diff --git a/.Rbuildignore b/.Rbuildignore index 56d974e2..34e575c9 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -43,9 +43,20 @@ input.shk INTER LINK.LNK README.html +inst/examples/nonmem/*.msf +inst/examples/nonmem/*.xml +inst/examples/nonmem/xgxr002.* +;;; used in vignettes/NMscanData.Rmd +;; inst/examples/nonmem/xgxr014.* tests/testthat/testOutput/simulations/nonmem tests/testthat/testOutput/simulations/NMsimData_xgxr.+\.rds tests/testthat/testData/simulations/xgxr..._subprobs/NMsim_xgxr..._subprobs_dir.+ +;; tests/testthat/testData/nonmem/xgxr005.* +;; tests/testthat/testData/nonmem/xgxr017.* +;; tests/testthat/testData/nonmem/xgxr018.* +;; tests/testthat/testData/nonmem/xgxr020.* +;; tests/testthat/testData/nonmem/xgxr021.* tests/testthat/testData/simulations/xgxr.*/.*.rds tests/testthat/testData/simulations/xgxr.*/.*.csv + .*_input.rds diff --git a/DESCRIPTION b/DESCRIPTION index ce832fbe..ce4da35c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: NMdata Type: Package Title: Preparation, Checking and Post-Processing Data for PK/PD Modeling -Version: 0.1.6.923 +Version: 0.1.7.905 Authors@R: c(person(given="Philip", family="Delff", email = "philip@delff.dk", @@ -33,6 +33,6 @@ Suggests: htmltools, spelling Encoding: UTF-8 -URL: https://philipdelff.github.io/NMdata/ BugReports: https://github.com/philipdelff/NMdata/issues Language: en-US +URL: https://philipdelff.github.io/NMdata/ diff --git a/NEWS.md b/NEWS.md index 03d1ace4..f1ecf469 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,30 @@ +# NMdata 0.1.8 -# 0.1.7 +## New features + +* If truncating columns in the csv file `NMwriteData()` accepts data + with commas in values, even when writing to csv files. + +* `NMscanTables()` includes model name in meta data table. Useful for + generation of overviews of output tables from multiple models. + +## Bugfixes + +* Support for data file names including substrings "ACCEPT" and "IGN" + is added. Before, such data set file names could lead to failure if + interpreting data subsetting filters (ACCEPT and IGN(ORE)) in Nonmem + control streams. + +## Other improvements + +* NMscanMultiple would sometimes print a bit of a messy overview of + the results. That has been fixed without implications on the results + returned. + +* dt2mat() now returns actual matrix objects. This provides + compatibility with the simpar package. + +# NMdata 0.1.7 ## New features * `NMreadPartab()` has been generalized to support comment formats very @@ -9,7 +34,7 @@ any structure should be supported as long as delimitors are not alphabetic or numeric (so any special characters should work). Notice, delimitors can change between fields . Example: - "$THETA 1.4 ; 3 - CL (Clearance) [L/h]" would be matched by + `"$THETA 1.4 ; 3 - CL (Clearance) [L/h]"` would be matched by `NMreadPartab(...,format="%init ;%idx-%symbol(%label)[%unit]")` which would then return a table including columns init, idx, symbol, label, and unit. The comments must be systematic within say `$THETA` @@ -22,8 +47,40 @@ that references THETA(1), `NMrelate()` will return a label `TVCL`. -* `mergeCheck()` has additional features available in the common.cols - argument. +* Improved support for character-coded `TIME` and `DATE` + arguments. The default behavior is to allow (not require) `TIME` and + `DATE` columns to be non-numeric. This is to support the Nonmem + character format of DATE and TIME. It affects sorting of columns + (`NMorderColumn()`) and the auto-generated `$INPUT` section + suggestions. Where applicable, the `allow.char.TIME` argument + controls this behavior. Set to `allow.char.TIME=FALSE` to require + `TIME` and `DATE` columns be numeric. Thanks to Sanaya Shroff for + the request, enabling `NMsim` to simulate using data sets with one + or more of these columns coded as character. + +* `mergeCheck(x,y)` has new options for handling common columns in + data sets. The `common.cols` argument replaces `fun.commoncols` with + added functionality. + + - `common.cols="merge.by"` to include them in by, even +if they are not provided in the `by` argument. + + - `common.cols="drop.x"` to drop the columns on the `x` and +overwrite with columns in y + + - `common.cols="drop.y"` to preserve in `x` + + + - `base::stop` The default value. Throw an error if common.columns +are not included in merge `by` options. + + - `common.cols=NULL` disabled handling and return columns as ".x" +and ".y". + + - Any function. `common.cols=warning` will issue a warning instead +of throwing an error. + + * `NMreadExt()` separates objective function values into a separate list element. The `return` argument is used to control what data to @@ -32,7 +89,9 @@ objective funtion value, or "all" for a list with all of those. * `NMreadExt()` adds block information to `OMEGA` and `SIGMA` elements - based on off-diagonal values. + based on off-diagonal values. `iblock` identifies which block the + element is in. `blocksize` is the size of the block the element is + in. Thank you Brian Reilly for contributing to this. * `NMreadExt()` adds a `par.name` column which is provides consistent parameter naming. Instead of Nonmem's `THETA1` which is found in the @@ -61,14 +120,16 @@ * `NMreadExt()` would mess up iterations and parameter estimates if `as.fun` was set to returning something else than `data.table`s. Fixed. -# 0.1.6 + + +# NMdata 0.1.6 ## New features * Function `NMreadShk()` to read and format `.shk` (shrinkage) files. * Functions `mat2dt()` and `dt2mat()` included to convert between - matrices and data.frame format of matrix data - especially for + matrices and `data.frame` format of matrix data - especially for symmetric matrices. * Function `addOmegaCorr()` adds estimated correlation between ETAs to @@ -87,7 +148,7 @@ `ADDL` and `II`) followed by other doses. Fixed. Thanks to Simone Cassani for catching it. -# 0.1.5 +# NMdata 0.1.5 ## New features * `countFlags` no longer needs a table of flags. By default it will summarize the ones found in data. If additional flags wanted in @@ -121,7 +182,9 @@ so). Now `NMdataConf(reset=TRUE)` makes sure to wipe all such configuration if exists. -# 0.1.4 + + +# NMdata 0.1.4 ## New functions * `NMreadParsText()` is a new function to extract comments to @@ -157,7 +220,7 @@ tables. * `NMreadText` would fail to disregard some comment lines when `keep.comments=FALSE`. Fixed. -# 0.1.3 +# NMdata 0.1.3 * Better support for models with multiple estimation steps. Particularly reading output tables now better distinguishes between Nonmem table numbers and repetitions (like @@ -167,7 +230,7 @@ tables. * Improved support for reading multiple models with NMreadExt and NMreadPhi. -# 0.1.2 +# NMdata 0.1.2 ## New features * NMreadExt is a new function that reads parameter estimates, uncertainties if available, estimation iterations and other @@ -186,7 +249,7 @@ NMreadPhi. arguments. -# 0.1.1 +# NMdata 0.1.1 ## New features * NMwriteSection can now handle functions to perform control stream editing. NMwriteSection provides methods to edit control @@ -202,7 +265,7 @@ NMreadPhi. with a directory (`dir`) only. * Minor bugfix in compareCols in case input is an unnamed list -# 0.1.0 +# NMdata 0.1.0 ## New features * The super fast `fst` format is now supported. Data sets can be @@ -271,7 +334,7 @@ This release provides a few bugfixes, nothing major. cumulative number and it aligns with col.doscuma which is the cumulative amount. -# 0.0.16 +# NMdata 0.0.16 ## New features * `NMwriteSection()` includes argument `location`. In combination with `section`, this determines where the new section is @@ -295,11 +358,11 @@ on file. This has been fixed to support cases where renaming or a pseudonym is being used to generate an `ID` column in `$INPUT`. -# 0.0.15 +# NMdata 0.0.15 This update is of no difference to users. A technicality has been chaned to ensure consistent test results once data.table 1.14.7 is -# 0.0.14 +# NMdata 0.0.14 ## New features * `fnExtension()` has been generalized. It now ignores leading spaces in new extension, and extensions with zero or one leading period are @@ -362,9 +425,13 @@ chaned to ensure consistent test results once data.table 1.14.7 is identifier is simplified. * NMdata version added to welcome message. -# 0.0.13 + + + +# NMdata 0.0.13 ## New functions + * `NMexpandDoses()` - Transform repeated dosing events (`ADDL`/`II`) to individual dosing events * `addTAPD()` - Add cumulative number of doses, time of last dose, @@ -374,12 +441,14 @@ chaned to ensure consistent test results once data.table 1.14.7 is has long been part of NMdata but has not been exported until now. ## New data + * A new data set called mad is included. It is based on the mad_missing_duplicates from the `xgxr` package. Doses are implemented using ADDL and II (so only one dosing row per subject). It is included for testing the new NMexpandDoses and addTAPD functions. ## Bugfixes + * Non-critical bugfix in mergeCheck dimensions overview printed to console. One column too many was reported in input and result data. No implications on results from mergeCheck. diff --git a/R/NMapplyFilters.R b/R/NMapplyFilters.R index 91bd0df3..5023cfb5 100644 --- a/R/NMapplyFilters.R +++ b/R/NMapplyFilters.R @@ -31,7 +31,7 @@ NMapplyFilters <- function(data,file,text,lines,invert=FALSE,as.fun,quiet) { value <- NULL ### Section end: Dummy variables, only not to get NOTE's in pacakge checks - + if(missing(quiet)) quiet <- NULL quiet <- NMdataDecideOption("quiet",quiet) @@ -71,11 +71,19 @@ NMapplyFilters <- function(data,file,text,lines,invert=FALSE,as.fun,quiet) { ## simplifying so IGNORE/IGN is always IGN text3 <- gsub("IGNORE","IGN",text3) - conds.sc <- regmatches(text3, gregexpr("(?:IGN) *=* *[^ (+=]",text3)) + + ## ^(.* )* : if anything before IGN, there must be a space in between + ## conds.sc <- regmatches(text3, gregexpr("^(.* )*(?:IGN) *=* *[^ (+=]",text3)) + conds.sc <- regmatches(text3, gregexpr("(?0){ + } else if(width>0){ text.nm.input <- strwrap( text.nm.input ,width=width diff --git a/R/NMorderColumns.R b/R/NMorderColumns.R index 2d3026ea..f0527413 100644 --- a/R/NMorderColumns.R +++ b/R/NMorderColumns.R @@ -47,6 +47,10 @@ ##' configured with `NMdataConf()`. ##' @param col.dv a vector of column names to put early to represent ##' dependent variable(s). Default is DV. +##' @param allow.char.TIME For the $INPUT text proposal only. Assume +##' Nonmem can read TIME and DATE even if it can't be translated to +##' numeric. This is necessary if using the 00:00 format. Default +##' is TRUE. ##' @param as.fun The default is to return a data.table if data is a ##' data.table and return a data.frame in all other cases. Pass a ##' function in as.fun to convert to something else. The default @@ -91,6 +95,7 @@ NMorderColumns <- function(data, col.row, col.flagn, col.dv="DV", + allow.char.TIME=TRUE, as.fun=NULL, quiet){ @@ -129,7 +134,7 @@ NMorderColumns <- function(data, if(missing(first)) first <- NULL if(missing(last)) last <- NULL - first1 <- c(col.row,col.id,col.nomtime,col.time,"EVID","CMT","AMT","II","ADDL","RATE", + first1 <- c(col.row,col.id,col.nomtime,"DATE",col.time,"EVID","CMT","AMT","II","ADDL","RATE", "SS",col.dv,"MDV") first2 <- c(col.flagn,"OCC","GRP","TRIAL","STUDY","DRUG","ROUTE") @@ -137,20 +142,25 @@ NMorderColumns <- function(data, nms <- names(data) nms.dup <- nms[duplicated(nms)] if(!quiet && length(nms.dup)) messageWrap(paste0("Duplicated column names:\n",paste(nms.dup,collapse=", ")),fun.msg=warning) -### these checks are now done in NMcheckData - ## missing <- setdiff(setdiff(first1,c("II","ADDL","RATE","SS")),nms) - ## if(!quiet && length(missing)) messageWrap(paste0("These standard Nonmem columns were not found in data:\n",paste(missing,collapse="\n")),fun.msg=message) first <- c(first1,first) dt.names <- data.table(name=colnames(data)) if(chars.last){ +### Accept TIME and DATE even if not numeric + ## chars.last: If columns cannot be converted to numerics dt.num.w <- data[,lapply(.SD,NMisNumeric)] + dt.names[,isnum:=as.logical(dt.num.w[1,])] + if(allow.char.TIME){ + dt.names[,isnum:=name%in%c("DATE","TIME")|as.logical(dt.num.w[1,])] + } } else { dt.names[,isnum:=TRUE] } + + dt.names[,nfirst:=match(name,first)] dt.names[,nfirst2:=match(name,first2)] dt.names[,nlast:=match(name,last)] diff --git a/R/NMreadExt.R b/R/NMreadExt.R index 1ed3b222..9e143029 100644 --- a/R/NMreadExt.R +++ b/R/NMreadExt.R @@ -78,25 +78,29 @@ NMreadExt <- function(file,return,as.fun,modelname,col.model,auto.ext,tableno="m #### Section start: Dummy variables, only not to get NOTE's in pacakge checks #### + . <- NULL + blocksize <- NULL + cond <- NULL + eigCor <- NULL + est <- NULL + FIX <- NULL + i <- NULL + iblock <- NULL + imin <- NULL + j <- NULL ITERATION <- NULL - variable <- NULL NMREP <- NULL model <- NULL par.type <- NULL parameter <- NULL - i <- NULL - j <- NULL TABLENO <- NULL table.step <- NULL - FIX <- NULL - est <- NULL - cond <- NULL - eigCor <- NULL partLik <- NULL se <- NULL seStdDevCor <- NULL stdDevCor <- NULL value <- NULL + variable <- NULL ### Section end: Dummy variables, only not to get NOTE's in pacakge checks diff --git a/R/NMreadSection.R b/R/NMreadSection.R index 02270aa2..ff8205a1 100644 --- a/R/NMreadSection.R +++ b/R/NMreadSection.R @@ -40,7 +40,6 @@ ##' @param keepEmpty Deprecated. See keep.empty. ##' @param keepName Deprecated. See keep.name. ##' @param asOne Deprecated. See as.one. -##' @param cleanSpaces Deprecated. See clean.spaces. ##' @return character vector with extracted lines. ##' @param ... Additional arguments passed to NMextractText ##' @return character vector with extracted lines. @@ -57,12 +56,13 @@ NMreadSection <- function(file=NULL, lines=NULL, text=NULL, section, return="tex ## deprecated arguments keepEmpty, keepName, keepComments, asOne, - cleanSpaces, ...){ + ...){ ## args <- getArgs() args <- getArgs(sys.call(),parent.frame()) as.one <- deprecatedArg("asOne","as.one",args=args) - clean.spaces <- deprecatedArg("cleanSpaces","clean.spaces",args=args) + ## clean.spaces <- deprecatedArg("cleanSpaces","clean.spaces",args=args) + ## if(!missing(cleanSpaces)) rm(cleanSpaces) keep.empty <- deprecatedArg("keepEmpty","keep.empty",args=args) keep.name <- deprecatedArg("keepName","keep.name",args=args) keep.comments <- deprecatedArg("keepComments","keep.comments",args=args) @@ -78,6 +78,12 @@ NMreadSection <- function(file=NULL, lines=NULL, text=NULL, section, return="tex section <- toupper(section) } + match.exactly <- FALSE + if(section!="."){ + string.start <- substring(sub("^\\$","",cleanSpaces(section)),1,3) + match.exactly <- !string.start%in%c("COV","EST","SIM") + } + res <- NMextractText(file=file, lines=lines, text=text, section=section, ## this wrapper is especially made for "$" sections char.section="\\$", @@ -90,7 +96,8 @@ NMreadSection <- function(file=NULL, lines=NULL, text=NULL, section, return="tex clean.spaces=clean.spaces, ## we only consider the model definition, not results. type="mod", - match.exactly=FALSE, + ## match.exactly=FALSE, + match.exactly=match.exactly, ## deprecated args ## keepEmpty=keepEmpty, ## keepName=keepName, diff --git a/R/NMrelateOne.R b/R/NMrelateOne.R index 3270bae5..f6c83434 100644 --- a/R/NMrelateOne.R +++ b/R/NMrelateOne.R @@ -44,7 +44,7 @@ NMrelateOne <- function(file,lines,par.type="OMEGA",sections=c("PRED","PK","ERRO ,SIGMA="(SIGMA|ERR|EPS)" ) str.regex.find <- paste0("[^[:alnum:]]",str.regex) - + lines.list <- NMreadSection(lines=lines,keep.comments=FALSE) lines.list <- lines.list[names(lines.list)%in%sections] @@ -65,7 +65,11 @@ NMrelateOne <- function(file,lines,par.type="OMEGA",sections=c("PRED","PK","ERRO ## determine found variable type? - dt.code <- dt.code[,.(varname=regmatches(line2, gregexpr(paste0(str.regex.find,"\\(([0-9]+(,[0-9]+)*)\\)"),line2)) |> unlist()),by=.(line.var,line2)] + dt.code <- dt.code[,.(varname=unlist( + regmatches(line2, + gregexpr(paste0(str.regex.find,"\\(([0-9]+(,[0-9]+)*)\\)"),line2)) + )), + by=.(line.var,line2)] dt.code[,varname:=sub("^[^[:alnum:]]","",varname)] dt.code[,var.type:=sub(sprintf("(%s).*",str.regex),"\\1",varname)][,lineno:=.I] diff --git a/R/NMscanData.R b/R/NMscanData.R index 09bf71a4..e51b1f56 100644 --- a/R/NMscanData.R +++ b/R/NMscanData.R @@ -247,6 +247,13 @@ NMscanData <- function(file, col.row, use.input, merge.by.row, formats.read <- setdiff(formats.read,c("rds")) } + if(missing(col.model)||!is.null(col.model)) { + if(missing(col.model)) { + col.model <- NULL + } + col.model <- NMdataDecideOption("col.model",col.model) + } + ### deprecated before 2023-06-12 ## if(!missing(tab.count)) .Deprecated("col.tableno",old="tab.count") @@ -322,7 +329,7 @@ NMscanData <- function(file, col.row, use.input, merge.by.row, #### Section start: read all output tables and add to meta data #### ## tables <- NMscanTables(file,quiet=TRUE,as.fun="data.table",col.row=col.row,col.id=col.id,col.tableno=col.tableno) - tables <- NMscanTables(file,quiet=TRUE,as.fun="data.table",col.row=col.row,col.id=col.id,col.tableno=col.tableno,col.nmrep=TRUE,skip.absent=skip.absent) + tables <- NMscanTables(file,quiet=TRUE,as.fun="data.table",col.row=col.row,col.id=col.id,col.tableno=col.tableno,col.nmrep=TRUE,skip.absent=skip.absent,modelname=modelname,col.model=col.model) meta.output <- copy(NMinfoDT(tables)$tables) @@ -380,13 +387,6 @@ NMscanData <- function(file, col.row, use.input, merge.by.row, cnames.input.result <- nminfo.input$colnames[,result] outnames <- unlist(lapply(tables,colnames)) allnames <- c(outnames,cnames.input.result) - - if(missing(col.model)||!is.null(col.model)) { - if(missing(col.model)) { - col.model <- NULL - } - col.model <- NMdataDecideOption("col.model",col.model) - } if(!is.null(col.model) && col.model%in%allnames){ diff --git a/R/NMscanInput.R b/R/NMscanInput.R index 7110a2da..9d0ed016 100644 --- a/R/NMscanInput.R +++ b/R/NMscanInput.R @@ -101,6 +101,7 @@ NMscanInput <- function(file, formats.read, file.mod, dir.data=NULL, #### Section start: Dummy variables, only not to get NOTE's in pacakge checks #### datafile <- NULL + info <- NULL nid <- NULL input <- NULL result <- NULL @@ -167,8 +168,12 @@ NMscanInput <- function(file, formats.read, file.mod, dir.data=NULL, break } } - if(is.null(type.file)) stop("None of the allowed file formats found.") - path.data.input <- info.datafile[[paste0("path.",type.file)]] + if(is.null(type.file)){ + message(paste0("$DATA section extracted\n",info$datafile$DATA)) + message("Based on that, data files related to this file were expected:\n",info$datafile$string) + stop("None of the allowed file formats found.") + } + path.data.input <- info.datafile[[paste0("path.",type.file)]] data.input <- NMreadCsv(path.data.input,as.fun="data.table",args.fread=args.fread,args.fst=args.fst,format=type.file) diff --git a/R/NMscanMultiple.R b/R/NMscanMultiple.R index 00efe52d..a4cd5703 100644 --- a/R/NMscanMultiple.R +++ b/R/NMscanMultiple.R @@ -45,6 +45,10 @@ NMscanMultiple <- function(files,dir,file.pattern,as.fun,...){ if(missing(as.fun)) as.fun <- NULL as.fun <- NMdataDecideOption("as.fun",as.fun) + + quiet <- list(...)$quiet + quiet <- NMdataDecideOption("quiet",quiet) + #### Section start: Define ad-hoc functions #### catchAnything <- function(fun){ @@ -84,7 +88,7 @@ NMscanMultiple <- function(files,dir,file.pattern,as.fun,...){ all.files <- getFilePaths(files=files,file.pattern=file.pattern,dir=dir) if(length(all.files)==0) { - cat("No files matched path/pattern criteria\n") + message("No files matched path/pattern criteria") return(NULL) } @@ -114,7 +118,7 @@ NMscanMultiple <- function(files,dir,file.pattern,as.fun,...){ } dims.res <- dims(list.data=res.all.list[dt.lst[,which(success)]]) dt.lst <- mergeCheck(dt.lst,dims.res,by.x="lst",by.y="data",all.x=T,quiet=TRUE) - + info.list <- lapply(res.all.list,NMinfo) names(info.list) <- all.files @@ -123,12 +127,14 @@ NMscanMultiple <- function(files,dir,file.pattern,as.fun,...){ res.all <- rbindlist(res.all.list[dt.lst[,which(success)]],fill=TRUE) writeNMinfo(res.all,info.list) -### quiet would have to be looked for in ... - ## if(!quiet){ - setcolorder(dt.lst,cc(lst,nrows,ncols,success,warning)) - cat("\nOverview of model scanning results:\n") - print(dt.lst) - ## } + + setcolorder(dt.lst,cc(lst,nrows,ncols,success,warning)) + + if(!quiet){ + message("\nOverview of model scanning results:\n") + message(paste0(capture.output(dt.lst), collapse = "\n")) + #message(print(dt.lst)) + } ## run as.fun res.all <- as.fun(res.all) diff --git a/R/NMscanTables.R b/R/NMscanTables.R index db4a9fda..d95255e7 100644 --- a/R/NMscanTables.R +++ b/R/NMscanTables.R @@ -10,10 +10,10 @@ ##' NMdataConf. ##' @param col.tableno Nonmem includes a counter of tables in the ##' written data files. These are often not useful. However, if -##' col.tableno is TRUE (not default), this will be carried forward -##' and added as a column called NMREP. Even if NMREP is generated -##' by NMscanTables, it is treated like any other table column in -##' meta (?NMinfo) data. +##' col.tableno is TRUE (not default), this will be carried +##' forward and added as a column called NMREP. Even if NMREP is +##' generated by NMscanTables, it is treated like any other table +##' column in meta (?NMinfo) data. ##' @param col.nmrep col.nmrep If tables are repeated, include a ##' counter? It does not relate to the order of the $TABLE ##' statements but to cases where a $TABLE statement is run @@ -40,6 +40,21 @@ ##' meta information. Notice, not all meta information (e.g., ##' dimensions) are available because the tables need to be read ##' to derive that. +##' @param modelname Only affects meta data table. The model name to +##' be stored if col.model is not NULL. If not supplied, the name +##' will be taken from the control stream file name by omitting +##' the directory/path and deleting the .lst extension +##' (path/run001.lst becomes run001). This can be a character +##' string or a function which is called on the value of file +##' (file is another argument to NMscanData). The function must +##' take one character argument and return another character +##' string. As example, see NMdataConf()$modelname. The default +##' can be configured using NMdataConf. +##' @param col.model Only affects meta data table. A column of this +##' name containing the model name will be included in the +##' returned data. The default is to store this in a column called +##' "model". See argument "modelname" as well. Set to NULL if not +##' wanted. Default can be configured using NMdataConf. ##' @return A list of all the tables as data.frames. If details=TRUE, ##' this is in one element, called data, and meta is another ##' element. If not, only the data is returned. @@ -49,7 +64,8 @@ ##' @import data.table ##' @export -NMscanTables <- function(file,as.fun,quiet,col.nmrep=TRUE,col.tableno=FALSE,col.id="ID",col.row,details,skip.absent=FALSE,meta.only=FALSE){ +NMscanTables <- function(file,as.fun,quiet,col.nmrep=TRUE,col.tableno=FALSE,col.id="ID",col.row,details,skip.absent=FALSE,meta.only=FALSE,modelname, + col.model){ #### Section start: Dummy variables, only not to get NOTE's in package checks #### @@ -87,6 +103,16 @@ NMscanTables <- function(file,as.fun,quiet,col.nmrep=TRUE,col.tableno=FALSE,col. ## args <- getArgs() args <- getArgs(sys.call(),parent.frame()) deprecatedArg(oldarg="details",args=args) + + + if(missing(col.model)||!is.null(col.model)) { + if(missing(col.model)) { + col.model <- NULL + } + col.model <- NMdataDecideOption("col.model",col.model) + } + modelname <- NMdataDecideOption("modelname",modelname) + dir <- dirname(file) extract.info <- function(x,NAME,default){ @@ -135,9 +161,13 @@ NMscanTables <- function(file,as.fun,quiet,col.nmrep=TRUE,col.tableno=FALSE,col. meta[,exists:=file.exists(file)] meta[,filetype:="output"] meta[,file.mtime:=file.mtime(file)] + if(!is.null(col.model)) { + runname <- modelname(file) + meta[,c(col.model):=runname] + } if(meta.only){ - setcolorder(meta,intersect(c("source","name","nrow","ncol","nid","level","scope","has.col.row","has.col.id","full.length","filetype","format", + setcolorder(meta,intersect(c(col.model,"source","name","nrow","ncol","nid","level","scope","has.col.row","has.col.id","full.length","filetype","format", "file.mtime","file"),colnames(meta))) return(as.fun(meta)) } @@ -235,7 +265,7 @@ NMscanTables <- function(file,as.fun,quiet,col.nmrep=TRUE,col.tableno=FALSE,col. ## sep not used so omitted - setcolorder(meta,intersect(c("source","name","nrow","ncol","nid","level","scope","has.col.row","has.col.id","full.length","filetype","format", + setcolorder(meta,intersect(c(col.model,"source","name","nrow","ncol","nid","level","scope","has.col.row","has.col.id","full.length","filetype","format", "file.mtime","file"),colnames(meta))) diff --git a/R/NMwriteData.R b/R/NMwriteData.R index 5493659e..e584dda9 100644 --- a/R/NMwriteData.R +++ b/R/NMwriteData.R @@ -299,17 +299,6 @@ NMwriteData <- function(data,file,formats.write=c("csv","rds"), data.dt <- copy(as.data.table(data)) - ## Check if character variables contain commas - ## This would cause trouble when writing csv - - has.no.comma <- data.dt[,lapply(.SD,function(x){is.numeric(x)||!any(grepl(",",as.character(x)))})] - comma.ok <- as.logical(has.no.comma[1]) - - if(any(!comma.ok)){ - messageWrap(paste("You must avoid commas in data values. They will corrupt the csv file, so get rid of them before saving data. Comma found in column(s):",paste(colnames(data.dt)[comma.ok==FALSE],sep=", ")), - fun.msg=stop) - } - ## if any repetetions, give warning, and add numbers @@ -348,6 +337,27 @@ NMwriteData <- function(data,file,formats.write=c("csv","rds"), n.cols.trunc <- length(strsplit(string.trunc,split=" ")[[1]]) data.csv <- data[,1:n.cols.trunc] } + + ## Check if character variables contain commas + ## This would cause trouble when writing csv + has.no.comma <- data.csv[,lapply(.SD,function(x){is.numeric(x)||!any(grepl(",",as.character(x)))})] + comma.ok <- as.logical(has.no.comma[1]) + + if(any(!comma.ok)){ + + messageWrap( + "When writing csv, You must avoid commas in data values. They will corrupt the csv file. You can + +1) avoid csv using formats.write=\"rds\" or +2) drop columns containing commas or +3) remove or replace commas in data values before saving data. ?editCharCols can help with option 3.", +paste(" + +Comma found in column(s):",paste(colnames(data.csv)[comma.ok==FALSE],collapse=", ")), +fun.msg=stop) + } +### Check for commas done + do.call(fwrite,append(list(x=data.csv,file=file.csv),args.fwrite)) diff --git a/R/NMwriteSectionOne.R b/R/NMwriteSectionOne.R index 9dfb15f7..428aa712 100644 --- a/R/NMwriteSectionOne.R +++ b/R/NMwriteSectionOne.R @@ -4,7 +4,7 @@ NMwriteSectionOne <- function(file0,lines,section,location="replace", newlines,list.sections,newfile, backup=TRUE,blank.append=TRUE,write, quiet=FALSE){ - + after <- NULL before <- NULL mad.dl <- NULL @@ -63,7 +63,7 @@ NMwriteSectionOne <- function(file0,lines,section,location="replace", keep.name=TRUE,keep.comments=TRUE,as.one=TRUE, clean.spaces=FALSE) - if(length(idx.dlines)==0&location%in%cc(replace,before,after)) { + if(length(idx.dlines)==0 && location%in%cc(replace,before,after)) { if(!quiet) message("Section not found. Nothing to be done.") return(lines) } @@ -108,11 +108,13 @@ NMwriteSectionOne <- function(file0,lines,section,location="replace", } } if(location=="after"){ + all.lines <- c(lines,newlines) if(min.dl>1){ all.lines <- c(lines[1:(max.dl)], newlines, - lines[(max.dl+1):length(lines)] + lines[-(1:(max.dl))] + ## lines[max((max.dl+1),length(lines)):length(lines)] ) } else { all.lines <- lines diff --git a/R/dt2mat.R b/R/dt2mat.R index b213e781..330313a6 100644 --- a/R/dt2mat.R +++ b/R/dt2mat.R @@ -8,7 +8,10 @@ ##' @param dt.subset Specifies whether pars contains only a lower or ##' upper triangle of an assumed symmetric matrix (most often the ##' case for variance-covariance matrices), or it contains the -##' full matrix. +##' full matrix. `dt.subset="unique"` (default) means that `pars` only +##' contains either upper or lower diagonal matrix (including +##' diagonal), `dt.subset="all"` means `pars` contains both upper +##' and lower triangles. See details. ##' @param max.i By default, the maximum row number is derived as he ##' maximum value in the `i` column. If more (empty ones) are ##' needed, specify the maximum row number with `max.i`. This can @@ -21,9 +24,9 @@ ##' output from `NMreadExt()`. ##' @details If pars does not contain all `i` values, they will be ##' imputed with zeros. The desired matrix dimension is inferred -##' from `min(i)` and `max(i)`. In case `dt.subset=="unique"` +##' from `min(i)` and `max(i)`. In case `dt.subset=="unique"` ##' missing `j` elements will also give imputations of missing -##' elements. +##' elements. ##' @import data.table ##' @return a matrix ##' @export @@ -62,8 +65,21 @@ dt2mat <- function(pars,dt.subset="unique",max.i,fill=0,col.value) { i.missing <- setdiff(min(pars$i):max.i,pars$i) pars.mat <- rbind(pars.mat,data.table(i=i.missing,j=i.missing),fill=TRUE) + + ## note, dcast returns a keyed data.table (keys are LHS vars) so it is always ordered by i. - matrix.pars <- as.matrix(dcast(pars.mat,i~j,value.var="value")[,!("i")]) + pars.matshape <- dcast(pars.mat,i~j,value.var="value")[,!("i")] + matrix.pars <- matrix(unlist(pars.matshape),ncol=nrow(pars.matshape)) + + if(F){ + if(nrow(pars.matshape)==1){ + ## matrix.pars <- matrix(pars.matshape) + matrix.pars <- matrix(as.numeric(unlist(pars.matshape))) + } else { + matrix.pars <- as.matrix(pars.matshape) + } + } + if(!isFALSE(fill)){ matrix.pars[is.na(matrix.pars)] <- fill } diff --git a/R/mergeCheck.R b/R/mergeCheck.R index b3abbb8f..bbaeb762 100644 --- a/R/mergeCheck.R +++ b/R/mergeCheck.R @@ -125,9 +125,8 @@ ##' dt.cov <- pk[,.(ID=unique(ID))] ##' dt.cov[,COV:=sample(1:5,size=.N,replace=TRUE)] ##' dt.cov <- dt.cov[c(1,1:(.N-1))] -##' dim(pk) ##' res.merge <- merge(pk,dt.cov,by="ID") -##' dim(res.merge) +##' dims(pk,dt.cov,res.merge) ##' mergeCheck(pk,dt.cov,by="ID") ##' } ##' @export @@ -274,7 +273,8 @@ mergeCheck <- function(x,y,by,by.x,by.y,common.cols=base::warning,ncols.expect,t commoncols.found <- FALSE fun.commoncols <- common.cols - if(is.character(fun.commoncols)) fun.commoncols <- stop + ## if common.cols was one of drop.x etc, that handling must be sufficient to avoid findings +if(is.character(fun.commoncols)) fun.commoncols <- stop if(length(cols.common.notby)) { messageWrap(paste0("x and y have common column names not being merged by. This will create new column names in output. Common but not merged by: ",paste(cols.common.notby,collapse=", "),"."), diff --git a/README.md b/README.md index 9b5ff66e..66419035 100644 --- a/README.md +++ b/README.md @@ -157,20 +157,6 @@ read multiple models and compare their predictions. ``` r res <- NMscanMultiple(dir=system.file("examples/nonmem", package="NMdata"), file.pattern="xgxr.*\\.lst",as.fun="data.table",quiet=TRUE) -#> -#> Overview of model scanning results: -#> lst nrows -#> 1: /data/home/philipde/wdirs/NMdata/inst/examples/nonmem/xgxr001.lst 905 -#> 2: /data/home/philipde/wdirs/NMdata/inst/examples/nonmem/xgxr002.lst 905 -#> 3: /data/home/philipde/wdirs/NMdata/inst/examples/nonmem/xgxr003.lst 905 -#> 4: /data/home/philipde/wdirs/NMdata/inst/examples/nonmem/xgxr014.lst 905 -#> 5: /data/home/philipde/wdirs/NMdata/inst/examples/nonmem/xgxr018.lst 905 -#> ncols success warning -#> 1: 40 TRUE FALSE -#> 2: 34 TRUE FALSE -#> 3: 34 TRUE FALSE -#> 4: 36 TRUE FALSE -#> 5: 33 TRUE FALSE gmean <- function(x)exp(mean(log(x))) res.mean <- res[,.(gmeanPRED=gmean(PRED)),by=.(model,NOMTIME)] obs.all <- unique(res[,.(ID,NOMTIME,TIME,DV)]) diff --git a/devel/check_package.R b/devel/check_package.R index 3d893321..d3b542d9 100644 --- a/devel/check_package.R +++ b/devel/check_package.R @@ -2,6 +2,7 @@ remotes::install_github("thinkr-open/checkhelper") library(checkhelper) path.pkg <- "~/wdirs/NMdata" finds <- find_missing_tags(path.pkg) +as.data.table(finds) file.csv <- tempfile() fwrite(finds,file=file.csv) as.data.table(finds) diff --git a/devel/overview_function_tags.R b/devel/overview_function_tags.R index b1a869b3..a0fa720a 100644 --- a/devel/overview_function_tags.R +++ b/devel/overview_function_tags.R @@ -1,11 +1,62 @@ -dir.r <- "~/wdirs/NMdata/R" +library(stringi) + +dir.r <- "~/wdirs/NMdata/tests/testthat" files.r <- list.files(dir.r,pattern=".*\\.r",full.names=T,ignore.case=TRUE) +fdt <- data.table(file=files.r) -dt.fams <- lapply(files.r,function(file){ - lines <- readLines(file) - dt <- data.table(file=basename(file),line.fam=lines[grepl(".*family.*",lines)]) - dt[,family:=sub(".*family *","",line.fam)] +fun.grab.model <- function(file){ + + lines <- try(readLines(file)) + if("try-error" %in%class(lines)){ + return(NULL) + } + + dt.lines <- data.table(file=file,code=lines) + + dt.lines[,ROW:=.I] + dt.lines <- dt.lines[grepl(".*xgxr...\\..*",code)] + if(nrow(dt.lines)==0) return(NULL) + + ## dt.lines[,file=basename(file),line.model=lines[grepl(".*xgxr???\\..*",lines)]) + dt.lines[,file.model:=stri_extract_all_regex(code,pattern="xgxr...\\....")] + dt.lines[,fnExt:=fnExtension(file.model)] + dt.lines[,run:=fnExtension(file.model,"")] + + dt.lines[] } -) |> rbindlist() -dt.fams[,.N,by=.(family)] +file <- "/data/home/philipde/wdirs/NMdata/tests/testthat/test_addTAPD.R" +res <- fun.grab.model(file="/data/home/philipde/wdirs/NMdata/tests/testthat/test_NMscanTables.R") + + +## dir.r <- "~/wdirs/NMdata/tests/testthat" +dir.r <- "~/wdirs/NMdata/R" +files.r <- list.files(dir.r,pattern=".*\\.r",full.names=T,ignore.case=TRUE) +fdt <- data.table(file=files.r) + + +odt.fams <- lapply(files.r,fun.grab.model) +dt.calls <- rbindlist(odt.fams) +dt.calls +dt.calls[,.N,by=.(run)][order(N)] +dt.calls[,.N,by=.(run,fnExt)][order(N)] + +## dir.inst <- "../tests/testthat/testData/nonmem" +dir.inst <- "../inst/examples/nonmem" +dt.found <- data.table(file.lst=list.files(dir.inst,pattern=".*\\.lst"))[ + ,run:=fnExtension(file.lst,"")][ + ,found:=TRUE] + +dt.cf <- merge(dt.found,dt.calls,by="run",all=T) + +dt.cf[,.N,by=.(run,found)][order(N)] +## dt.cf[,.N,by=.(run,fnExt,found)][order(N)] + + +dt.cf[run=="xgxr002"] +## trimmed to only mod and ext +dt.cf[run=="xgxr031"] +## left out by rbuildignore +dt.cf[run=="xgxr005"] + +## try omit 002 014 diff --git a/devel/scripts/check_NMdata.R b/devel/scripts/check_NMdata.R index ba55d69e..bd1d69d9 100644 --- a/devel/scripts/check_NMdata.R +++ b/devel/scripts/check_NMdata.R @@ -1,6 +1,17 @@ + + library(devtools) load_all() res.test <- test() res.chek <- check() + + +devtools::build_readme() +setwd("~/wdirs/NMdata") +library(rmarkdown) +render("NEWS.md") + +library(pkgdown) +pkgdown::build_news() diff --git a/devel/scripts/dsCreate_1.R b/devel/scripts/dsCreate_1.R index ae540832..d89a4c78 100644 --- a/devel/scripts/dsCreate_1.R +++ b/devel/scripts/dsCreate_1.R @@ -15,6 +15,7 @@ library(ggplot2) ## install_github("philipdelff/NMdata") ## library(NMdata) +setwd("~/wdirs/NMdata/devel/scripts/") library(devtools) load_all("~/wdirs/NMdata") @@ -310,3 +311,13 @@ NMwriteSection(file.nm("xgxr001dir/input.txt"),section="DATA",newlines=sec.data. ### Section end: Create xgxr001dir +#### Section start: Version with AMT in microgram #### + +### xgxgr002: CYCLE=DROP, BBW for WEIGHTB +pk2 <- copy(pk) +pk2[,AMT:=AMT*1000] +nmcode <- NMwriteData(pk2,file=file.data.test("xgxr12.csv"),script=script.1,args.stamp = list(description="AMT in micrograms")) + + +### Section end: Version with AMT in microgram + diff --git a/devel/todo.org b/devel/todo.org index a8faf0fd..ca09e4e2 100644 --- a/devel/todo.org +++ b/devel/todo.org @@ -40,7 +40,7 @@ With load_all(): function is called from other functions. Possible to distinguish somehow? ** High level features -*** TODO [#A] Support for DATE type columns +*** DONE Support for DATE type columns ** New functions *** document columns **** TODO Check for existence of char column in values @@ -439,7 +439,7 @@ if return="iterations" only return iterations *** NMreadTabSlow **** TODO [#A] Only handle Table numbers if "TABLE..." strings found *** NMreadParsText -**** DONE [#A] order columns - created ones to the right +**** DONE order columns - created ones to the right **** DONE change num to idx and include a field.idx so user can specify what to use. If idx is not taken from fields, it should not come out in the results. @@ -449,7 +449,7 @@ in which case "; [" is a delimiter **** DONE Empty fields make it break Like ;1;CL;;;mL/h **** TODO [#B] Handle SAME -***** DONE [#A] Include test so we at least know what happens +***** DONE Include test so we at least know what happens *** NMreadSection **** DONE error returned when return="idx" and no section specified :Bug: **** TODO [#B] return="text"/"idx" should be return.idx=TRUE/FALSE instead diff --git a/man/NMgenText.Rd b/man/NMgenText.Rd index 3b8235fa..e4ee219a 100644 --- a/man/NMgenText.Rd +++ b/man/NMgenText.Rd @@ -72,7 +72,7 @@ used (probably only interesting if character values are supplied).