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An input data object. Could be read with NMreadCsv orNMscanInput.

Path to mod/lst file. Only one of file or linesto be given. See '?NMreadSection' for understanding when to use,file, or lines. Only used when 'filters' not provided.

The mod/lst as character, line by line.

A 'data.frame' with filters as returned by'NMreadFilters()'. If not supplied, filters will be read from'file'/'lines'.

Invert the filters? This means read what Nonmemwould disregard, and disregard what Nonmem would read.

The default is to return data as a data.frame. Passa function (say tibble::as_tibble) in as.fun to convert tosomething else. If data.tables are wanted, useas.fun="data.table". The default can be configured usingNMdataConf.

Don't report information along the way if no warningsor errors. Default is FALSE.

A Nonmem control stream or list file

See ?NMdataConf

Additional arguments passed to

The data to check.data.frame,data.table,tibble, anything that can beconverted todata.table.

Alternatively to checking a data object, you can usefile to specify a control stream to check. This can either bea (working or non-working) input control stream or an outputcontrol stream. In this case,NMdataCheck checks columnnames in data against control stream (seeNMcheckColnames), reads the data as Nonmem would do,and do the same checks on the data as NMdataCheck would dousing the data argument.col.flagn is ignored in thiscase - instead, ACCEPT/IGNORE statements in control stream areapplied. The file argument is useful for debugging a Nonmemmodel.

columns that contain subject-level covariates. Theyare expected to be non-missing, numeric and not varying withinsubjects.

A list specifying columns that containsubject:occasion-level covariates. They are expected to benon-missing, numeric and not varying within combinations ofsubject and occasion.covs.occ=list(PERIOD=c("FED"))means thatFED is the covariate, whilePERIODindicates the occasion.

Columns that are expected to be present, numericand non-NA. If a character vector is given, the columns areexpected to be used in all rows. If a column is only used fora subset of rows, use a list and name the elements bysubsetting strings. See examples.

The name of the column that holds the subjectidentifier. Default is "ID".

The name of the column holding actual time.

The name of the column holding the dependentvariable. For now, only one column can be specified, andMDV is assumed to match this column. Default isDV.

The name of the column holding the binary indicatorof the dependent variable missing. Default isMDV.

The name(s) of the compartment column(s). Thesewill be checked to be positive integers for all rows. They arealso used in checks for row duplicates.

The name of the dose amount column.

Optionally, the name of the column holdingnumeric exclusion flags. Default value isFLAG and canbe configured usingNMdataConf. Even thoughFLAGis the default value, no finding will be returned if thecolumn is missing unless explicitly defined ascol.flagn="FLAG". This is because this way of usingexclusion flags is only one of many ways you could choose tohandle exclusions. Disable completely by usingcol.flagn=FALSE.

A column with a unique value for each row. Such acolumn is recommended to use if possible. Default("ROW") can be modified usingNMdataConf.

Optional unique subject identifier. It isrecommended to keep a unique subject identifier (typically acharacter string including an abbreviated study name and thesubject id) from the clinical datasets in the analysis set. Ifyou supply the name of the column holding this identifier,NMcheckData will check that it is non-missing, that it isunique within values of col.id (i.e. that the analysis subjectID's are unique across actual subjects), and that col.id isunique within the unique subject ID (a violation of the latteris less likely).

Additional column names to consider in search ofduplicate events.col.id,col.cmt,col.evid, andcol.time are always considered iffound in data, andcols.dup is added to this list ifprovided.

"est" for estimation data (default), and"sim" for simulation data. Differences are thatcol.row is not expected for simulation data, andsubjects will be checked to haveEVID==0 rows forestimation data andEVID==2 rows for simulation data.

Columns to not check. This is particularlyuseful when checking data sets that do not include i.e. 'CMT','EVID', and others. To skip checking specific columns, providetheir names like 'cols.disable=c("CMT","EVID")'.

Strings to be accepted when trying to convertcharacters to numerics. This will typically be a string thatrepresents missing values. Default is ".". Notice, actualNA, i.e. not a string, is allowed independently ofna.strings. See?NMisNumeric.

If TRUE (not default), the table summarythat is printed ifquiet=FALSE is returned as well. Inthat case, a list is returned, and the findings are in anelement called findings.

Keep quiet? Default is not to.

The default is to return data as adata.frame. Pass a function (saytibble::as_tibble) in as.fun to convert to somethingelse. Ifdata.tables are wanted, useas.fun="data.table". The default can be configuredusingNMdataConf.

a model file (input or output control stream)

row identifier

subject identifier

Prioritized input data file formats to lookfor and use if found. Default is c("csv") which meansrds andfst will _not_ be used. Typically onlythe csv file is wanted because we want to test the input dataas read by Nonmem.

Keep quiet? Default is FALSE.

How to find the input control stream if you areusing the output control stream.

The data directory can only be read from thecontrol stream (.mod) and not from the output file (.lst). Soif you only have the output control stream, use dir.data totell in which directory to find the data file. If dir.data isprovided, the .mod file is not used at all.

The function to run results through before returningthem.

Deprecated. Use formats.read instead.

passed to NMcheckData

the Nonmem code.

NMdata options to modify. These are named arguments,like for base::options. Normally, multiple arguments can beused. The exception is if reset=TRUE is used which means alloptions are restored to default values. If NULL is passed toan argument, the argument is reset to default. is Seeexamples for how to use.

Allow to store configuration of variablesthat are not pre-defined in NMdata. This should only be neededin cases where say another package wants to use the NMdataconfiguration system for variables unknown to NMdata.

IfTRUE, an overview of the configurationchanges is summarized in a printed table. This is useful fortransparency when sourcing a file with configuration. DefaultisFALSE.

Optionally, a single parameter name (say "as.fun").

Allow access to configuration of variablesthat are not pre-defined in NMdata. This should only be neededin cases where say another package wants to use the NMdataconfiguration system for variables unknown to NMdata.

The name of the parameter, say "as.fun"

The value to pass. If missing or NULL, the value returned by NMdataConf/NMdataGetOption will typically be used.

argument to look up. Only one argument can be looked up.

an NMdata object

arguments passed to other methods.

The data set to expand

The name of the column holding the time on whichtime since previous dose will be based. This is typicallyactual or nominal time since first dose.

The subject identifier. All new columns will bederived within unique values of this column.

The name of the event ID column. This must existin data. Default is EVID.

Keep track of what rows were in dataoriginally and which ones are added by NMexpandDoses byincluding a column called nmexpand? nmexpand will be TRUE ifthe row is "generated" by NMexpandDoses.

A string that will be evaluated as a customexpression to identify relevant events.

Suppress messages back to user (default is FALSE)

The default is to return data as a data.frame. Passa function (say tibble::as_tibble) in as.fun to convert tosomething else. If data.tables are wanted, useas.fun="data.table". The default can be configured usingNMdataConf.

The input control stream or the list file.

See NMscanInput. If used, only the file namementioned in $DATA is used. dir.data will be used as the path,and the existence of the file in that directory is notchecked.

The input control stream. Default is to look for\"file\" with extension changed to '.mod' (PSN style). You canalso supply the path to the file, or you can provide afunction that translates the output file path to the inputfile path. The default behavior can be configured usingNMdataConf. See dir.data too.

Specification of the data file path. When this isused, the control streams are not used at all.

A file path to read from. Normally a .mod or .lst. Seelines and text as well.

Text lines to process. This is an alternative tousing the file and text arguments.

Use this argument if the text to process is one longcharacter string, and indicate the line separator with thelinesep argument. Use only one of file, lines, and text.

The name of section to extract. Examples: "INPUT","PK", "TABLE", etc. It can also be result sections like"MINIMIZATION".

The section denoted as a string compatiblewith regular expressions. "$" (remember to escape properly)for sections in .mod files, "0" for results in .lst files.

A regular expression to capture the end of thesection. The default is to look for the next occurrence ofchar.section.

If "text", plain text lines are returned. If "idx",matching line numbers are returned. "text" is default.

Keep empty lines in output? Default isFALSE. Notice, comments are removed before empty lines arehandled if 'keep.comments=TRUE'.

