documentation

R/NMextractText.R

@@ -25,7 +25,9 @@
 ##' @param keep.empty Keep empty lines in output? Default is FALSE.
 ##' @param keep.name Keep the section name in output (say, "$PROBLEM")
 ##'     Default is TRUE. It can only be FALSE, if return="text".
-##' @param keep.comments Keep comment lines?
+##' @param keep.comments Keep comment lines? This concerns lines that
+##'     consist of only white space and comments; comments after
+##'     actual contents are not concerned.
 ##' @param as.one If multiple hits, concatenate into one. This will
 ##'     most often be relevant with name="TABLE". If FALSE, a list
 ##'     will be returned, each element representing a table. Default

R/NMreadSection.R

@@ -20,7 +20,9 @@
 ##' @param keep.empty Keep empty lines in output? Default is FALSE.
 ##' @param keep.name Keep the section name in output (say, "$PROBLEM")
 ##'     Default is FALSE. It can only be FALSE, if return="text".
-##' @param keep.comments Keep comment lines?
+##' @param keep.comments Keep comment lines? This concerns lines that
+##'     consist of only white space and comments; comments after
+##'     actual contents are not concerned.
 ##' @param as.one If multiple hits, concatenate into one. This will
 ##'     most often be relevant with name="TABLE". If FALSE, a list
 ##'     will be returned, each element representing a table. Default

R/NMscanData.R

@@ -218,6 +218,7 @@ NMscanData <- function(file, col.row, use.input, merge.by.row,
     if(missing(check.time)) check.time <- NULL
     if(missing(tz.lst)) tz.lst <- NULL
     if(missing(as.fun)) as.fun <- NULL
+    ## if(missing(modelname)) modelname <- NULL
     if(missing(quiet)) quiet <- NULL
     if(missing(formats.read)) formats.read <- NULL
     if(missing(args.fread)) args.fread <- NULL

devel/todo.org

@@ -38,6 +38,18 @@ With load_all():
     function is called from other functions. Possible to distinguish
     somehow?
 ** New functions
+*** document columns
+**** TODO Check for existence of char column in values
+If a data.frame specifies the num/char relationship, the char column
+should not be present in data. That would at least be a warning.
+**** TODO A regex argument to search for character values
+**** TODO Additional standard Nonmem columns 
+RATE,II, ADDL
+**** TODO addTAPD columns
+**** TODO If specified variable does not exist, send a message
+*** xml processer
+library(XML)
+XML::xmlParse("models/run1005_hi005.xml") |> xmlToList()
 *** DONE Remove commas from character strings
 Added editCharCols
 
@@ -461,6 +473,11 @@ A way to limit rows read into nonmem
 ***** tolower(nonmem)==tolower(input) OK
 ***** diff
 ***** off
+*** NMreadTab
+**** TODO [#B] Include metadata
+***** TODO Include path to file
+***** TODO Include $TABLE statement
+***** TODO Potentially include info generated by NMscanTables that should belong to NMreadTab
 *** NMscanTables
 **** DONE Don't throw an error when no tables found
 Just return NULL. and a message if !silent. To find where, look for
@@ -471,6 +488,7 @@ xgxr028.mod created and it works
 **** TODO [#B] Integrate the reduction into one table from NMscanData
 **** DONE Lastonly does the same as firstonly
 *** NMscanData
+**** TODO [#A] EXCLUDE_BY option is not suported in $TABLE if using merge_by_row=FALSE
 **** DONE Rename TABLENO to NMREP
 **** DONE Deprecate tab.count
 **** DONE Make clear how TABLENO is being counted
@@ -562,6 +580,7 @@ It now throws a weird error
 **** TODO [#A] Check if input data can be reused across models
 In that case, do the merge in the end
 *** NMwriteData
+**** TODO If NMgenText is run, results should go into metaData
 **** DONE Support writing fst
 ***** TODO formats.read instead of use.formats
 ***** TODO deprecate use.rds everywhere