} \item{allow.char.TIME}{For the $INPUT text proposal only. Assume -Nonmem can read TIME even if it can't be translated to +Nonmem can read TIME and DATE even if it can't be translated to numeric. This is necessary if using the 00:00 format. Default is TRUE.} diff --git a/man/NMorderColumns.Rd b/man/NMorderColumns.Rd index 014ba668..3f98e162 100644 --- a/man/NMorderColumns.Rd +++ b/man/NMorderColumns.Rd @@ -17,6 +17,7 @@ NMorderColumns( col.row, col.flagn, col.dv = "DV", + allow.char.TIME = TRUE, as.fun = NULL, quiet ) @@ -77,6 +78,11 @@ configured with `NMdataConf()`.} \item{col.dv}{a vector of column names to put early to represent dependent variable(s). Default is DV.} +\item{allow.char.TIME}{For the $INPUT text proposal only. Assume +Nonmem can read TIME and DATE even if it can't be translated to +numeric. This is necessary if using the 00:00 format. Default +is TRUE.} + \item{as.fun}{The default is to return a data.table if data is a data.table and return a data.frame in all other cases. Pass a function in as.fun to convert to something else. The default diff --git a/man/NMreadExt.Rd b/man/NMreadExt.Rd index 8a5c4db5..9ed03f19 100644 --- a/man/NMreadExt.Rd +++ b/man/NMreadExt.Rd @@ -23,7 +23,9 @@ estimates and iterations of the estimates. If \code{return="pars"} (default) the final estimates are returned in addition to what other parameter-level information is found, like FIX, sd etc. as columns. If -\code{return="iterations"}, the iterations are returned. If +\code{return="iterations"}, the iterations are returned +(including objective function value). If \code{return="obj"} +objective function value at final estimate is returned. If \code{return="all"}, all er returned, though in separate data.frames compiled in a list.} diff --git a/man/NMreadParsText.Rd b/man/NMreadParsText.Rd index 4f1ef703..b956bb51 100644 --- a/man/NMreadParsText.Rd +++ b/man/NMreadParsText.Rd @@ -111,7 +111,7 @@ $SIGMA 1 res <- NMreadParsText(lines=lines, format="\%init;[\%num];\%symbol", -format.omega="\%init \%symbol ; \%num ; \%type ; \%label ; \%unit", +format.omega="\%init; \%symbol ; \%num ; \%type ; \%label ; \%unit", field.idx="num") ## BLOCK() SAME are skipped diff --git a/man/NMreadSection.Rd b/man/NMreadSection.Rd index 48bdb876..9dfc0d9e 100644 --- a/man/NMreadSection.Rd +++ b/man/NMreadSection.Rd @@ -21,7 +21,6 @@ NMreadSection( keepName, keepComments, asOne, - cleanSpaces, ... ) @@ -79,8 +78,6 @@ probably want FALSE.} \item{asOne}{Deprecated. See as.one.} -\item{cleanSpaces}{Deprecated. See clean.spaces.} - \item{...}{Additional arguments passed to NMextractText} } \value{ diff --git a/man/NMscanTables.Rd b/man/NMscanTables.Rd index 47c6b6f1..63fe5576 100644 --- a/man/NMscanTables.Rd +++ b/man/NMscanTables.Rd @@ -14,7 +14,9 @@ NMscanTables( col.row, details, skip.absent = FALSE, - meta.only = FALSE + meta.only = FALSE, + modelname, + col.model ) } \arguments{ @@ -44,10 +46,10 @@ with a different name. The argument is passed to NMscanTables.} \item{col.tableno}{Nonmem includes a counter of tables in the written data files. These are often not useful. However, if -col.tableno is TRUE (not default), this will be carried forward -and added as a column called NMREP. Even if NMREP is generated -by NMscanTables, it is treated like any other table column in -meta (?NMinfo) data.} +col.tableno is TRUE (not default), this will be carried +forward and added as a column called NMREP. Even if NMREP is +generated by NMscanTables, it is treated like any other table +column in meta (?NMinfo) data.} \item{col.id}{name of the subject ID column. Used for calculation of the number of subjects in each table.} @@ -68,6 +70,23 @@ returned showing what tables were found and some available meta information. Notice, not all meta information (e.g., dimensions) are available because the tables need to be read to derive that.} + +\item{modelname}{Only affects meta data table. The model name to +be stored if col.model is not NULL. If not supplied, the name +will be taken from the control stream file name by omitting +the directory/path and deleting the .lst extension +(path/run001.lst becomes run001). This can be a character +string or a function which is called on the value of file +(file is another argument to NMscanData). The function must +take one character argument and return another character +string. As example, see NMdataConf()$modelname. The default +can be configured using NMdataConf.} + +\item{col.model}{Only affects meta data table. A column of this +name containing the model name will be included in the +returned data. The default is to store this in a column called +"model". See argument "modelname" as well. Set to NULL if not +wanted. Default can be configured using NMdataConf.} } \value{ A list of all the tables as data.frames. If details=TRUE, diff --git a/man/dt2mat.Rd b/man/dt2mat.Rd index 2b82bac4..f4e56a7c 100644 --- a/man/dt2mat.Rd +++ b/man/dt2mat.Rd @@ -14,7 +14,10 @@ and `j` with row and column indexes and `est` with parameter \item{dt.subset}{Specifies whether pars contains only a lower or upper triangle of an assumed symmetric matrix (most often the case for variance-covariance matrices), or it contains the -full matrix.} +full matrix. `dt.subset="unique"` (default) means that `pars` only +contains either upper or lower diagonal matrix (including +diagonal), `dt.subset="all"` means `pars` contains both upper +and lower triangles. See details.} \item{max.i}{By default, the maximum row number is derived as he maximum value in the `i` column. If more (empty ones) are @@ -39,7 +42,7 @@ further calculations. \details{ If pars does not contain all `i` values, they will be imputed with zeros. The desired matrix dimension is inferred - from `min(i)` and `max(i)`. In case `dt.subset=="unique"` + from `min(i)` and `max(i)`. In case `dt.subset=="unique"` missing `j` elements will also give imputations of missing elements. } diff --git a/man/figures/README-unnamed-chunk-2-1.png b/man/figures/README-unnamed-chunk-2-1.png index f3c25af0..e788b6b6 100644 Binary files a/man/figures/README-unnamed-chunk-2-1.png and b/man/figures/README-unnamed-chunk-2-1.png differ diff --git a/man/mergeCheck.Rd b/man/mergeCheck.Rd index 53654456..1a332d80 100644 --- a/man/mergeCheck.Rd +++ b/man/mergeCheck.Rd @@ -45,8 +45,8 @@ named like col.x and col.y in result (see ?merge). Often, this is a mistake, and the default is to throw a warning if this happens. If using mergeCheck in programming, you may want to make sure this is not happening and use -fun.commoncols=stop. If you want nothing to happen, you can do -fun.commoncols=NULL. You can also use `common.cols="drop.x"` +common.cols=stop. If you want nothing to happen, you can do +common.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 the conflicts. The last option is to use `common.cols="merge.by"` @@ -166,9 +166,8 @@ pk <- readRDS(file=system.file("examples/data/xgxr2.rds",package="NMdata")) dt.cov <- pk[,.(ID=unique(ID))] dt.cov[,COV:=sample(1:5,size=.N,replace=TRUE)] dt.cov <- dt.cov[c(1,1:(.N-1))] -dim(pk) res.merge <- merge(pk,dt.cov,by="ID") -dim(res.merge) +dims(pk,dt.cov,res.merge) mergeCheck(pk,dt.cov,by="ID") } } diff --git a/tests/testthat/testData/nonmem/xgxr031.coi b/tests/testthat/testData/nonmem/xgxr031.coi deleted file mode 100644 index b10f839f..00000000 --- a/tests/testthat/testData/nonmem/xgxr031.coi +++ /dev/null @@ -1,25 +0,0 @@ -TABLE NO. 1: First Order Conditional Estimation with Interaction: Problem=1 Subproblem=0 Superproblem1=0 Iteration1=0 Superproblem2=0 Iteration2=0 - NAME THETA1 THETA2 THETA3 THETA4 THETA5 SIGMA(1,1) SIGMA(2,1) SIGMA(2,2) OMEGA(1,1) OMEGA(2,1) OMEGA(2,2) OMEGA(3,1) OMEGA(3,2) OMEGA(3,3) OMEGA(4,1) OMEGA(4,2) OMEGA(4,3) OMEGA(4,4) OMEGA(5,1) OMEGA(5,2) OMEGA(5,3) OMEGA(5,4) OMEGA(5,5) - THETA1 4.54869E+02 -2.28642E+02 -3.25645E+01 -6.20639E+01 1.63086E+02 -1.34353E+02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 5.22778E+01 0.00000E+00 0.00000E+00 7.58781E+01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - THETA2 -2.28642E+02 4.71550E+02 4.59125E+01 1.16380E+01 -1.86011E+01 -1.09784E+03 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.11131E+02 0.00000E+00 0.00000E+00 -1.35345E+01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - THETA3 -3.25645E+01 4.59125E+01 3.00469E+02 8.82571E+01 -1.02180E+02 -1.98131E+02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 4.05035E+01 0.00000E+00 0.00000E+00 1.53776E+01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - THETA4 -6.20639E+01 1.16380E+01 8.82571E+01 6.42597E+01 -1.15376E+02 -5.07557E+01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -1.66235E+01 0.00000E+00 0.00000E+00 -2.91471E+01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - THETA5 1.63086E+02 -1.86011E+01 -1.02180E+02 -1.15376E+02 5.31510E+02 3.26007E+02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 9.55387E+01 0.00000E+00 0.00000E+00 3.70844E+01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - SIGMA(1,1) -1.34353E+02 -1.09784E+03 -1.98131E+02 -5.07557E+01 3.26007E+02 3.65217E+04 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -2.36228E+02 0.00000E+00 0.00000E+00 -3.15360E+02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - SIGMA(2,1) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - SIGMA(2,2) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(1,1) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(2,1) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(2,2) 5.22778E+01 1.11131E+02 4.05035E+01 -1.66235E+01 9.55387E+01 -2.36228E+02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.08954E+03 0.00000E+00 0.00000E+00 1.80317E+02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(3,1) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(3,2) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(3,3) 7.58781E+01 -1.35345E+01 1.53776E+01 -2.91471E+01 3.70844E+01 -3.15360E+02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.80317E+02 0.00000E+00 0.00000E+00 5.74822E+02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(4,1) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(4,2) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(4,3) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(4,4) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(5,1) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(5,2) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(5,3) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(5,4) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(5,5) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 diff --git a/tests/testthat/testData/nonmem/xgxr031.cor b/tests/testthat/testData/nonmem/xgxr031.cor deleted file mode 100644 index 2a14cc35..00000000 --- a/tests/testthat/testData/nonmem/xgxr031.cor +++ /dev/null @@ -1,25 +0,0 @@ -TABLE NO. 1: First Order Conditional Estimation with Interaction: Problem=1 Subproblem=0 Superproblem1=0 