Keep the section name in output (say, "$PROBLEM")Default is TRUE. It can only be FALSE, if return="text".

Default is to keep comments. If FALSE, thewill be removed.

If multiple hits, concatenate into one. This willmost often be relevant with name="TABLE". If FALSE, a listwill be returned, each element representing a table. Defaultis TRUE. So if you want to process the tables separately, youprobably want FALSE here.

If TRUE, leading and trailing are removed, andmultiplied succeeding white spaces are reduced to single whitespaces.

If asOne=FALSE, do you want the result to besimplified if only one table is found? Default is TRUE whichis desirable for interactive analysis. For programming, youprobably want FALSE.

Default is to search for exact matches of'section'. If FALSE, only the first three characters arematched. E.G., this allows "ESTIMATION" to match "ESTIMATION"or "EST".

Either mod, res or NULL. mod is for information thatis given in .mod (.lst file can be used but results section isdisregarded). If NULL, NA or empty string, everything isconsidered.

If using the text argument, use linesep to indicatehow lines should be separated.

Deprecated. See keep.empty.

Deprecated. See keep.name.

Deprecated. See keep.comments.

Deprecated. See as.one.

The data that NONMEM will read. Either as a'data.frame', of if a path to an rds or a delimited text file,the data will automatically be read first.

Only used for generation of proposed text for INPUTsection. Columns to drop in Nonmem $INPUT. This has twoimplications. One is that the proposed $INPUT indicates =DROPafter the given column names. The other that in case it is anon-numeric column, succeeding columns will still be includedin $INPUT and can be read by NONMEM.

Name of a numeric column with zero value for rowsto include in Nonmem run, non-zero for rows to skip. Theargument is only used for generating the proposed $DATA textto paste into the Nonmem control stream. Default is defined by'NMdataConf()'. To skip this feature, use 'col.flagn=FALSE'.

For the $INPUT text proposal only. If you want torename columns in NONMEM $DATA, NMwriteData can adjust thesuggested $DATA text. If you plan to use BBW instead of BWBASEin Nonmem, consider rename=c(BBW="BWBASE"). The result willinclude BBW and not BWBASE.

For the $INPUT text proposal only. If you plan to useadditional names for columns in Nonmem $INPUT, NMwriteData canadjust the suggested $INPUT text. Say you plan to use CONC asDV in Nonmem, use copy=c(DV="CONC"),i.e. copy=c(newname="existing"). INPUT suggestion will in thiscase contain DV=CONC.

The file name NONMEM will read the data from (for the$DATA section). It can be a full path.

For the $DATA text proposal only. The path to theinput datafile to be used in the Nonmem $DATA section. Often,a relative path to the actual Nonmem run is wanted here. Ifthis is used, only the file name and not the path from thefile argument is used.

For the $INPUT text proposal only. If TRUE, allcolumn names in $INPUT text will be converted to capitalletters.

Use this to truncate the columns in $INPUT. until caneither be a character (column name) or a numeric (columnnumber). If a character is given, it is matched against theresulting column name representation in $INPUT, i.e. thiscould be "DV=CONC" if you are using in this case the copyargument. In case until is of length>1, the maximum will beused (probably only interesting if character values aresupplied).

For the $INPUT text proposal only. AssumeNonmem can read TIME and DATE even if it can't be translatedto numeric. This is necessary if using the 00:00format. Default is TRUE.

If positive, will be passed to strwrap for the $INPUTtext. If missing or NULL, strwrap will be called with defaultvalue. If negative or zero, strwrap will not be called.

Hold messages back? Default is defined by NMdataConf.

An object of class NMdata (a result of 'NMscanData()')

If not passed, all the metadata is returned. You canuse "details", "tables", or "columns" to get only thesesubsets. If info is "tables" or "columns"

The default is to return data as a 'data.frame'. Passa function (say 'tibble::as_tibble') in as.fun to convert tosomething else. If 'data.table's are wanted, use'as.fun="data.table"'. The default can be configured using'NMdataConf()'.

The vector to check Don't export

Tolerated strings that do not translate tonumerics. Default is to accept "." because it's common towrite missing values that way to Nonmem (even if Nonmem willhandle them as zeros rather than missing). Notice actual NA'sare accepted so you may want to use na.strings=NULL if youdon't code missings as "." and just do this when writing thedata set to a delimited file (like NMwriteData will do foryou).

Use each=TRUE to evaluate each element in a vectorindividually. The default (each=FALSE) is to return asingle-length logical for a vector x summarizing whether allthe elements are numeric-compatible.

The dataset which columns to reorder.

Columns that should come almost first. See details.

Columns to move to back of dataset. If you work with alarge dataset, and some columns are irrelevant for the Nonmemruns, you can use this argument.

Should columns which names contain lowercasecharacters be moved towards the back? Some people use astandard of lowercase variables (say "race") being characterrepresentations ("Asian", "Caucasian", etc.) variables and theuppercase (1,2,...) being the numeric representation forNonmem.

Should columns which cannot be converted tonumeric be put towards the end? A column can be a character ora factor in R, but still be valid in Nonmem (often the casefor ID which can only contain numeric digits but really is acharacter or factor). So rather than only looking at thecolumn class, the columns are attempted converted tonumeric. Notice, it will attempted to be converted to numericto test whether Nonmem will be able to make sense of it, butthe values in the resulting dataset will be untouched. Novalues will be edited. If TRUE, logicals will always be putlast. NA's must be NA or ".".

Sort columns alphabetically. Notice, this is the lastorder priority applied.

Name of the (numeric) unique subject ID. Can becontrolled with 'NMdataConf()'.

The name of the column containing nominaltime. If given, it will put the column quite far left, justafter row counter and 'col.id'. Default value is NOMTIME and can beconfigured with 'NMdataConf()'.

The name of the column containing actual time. Ifgiven, it will put the column quite far left, just after rowcounter, subject ID, and nominal time. Default value is 'TIME'. Can becontrolled with 'NMdataConf()'.

A row counter column. This will be the first columnin the dataset. Technically, you can use it for whatevercolumn you want first. Default value is 'ROW' and can beconfigured with 'NMdataConf()'.

The name of the column containing numerical flagvalues for data row omission. Default value is FLAG and can beconfigured with 'NMdataConf()'.

a vector of column names to put early to representdependent variable(s). Default is DV.

For the $INPUT text proposal only. AssumeNonmem can read TIME and DATE even if it can't be translated tonumeric. This is necessary if using the 00:00 format. Defaultis TRUE.

The default is to return a data.table if data is adata.table and return a data.frame in all other cases. Pass afunction in as.fun to convert to something else. The defaultcan be configured using 'NMdataConf()'. However, if data is adata.table, settings via 'NMdataConf()' are ignored.

If true, no warning will be given about missingstandard Nonmem columns.

The ".cov" covariance Nonmem matrix file to read

If 'TRUE' (default) the extension willautomatically be modified using 'NMdataConf()$file.cov'. Thismeans 'file' can be the path to an input or output controlstream, and 'NMreadCov()' will still read the '.cov' file.

The table number to read. The ".cov" file cancontain multiple tables and will often do so if using SAEM/IMPmethods. Default is "max" which means the last table isused. Alternative values are "min" and "all" or numericvalues. If "all" or multiple numeric values are used, a listis returned. However, see 'simplify' too.

If 'TRUE' (default) and only one table is returned(say using tableno="max") only that matrix is returned as amatrix object. If 'FALSE' or multiple tables are returned, theresult is a list.

The file to read. Must be pure text.

List of arguments passed to fread. Notice thatexcept for "file", you need to supply all arguments to freadif you use this argument. Default values can be configuredusing NMdataConf.

The default is to return data as a data.frame. Passa function (say tibble::as_tibble) in as.fun to convert tosomething else. If data.tables are wanted, useas.fun="data.table". The default can be configured usingNMdataConf.

