label default to "Etas"
+\item \strong{y:} y axis label default to empty
 }
 
 \strong{point} is a list that contains:
 \itemize{
-\item {\strong{shape:}} {default to 1}
-\item {\strong{color:}} {default to black}
-\item {\strong{size:}} {default to 1}
+\item \strong{shape:} default to 1
+\item \strong{color:} default to black
+\item \strong{size:} default to 1
 }
 }
 \concept{qq_plot}
diff --git a/man/pmx_read_nm_model.Rd b/man/pmx_read_nm_model.Rd
index 75438afb..ac33cfb1 100644
--- a/man/pmx_read_nm_model.Rd
+++ b/man/pmx_read_nm_model.Rd
@@ -24,16 +24,16 @@ pmx_read_nm_model(
 \item{dir}{directory of the model files.}
 }
 \value{
-A \code{\link[dplyr]{tibble}} of class \code{model} containing the following columns: 
+A \code{\link[dplyr]{tibble}} of class \code{model} containing the following columns:
 \itemize{
- \item{\strong{problem}}{: a numeric identifier for the $PROBLEM associated with the code.}
- \item{\strong{level}}{: a unique numeric identifier to each subroutine block associated with the code.}
- \item{\strong{subroutine}}{: a character identifier named after the 3 first letters of the subroutine name e.g. '$THETA' and 
- '$TABLE' will become 'the' and 'tab' respectively. In addition all output from the .lst is labeled 'lst', the general nonmem 
- output e.g. NM-TRAN messages are labelled 'oth'. With priors thp, tpv, omp, opd, sip, spd abbreviations are given to the THETAP, 
- THETAPV, OMEGAP, etc.}
- \item{\strong{code}}{: the code without comments or subroutine names e.g. '$THETA 0.5 ; TVCL' will return '0.5'.}
- \item{\strong{comment}}{: the last comment of a record e.g. '0.5 ; Clearance (L/h) ; TVCL' will return 'TVCL'.}
+ \item \strong{problem}: a numeric identifier for the $PROBLEM associated with the code.
+ \item \strong{level}: a unique numeric identifier to each subroutine block associated with the code.
+ \item \strong{subroutine}: a character identifier named after the 3 first letters of the subroutine name e.g. '$THETA' and
+ '$TABLE' will become 'the' and 'tab' respectively. In addition all output from the .lst is labeled 'lst', the general nonmem
+ output e.g. NM-TRAN messages are labelled 'oth'. With priors thp, tpv, omp, opd, sip, spd abbreviations are given to the THETAP,
+ THETAPV, OMEGAP, etc.
+ \item \strong{code}: the code without comments or subroutine names e.g. '$THETA 0.5 ; TVCL' will return '0.5'.
+ \item \strong{comment}: the last comment of a record e.g. '0.5 ; Clearance (L/h) ; TVCL' will return 'TVCL'.
 }
 }
 \description{
diff --git a/man/pmx_vpc_ci.Rd b/man/pmx_vpc_ci.Rd
index 532d223f..58ff0377 100644
--- a/man/pmx_vpc_ci.Rd
+++ b/man/pmx_vpc_ci.Rd
@@ -15,28 +15,28 @@ pmx_vpc_ci(
 \arguments{
 \item{show}{\code{charcater} how areas are displayed:
 \itemize{
-\item {\strong{show="all"}} {areas will be displayed for each of the 3 percentiles. }
-\item {\strong{show="median"}} {Show only median area.}
+\item \strong{show="all"} areas will be displayed for each of the 3 percentiles.
+\item \strong{show="median"} Show only median area.
 }}
 
 \item{interval}{\code{numeric} quantiles values default to \code{c(.05,.95)}}
 
 \item{method}{\code{charcater} which areas are displayed:
 \itemize{
-\item {\strong{method="ribbon"}} {areas are ribbons.}
-\item {\strong{method="rectangle"}} {ares are horizontal rectangles.}
+\item \strong{method="ribbon"} areas are ribbons.
+\item \strong{method="rectangle"} areas are horizontal rectangles.
 }}
 
 \item{median}{\code{list} containing: \cr
 \itemize{
-\item {\strong{fill}} { \code{character} Color of the area representing the CI for the median. Default: "#3388cc".}
-\item {\strong{alpha}} {\code{numeric} Transparency of the area representing the PI for the median. Default=0.3.}
+\item \strong{fill}  \code{character} Color of the area representing the CI for the median. Default: "#3388cc".
+\item \strong{alpha} \code{numeric} Transparency of the area representing the PI for the median. Default=0.3.
 }}
 