Iteration1=0 Superproblem2=0 Iteration2=0 - NAME THETA1 THETA2 THETA3 THETA4 THETA5 SIGMA(1,1) SIGMA(2,1) SIGMA(2,2) OMEGA(1,1) OMEGA(2,1) OMEGA(2,2) OMEGA(3,1) OMEGA(3,2) OMEGA(3,3) OMEGA(4,1) OMEGA(4,2) OMEGA(4,3) OMEGA(4,4) OMEGA(5,1) OMEGA(5,2) OMEGA(5,3) OMEGA(5,4) OMEGA(5,5) - THETA1 6.35305E-02 5.78566E-01 -2.40718E-01 3.08463E-01 -1.23949E-01 2.30215E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -1.14747E-01 0.00000E+00 0.00000E+00 -2.81536E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - THETA2 5.78566E-01 5.97575E-02 -2.07810E-01 1.92902E-01 -5.74709E-02 3.40281E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -1.95289E-01 0.00000E+00 0.00000E+00 5.44954E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - THETA3 -2.40718E-01 -2.07810E-01 8.12782E-02 -6.68455E-01 -1.98554E-01 -2.83950E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -3.60282E-02 0.00000E+00 0.00000E+00 -1.57328E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - THETA4 3.08463E-01 1.92902E-01 -6.68455E-01 2.22130E-01 5.42447E-01 3.93250E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -2.73520E-02 0.00000E+00 0.00000E+00 1.98147E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - THETA5 -1.23949E-01 -5.74709E-02 -1.98554E-01 5.42447E-01 5.82080E-02 -9.84697E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -8.63241E-02 0.00000E+00 0.00000E+00 9.75005E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - SIGMA(1,1) 2.30215E-01 3.40281E-01 -2.83950E-02 3.93250E-02 -9.84697E-02 5.61172E-03 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -4.11213E-02 0.00000E+00 0.00000E+00 6.59379E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - SIGMA(2,1) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - SIGMA(2,2) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(1,1) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(2,1) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(2,2) -1.14747E-01 -1.95289E-01 -3.60282E-02 -2.73520E-02 -8.63241E-02 -4.11213E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 3.20986E-02 0.00000E+00 0.00000E+00 -2.12913E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(3,1) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(3,2) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(3,3) -2.81536E-02 5.44954E-02 -1.57328E-01 1.98147E-01 9.75005E-02 6.59379E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -2.12913E-01 0.00000E+00 0.00000E+00 4.42140E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(4,1) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(4,2) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(4,3) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(4,4) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(5,1) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(5,2) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(5,3) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(5,4) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(5,5) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 diff --git a/tests/testthat/testData/nonmem/xgxr031.cov b/tests/testthat/testData/nonmem/xgxr031.cov deleted file mode 100644 index dbfd7823..00000000 --- a/tests/testthat/testData/nonmem/xgxr031.cov +++ /dev/null @@ -1,25 +0,0 @@ -TABLE NO. 1: First Order Conditional Estimation with Interaction: Problem=1 Subproblem=0 Superproblem1=0 Iteration1=0 Superproblem2=0 Iteration2=0 - NAME THETA1 THETA2 THETA3 THETA4 THETA5 SIGMA(1,1) SIGMA(2,1) SIGMA(2,2) OMEGA(1,1) OMEGA(2,1) OMEGA(2,2) OMEGA(3,1) OMEGA(3,2) OMEGA(3,3) OMEGA(4,1) OMEGA(4,2) OMEGA(4,3) OMEGA(4,4) OMEGA(5,1) OMEGA(5,2) OMEGA(5,3) OMEGA(5,4) OMEGA(5,5) - THETA1 4.03613E-03 2.19648E-03 -1.24298E-03 4.35303E-03 -4.58360E-04 8.20753E-05 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -2.33997E-04 0.00000E+00 0.00000E+00 -7.90815E-05 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - THETA2 2.19648E-03 3.57096E-03 -1.00933E-03 2.56057E-03 -1.99905E-04 1.14111E-04 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -3.74591E-04 0.00000E+00 0.00000E+00 1.43983E-04 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - THETA3 -1.24298E-03 -1.00933E-03 6.60615E-03 -1.20685E-02 -9.39367E-04 -1.29513E-05 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -9.39946E-05 0.00000E+00 0.00000E+00 -5.65381E-04 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - THETA4 4.35303E-03 2.56057E-03 -1.20685E-02 4.93415E-02 7.01368E-03 4.90198E-05 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -1.95021E-04 0.00000E+00 0.00000E+00 1.94605E-03 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - THETA5 -4.58360E-04 -1.99905E-04 -9.39367E-04 7.01368E-03 3.38817E-03 -3.21648E-05 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -1.61287E-04 0.00000E+00 0.00000E+00 2.50928E-04 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - SIGMA(1,1) 8.20753E-05 1.14111E-04 -1.29513E-05 4.90198E-05 -3.21648E-05 3.14914E-05 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -7.40711E-06 0.00000E+00 0.00000E+00 1.63603E-05 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - SIGMA(2,1) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - SIGMA(2,2) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(1,1) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(2,1) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(2,2) -2.33997E-04 -3.74591E-04 -9.39946E-05 -1.95021E-04 -1.61287E-04 -7.40711E-06 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.03032E-03 0.00000E+00 0.00000E+00 -3.02167E-04 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(3,1) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(3,2) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(3,3) -7.90815E-05 1.43983E-04 -5.65381E-04 1.94605E-03 2.50928E-04 1.63603E-05 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -3.02167E-04 0.00000E+00 0.00000E+00 1.95487E-03 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(4,1) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(4,2) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(4,3) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(4,4) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(5,1) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(5,2) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(5,3) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(5,4) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 - OMEGA(5,5) 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 diff --git a/tests/testthat/testData/nonmem/xgxr031.lst b/tests/testthat/testData/nonmem/xgxr031.lst deleted file mode 100644 index 466fd2f5..00000000 --- a/tests/testthat/testData/nonmem/xgxr031.lst +++ /dev/null @@ -1,842 +0,0 @@ -Thu Nov 2 03:13:03 PM EDT 2023 -$PROBLEM 021 mu-ref -$INPUT ROW ID NOMTIME TIME EVID CMT AMT DV FLAG STUDY BLQ CYCLE - DOSE PART PROFDAY PROFTIME WEIGHTB eff0 -$DATA xgxr2.csv IGNORE=@ IGNORE=(FLAG.NE.0) IGNORE(DOSE.LT.30) -$SUBROUTINE ADVAN4 TRANS4 -$PK -LTVKA=THETA(1) -LTVV2=THETA(2) -LTVCL=THETA(3) -LTVV3=THETA(4) -LTVQ=THETA(5) - -MU_1=LTVKA -KA=EXP(MU_1+ETA(1)) -MU_2=LTVV2 -V2=EXP(MU_2+ETA(2)) -MU_3=LTVCL -CL=EXP(MU_3+ETA(3)) -MU_4=LTVV3 -V3=EXP(MU_4+ETA(4)) -MU_5 = LTVQ -Q =EXP(MU_5+ETA(5)) -S2=V2 - -$ERROR - IPRED=F - IRES=DV-IPRED - - IF (IPRED.GT.1) THEN - W = SQRT(IPRED**2*SIGMA(1,1) + SIGMA(2,2)) - ELSE - W=1 - ENDIF - - IWRES=IRES/W - Y=F+F*ERR(1)+ERR(2) - -;-----------------------INITIAL ESTIMATES--------------------------------- -$THETA .1 ; LTVKA -$THETA 3 ; LTVV2 -$THETA 1 ; LTVCL -$THETA 4 ; LTVV3 -$THETA -1 ; LTVQ -$OMEGA 0 FIX -$OMEGA 0.1 -$OMEGA 0.1 -$OMEGA 0 FIX -$OMEGA 0 FIX -$SIGMA 0.1 -$SIGMA 0 FIX -$ESTIMATION METHOD=1 POSTHOC INTER MAXEVAL=9999 NSIG=2 SIGL=9 PRINT=10 - NOABORT MSFO=xgxr031.msf -$COVARIANCE -$TABLE ROW KA V2 V3 CL Q PRED IPRED Y NOPRINT - FILE=xgxr031_res.txt - - -NM-TRAN MESSAGES - - WARNINGS AND ERRORS (IF ANY) FOR PROBLEM 1 - - (WARNING 2) NM-TRAN INFERS THAT THE DATA ARE POPULATION. - - (WARNING 79) SIGMA IS USED ON THE RIGHT. WITH A SUBSEQUENT RUN, IF AN - INITIAL ESTIMATE OF A DIAGONAL BLOCK OF SIGMA IS TO BE COMPUTED BY - NONMEM, THAT BLOCK WILL BE SET TO AN IDENTITY MATRIX DURING THAT - COMPUTATION. THIS COULD LEAD TO AN ARITHMETIC EXCEPTION.* - - * THE MAXIMUM NUMBER OF WARNINGS OF ONE OR MORE TYPES WAS REACHED. - IT IS POSSIBLE THAT SOME WARNING MESSAGES WERE SUPPRESSED. - -Note: Analytical 2nd Derivatives are constructed in FSUBS but are never used. - You may insert $ABBR DERIV2=NO after the first $PROB to save FSUBS construction and compilation time - - -License Registered to: Philip Harder Delff for developing R packages that Interact with NONMEM -Expiration Date: 14 SEP 2024 -Current Date: 2 NOV 2023 -Days until program expires : 317 -1NONLINEAR MIXED EFFECTS MODEL PROGRAM (NONMEM) VERSION 7.5.1 - ORIGINALLY DEVELOPED BY STUART BEAL, LEWIS SHEINER, AND ALISON BOECKMANN - CURRENT DEVELOPERS ARE ROBERT BAUER, ICON DEVELOPMENT SOLUTIONS, - AND ALISON BOECKMANN. IMPLEMENTATION, EFFICIENCY, AND STANDARDIZATION - PERFORMED BY NOUS INFOSYSTEMS. - - PROBLEM NO.: 1 - 021 mu-ref -0DATA CHECKOUT RUN: NO - DATA SET LOCATED ON UNIT NO.: 2 - THIS UNIT TO BE REWOUND: NO - NO. OF DATA RECS IN DATA SET: 731 - NO. OF DATA ITEMS IN DATA SET: 19 - ID DATA ITEM IS DATA ITEM NO.: 2 - DEP VARIABLE IS DATA ITEM NO.: 8 - MDV DATA ITEM IS DATA ITEM NO.: 19 -0INDICES PASSED TO SUBROUTINE PRED: - 5 4 7 0 0 0 6 0 0 0 0 -0LABELS FOR DATA ITEMS: - ROW ID NOMTIME TIME EVID CMT AMT DV FLAG STUDY BLQ CYCLE DOSE PART PROFDAY PROFTIME WEIGHTB eff0 MDV -0(NONBLANK) LABELS FOR PRED-DEFINED ITEMS: - KA V2 CL V3 Q IPRED Y -0FORMAT FOR DATA: - (2(8E9.0/),2E9.0,1F2.0) - - TOT. NO. OF OBS RECS: 641 - TOT. NO. OF INDIVIDUALS: 90 -0LENGTH OF THETA: 5 -0DEFAULT THETA BOUNDARY TEST OMITTED: NO -0OMEGA HAS BLOCK FORM: - 1 - 0 2 - 0 0 3 - 0 0 0 4 - 0 0 0 0 5 -0DEFAULT OMEGA BOUNDARY TEST OMITTED: NO -0SIGMA HAS BLOCK FORM: - 1 - 0 2 -0DEFAULT SIGMA BOUNDARY TEST OMITTED: NO -0INITIAL ESTIMATE OF THETA: - 0.1000E+00 0.3000E+01 0.1000E+01 0.4000E+01 -0.1000E+01 -0INITIAL ESTIMATE OF OMEGA: - BLOCK SET NO. BLOCK FIXED - 1 YES - 0.0000E+00 - 2 NO - 0.1000E+00 - 3 NO - 0.1000E+00 - 4 YES - 0.0000E+00 - 5 YES - 0.0000E+00 -0INITIAL ESTIMATE OF SIGMA: - BLOCK SET NO. BLOCK FIXED - 1 NO - 0.1000E+00 - 2 YES - 0.0000E+00 -0COVARIANCE STEP OMITTED: NO - EIGENVLS. PRINTED: NO - SPECIAL COMPUTATION: NO - COMPRESSED FORMAT: NO - GRADIENT METHOD USED: NOSLOW - SIGDIGITS ETAHAT (SIGLO): -1 - SIGDIGITS GRADIENTS (SIGL): -1 - EXCLUDE COV FOR FOCE (NOFCOV): NO - Cholesky Transposition of R Matrix (CHOLROFF):0 - KNUTHSUMOFF: -1 - RESUME COV ANALYSIS (RESUME): NO - SIR SAMPLE SIZE (SIRSAMPLE): - NON-LINEARLY TRANSFORM THETAS DURING COV (THBND): 1 - PRECONDTIONING CYCLES (PRECOND): 0 - PRECONDTIONING TYPES (PRECONDS): TOS - FORCED PRECONDTIONING CYCLES (PFCOND):0 - PRECONDTIONING TYPE (PRETYPE): 0 - FORCED POS. DEFINITE SETTING DURING PRECONDITIONING: (FPOSDEF):0 - SIMPLE POS. DEFINITE SETTING: (POSDEF):-1 -0TABLES STEP OMITTED: NO - NO. OF TABLES: 1 - SEED NUMBER (SEED): 11456 - NPDTYPE: 0 - INTERPTYPE: 0 - RANMETHOD: 3U - MC SAMPLES (ESAMPLE): 300 - WRES SQUARE ROOT TYPE (WRESCHOL): EIGENVALUE -0-- TABLE 1 -- -0RECORDS ONLY: ALL -04 COLUMNS APPENDED: YES - PRINTED: NO - HEADER: YES - FILE TO BE FORWARDED: NO - FORMAT: S1PE11.4 - IDFORMAT: - LFORMAT: - RFORMAT: - FIXED_EFFECT_ETAS: -0USER-CHOSEN ITEMS: - ROW KA V2 V3 CL Q IPRED Y -1DOUBLE PRECISION PREDPP VERSION 7.5.1 - - TWO COMPARTMENT MODEL WITH FIRST-ORDER ABSORPTION (ADVAN4) -0MAXIMUM NO. OF BASIC PK PARAMETERS: 5 -0BASIC PK PARAMETERS (AFTER TRANSLATION): - BASIC PK PARAMETER NO. 1: ELIMINATION RATE (K) - BASIC PK PARAMETER NO. 2: CENTRAL-TO-PERIPH. RATE (K23) - BASIC PK PARAMETER NO. 3: PERIPH.