Format of file to read. Can be of length>1 in whichcase the first format found will be used (i.e. format is aprioritized vector). If not one of "rds" or "fst", it isassumed to be a delimited text file. Default is to determinethis from the file name extension. Notice, if a delimitedformat is used, the extension can very well be different from"csv" (say file name is"input.tab")". This will work for any delimited format supported by fread.

Optional arguments to pass toread_fst ifformat="fst" is used.

Path to the ext file

The .ext file contains both final parameterestimates and iterations of the estimates. Ifreturn="pars" (default) the final estimates arereturned in addition to what other parameter-level informationis found, like FIX, sd etc. as columns. Ifreturn="iterations", the iterations are returned(including objective function value). Ifreturn="obj"objective function value at final estimate is returned. Ifreturn="all", all er returned, though in separatedata.frames compiled in a list.

The default is to return data as adata.frame. Passa function in as.fun to convert tosomething else. If 'data.table's are wanted, use'as.fun="data.table"'. The default can be configured usingNMdataConf().

See '?NMscanData'

See '?NMscanData'

If 'TRUE' (default) the extension willautomatically be modified usingNMdataConf()$file.ext. Thismeans 'file' can be the path to an input or output controlstream, andNMreadExt will still read the '.ext' file.

In case the ext file contains multiple tables, thisargument controls which one to choose. The options are

• "max" (default) Pick the table with the highest tablenumber. This typically means the results from the last'$ESTIMATION' step are used.

• "min" Pick results from the first table available.

• "all" Keep all results. The tables can be distinguished bythetableno column.

• an integer greater than 0, in which case the table with thistable number will be picked.

Deprecated. Please usefile instead.

Use a slow but more robust method to read tables? Ifmissing or 'NULL', the fast method will be tried first, and ifany issues are seen, the method will switch to 'slow=TRUE'. If'FALSE',it will also switch in case of issues, but a warning isissued. In other words, it should be safe to not use thisargument.

Control stream path

Control stream lines if already read from file

Return the filters only or also return the remaining text in a separate object? If 'FALSE', a list with the two objects is returned.

Function to run on the tables with filters.

Path to a control stream. See 'lines' too.

A control stream as text lines. Use this or 'file'.

The section to read. Typically, "theta", "omega",or "sigma". Default is those three.

By default (whenreturn="pars", a parametertable with initial values, FIX, lower and upper bounds etc. Inmost cases, that is what is needed to derive information aboutparameter definitions. Ifreturn="all", two additionaltables are returned which can be used if the aim is to modifyand write the resulting parameters to a control stream.

See ?NMscanData

Path to the control stream to read.

As an alternative to 'file', the control stream orselected lines of the control stream can be provided as avector of lines.

Defines naming and splitting of contents of lines inparameter sections. Default is"%init;%idx;%symbol;%label;%unit". Be careful toremember percentage symbols in front of any variable names.

Like 'format', applied to '$OMEGA'section. Default is to reuse 'format'.

Like 'format', applied to '$SIGMA'section. Default is to reuse 'format.omega'.

Is a blank in 'fields' to be treated as afield separator? Default is not to (i.e. neglect spaces in'fields').

If TRUE, each line in the control stream isassigned to one parameter, at most. This means, if twoparameters are listed in one line, the comments will only beused for one of the parameters, and only that parameter willbe kept in output. Where this will typically happen is in'$OMEGA' and '$SIGMA' sections where off-diagonal may be puton the same line as diagonal elements. Since the off-diagonalelements are covariances of variables that have already beenidentified by the diagonals, the off-diagonal elements can beautomatically described. For example, if 'OMEGA(1,1)' isbetween-subject variability (BSV) on CL and 'OMEGA(2,2) is BSVon V, then we know that 'OMEGA(2,1)' is covariance of (BSV on)CL and V.

If an index field is manually provided in thecontrol stream comments, define the name of that field in'format' and tell 'NMreadParsText()' to use this idx toorganize especially OMEGA and SIGMA elements by pointing to itwith 'field.idx'. The default is to look for a variable called'idx'. If the index has values like 1-2 on an OMEGA or SIGMArow, the row is interpreted as the covariance betweenOMEGA/SIGMA 1 and 2.

The default method is to automatically identifyelement numbering ('i' for THETAs, 'i' and 'j' for OMEGAs andSIGMAs). The automated method is based on identification of'BLOCK()' structures and numbers of initial values. Shouldthis fail, or should you want to control this manually, youcan include a parameter counter in the comments and have'NMreadParsText()' use that to assign thenumbering. 'use.idx=FALSE' is default and means all blocks arehandled automatically, 'use.idx=TRUE' assumes you have acounter in all sections, and a character vector like'use.idx="omega"' can be used to denote which sections usesuch a counter from the control stream. When using a counteron OMEGA and SIGMA, off-diagonal elements MUST be denoted by'i-j', like '2-1' for OMEGA(2,1). See 'field.idx' too.

If 'TRUE' (default), a field will automatically beadded to the formats for the initial value string. This willbe called "initstr". It will only happen if the first field isnot called either "initstr" or "init". The only situationwhere one would use 'add.init=FALSE' is if a different namefor the initial value field is already included in formats.

See ?NMscanData

See ?NMscanData

See ?NMscanData

If an index field in comments should be usedto number thetas. The index field is used to organize'$OMEGA's and '$SIGMA's because they are matrices but I do notsee where this is advantageous to do for '$THETA's. Default'use.theta.idx=FALSE' which means '$THETA's are simplycounted.

Deprecated. Use 'format'.

Deprecated. Use 'format.omega'.

Deprecated. Use 'format.sigma'.

Path to the phi file. See 'auto.ext' too.

The default is to return data as a data.frame. Passa function (say tibble::as_tibble) in as.fun to convert tosomething else. If data.tables are wanted, useas.fun="data.table". The default can be configured usingNMdataConf.

See ?NMscanData

See ?NMscanData

If 'auto.ext=TRUE', the file name extension willautomatically be changed using the setting in'NMdataConf()$file.phi' - this by default means that the'.phi' extension will be used no matter what extension theprovided file name has.

Deprecated. Use 'file'.

A file path to read from. Normally a .mod or .lst. Seelines also.

Text lines to process. This is an alternative tousing the file argument.

Deprecated, use 'lines'. Use this argument if the textto process is one long character string, and indicate the lineseparator with the linesep argument (handled byNMextractText). Use only one of file, lines, and text.

The name of section to extract without"$". Examples: "INPUT", "PK", "TABLE", etc. Not casesensitive.

If "text", plain text lines are returned. If "idx",matching line numbers are returned. "text" is default.

Keep empty lines in output? Default isFALSE. Notice, comments are removed before empty lines arehandled if 'keep.comments=TRUE'.

Keep the section name in output (say, "$PROBLEM")Default is FALSE. It can only be FALSE, if return="text".

Default is to keep comments. If FALSE, thewill be removed. See keep.empty too. Notice, there is no wayfor NMreadSection to keep comments and also drop lines thatonly contain comments.

If multiple hits, concatenate into one. This willmost often be relevant with name="TABLE". If FALSE, a listwill be returned, each element representing a table. Defaultis TRUE. So if you want to process the tables separately, youprobably want FALSE here.

If TRUE, leading and trailing are removed, andmultiplied succeeding white spaces are reduced to single whitespaces.

If asOne=FALSE, do you want the result to besimplified if only one section is found? Default is TRUE whichis desirable for interactive analysis. For programming, youprobably want FALSE.

Deprecated. See keep.empty.

Deprecated. See keep.name.

Deprecated. See keep.comments.

Deprecated. See as.one.

Additional arguments passed to NMextractText

A model file. Extension will be replaced by ".shk".

If 'TRUE' (default) the extension will automaticallybe modified using 'NMdataConf()$file.shk'. This means 'file'can be the path to an input or output control stream, and'NMreadShk' will still read the '.shk' file.

See ?NMdataConf

Control stream path.