 \item{extreme}{\code{list} containing: \cr
 \itemize{
-\item {\strong{fill}} {\code{character} Color of the area representing the CI for the extreme percentiles. Default: "#3388cc".}
-\item {\strong{alpha}} {\code{numeric} Transparency of the area representing the PI for the extreme percentiles. Default=0.3.}
+\item \strong{fill} \code{character} Color of the area representing the CI for the extreme percentiles. Default: "#3388cc".
+\item \strong{alpha} \code{numeric} Transparency of the area representing the PI for the extreme percentiles. Default=0.3.
 }}
 }
 \description{
diff --git a/man/pmx_vpc_pi.Rd b/man/pmx_vpc_pi.Rd
index 29587819..975c9de2 100644
--- a/man/pmx_vpc_pi.Rd
+++ b/man/pmx_vpc_pi.Rd
@@ -15,10 +15,10 @@ pmx_vpc_pi(
 \arguments{
 \item{show}{\code{charcater} how lines are displayed:
 \itemize{
-\item {\strong{show=all}} {lines will be displayed for each of
-the 3 percentiles. with a shaded area.}
-\item {\strong{show=median}} {Show only median line.}
-\item {\strong{show=area}} {Show only median line and the shaded area}
+\item \strong{show=all} lines will be displayed for each of
+the 3 percentiles. with a shaded area.
+\item \strong{show=median} Show only median line.
+\item \strong{show=area} Show only median line and the shaded area
 }}
 
 \item{interval}{\code{numeric} quantiles values default
@@ -26,24 +26,24 @@ to \code{c(.05,.95)}}
 
 \item{median}{\code{list} containing: \cr
 \itemize{
-\item {\strong{color}} {\code{charcater}  Color of the median percentile line. Default: "#000000". }
-\item {\strong{linewidth}} {\code{numeric}  Thickness of the median percentile line. Default: 1.}
-\item {\strong{alpha}} {\code{numeric} Transparency of the median percentile line. Default: 0.7.}
-\item {\strong{linetype}} {\code{charcater} Linetype of the median percentile line. Default: "solid".}
+\item \strong{color} \code{charcater}  Color of the median percentile line. Default: "#000000".
+\item \strong{linewidth} \code{numeric}  Thickness of the median percentile line. Default: 1.
+\item \strong{alpha} \code{numeric} Transparency of the median percentile line. Default: 0.7.
+\item \strong{linetype} \code{charcater} Linetype of the median percentile line. Default: "solid".
 }}
 
 \item{extreme}{\code{list} containing: \cr
 \itemize{
-\item {\strong{color}} {\code{charcater} Color of the median percentile line. Default: "#000000". }
-\item {\strong{linewidth}} {\code{numeric} Thickness of the median percentile line. Default: 1.}
-\item {\strong{alpha}} {\code{numeric} Transparency of the median percentile line. Default: 0.7.}
-\item {\strong{linetype}} {\code{charcater} Linetype of the median percentile line. Default: "solid"}
+\item \strong{color} \code{charcater} Color of the median percentile line. Default: "#000000".
+\item \strong{linewidth} \code{numeric} Thickness of the median percentile line. Default: 1.
+\item \strong{alpha} \code{numeric} Transparency of the median percentile line. Default: 0.7.
+\item \strong{linetype} \code{charcater} Linetype of the median percentile line. Default: "solid"
 }}
 
 \item{area}{\code{list} containing: \cr
 \itemize{
-\item {\strong{fill}} {\code{charcater}  Color of the shaded area. Default: "blue". }
-\item {\strong{alpha}} {\code{numeric} Transparency of the sahded area. Default: 0.1.}
+\item \strong{fill} \code{charcater}  Color of the shaded area. Default: "blue".
+\item \strong{alpha} \code{numeric} Transparency of the sahded area. Default: 0.1.
 }}
 }
 \description{
diff --git a/man/read_extfile.Rd b/man/read_extfile.Rd
index d3d8d535..6338d149 100644
--- a/man/read_extfile.Rd
+++ b/man/read_extfile.Rd
@@ -27,15 +27,15 @@ read_extfile(
 \item{quiet}{Logical, if \code{FALSE} messages are printed to the console.}
 }
 \value{
-A list with param, omega, and sigma in a format 
+A list with param, omega, and sigma in a format
 ready to be used.
 }
 \description{
 Reads .ext files generated by NONMEM
 }
 \examples{
-#project <- system.file("nonmem", package = "mrgsolve") 
-#est <- read_nmext(1005, project = project) 
+#project <- system.file("nonmem", package = "mrgsolve")
+#est <- read_nmext(1005, project = project)
 }
 \author{
 This function is based on read_nmext from mrgsolve, Original Author: Kyle T Baron.
diff --git a/man/residual.Rd b/man/residual.Rd
index 20278095..3b2abd20 100644
--- a/man/residual.Rd
+++ b/man/residual.Rd
@@ -54,17 +54,17 @@ Some parameters are a list of parameters :
 
 \strong{point} is a list that contains:
 \itemize{
-\item {\strong{shape:}} {default to 1}
-\item {\strong{color:}} {default to black}
-\item {\strong{size:}} {default to 1}
+\item \strong{shape:} default to 1
+\item \strong{color:} default to black
+\item \strong{size:} default to 1
 }
 
 \strong{labels} is a list that contains:
 \itemize{
-\item {\strong{title:}} {plot title default to AES_X versus AES_Y}
-\item {\strong{subtitle:}} {plot subtitle default empty}
-\item {\strong{x:}} {x axis label default to AES_X}
-\item {\strong{y:}} {y axis label default to AES_Y}
+\item \strong{title:} plot title default to AES_X versus AES_Y
+\item \strong{subtitle:} plot subtitle default empty
+\item \strong{x:} x axis label default to AES_X
+\item \strong{y:} y axis label default to AES_Y
 }
 }
 \seealso{