-TO-CENTRAL RATE (K32) - BASIC PK PARAMETER NO. 5: ABSORPTION RATE (KA) - TRANSLATOR WILL CONVERT PARAMETERS - CL, V2, Q, V3 TO K, K23, K32 (TRANS4) -0COMPARTMENT ATTRIBUTES - COMPT. NO. FUNCTION INITIAL ON/OFF DOSE DEFAULT DEFAULT - STATUS ALLOWED ALLOWED FOR DOSE FOR OBS. - 1 DEPOT OFF YES YES YES NO - 2 CENTRAL ON NO YES NO YES - 3 PERIPH. ON NO YES NO NO - 4 OUTPUT OFF YES NO NO NO -1 - ADDITIONAL PK PARAMETERS - ASSIGNMENT OF ROWS IN GG - COMPT. NO. INDICES - SCALE BIOAVAIL. ZERO-ORDER ZERO-ORDER ABSORB - FRACTION RATE DURATION LAG - 1 * * * * * - 2 6 * * * * - 3 * * * * * - 4 * - - - - - - PARAMETER IS NOT ALLOWED FOR THIS MODEL - * PARAMETER IS NOT SUPPLIED BY PK SUBROUTINE; - WILL DEFAULT TO ONE IF APPLICABLE -0DATA ITEM INDICES USED BY PRED ARE: - EVENT ID DATA ITEM IS DATA ITEM NO.: 5 - TIME DATA ITEM IS DATA ITEM NO.: 4 - DOSE AMOUNT DATA ITEM IS DATA ITEM NO.: 7 - COMPT. NO. DATA ITEM IS DATA ITEM NO.: 6 - -0PK SUBROUTINE CALLED WITH EVERY EVENT RECORD. - PK SUBROUTINE NOT CALLED AT NONEVENT (ADDITIONAL OR LAGGED) DOSE TIMES. -0ERROR SUBROUTINE CALLED WITH EVERY EVENT RECORD. -1 - - - #TBLN: 1 - #METH: First Order Conditional Estimation with Interaction - - ESTIMATION STEP OMITTED: NO - ANALYSIS TYPE: POPULATION - NUMBER OF SADDLE POINT RESET ITERATIONS: 0 - GRADIENT METHOD USED: NOSLOW - CONDITIONAL ESTIMATES USED: YES - CENTERED ETA: NO - EPS-ETA INTERACTION: YES - LAPLACIAN OBJ. FUNC.: NO - NO. OF FUNCT. EVALS. ALLOWED: 9999 - NO. OF SIG. FIGURES REQUIRED: 2 - INTERMEDIATE PRINTOUT: YES - ESTIMATE OUTPUT TO MSF: YES - ABORT WITH PRED EXIT CODE 1: NO - IND. OBJ. FUNC. VALUES SORTED: NO - NUMERICAL DERIVATIVE - FILE REQUEST (NUMDER): NONE - MAP (ETAHAT) ESTIMATION METHOD (OPTMAP): 0 - ETA HESSIAN EVALUATION METHOD (ETADER): 0 - INITIAL ETA FOR MAP ESTIMATION (MCETA): 0 - SIGDIGITS FOR MAP ESTIMATION (SIGLO): 9 - GRADIENT SIGDIGITS OF - FIXED EFFECTS PARAMETERS (SIGL): 9 - NOPRIOR SETTING (NOPRIOR): 0 - NOCOV SETTING (NOCOV): OFF - DERCONT SETTING (DERCONT): OFF - FINAL ETA RE-EVALUATION (FNLETA): 1 - EXCLUDE NON-INFLUENTIAL (NON-INFL.) ETAS - IN SHRINKAGE (ETASTYPE): NO - NON-INFL. ETA CORRECTION (NONINFETA): 0 - RAW OUTPUT FILE (FILE): psn.ext - EXCLUDE TITLE (NOTITLE): NO - EXCLUDE COLUMN LABELS (NOLABEL): NO - FORMAT FOR ADDITIONAL FILES (FORMAT): S1PE12.5 - PARAMETER ORDER FOR OUTPUTS (ORDER): TSOL - KNUTHSUMOFF: 0 - INCLUDE LNTWOPI: NO - INCLUDE CONSTANT TERM TO PRIOR (PRIORC): NO - INCLUDE CONSTANT TERM TO OMEGA (ETA) (OLNTWOPI):NO - ADDITIONAL CONVERGENCE TEST (CTYPE=4)?: NO - EM OR BAYESIAN METHOD USED: NONE - - - THE FOLLOWING LABELS ARE EQUIVALENT - PRED=PREDI - RES=RESI - WRES=WRESI - IWRS=IWRESI - IPRD=IPREDI - IRS=IRESI - - MONITORING OF SEARCH: - - -0ITERATION NO.: 0 OBJECTIVE VALUE: 1257.18214438728 NO. OF FUNC. EVALS.: 8 - CUMULATIVE NO. OF FUNC. EVALS.: 8 - NPARAMETR: 1.0000E-01 3.0000E+00 1.0000E+00 4.0000E+00 -1.0000E+00 1.0000E-01 1.0000E-01 1.0000E-01 - PARAMETER: 1.0000E-01 1.0000E-01 1.0000E-01 1.0000E-01 -1.0000E-01 1.0000E-01 1.0000E-01 1.0000E-01 - GRADIENT: 3.9332E+02 -3.9841E+04 -1.1159E+04 5.0036E+02 -9.8138E+02 -1.0064E+03 -8.9015E+02 -2.2864E+03 - -0ITERATION NO.: 10 OBJECTIVE VALUE: -1284.15137643419 NO. OF FUNC. EVALS.: 93 - CUMULATIVE NO. OF FUNC. EVALS.: 101 - NPARAMETR: 1.3607E+00 5.0146E+00 2.9952E+00 1.3186E+00 -1.1664E+00 1.1330E-01 1.0537E-01 1.8831E-01 - PARAMETER: 1.3607E+00 1.6715E-01 2.9952E-01 3.2966E-02 -1.1664E-01 1.6242E-01 1.2614E-01 4.1647E-01 - GRADIENT: -4.2253E+01 1.0158E+04 1.9796E+03 9.3052E+00 -1.2320E+02 -6.7092E+01 -6.3143E+01 -6.0266E-01 - -0ITERATION NO.: 20 OBJECTIVE VALUE: -1708.20916827306 NO. OF FUNC. EVALS.: 98 - CUMULATIVE NO. OF FUNC. EVALS.: 199 - NPARAMETR: 7.9682E-01 4.3506E+00 2.5771E+00 5.1732E+00 2.1974E+00 1.5425E-01 2.7878E-01 8.2792E-02 - PARAMETER: 7.9682E-01 1.4502E-01 2.5771E-01 1.2933E-01 2.1974E-01 3.1672E-01 6.1262E-01 5.5790E-03 - GRADIENT: 5.0250E+00 3.6404E+02 -1.0464E+02 -2.3706E+02 2.3547E+02 -1.8483E+01 2.5738E+00 -1.9502E+00 - -0ITERATION NO.: 28 OBJECTIVE VALUE: -1709.70777266441 NO. OF FUNC. EVALS.: 103 - CUMULATIVE NO. OF FUNC. EVALS.: 302 - NPARAMETR: 7.7162E-01 4.3278E+00 2.6293E+00 5.0435E+00 2.1483E+00 1.7872E-01 2.5423E-01 8.2122E-02 - PARAMETER: 7.7162E-01 1.4426E-01 2.6293E-01 1.2609E-01 2.1483E-01 3.9031E-01 5.6654E-01 1.5149E-03 - GRADIENT: -2.6407E+00 4.4387E+01 -1.7935E-01 2.2766E+01 1.8464E+01 2.1266E-01 5.2574E-01 -1.5856E+00 - - #TERM: -0MINIMIZATION SUCCESSFUL - NO. OF FUNCTION EVALUATIONS USED: 302 - NO. OF SIG. DIGITS IN FINAL EST.: 2.4 - - ETABAR IS THE ARITHMETIC MEAN OF THE ETA-ESTIMATES, - AND THE P-VALUE IS GIVEN FOR THE NULL HYPOTHESIS THAT THE TRUE MEAN IS 0. - - ETABAR: 0.0000E+00 -9.9951E-03 2.3931E-02 0.0000E+00 0.0000E+00 - SE: 0.0000E+00 4.1156E-02 5.0374E-02 0.0000E+00 0.0000E+00 - N: 90 90 90 90 90 - - P VAL.: 1.0000E+00 8.0811E-01 6.3474E-01 1.0000E+00 1.0000E+00 - - ETASHRINKSD(%) 0.0000E+00 7.6433E+00 5.2221E+00 0.0000E+00 0.0000E+00 - ETASHRINKVR(%) 0.0000E+00 1.4702E+01 1.0172E+01 0.0000E+00 0.0000E+00 - EBVSHRINKSD(%) 0.0000E+00 6.4391E+00 6.5552E+00 0.0000E+00 0.0000E+00 - EBVSHRINKVR(%) 0.0000E+00 1.2464E+01 1.2681E+01 0.0000E+00 0.0000E+00 - RELATIVEINF(%) 0.0000E+00 8.7517E+01 8.7300E+01 0.0000E+00 0.0000E+00 - EPSSHRINKSD(%) 1.0726E+01 1.0000E+02 - EPSSHRINKVR(%) 2.0302E+01 1.0000E+02 - - - TOTAL DATA POINTS NORMALLY DISTRIBUTED (N): 641 - N*LOG(2PI) CONSTANT TO OBJECTIVE FUNCTION: 1178.0791995683903 - OBJECTIVE FUNCTION VALUE WITHOUT CONSTANT: -1709.7077726644116 - OBJECTIVE FUNCTION VALUE WITH CONSTANT: -531.62857309602123 - REPORTED OBJECTIVE FUNCTION DOES NOT CONTAIN CONSTANT - - TOTAL EFFECTIVE ETAS (NIND*NETA): 180 - - #TERE: - Elapsed estimation time in seconds: 2.52 - Elapsed covariance time in seconds: 1.70 - Elapsed postprocess time in seconds: 0.02 -1 - - - - - - - - - - - - - - - - - - - - - ************************************************************************************************************************ - ******************** ******************** - ******************** FIRST ORDER CONDITIONAL ESTIMATION WITH INTERACTION ******************** - #OBJT:************** MINIMUM VALUE OF OBJECTIVE FUNCTION ******************** - ******************** ******************** - ************************************************************************************************************************ - - - - - - - #OBJV:******************************************** -1709.708 ************************************************** -1 - ************************************************************************************************************************ - ******************** ******************** - ******************** FIRST ORDER CONDITIONAL ESTIMATION WITH INTERACTION ******************** - ******************** FINAL PARAMETER ESTIMATE ******************** - ******************** ******************** - ************************************************************************************************************************ - - - - THETA - VECTOR OF FIXED EFFECTS PARAMETERS ********* - - - TH 1 TH 2 TH 3 TH 4 TH 5 - - 7.72E-01 4.33E+00 2.63E+00 5.04E+00 2.15E+00 - - - - OMEGA - COV MATRIX FOR RANDOM EFFECTS - ETAS ******** - - - ETA1 ETA2 ETA3 ETA4 ETA5 - - ETA1 -+ 0.00E+00 - - ETA2 -+ 0.00E+00 1.79E-01 - - ETA3 -+ 0.00E+00 0.00E+00 2.54E-01 - - ETA4 -+ 0.00E+00 0.00E+00 0.00E+00 0.00E+00 - - ETA5 -+ 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 - - - - SIGMA - COV MATRIX FOR RANDOM EFFECTS - EPSILONS **** - - - EPS1 EPS2 - - EPS1 -+ 8.21E-02 - - EPS2 -+ 0.00E+00 0.00E+00 - -1 - - - OMEGA - CORR MATRIX FOR RANDOM EFFECTS - ETAS ******* - - - ETA1 ETA2 ETA3 ETA4 ETA5 - - ETA1 -+ 0.00E+00 - - ETA2 -+ 0.00E+00 4.23E-01 - - ETA3 -+ 0.00E+00 0.00E+00 5.04E-01 - - ETA4 -+ 0.00E+00 0.00E+00 0.00E+00 0.00E+00 - - ETA5 -+ 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 - - - - SIGMA - CORR MATRIX FOR RANDOM EFFECTS - EPSILONS *** - - - EPS1 EPS2 - - EPS1 -+ 2.87E-01 - - EPS2 -+ 0.00E+00 0.00E+00 - -1 - ************************************************************************************************************************ - ******************** ******************** - ******************** FIRST ORDER CONDITIONAL ESTIMATION WITH INTERACTION ******************** - ******************** STANDARD ERROR OF ESTIMATE ******************** - ******************** ******************** - ************************************************************************************************************************ - - - - THETA - VECTOR OF FIXED EFFECTS PARAMETERS ********* - - - TH 1 TH 2 TH 3 TH 4 TH 5 - - 6.35E-02 5.98E-02 8.13E-02 2.22E-01 5.82E-02 - - - - OMEGA - COV MATRIX FOR RANDOM EFFECTS - ETAS ******** - - - ETA1 ETA2 ETA3 ETA4 ETA5 - - ETA1 -+ ......... - - ETA2 -+ ......... 3.21E-02 - - ETA3 -+ ......... ......... 4.42E-02 - - ETA4 -+ ......... ......... ......... ......... - - ETA5 -+ ......... ......... ......... ......... ......... - - - - SIGMA - COV MATRIX FOR RANDOM EFFECTS - EPSILONS **** - - - EPS1 EPS2 - - EPS1 -+ 5.61E-03 - - EPS2 -+ ......... ......... - -1 - - - OMEGA - CORR MATRIX FOR RANDOM EFFECTS - ETAS ******* - - - ETA1 ETA2 ETA3 ETA4 ETA5 - - ETA1 -+ ......... - - ETA2 -+ ......... 3.80E-02 - - ETA3 -+ ......... ......... 4.38E-02 - - ETA4 -+ ......... ......... ......... ......... - - ETA5 -+ ......... ......... ......... ......... ......... - - - - SIGMA - CORR MATRIX FOR RANDOM EFFECTS - EPSILONS *** - - - EPS1 EPS2 - - EPS1 -+ 9.79E-03 - - EPS2 -+ ......... ......... - -1 - ************************************************************************************************************************ - ******************** ******************** - ******************** FIRST ORDER CONDITIONAL ESTIMATION WITH INTERACTION ******************** - ******************** COVARIANCE MATRIX OF ESTIMATE ******************** - ******************** ******************** - ************************************************************************************************************************ - - - TH 1 TH 2 TH 3 TH 4 TH 5 OM11 OM12 OM13 OM14 OM15 OM22 OM23 - OM24 OM25 OM33 OM34 OM35 OM44 OM45 OM55 SG11 SG12 SG22 - - TH 1 -+ 4.04E-03 - - TH 2 -+ 2.20E-03 3.57E-03 - - TH 3 -+ -1.24E-03 -1.01E-03 6.61E-03 - - TH 4 -+ 4.35E-03 2.56E-03 -1.21E-02 4.93E-02 - - TH 5 -+ -4.58E-04 -2.00E-04 -9.39E-04 7.01E-03 3.39E-03 - - OM11 -+ ......... ......... ......... ......... ......... ......... - - OM12 -+ ......... ......... ......... ......... ......... ......... ......... - - OM13 -+ ......... ......... ......... ......... ......... ......... ......... ......... - - OM14 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... - - OM15 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - - OM22 -+ -2.34E-04 -3.75E-04 -9.40E-05 -1.95E-04 -1.61E-04 ......... ......... ......... ......... ......... 1.03E-03 - - OM23 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - - OM24 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - ......... - - OM25 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - ......... ......... - - OM33 -+ -7.91E-05 1.44E-04 -5.65E-04 1.95E-03 2.51E-04 ......... ......... ......... ......... ......... -3.02E-04 ......... - ......... ......... 1.95E-03 - - OM34 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - ......... ......... ......... ......... - - OM35 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - ......... ......... ......... ......... ......... - - OM44 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - ......... ......... ......... ......... ......... ......... - - OM45 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - ......... ......... ......... ......... ......... ......... ......... - -1 - - TH 1 TH 2 TH 3 TH 4 TH 5 OM11 OM12 OM13 OM14 OM15 OM22 OM23 - OM24 OM25 OM33 OM34 OM35 OM44 OM45 OM55 SG11 SG12 SG22 - - OM55 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - ......... ......... ......... ......... ......... ......... ......... ......... - - SG11 -+ 8.21E-05 1.14E-04 -1.30E-05 4.90E-05 -3.22E-05 ......... ......... ......... ......... ......... -7.41E-06 ......... - ......... ......... 1.64E-05 ......... ......... ......... ......... ......... 