Character vector with control stream file.

path to Nonmem table file

In case of simulations where tables are beingrepeated, a counter of the repetition number can be useful toinclude in the output. For now, this will only work if theNOHEADER option is not used. This is because NMreadTabsearches for the "TABLE NO..." strings in Nonmem outputtables. If col.tableno is TRUE (default), a counter of tablesis included as a column called NMREP. Notice, the tablenumbers in NMREP are cumulatively counting the number oftables reported in the file. NMREP is not the actual tablenumber as given by Nonmem.

col.nmrep If tables are repeated, include acounter? It does not relate to the order of the $TABLEstatements but to cases where a $TABLE statement is runrepeatedly. E.g., in combination with the SUBPROBLEMS featurein Nonmem, it is useful to keep track of the table(repetition) number. If col.nmrep is TRUE, this will becarried forward and added as a column called NMREP. This isdefault behavior when more than one $TABLE repetition is foundin data. Set it to a different string to request the columnwith a different name. The argument is passed to NMscanTables.

The name of a column containing the name ordescription of the table (generated by Nonmem). The default is"table.name". Use FALSE not to include this column.

Use header=FALSE if table was created with NOHEADERoption in $TABLE.

The number of rows to skip. The default is skip=1 ifheader==TRUE and skip=0 if header==FALSE.

logical stating whether or not information is printedabout what is being done. Default can be configured usingNMdataConf.

The default is to return data as a data.frame. Passa function (say tibble::as_tibble) in as.fun to convert tosomething else. If data.tables are wanted, useas.fun="data.table". The default can be configured usingNMdataConf.

Arguments passed todata.table::fread().

A Nonmem table file. Can be output tables, or one ofthe several different results files from Nonmem.

Name of the column (to be created)containing the "table name" which is derived from the Nonmemdescription of the table sometimes pasted above the tabledata.

Path to a control stream to process. See 'lines' too.

If the control stream has been read already, the textcan be provided here instead of using the 'file'argument. Character vector of text lines.

Either a model name (like "Base") or a functionthat derives the model name from the control stream filepath. The default is dropping the file name extension on thecontrol stream file name.

Parameter type(s) to include. Default is all threepossible which isc("THETA","OMEGA","SIGMA").

Name of the column containing the model name.

Sections of the control stream toconsider. Default is all ofc("PRED","PK","ERROR").

The default is to return data as a data.frame. Passa function (say tibble::as_tibble) in as.fun to convert tosomething else. If data.tables are wanted, useas.fun="data.table". The default can be configured usingNMdataConf.

Paths to input control streams to modify. Seefile.pattern and dir too.

A pattern to look for if 'dir' is supplied too(and not 'file.mod'). This is used to modify multiple inputcontrol streams at once.

Directory in which to look for 'file.pattern'. Notice,use either just 'file.mod' or both 'dir' and 'file.pattern'.

Path to input control stream to use in newfile

A path to a new control stream to write to (anddon't edit contents of 'file.mod'). Default is to overwrite 'file.mod'.

Additional arguments to pass to NMwriteSection.

Path to a Nonmem control stream or output file fromNonmem (.mod or .lst)

A column with a unique value for each row. Such acolumn is recommended to use if possible. See merge.by.row anddetails as well. Default ("ROW") can be modified usingNMdataConf.

Should the input data be added to the outputdata. Only column names that are not found in output data willbe retrieved from the input data. Default is TRUE which can bemodified using NMdataConf. See merge.by.row too.

If use.input=TRUE, this argument determinesthe method by which the input data is added to outputdata. The default method (merge.by.row=FALSE) is to interpretthe Nonmem code to imitate the data filtering (IGNORE andACCEPT statements), but the recommended method ismerge.by.row=TRUE which means that data will be merged by aunique row identifier. The row identifier must be present ininput and at least one full length output data table. Seeargument col.row too.

Include rows from input data files that do notexist in output tables? This will be added to the $row datasetonly, and $run, $id, and $occ datasets are created before thisis taken into account. A column called nmout will be TRUE whenthe row was found in output tables, and FALSE whennot. Default is FALSE and can be configured using NMdataConf.

The input control stream file path. Default is tolook for \"file\" with extension changed to .mod (PSNstyle). You can also supply the path to the file, or you canprovide a function that translates the output file path to theinput file path. The default behavior can be configured usingNMdataConf. See dir.data too.

The data directory can only be read from thecontrol stream (.mod) and not from the output file (.lst). Soif you only have the output control stream, use dir.data totell in which directory to find the data file. If dir.data isprovided, the .mod file is not used at all.

Specification of the data file path. When this isused, the control streams are not used at all.

Default is TRUE, meaning that input datacolumn names are translated according to $INPUT section inNonmem listing file.

The default is to give some information along the wayon what data is found. But consider setting this to TRUE fornon-interactive use. Default can be configured usingNMdataConf.

Prioritized input data file formats to lookfor and use if found. Default is c("rds","csv") which meansrds will be used if found, andcsv ifnot.fst is possible too. Default can be modified usingNMdataConf().

List of arguments passed to when reading _input_data. Notice that except for "input" and "file", you need tosupply all arguments to fread if you use thisargument. Default values can be configured using NMdataConf.

The default is to return data as a data.frame. Passa function (say tibble::as_tibble) in as.fun to convert tosomething else. If data.tables are wanted, useas.fun="data.table". The default can be configured usingNMdataConf.

The name of the subject ID variable, default is"ID".

The model name to be stored if col.model is notNULL. If not supplied, the name will be taken from the controlstream file name by omitting the directory/path and deletingthe .lst extension (path/run001.lst becomes run001). This canbe a character string or a function which is called on thevalue of file (file is another argument to NMscanData). Thefunction must take one character argument and return anothercharacter string. As example, see NMdataConf()$modelname. Thedefault can be configured using NMdataConf.

A column of this name containing the model namewill be included in the returned data. The default is to storethis in a column called "model". See argument "modelname" aswell. Set to NULL if not wanted. Default can be configuredusing NMdataConf.

A column of this name will be a logicalrepresenting whether row was in output table or not. Defaultcan be modified using NMdataConf.

If tables are repeated, include a counter? Itdoes not relate to the order of the $TABLE statements but tocases where a $TABLE statement is run repeatedly. E.g., incombination with the SUBPROBLEMS feature in Nonmem, it isuseful to keep track of the table (repetition) number. Ifcol.nmrep is TRUE, this will be carried forward and added as acolumn called NMREP. This is default behavior when more thanone $TABLE repetition is found in data. Set it to a differentstring to request the column with a different name. Theargument is passed to NMscanTables.

If TRUE (default), NMorderColumns is used toreorder the columns before returning the data. NMorderColumnswill be called with alpha=FALSE, so columns are not sortedalphabetically. But standard Nonmem columns like ID, TIME, andother will be first. If col.row is used, this will be passedto NMorderColumns too.

If TRUE (default) and if input data is used,input control stream and input data are checked to be newerthan output control stream and output tables. These areimportant assumptions for the way information is merged byNMscanData. However, if data has been transferred from anothersystem where Nonmem was run, these checks may not make sense,and you may not want to see these warnings. The default can beconfigured using NMdataConf. For the output control stream,the time stamp recorded by Nonmem is used if possible, and ifthe input data is created with NMwriteData, the recordedcreation time is used if possible. If not, and for all otherfiles, the file modification times are used.

If supplied, the timezone to be used when readingthe time stamp in the output control stream. Please supplysomething listed in OlsonNames(). Can be configured usingNMdataConf() too.

Skip missing output table files with a warning?Default is FALSE in which case an error is thrown.

Deprecated. Usecol.tableno.

Deprecated - useformats.read instead. Ifprovided (though not recommended), this will overwriteformats.read, and only formatsrds andcsv can be used.

a .lst (output) or a .mod (input) control streamfile. The filename does not need to end in .lst. It isrecommended to use the output control stream because itreflects the model as it was run rather than how it is plannedfor next run. However, see file.mod and dir.data.

Prioritized input data file formats to lookfor and use if found. Default is c("rds","csv") which meansrds will be used if found, andcsv ifnot.fst is possible too. Default can be modified usingNMdataConf().

The input control stream file path. Default is tolook for \"file\" with extension changed to .mod (PSNstyle). You can also supply the path to the file, or you canprovide a function that translates the output file path to theinput file path. If dir.data is missing, the input controlstream is needed. This is because the .lst does not containthe path to the data file. The .mod file is only used forfinding the data file. How to interpret the datafile is readfrom the .lst file. The default can be configured usingNMdataConf. See dir.data too.

The data directory can only be read from thecontrol stream (.mod) and not from the output file (.lst). Soif you only have the output file, use dir.data to tell inwhich directory to find the data file. If dir.data isprovided, the .mod file is not used at all.

Specification of the data file path. When this isused, the control streams are not used at all.

If TRUE (default), IGNORE and ACCEPTstatements in the Nonmem control streams are applied beforereturning the data. This affects what rows are returned, notcolumns.

If TRUE (default), data columns are named asinterpreted by Nonmem (in '$INPUT'). See details.

recover columns that were not used in theNonmem control stream? This means adding column from the inputdata file that are not used in '$INPUT'. If data file containsmore columns than mentioned in '$INPUT', these will be namedas in data file (if data file contains named variables). Thisaffects what columns are returned, not rows.

If TRUE, metadata is added to output. In this case,you get a list. Typically, this is mostly useful ifprogramming up functions which behavior must depend onproperties of the output. See details.

The name of the subject ID column. Optional and onlyused to calculate number of subjects in data. Default ismodified by NMdataConf.

The name of the row counter column. Optional andonly used to check whether the row counter is in the data.

Default is to inform a little, but TRUE is useful fornon-interactive stuff.

List of arguments passed to fread. Notice thatexcept for "input" and "file", you need to supply allarguments to fread if you use this argument. Default valuescan be configured using 'NMdataConf()'.

If TRUE, the data rows that are dismissed by theNonmem data filters (ACCEPT and IGNORE) and only this will bereturned. Only used if 'apply.filters' is 'TRUE'.

Only affects meta data table. The model name tobe stored if col.model is not NULL. If not supplied, the namewill be taken from the control stream file name by omittingthe directory/path and deleting the .lst extension(path/run001.lst becomes run001). This can be a characterstring or a function which is called on the value of file(file is another argument to NMscanData). The function musttake one character argument and return another characterstring. As example, see NMdataConf()$modelname. The defaultcan be configured using NMdataConf.

Only affects meta data table. A column of thisname containing the model name will be included in thereturned data. The default is to store this in a column called"model". See argument "modelname" as well. Set to NULL if notwanted. Default can be configured using NMdataConf.

The default is to return data as a data.frame. Passa function (say tibble::as_tibble) in as.fun to convert tosomething else. If data.tables are wanted, useas.fun="data.table". The default can be configured usingNMdataConf.

Deprecated - use apply.filters.

Deprecated - useformats.read instead. Ifprovided (though not recommended), this will overwriteformats.read, and only formatsrds andcsv can be used.

File paths to the models (control stream) toedit. See file.pattern too.

The directory in which to find the models. Passed tolist.files(). See file.pattern argument too.

The pattern used to match the filenames toread with NMscanData. Passed to list.files(). Ifdir issupplied andfiles is not (or isNULL), thedefault is".*\.lst" which means all files ending in'.lst'. Seedir argument too.

The default is to return data as a data.frame. Passa function (say tibble::as_tibble) in as.fun to convert tosomething else. If data.tables are wanted, useas.fun="data.table". The default can be configured usingNMdataConf.

Additional arguments passed to NMscanData.

the Nonmem file to read (normally .mod or .lst)

The default is to return data as a data.frame. Passa function (say tibble::as_tibble) in as.fun to convert tosomething else. If data.tables are wanted, useas.fun="data.table". The default can be configured usingNMdataConf.

The default is to give some information along the wayon what data is found. But consider setting this to TRUE fornon-interactive use. Default can be configured usingNMdataConf.

col.nmrep If tables are repeated, include acounter? It does not relate to the order of the $TABLEstatements but to cases where a $TABLE statement is runrepeatedly. E.g., in combination with the SUBPROBLEMS featurein Nonmem, it is useful to keep track of the table(repetition) number. If col.nmrep is TRUE, this will becarried forward and added as a column called NMREP. This isdefault behavior when more than one $TABLE repetition is foundin data. Set it to a different string to request the columnwith a different name. The argument is passed to NMscanTables.

Nonmem includes a counter of tables in thewritten data files. These are often not useful. However, ifcol.tableno is TRUE (not default), this will be carriedforward and added as a column called NMREP. Even if NMREP isgenerated by NMscanTables, it is treated like any other tablecolumn in meta (?NMinfo) data.

name of the subject ID column. Used for calculationof the number of subjects in each table.

The name of the row counter column. Optional andonly used to check whether the row counter is in the data.

If TRUE, metadata is added to output. In this case,you get a list. Typically, this is mostly useful ifprogramming up functions which behavior must depend onproperties of the output.

Skip missing output table files with a warning?Default is FALSE in which case an error is thrown.

If TRUE, tables are not read, only a table isreturned showing what tables were found and some availablemeta information. Notice, not all meta information (e.g.,dimensions) are available because the tables need to be readto derive that.

Only affects meta data table. The model name tobe stored if col.model is not NULL. If not supplied, the namewill be taken from the control stream file name by omittingthe directory/path and deleting the .lst extension(path/run001.lst becomes run001). This can be a characterstring or a function which is called on the value of file(file is another argument to NMscanData). The function musttake one character argument and return another characterstring. As example, see NMdataConf()$modelname. The defaultcan be configured using NMdataConf.

Only affects meta data table. A column of thisname containing the model name will be included in thereturned data. The default is to store this in a column called"model". See argument "modelname" as well. Set to NULL if notwanted. Default can be configured using NMdataConf.

The dataset to stamp.

path to the script where the dataset was generated.

the time stamp to attach. Default is to use cpu clock.

other named metadata elements to add to the dataset. Example:Description="PK data for phase 1 trials in project".

the data to translate

the list file or control stream

Do translation according to Nonmem code or not(default 'TRUE')? If not, an overview of column names in dataand in Nonmem code is still returned with the data.

recover columns that were not used in theNONMEM control stream? Default is TRUE. Can only be negativewhen translate=FALSE.

Suppress warnings about data columns?

The dataset to write to file for use in Nonmem.

The file to write to. The extension (everything afterand including last ".") is dropped. csv, rds and otherstandard file name extensions are added.

character vector of formats.write. Default isc("csv","rds"). "fst" is possible too. Default can be modifiedwithNMdataConf().

If provided, the object will be stamped with thisscript name before saved to rds or RData. See ?NMstamp.

A list of arguments to be passed to NMstamp.

List of arguments passed to fwrite. Notice thatexcept for "x" and "file", you need to supply all arguments tofwrite if you use this argument. Default values can beconfigured using NMdataConf.

A list of arguments to be passed to saveRDS.

A list of arguments to be passed to save. Pleasenote that writing RData is deprecated.

An optional list of arguments to be passedto write_fst.

The default is to give some information along the wayon what data is found. But consider setting this to TRUE fornon-interactive use. Default can be configured usingNMdataConf.

List of arguments to pass to NMgenText - thefunction that generates text suggestion for INPUT and DATAsections in the Nonmem control stream. You can use thesearguments to get a text suggestion you an use directly inNonmem - andNMwriteSection can even update multipleNonmem control streams based on the result. This will updateyour control streams to match your new data file with just onecommand.

If TRUE, csv file will be truncatedhorizontally (columns will be dropped) to match the $INPUTtext generated for Nonmem (genText must be TRUE for thisoption to be allowed). This can be a great advantage whendealing with large datasets that can create problems inparallellization. Combined with write.rds=TRUE, the full dataset will still be written to an rds file, so this can be usedwhen combining output and input data when reading modelresults. This is done by default by NMscanData. This meanswriting a lean (narrow) csv file for Nonmem while keepingcolumns of non-numeric class like character and factor forpost-processing.

Run and report results of NMgenText? Default is'TRUE' if a csv file is written, otherwise 'FALSE'. You maywant to disable this if data set is not for Nonmem.

Save defined files? Default is TRUE. If a variable isused to control whether a script generates outputs (saywriteOutputs=TRUE/FALSE), if you usesave=writeOutputs to comply with this.

Write to csv file? Deprecated, use'formats.write' instead.

write an rds file? Deprecated, use'formats.write' instead.

Deprecated and not recommended - will beremoved. RData is not a adequate format for a dataset (but isfor environments). Please use write.rds instead.

Deprecated, useargs.NMgenText=list(drop=c("column")) instead.

Deprecated, useargs.NMgenText=list(dir.data="your/path") instead.

Deprecated, useargs.NMgenText=list(col.flagn="column.name"). Name of anumeric column with zero value for rows to include in Nonmemrun, non-zero for rows to skip. The argument is only used forgenerating the proposed $DATA text to paste into the Nonmemcontrol stream. To skip this feature, use 'col.flagn=FALSE'.

Deprecated, useargs.NMgenText=list(rename=c(newname="existing")) instead.

Deprecated, useargs.NMgenText=list(copy=c(newname="existing")) instead.

Deprecated, useargs.NMgenText=list(capitalize=TRUE) instead.

Deprecated, useargs.NMgenText=list(allow.char.TIME=TRUE) instead.

File paths to the models (control stream) toedit. See file.pattern too.

Alternatively to files, you can supply aregular expression which will be passed to list.files as thepattern argument. If this is used, use 'dir' argument aswell. Also see data.file to only process models that use aspecific data file.

If file.pattern is used, 'dir' is the directory to searchin.

The name of the section to update with or without"$". Example: 'section="EST"' or 'section="$EST"' to edit thesections starting by '$EST'. Section specification is notcase-sensitive. See '?NMreadSection' too.

The new text (including "$SECTION"). Better bebroken into lines in a character vector since this is simplypast towriteLines().

Named list of new sections, each elementcontaining a section. Names must be section names, contents ofeach element are the new section lines for each section.

In combination with 'section', this determineswhere the new section is inserted. Possible values are"replace" (default), "before", "after", "first", "last".

path and filename to new run. If missing, theoriginal file (fromfiles orfile.pattern) isoverwritten (see thebackup option below). If NULL,output is returned as a character vector rather than written.

In case you are overwriting the old file, do youwant to backup the file (to say, backup_run001.mod)?

Append a blank line to output?

Use this to limit the scope of models to thosethat use a specific input data data file. The string has toexactly match the one in '$DATA' or '$INFILE' in Nonmem.

Default is to write to file. If write=FALSE,'NMwriteSection()' returns the resulting input.txt without writingit to disk. Default is 'TRUE'.

The default is to give some information along the wayon what data is found. But consider setting this to TRUE fornon-interactive use. Default can be configured using'NMdataConf()'.

If TRUE (default) and only one file is edited, theresulting rows are returned directly. If more than one file isedited, the result will always be a list with one element perfile.

The parameter, as returned by 'NMreadExt()'

Name of the model name column.

A parameter table, like returned by 'NMreadExt()'.

The name of a column, as a string. Calculate thecorrelations within a grouping variable? This will often be acolumn containing the model name.

See '?NMdataConf'

The name of the column from which to take the'OMEGA' values. Default is "value" in alignment with theoutput from 'NMreadExt()'.

Passed to addCor

Table of parameters to augment with additional columns

Optional string to add to all new columnnames. Maybe except 'i' and 'j'.

Add 'i' and 'j'? Default is 'TRUE' if no suffix is supplied, and 'FALSE' if a suffix is specified.

Overwrite non-missing values? Default is 'FALSE'.

Table of parameters to augment with additional columns.

Overwrite non-missing values? Default is 'FALSE'.

Table of initial values as created by NMreadInits().

The data set to add the variables to.

The name of the column with the subjectidentifier. All calculations are by default done by subject,so this column name must be provided. Default is controlled by'?NMdataConf()'.

Name of time column on which calculations ofrelative times will be based. Default it"TIME".Default is controlled by '?NMdataConf()'.

The name of the event ID column. This must existin data. Default is EVID.

col.evid The name of the dose amount column. Thismust exist in data. Default is AMT.

Name of the time of previous dose column (createdbyaddTAPD()). Default is"TPDOS". Set toNULL to not create this column.

Name of the time of previous dose column (createdbyaddTAPD()). Default is"TAPD". Set toNULL to not create this column.

The name of the column to be created holdingthe previous dose amount. Set to NULL to not create thiscolumn.

The name of the column to be created holdingthe cumulative dose amount. Set to NULL to not create thiscolumn.

The name of the column (created by addTAPD)that holds the cumulative number of doses administered to thesubject. Set to NULL to not create this column.

String to be prepended to all generated columnnames, that is each of col.tpdos, col.tapd, col.ndoses,col.pdosamt, col.doscuma that are not NULL.

String to be appended to all generated columnnames, that is each of col.tpdos, col.tapd, col.ndoses,col.pdosamt, col.doscuma that are not NULL.

A string that will be evaluated as a customexpression to identify relevant events. See subset.is.completeas well.

Only used in combination withnon-missing subset.dos. By default, subset.dos is used inaddition to the impact of col.evid (must be 1 or 4) andcol.amt (greater than zero). If subset.is.complete=TRUE,subset.dos is used alone, and col.evid and col.amt arecompletely ignored. This is typically useful if the events arenot doses but other events that are not expressed as a typicaldose combination of EVID and AMT columns.

Order of events. This will only matter if thereare simultaneous events of different event types withinsubjects. Typically if using nominal time, it may be importantto specify whether samples at dosing times are pre-dosesamples. The default is 'c(3,0,4,1,2)' - i.e. samples andsimulations are pre-dose. See details.

Columns to do calculations within. Default is ID.

Scaling value for columns related to dose amount,relative to AMT values. col.pdosamt and col.doscuma areaffected and will be derived as AMT/SDOSE.

Suppress messages? Default can be set using 'NMdataConf()'.

The default is to return data as a data.frame. Passa function (say 'tibble::as_tibble') in as.fun to convert tosomething else. If data.tables are wanted, use'as.fun="data.table"'. The default can be configured usingNMdataConf.

Deprecated. Use col.doscumn instead.

object to convert

Not used

The unquoted names that will become character values inthe returned vector.

The name of the unique row identifier (say "ROW").

a list file or input control stream file path.

unique elements or vectors with unique elements

A vector of character strings to modify

Replace any number of consecutive blank spaces by asingle blank. Default is TRUE.

Drop spaces before first non-empty character. Defaultis TRUE.

Drop spaces after last non-empty character. Defaultis TRUE.

object with elements containing label attributes.

If sort="alpha", results are sorted alphabetically.

objects which element names to compare

As alternative to ..., you can supply the datasets in a list here.

If TRUE, the original dataset names are used inreported table. If not, generic x1, x2,... are used. Thelatter may be preferred for readability.

Do you just want a TRUE/FALSE to whether thenames of the two objects are the same? Default is FALSE whichmeans to return an overview for interactive use. You mightwant to use TRUE in programming. However, notice that thischeck may be overly rigorous. Many classes are compatibleenough (say numeric and integer), and compareCols doesn't takethis into account.

If TRUE, don't report columns where no differencefound. Default is TRUE if number of data sets supplied isgreater than one. If only one data set is supplied, the fulllist of columns is shown by default.

Columns of special interest. These will alwaysbe included in overview and indicated by a prepended * to thecolumn names. This argument is often useful when you start bydefining a set of columns that you want to end up with bycombining a number of data sets.

the function that will be run on each column tocheck for differences.base::class is default. Notice that thealternativebase::typeof is different in certain ways. Forinstance,typeof will not report a difference on numeric vsdifftime. You could basically submit any function that takes avector and returns a single value.

The default is to give some information along the wayon what data is found. But consider setting this to TRUE fornon-interactive use. Default can be configured usingNMdataConf.

A function that will be run on the result beforereturning. If first input data set is a data.table, thedefault is to return a data.table, if not the default is toreturn a data.frame. Use whatever to get what fits in withyour workflow. Default can be configured with NMdataConf.

Deprecated. Use keep.names instead.

Deprecated. Use test.equal instead.

elements as detected by 'NMreadInits()'

data set to transpose (widen)

left-hand side variables as character vector. Result willbe long/vertical in these variables.

left-hand side variables as character vector. Result willbe wide in these variables.

Additional arguments passed to 'data.table::dcast()'.

The deprecated argument name (a character string).

The non-deprecated argument name (a characterstring).

List of arguments in the function call to look foroldarg and newarg. See '?getArgs'. If missing, 'getArgs()'will be called from within 'deprecatedArg'. See 'which' too.

If calling 'getArgs' this is passed along, referringto how many environments to jump to look at arguments.

data sets

As alternative to ..., you can supply the datasets in a list here.

If TRUE, the original dataset names are used inreported table. If not, generic x1, x2,... are used. Thelatter may be preferred for readability in some cases.

A function that will be run on the result beforereturning. If first input data set is a data.table, thedefault is to return a data.table, if not the default is toreturn a data.frame. Use whatever to get what fits in withyour workflow. Default can be configured with NMdataConf.

Deprecated. Use keep.names instead.

A data.table with parameters. Must contain columns 'i'and 'j' with row and column indexes and 'est' with parameter(matrix) values.

Specifies whether pars contains only a lower orupper triangle of an assumed symmetric matrix (most often thecase for variance-covariance matrices), or it contains thefull matrix. 'dt.subset="unique"' (default) means that 'pars' onlycontains either upper or lower diagonal matrix (includingdiagonal), 'dt.subset="all"' means 'pars' contains both upperand lower triangles. See details.

By default, the maximum row number is derived as hemaximum value in the 'i' column. If more (empty ones) areneeded, specify the maximum row number with 'max.i'. This canbe necessary in cases where only estimated elements areavailable but a full matrix including elements related tofixed parameters is needed.

Value to insert for missing elements

The name of the column from which to take the'OMEGA' values. Default is "value" in alignment with theoutput from 'NMreadExt()'.

Vectors to put into data.table

Like for 'lapply()', an object to process (typically avector or a list). Passed to 'lapply()'.

Function to run for each element in 'X'. Passed to'lapply()'.

If supplied, setnames will be run on eachelement returned by lapply wit value.names as the 'new'argument.

What to call the column holding the values orthe names of 'X'? Default is "element". What goes into thiscolumn depends on the class of 'X'. If 'X' is a charactervector, it will be the values of 'X'. If 'X' is a list, itwill be the names of the elements in the list.

Fill resulting data with 'NA's in order to combineinto a single 'data.frame'? Default is TRUE.

The default is to return data as a data.frame. Passa function in as.fun to convert to something else. Ifdata.tables are wanted, use 'as.fun="data.table"'. The defaultcan be configured using 'NMdataConf()'.

arguments passed to lapply

The data set to edit.

Pattern to search for in character columns. Passedto 'gsub()'. By default, 'gsub()' works with regularexpressions. See ... for how to disable this if you want toreplace a specific string.

pattern or string to replace with. Passed to'gsub()'.

The default is to return data as a data.frame. Passa function (say tibble::as_tibble) in as.fun to convert tosomething else. If data.tables are wanted, useas.fun="data.table". The default can be configured usingNMdataConf.

Additional arguments passed to 'gsub()'. Especially,notice fixed=TRUE will disable interpretation of 'pattern' and'replace' as regular expressions.

a data.table.

another data.table.

The default is to give some information along the wayon what data is found. But consider setting this to TRUE fornon-interactive use. Default can be configured usingNMdataConf.

additional arguments passed to file.path().

data.frame in which to look for covariates

covariates will be searched for in combinations of values inthese columns. Often by will be either empty or ID. But it can alsobe both say c("ID","DRUG") or c("ID","TRT").

Deprecated. Use by instead.

The default is to return a data.table if data is a data.tableand return a data.frame in all other cases. Pass a function in as.fun toconvert to something else. If data is not a data.table, the default canbe configured using NMdataConf.

data.frame in which to look for covariates

optional covariates will be searched for in combinations ofvalues in these columns. Often by will be either empty or ID. Butit can also be both say c("ID","DRUG") or c("ID","TRT").

Deprecated. Use by instead.

The default is to return a data.table if data is a data.tableand return a data.frame in all other cases. Pass a function in as.fun toconvert to something else. If data is not a data.table, the default canbe configured using NMdataConf.

The dataset to assign flags to.

A data.frame containing at least these namedcolumns: FLAG, flag, condition. Condition is disregarded forFLAG==0. FLAG must be numeric and non-negative, flag andcondition are characters.

An optional string that provides a subset ofdata to assign flags to. A common example issubset=\"EVID==0\" to only assign to observations. Numericaland character flags will be missing in rows that are notmatched by this subset.

The name of the column containing the numericalflag values in tab.flags. This will be added to data. Defaultvalue is FLAG and can be configured using NMdataConf.

The name of the column containing the characterflag values in tab.flags. This will be added to data. Defaultvalue is flag and can be configured using NMdataConf.

The flags are applied by either decreasing(default) or increasing value of col.flagn. Decreasing ordermeans that conditions associated with higher values ofcol.flagn will be evaluated first. By using decreasing order,you can easily adjust the Nonmem IGNORE statement fromIGNORE(FLAG.NE.0) to say IGNORE(FLAG.GT.10) if BLQ's haveFLAG=10, and you decide to include these in the analysis.

Column(s) that distinct incompatible subsets ofdata. Default is "EVID" meaning that if different values ofEVID are found in data, the function will return anerror. This is a safeguard not to mix data unintentionallywhen counting flags.

The character flag to assign to rows that are notmatched by exclusion conditions (numerical flag 0).

The default is to return data.tables if input datais a data.table, and return a data.frame for all other inputclasses. Pass a function in as.fun to convert to somethingelse. If return.all=FALSE, this is applied to data andtab.flags independently.

The dataset including both FLAG and flag columns.

A data.frame containing at least these namedcolumns: FLAG, flag, condition. Condition is disregarded forFLAG==0.

A file to write the table of flag counts to. Willprobably be removed and put in a separate function.

The name of the subject ID column. Default is "ID".

The name of the column containing the numericalflag values in tab.flags. This will be added to data. Use thesame as when flagsAssign was called (if that wasused). Default value is FLAG and can be configured usingNMdataConf.

The name of the column containing the characterflag values in data and tab.flags. Use the same as whenflagsAssign was called (if that was used). Default value isflag and can be configured using NMdataConf.

An optional column to group the counting by. This couldbe "STUDY", "DRUG", "EVID", or a combination of multiplecolumns.

The flags are applied by either decreasing(default) or increasing value of col.flagn. By usingdecreasing order, you can easily adjust the Nonmem IGNOREstatement from IGNORE(FLAG.NE.0) to say IGNORE(FLAG.GT.10) ifBLQ's have FLAG=10, and you decide to include these in theanalysis.

The character flag to assign to rows that are notmatched by exclusion conditions (numerical flag 0).

What to call the total set of data beforeapplying exclusion flags. Default is "All available data".

Column(s) that distinct incompatible subsets ofdata. Default is "EVID" meaning that if different values ofEVID are found in data, the function will return anerror. This is a safeguard not to mix data unintentionallywhen counting flags.

Save file? Default is TRUE, meaning that a file willbe written if file argument is supplied.

Suppress non-critical messages? Default is 'FALSE'.

The default is to return a data.table if input datais a data.table, and return a data.frame for all other inputclasses. Pass a function in as.fun to convert to somethingelse. If data is not a data.table, default can be configuredusing NMdataConf.

The file name or file names to modify.

A character string or a numeric to add to the filename. If a vector, the vector is collapsed to a single string,using 'sep' as separator in the collapsed string.

In case x is numeric, a number of zeros to pad beforethe appended number. This is useful if you are generating saymore than 10 files, and your counter will be 01, 02,..,10,... and not 1, 2,...,10,...

The separator between the existing file name (untilextension) and the addition.

If 'x' is of length greater than 1, the default isto collapse the elements to a single string using 'sep' asseparator. See the 'collapse' argument to '?paste'. If youwant to treat them as separate strings, use 'collapse=NULL'which will lead to generation of separate file names. However,currently 'fn' or 'x' must be of length 1.

"append" (default) or "prepend".

Allow 'fn' to be string(s) without extensions?Default is 'FALSE' in which case an error will be thrown if'fn' contains strings without extensions. If 'TRUE', 'x' willbe appended to fn in these cases.

file name. Often ending in an extension after a periodbut the extension is not needed.

new file name extension. If omitted or NULL, theextension of fn is returned.

Function call as provided bysys.call().

Environment in which to evaluate the arguments.

character vector of full file paths. Specify eitherfiles or both file.pattern and dir.

A regular expression to look for in dir. Ifused, dir must also be supplied.

The directory i which to look for file.pattern. dir ispassed to list.files as pattern. If supplied, file.patternmust also be supplied.

The default is not to be quiet.

A file path to a a text file to read.

Text lines if file was already read.

If the 'file' argument is used and if 'as.one' isTRUE, the file(s) are read and put into a 'data.table' with amodel column and a 'text' column. Default is FALSE. Be carefulwith this, as it returns different formats whether the 'file'or the 'lines' argument is used.

The elements object produced by 'NMreadInits()'.

Any object

Data set to process. Must be a data.frame-like structure.

Column to split data by.

function to pass to 'lapply()'.

If some subsets return NULL, drop the emptyelements in the returned list?

The data to look into.

The columns to look for missings in.

If supplied, we are keeping track of the missings withinthe values of the by columns. In summary, by is included too.

Strings that should be interpreted asmissing. All spaces will be removed before we compare tona.strings. The default is c("",".") so say " . " is amissing by default.

Keep quiet? Default is not to.

A function that will be run on the result beforereturning. If first input data set is a data.table, thedefault is to return a data.table, if not the default is toreturn a data.frame. Use whatever to get what fits in withyour workflow. Default can be configured with NMdataConf.

path to output control stream

The time zone of the time stamp from Nonmem. Thedefault ("as.is") is to try to extract it or take it from thesystem on which this function is run. See details.

A matrix

Either '"lower"' (default) or '"upper"', or'"all"' for which triangle to return. '"lower"' and '"upper"'are equivalent for covariance or correlation matrices but thereturned indexes will differ. '"all"' will return the fullmatrix which mostly makes sense if matrix is not a covarianceor correlation matrix.

See '?NMdataConf'

A data.frame with the number of rows must should beobtained from the merge. The resulting data.frame will beordered like x.

A data.frame that will be merged onto x.

The column(s) to merge by. Character string (vector). byor by.x and by.y must be supplied.

If the columns to merge by in x and y are nameddifferently. by or by.x and by.y must be supplied.

If the columns to merge by in x and y are nameddifferently. by or by.x and by.y must be supplied.

If common columns are found in x and y, andthey are not used in 'by', this will by default create columnsnamed like col.x and col.y in result (see ?merge). Often, thisis a mistake, and the default is to throw a warning if thishappens. If using 'mergeCheck' in programming, you may want tomake sure this is not happening and usecommon.cols=stop. If you want nothing to happen, you can docommon.cols=NULL. You can also use 'common.cols="drop.x"'to drop "non-by" columns in 'x' with identical column names in'y'. Use "drop.y" to drop them in 'y' and avoid theconflicts. The last option is to use 'common.cols="merge.by"'which means 'by' will automatically be extended to include allcommon column names.

If you want to include a check of the numberof columns being added to the dimensions of 'x'. So ifncols.expect=1, the resulting data must have exactly onecolumn more than 'x' - if not, an error will be returned.

If using 'mergeCheck' inside other functions, itcan be useful to use track.msg=TRUE. This will add informationto messages/warnings/errors that they came from 'mergeCheck()'.

If FALSE, the names of the added columns arereported. Default value controlled by NMdataConf.

Deprecated. Use x.

Deprecated. Use y.

Not implemented.

If NA's are found in (matched) by columns in bothx and why, what should we do? This could be OK, but in manycases, it's because something unexpected is happening. Usefun.na.by=NULL if you don't want to be notified and want to goahead regardless.

The default is to return a data.table if x is adata.table and return a data.frame in all other cases. Pass afunction in as.fun to convert to something else.

Deprecated. Please use 'common.cols'.

additional arguments passed to data.table::merge. Ifall is among them, an error will be returned.

parameters to pass to strwrap

The function to pass the text through. Typically,message, warning, or stop. If NULL, nothing will happen, andNULL is invisibly returned.

Passed to strwrap. Default is "\n".

Passed to strwrap. Default is an empty string.

Passed to strwrap. Default is 80.

If TRUE, the name of the function throwing themessage/warning/error is mentioned. This is not default butuseful when using function inside other functions.

a data.table or something to be converted to adata.table.

passed to print.data.table.

The summary object to be printed. See ?summary.NMdata

Arguments passed to other print methods.

object to read.

Not used.

Object from NMscanTables

The name of the column holding logical of whetherrow was found in output tables.

data.frame in which to rename columns

Function that returns TRUE for columns to berenamed.

Function that takes the existing column name andreturns the new one.

Rename those where FALSE is returned fromfun.test.

The default is to return data as a data.frame. Passa function (say tibble::as_tibble) in as.fun to convert tosomething else. If data.tables are wanted, useas.fun="data.table". The default can be configured usingNMdataConf.

a .lst (output) or a .mod (input) control streamfile. The filename does not need to end in .lst. It isrecommended to use the output control stream because itreflects the model as it was run rather than how it is plannedfor next run. However, see file.mod and dir.data.

The input control stream file path. Default is tolook for \"file\" with extension changed to .mod (PSNstyle). You can also supply the path to the file, or you canprovide a function that translates the output file path to theinput file path. If dir.data is missing, the input controlstream is needed. This is because the .lst does not containthe path to the data file. The .mod file is only used forfinding the data file. How to interpret the datafile is readfrom the .lst file. The default can be configured usingNMdataConf. See dir.data too.

The data directory can only be read from thecontrol stream (.mod) and not from the output file (.lst). Soif you only have the output file, use dir.data to tell inwhich directory to find the data file. If dir.data isprovided, the .mod file is not used at all.

Specification of the data file path. When this isused, the control streams are not used at all.

If TRUE (default), data columns are namedas interpreted by Nonmem (in $INPUT). If data file containsmore columns than mentioned in $INPUT, these will be named asin data file (if data file contains named variables).

List of arguments passed to fread. Notice thatexcept for "input" and "file", you need to supply allarguments to fread if you use this argument. Default valuescan be configured using NMdataConf.

The name of the subject ID column. Optional and onlyused to calculate number of subjects in data. Default ismodified by NMdataConf.

row-level data

An NMdata object (from NMscanData).

Only passed to the summary generic if object is missing NMdatameta data (this should not happen anyway).

The dataset to find a new element name for

Character vector of names that must not bematched. Only one of data and names can be supplied.

The base name of the new element. A number willappended to this string that will ensure that the new elementname is not already in use.

Where to start the search for a smallest available indexnumber to add to 'base' if necessary.

Delimiter to use when appending integers. Default is none.

Maximum number of iterations on element name.

If base isn't in use already, use it without adigit appended?

The length of the diagonal. Same as number of rowsor columns.

The expression to catch errors, warnings, messages from

Catch messages? Default is 'FALSE'.

Catch warnings? Default is 'TRUE'.

Catch errors? Default is 'TRUE'.

An 'NMdata' object.

A vector, either numeric or character.

Require one unique value? If 'TRUE' (default), anerror is thrown if non-unique values found. If 'FALSE', allthe unique values are returned.

In addition to NA-elements, what text stringsshould be considered missing? Default is empty strings andstrings only containing white spaces ('na.pattern="^ *$"').

A data set

The meta data to attach

If FALSE, the existing meta data will be removed. IfTRUE, metadata will be appended to existing metadata. However,this will not work recursively.

Should always be TRUE.