3.15E-05 - - SG12 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - - SG22 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - -1 - ************************************************************************************************************************ - ******************** ******************** - ******************** FIRST ORDER CONDITIONAL ESTIMATION WITH INTERACTION ******************** - ******************** CORRELATION MATRIX OF ESTIMATE ******************** - ******************** ******************** - ************************************************************************************************************************ - - - TH 1 TH 2 TH 3 TH 4 TH 5 OM11 OM12 OM13 OM14 OM15 OM22 OM23 - OM24 OM25 OM33 OM34 OM35 OM44 OM45 OM55 SG11 SG12 SG22 - - TH 1 -+ 6.35E-02 - - TH 2 -+ 5.79E-01 5.98E-02 - - TH 3 -+ -2.41E-01 -2.08E-01 8.13E-02 - - TH 4 -+ 3.08E-01 1.93E-01 -6.68E-01 2.22E-01 - - TH 5 -+ -1.24E-01 -5.75E-02 -1.99E-01 5.42E-01 5.82E-02 - - OM11 -+ ......... ......... ......... ......... ......... ......... - - OM12 -+ ......... ......... ......... ......... ......... ......... ......... - - OM13 -+ ......... ......... ......... ......... ......... ......... ......... ......... - - OM14 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... - - OM15 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - - OM22 -+ -1.15E-01 -1.95E-01 -3.60E-02 -2.74E-02 -8.63E-02 ......... ......... ......... ......... ......... 3.21E-02 - - OM23 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - - OM24 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - ......... - - OM25 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - ......... ......... - - OM33 -+ -2.82E-02 5.45E-02 -1.57E-01 1.98E-01 9.75E-02 ......... ......... ......... ......... ......... -2.13E-01 ......... - ......... ......... 4.42E-02 - - OM34 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - ......... ......... ......... ......... - - OM35 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - ......... ......... ......... ......... ......... - - OM44 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - ......... ......... ......... ......... ......... ......... - - OM45 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - ......... ......... ......... ......... ......... ......... ......... - -1 - - TH 1 TH 2 TH 3 TH 4 TH 5 OM11 OM12 OM13 OM14 OM15 OM22 OM23 - OM24 OM25 OM33 OM34 OM35 OM44 OM45 OM55 SG11 SG12 SG22 - - OM55 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - ......... ......... ......... ......... ......... ......... ......... ......... - - SG11 -+ 2.30E-01 3.40E-01 -2.84E-02 3.93E-02 -9.85E-02 ......... ......... ......... ......... ......... -4.11E-02 ......... - ......... ......... 6.59E-02 ......... ......... ......... ......... ......... 5.61E-03 - - SG12 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - - SG22 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - -1 - ************************************************************************************************************************ - ******************** ******************** - ******************** FIRST ORDER CONDITIONAL ESTIMATION WITH INTERACTION ******************** - ******************** INVERSE COVARIANCE MATRIX OF ESTIMATE ******************** - ******************** ******************** - ************************************************************************************************************************ - - - TH 1 TH 2 TH 3 TH 4 TH 5 OM11 OM12 OM13 OM14 OM15 OM22 OM23 - OM24 OM25 OM33 OM34 OM35 OM44 OM45 OM55 SG11 SG12 SG22 - - TH 1 -+ 4.55E+02 - - TH 2 -+ -2.29E+02 4.72E+02 - - TH 3 -+ -3.26E+01 4.59E+01 3.00E+02 - - TH 4 -+ -6.21E+01 1.16E+01 8.83E+01 6.43E+01 - - TH 5 -+ 1.63E+02 -1.86E+01 -1.02E+02 -1.15E+02 5.32E+02 - - OM11 -+ ......... ......... ......... ......... ......... ......... - - OM12 -+ ......... ......... ......... ......... ......... ......... ......... - - OM13 -+ ......... ......... ......... ......... ......... ......... ......... ......... - - OM14 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... - - OM15 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - - OM22 -+ 5.23E+01 1.11E+02 4.05E+01 -1.66E+01 9.55E+01 ......... ......... ......... ......... ......... 1.09E+03 - - OM23 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - - OM24 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - ......... - - OM25 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - ......... ......... - - OM33 -+ 7.59E+01 -1.35E+01 1.54E+01 -2.91E+01 3.71E+01 ......... ......... ......... ......... ......... 1.80E+02 ......... - ......... ......... 5.75E+02 - - OM34 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - ......... ......... ......... ......... - - OM35 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - ......... ......... ......... ......... ......... - - OM44 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - ......... ......... ......... ......... ......... ......... - - OM45 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - ......... ......... ......... ......... ......... ......... ......... - -1 - - TH 1 TH 2 TH 3 TH 4 TH 5 OM11 OM12 OM13 OM14 OM15 OM22 OM23 - OM24 OM25 OM33 OM34 OM35 OM44 OM45 OM55 SG11 SG12 SG22 - - OM55 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - ......... ......... ......... ......... ......... ......... ......... ......... - - SG11 -+ -1.34E+02 -1.10E+03 -1.98E+02 -5.08E+01 3.26E+02 ......... ......... ......... ......... ......... -2.36E+02 ......... - ......... ......... -3.15E+02 ......... ......... ......... ......... ......... 3.65E+04 - - SG12 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - - SG22 -+ ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... ......... - - Elapsed finaloutput time in seconds: 0.02 - #CPUT: Total CPU Time in Seconds, 4.329 -Stop Time: -Thu Nov 2 03:13:11 PM EDT 2023 diff --git a/tests/testthat/testData/nonmem/xgxr031.msf b/tests/testthat/testData/nonmem/xgxr031.msf deleted file mode 100644 index 40811dd4..00000000 Binary files a/tests/testthat/testData/nonmem/xgxr031.msf and /dev/null differ diff --git a/tests/testthat/testData/nonmem/xgxr031.phi b/tests/testthat/testData/nonmem/xgxr031.phi deleted file mode 100644 index 95949b1a..00000000 --- a/tests/testthat/testData/nonmem/xgxr031.phi +++ /dev/null @@ -1,92 +0,0 @@ -TABLE NO. 1: First Order Conditional Estimation with Interaction: Problem=1 Subproblem=0 Superproblem1=0 Iteration1=0 Superproblem2=0 Iteration2=0 - SUBJECT_NO ID ETA(1) ETA(2) ETA(3) ETA(4) ETA(5) ETC(1,1) ETC(2,1) ETC(2,2) ETC(3,1) ETC(3,2) ETC(3,3) ETC(4,1) ETC(4,2) ETC(4,3) ETC(4,4) ETC(5,1) ETC(5,2) ETC(5,3) ETC(5,4) ETC(5,5) OBJ - 1 91 0.00000E+00 -8.11959E-01 -5.75164E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.57078E-02 0.00000E+00 5.24577E-04 7.24110E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -9.5306079213908443 - 2 92 0.00000E+00 3.82693E-01 -1.98926E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.99810E-02 0.00000E+00 -6.18520E-03 7.47890E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -31.283986356134818 - 3 93 0.00000E+00 -9.79425E-02 9.00282E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.47617E-02 0.00000E+00 7.01858E-03 2.28144E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -21.841031808379320 - 4 94 0.00000E+00 2.58037E-01 5.66266E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 3.09455E-02 0.00000E+00 -8.67370E-03 7.18198E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -16.413444226434247 - 5 95 0.00000E+00 2.67915E-01 -2.36959E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.90309E-02 0.00000E+00 2.74156E-03 3.14348E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -34.506467407518905 - 6 96 0.00000E+00 2.30095E-01 2.16433E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.26563E-02 0.00000E+00 -1.16117E-02 1.00995E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -20.447328304379226 - 7 97 0.00000E+00 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-3.66385E-01 -1.78721E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.22683E-02 0.00000E+00 6.70873E-03 1.25820E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -21.599479602640837 - 56 146 0.00000E+00 -2.02450E-01 -2.14276E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 3.00366E-02 0.00000E+00 6.39593E-03 1.26364E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -23.598289724571554 - 57 147 0.00000E+00 2.43297E-01 9.78775E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.92107E-02 0.00000E+00 6.43737E-03 1.29187E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -33.336614797265398 - 58 148 0.00000E+00 1.26061E-02 -2.80368E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.89744E-02 0.00000E+00 4.92430E-03 1.21934E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -33.946352766577213 - 59 149 0.00000E+00 -4.85078E-01 2.53335E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.90785E-02 0.00000E+00 8.99688E-03 9.45136E-03 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -25.471796325601854 - 60 150 0.00000E+00 1.47278E-01 5.52764E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.07168E-02 0.00000E+00 8.23166E-03 1.79175E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -17.994720790822118 - 61 151 0.00000E+00 1.86224E-01 -1.21888E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.75774E-02 0.00000E+00 -1.71050E-03 5.04140E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.7615012129130623 - 62 152 0.00000E+00 2.04480E-01 -2.63058E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.76781E-02 0.00000E+00 4.55124E-03 1.34474E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -8.2460354540261829 - 63 153 0.00000E+00 -8.54724E-01 5.77901E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.01405E-02 0.00000E+00 5.45591E-03 6.34022E-03 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -8.6854475985797350 - 64 154 0.00000E+00 2.42720E-01 -2.60753E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.78074E-02 0.00000E+00 4.43248E-03 1.37737E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -16.004227463868961 - 65 155 0.00000E+00 2.63726E-01 2.21866E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.81085E-02 0.00000E+00 5.77885E-03 8.76528E-03 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -19.911013267991688 - 66 156 0.00000E+00 -8.42926E-02 8.22959E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.03130E-02 0.00000E+00 1.01396E-02 1.40226E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -6.5026792415701857 - 67 157 0.00000E+00 -5.48669E-01 -1.92331E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.14963E-02 0.00000E+00 5.35184E-03 9.06737E-03 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -9.3485228030208525 - 68 158 0.00000E+00 6.89363E-02 -2.92200E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.88696E-02 0.00000E+00 4.78802E-03 1.27359E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -4.3426589373690172 - 69 159 0.00000E+00 8.50269E-02 -6.72061E-03 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.00900E-02 0.00000E+00 5.75152E-03 9.58495E-03 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -7.1983270119934604 - 70 160 0.00000E+00 -1.44074E-01 8.39724E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.28457E-02 0.00000E+00 1.09632E-02 1.29441E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 3.7297328217927319 - 71 161 0.00000E+00 -4.07011E-01 -6.44158E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.20117E-02 0.00000E+00 4.79261E-03 1.46347E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 7.2759645895866676 - 72 162 0.00000E+00 4.05655E-01 8.24693E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.11805E-02 0.00000E+00 9.54900E-03 1.12708E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -8.0909090116574909 - 73 163 0.00000E+00 3.88244E-01 6.59459E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.80341E-02 0.00000E+00 6.34732E-03 6.86568E-03 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -24.516110830681491 - 74 164 0.00000E+00 -1.13592E-01 -2.93573E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.95994E-02 0.00000E+00 5.05129E-03 1.16057E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -1.3439770195808454 - 75 165 0.00000E+00 -2.14503E-01 9.41487E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.13833E-02 0.00000E+00 8.07640E-03 8.36706E-03 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -2.8776886139489286 - 76 166 0.00000E+00 -1.33338E-01 2.99398E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.03447E-02 0.00000E+00 5.96912E-03 7.00995E-03 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -19.088401167557187 - 77 167 0.00000E+00 -2.89310E-01 4.10227E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.27586E-02 0.00000E+00 6.12389E-03 6.30547E-03 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -21.523689581544176 - 78 168 0.00000E+00 -4.36881E-01 1.37326E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.01172E-02 0.00000E+00 5.29974E-03 7.18414E-03 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -11.611109626131002 - 79 169 0.00000E+00 2.16798E-01 -2.00032E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.75488E-02 0.00000E+00 4.69806E-03 1.28489E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -13.948785157650420 - 80 170 0.00000E+00 7.74743E-02 7.00303E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.05508E-02 0.00000E+00 9.03432E-03 1.08962E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -7.6240428762605408 - 81 171 0.00000E+00 4.27124E-01 -4.03820E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.72922E-02 0.00000E+00 2.84634E-03 1.89258E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -14.109851160039923 - 82 172 0.00000E+00 -2.42398E-01 7.54545E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.31089E-02 0.00000E+00 8.91708E-03 9.16684E-03 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -13.731084132419038 - 83 173 0.00000E+00 -5.73948E-01 2.43174E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.00799E-02 0.00000E+00 4.93617E-03 6.47060E-03 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -7.7524854412233468 - 84 174 0.00000E+00 -1.44276E-01 -1.53357E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.02049E-02 0.00000E+00 5.50320E-03 1.02083E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -12.843119682610441 - 85 175 0.00000E+00 -6.57595E-01 3.70111E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.33277E-02 0.00000E+00 6.56474E-03 7.44315E-03 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -12.699040135415498 - 86 176 0.00000E+00 -5.04327E-02 -3.39037E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.86652E-02 0.00000E+00 4.83048E-03 1.28472E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -13.484226886505997 - 87 177 0.00000E+00 2.26628E-01 1.96472E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.81596E-02 0.00000E+00 5.40066E-03 1.00830E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -15.884086313896745 - 88 178 0.00000E+00 -2.18440E-01 -2.75354E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.94264E-02 0.00000E+00 5.52326E-03 8.90214E-03 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -16.297483233106707 - 89 179 0.00000E+00 -5.54084E-01 -2.00558E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.94851E-02 0.00000E+00 4.86196E-03 9.35216E-03 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -12.383972785058814 - 90 180 0.00000E+00 2.92204E-01 6.99993E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.90254E-02 0.00000E+00 6.49668E-03 6.45054E-03 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -22.240750853347318 diff --git a/tests/testthat/testData/nonmem/xgxr031.shk b/tests/testthat/testData/nonmem/xgxr031.shk deleted file mode 100644 index e98964fd..00000000 --- a/tests/testthat/testData/nonmem/xgxr031.shk +++ /dev/null @@ -1,13 +0,0 @@ -TABLE NO. 1: First Order Conditional Estimation with Interaction: Problem=1 Subproblem=0 Superproblem1=0 Iteration1=0 Superproblem2=0 Iteration2=0 -TYPE SUBPOP ETA(1) ETA(2) ETA(3) ETA(4) ETA(5) - 1 1 0.00000E+00 -9.99515E-03 2.39306E-02 0.00000E+00 0.00000E+00 - 2 1 0.00000E+00 4.11556E-02 5.03735E-02 0.00000E+00 0.00000E+00 - 3 1 1.00000E+00 8.08112E-01 6.34742E-01 1.00000E+00 1.00000E+00 - 4 1 0.00000E+00 7.64331E+00 5.22212E+00 0.00000E+00 0.00000E+00 - 5 1 1.07264E+01 1.00000E+02 0.00000E+00 0.00000E+00 0.00000E+00 - 6 1 0.00000E+00 6.43912E+00 6.55523E+00 0.00000E+00 0.00000E+00 - 7 1 9.00000E+01 9.00000E+01 9.00000E+01 9.00000E+01 9.00000E+01 - 8 1 0.00000E+00 1.47024E+01 1.01715E+01 0.00000E+00 0.00000E+00 - 9 1 0.00000E+00 1.24636E+01 1.26808E+01 0.00000E+00 0.00000E+00 - 10 1 2.03022E+01 1.00000E+02 0.00000E+00 0.00000E+00 0.00000E+00 - 11 1 0.00000E+00 8.75169E+01 8.72998E+01 0.00000E+00 0.00000E+00 diff --git a/tests/testthat/testData/nonmem/xgxr031_res.txt b/tests/testthat/testData/nonmem/xgxr031_res.txt deleted file mode 100644 index 7ac04e2c..00000000 --- a/tests/testthat/testData/nonmem/xgxr031_res.txt +++ /dev/null @@ -1,733 +0,0 @@ -TABLE NO. 1 - ROW KA V2 V3 CL Q IPRED Y DV PRED RES WRES - 6.0100E+02 2.1633E+00 3.3644E+01 1.5502E+02 7.8000E+00 8.5705E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 - 6.0200E+02 2.1633E+00 3.3644E+01 1.5502E+02 7.8000E+00 8.5705E+00 2.6843E-01 2.6843E-01 2.5706E-01 1.2128E-01 1.3578E-01 1.2557E-01 - 6.0300E+02 2.1633E+00 3.3644E+01 1.5502E+02 7.8000E+00 8.5705E+00 5.4173E-01 5.4173E-01 7.0798E-01 2.5660E-01 4.5138E-01 2.9397E+00 - 6.0400E+02 2.1633E+00 3.3644E+01 1.5502E+02 7.8000E+00 8.5705E+00 5.7640E-01 5.7640E-01 5.8570E-01 2.8905E-01 2.9665E-01 8.6302E-01 - 6.0500E+02 2.1633E+00 3.3644E+01 1.5502E+02 7.8000E+00 8.5705E+00 4.2165E-01 4.2165E-01 6.4982E-01 2.4738E-01 4.0244E-01 3.4008E+00 - 6.0600E+02 2.1633E+00 3.3644E+01 1.5502E+02 7.8000E+00 8.5705E+00 1.9300E-01 1.9300E-01 1.8526E-01 1.4962E-01 3.5637E-02 -1.6279E-01 - 6.1100E+02 2.1633E+00 1.1111E+02 1.5502E+02 1.1363E+01 8.5705E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 - 6.1200E+02 2.1633E+00 1.1111E+02 1.5502E+02 1.1363E+01 8.5705E+00 8.8507E-02 8.8507E-02 8.6748E-02 1.2828E-01 -4.1527E-02 -2.7005E-01 - 6.1300E+02 2.1633E+00 1.1111E+02 1.5502E+02 1.1363E+01 8.5705E+00 1.8901E-01 1.8901E-01 1.8008E-01 2.6500E-01 -8.4917E-02 -4.6226E-01 - 6.1400E+02 2.1633E+00 1.1111E+02 1.5502E+02 1.1363E+01 8.5705E+00 2.1558E-01 2.1558E-01 1.9879E-01 2.8861E-01 -8.9818E-02 -5.5239E-01 - 6.1500E+02 2.1633E+00 1.1111E+02 1.5502E+02 1.1363E+01 8.5705E+00 1.9710E-01 1.9710E-01 1.9367E-01 2.3741E-01 -4.3742E-02 -3.5813E-01 - 6.1600E+02 2.1633E+00 1.1111E+02 1.5502E+02 1.1363E+01 8.5705E+00 1.4633E-01 1.4633E-01 2.1215E-01 1.4483E-01 6.7321E-02 1.2894E+00 - 6.1700E+02 2.1633E+00 1.1111E+02 1.5502E+02 1.1363E+01 8.5705E+00 8.2431E-02 8.2431E-02 7.6733E-02 5.8912E-02 1.7821E-02 -2.1240E-01 - 6.2100E+02 2.1633E+00 6.8707E+01 1.5502E+02 3.4109E+01 8.5705E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 - 6.2200E+02 2.1633E+00 6.8707E+01 1.5502E+02 3.4109E+01 8.5705E+00 1.5107E-01 1.5107E-01 1.7612E-01 1.4214E-01 3.3983E-02 8.8146E-01 - 6.2300E+02 2.1633E+00 6.8707E+01 1.5502E+02 3.4109E+01 8.5705E+00 2.5373E-01 2.5373E-01 2.7860E-01 2.5721E-01 2.1385E-02 4.3077E-01 - 6.2400E+02 2.1633E+00 6.8707E+01 1.5502E+02 3.4109E+01 8.5705E+00 2.5898E-01 2.5898E-01 1.9066E-01 2.8894E-01 -9.8279E-02 -9.2056E-01 - 6.2500E+02 2.1633E+00 6.8707E+01 1.5502E+02 3.4109E+01 8.5705E+00 1.8102E-01 1.8102E-01 1.8520E-01 2.5653E-01 -7.1334E-02 -6.1054E-01 - 6.2600E+02 2.1633E+00 6.8707E+01 1.5502E+02 3.4109E+01 8.5705E+00 5.6795E-02 5.6795E-02 5.5120E-02 1.4927E-01 -9.4151E-02 -1.3274E+00 - 6.3100E+02 2.1633E+00 9.8084E+01 1.5502E+02 2.4424E+01 8.5705E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 - 6.3300E+02 2.1633E+00 9.8084E+01 1.5502E+02 2.4424E+01 8.5705E+00 1.4476E-01 1.4476E-01 1.3855E-01 1.8872E-01 -5.0174E-02 -3.3071E-01 - 6.3400E+02 2.1633E+00 9.8084E+01 1.5502E+02 2.4424E+01 8.5705E+00 2.0816E-01 2.0816E-01 1.6273E-01 2.7429E-01 -1.1156E-01 -8.5323E-01 - 6.3500E+02 2.1633E+00 9.8084E+01 1.5502E+02 2.4424E+01 8.5705E+00 1.9637E-01 1.9637E-01 2.5910E-01 2.6747E-01 -8.3710E-03 3.7262E-01 - 6.3600E+02 2.1633E+00 9.8084E+01 1.5502E+02 2.4424E+01 8.5705E+00 1.0529E-01 1.0529E-01 6.4629E-02 1.5660E-01 -9.1975E-02 -1.4047E+00 - 6.4100E+02 2.1633E+00 9.9058E+01 1.5502E+02 1.0939E+01 8.5705E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 - 6.4200E+02 2.1633E+00 9.9058E+01 1.5502E+02 1.0939E+01 8.5705E+00 6.0959E-02 6.0959E-02 5.6887E-02 7.9260E-02 -2.2373E-02 -2.1927E-01 - 6.4300E+02 2.1633E+00 9.9058E+01 1.5502E+02 1.0939E+01 8.5705E+00 2.1943E-01 2.1943E-01 1.1065E-01 2.7457E-01 -1.6392E-01 -1.5324E+00 - 6.4400E+02 2.1633E+00 9.9058E+01 1.5502E+02 1.0939E+01 8.5705E+00 2.3858E-01 2.3858E-01 3.5931E-01 2.8841E-01 7.0901E-02 1.1715E+00 - 6.4500E+02 2.1633E+00 9.9058E+01 1.5502E+02 1.0939E+01 8.5705E+00 2.1480E-01 2.1480E-01 2.0009E-01 2.3763E-01 -3.7539E-02 -3.2021E-01 - 6.4600E+02 2.1633E+00 9.9058E+01 1.5502E+02 1.0939E+01 8.5705E+00 1.4926E-01 1.4926E-01 1.2642E-01 1.3704E-01 -1.0617E-02 -4.7860E-01 - 6.4700E+02 2.1633E+00 9.9058E+01 1.5502E+02 1.0939E+01 8.5705E+00 8.0080E-02 8.0080E-02 7.3517E-02 5.5847E-02 1.7670E-02 -3.5702E-02 - 6.4800E+02 2.1633E+00 9.9058E+01 1.5502E+02 1.0939E+01 8.5705E+00 4.9710E-02 4.9710E-02 6.2952E-02 3.0890E-02 3.2062E-02 1.6326E+00 - 6.5100E+02 2.1633E+00 9.5382E+01 1.5502E+02 1.7214E+01 8.5705E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 - 6.5200E+02 2.1633E+00 9.5382E+01 1.5502E+02 1.7214E+01 8.5705E+00 7.1899E-02 7.1899E-02 6.8034E-02 9.0353E-02 -2.2319E-02 -3.6800E-01 - 6.5300E+02 2.1633E+00 9.5382E+01 1.5502E+02 1.7214E+01 8.5705E+00 1.9614E-01 1.9614E-01 1.6596E-01 2.4498E-01 -7.9025E-02 -6.9363E-01 - 6.5400E+02 2.1633E+00 9.5382E+01 1.5502E+02 1.7214E+01 8.5705E+00 2.3194E-01 2.3194E-01 2.0658E-01 2.8756E-01 -8.0976E-02 -5.8415E-01 - 6.5500E+02 2.1633E+00 9.5382E+01 1.5502E+02 1.7214E+01 8.5705E+00 2.1085E-01 2.1085E-01 3.1463E-01 2.5633E-01 5.8298E-02 1.1304E+00 - 6.5600E+02 2.1633E+00 9.5382E+01 1.5502E+02 1.7214E+01 8.5705E+00 1.2645E-01 1.2645E-01 5.5850E-02 1.4725E-01 -9.1402E-02 -1.5797E+00 - 6.6100E+02 2.1633E+00 9.0673E+01 1.5502E+02 2.5965E+01 8.5705E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 - 6.6300E+02 2.1633E+00 9.0673E+01 1.5502E+02 2.5965E+01 8.5705E+00 1.8636E-01 1.8636E-01 1.9210E-01 2.2788E-01 -3.5777E-02 -1.4012E-01 - 6.6400E+02 2.1633E+00 9.0673E+01 1.5502E+02 2.5965E+01 8.5705E+00 2.2853E-01 2.2853E-01 2.3065E-01 2.8888E-01 -5.8231E-02 -3.0888E-01 - 6.6500E+02 2.1633E+00 9.0673E+01 1.5502E+02 2.5965E+01 8.5705E+00 1.7555E-01 1.7555E-01 1.7834E-01 2.4162E-01 -6.3278E-02 -4.7750E-01 - 6.6600E+02 2.1633E+00 9.0673E+01 1.5502E+02 2.5965E+01 8.5705E+00 8.7457E-02 8.7457E-02 8.0614E-02 1.4244E-01 -6.1825E-02 -8.9529E-01 - 6.7100E+02 2.1633E+00 8.2592E+01 1.5502E+02 5.2430E+00 8.5705E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 - 6.7200E+02 2.1633E+00 8.2592E+01 1.5502E+02 5.2430E+00 8.5705E+00 9.7375E-02 9.7375E-02 1.3245E-01 1.0509E-01 2.7359E-02 1.4469E+00 - 6.7300E+02 2.1633E+00 8.2592E+01 1.5502E+02 5.2430E+00 8.5705E+00 2.2527E-01 2.2527E-01 1.0025E-01 2.3684E-01 -1.3659E-01 -1.4796E+00 - 6.7400E+02 2.1633E+00 8.2592E+01 1.5502E+02 5.2430E+00 8.5705E+00 2.8641E-01 2.8641E-01 3.1455E-01 2.8818E-01 2.6371E-02 5.2528E-01 - 6.7500E+02 2.1633E+00 8.2592E+01 1.5502E+02 5.2430E+00 8.5705E+00 2.7606E-01 2.7606E-01 2.3572E-01 2.4524E-01 -9.5243E-03 -3.7702E-01 - 6.7600E+02 2.1633E+00 8.2592E+01 1.5502E+02 5.2430E+00 8.5705E+00 2.0868E-01 2.0868E-01 2.5946E-01 1.4606E-01 1.1340E-01 1.1083E+00 - 6.7700E+02 2.1633E+00 8.2592E+01 1.5502E+02 5.2430E+00 8.5705E+00 1.2657E-01 1.2657E-01 1.3295E-01 5.8614E-02 7.4336E-02 -2.5204E-02 - 6.7800E+02 2.1633E+00 8.2592E+01 1.5502E+02 5.2430E+00 8.5705E+00 8.8698E-02 8.8698E-02 1.2596E-01 3.2327E-02 9.3633E-02 3.1225E+00 - 6.7900E+02 2.1633E+00 8.2592E+01 1.5502E+02 5.2430E+00 8.5705E+00 6.3053E-02 6.3053E-02 7.1785E-02 2.0224E-02 5.1561E-02 1.8788E+00 - 6.8000E+02 2.1633E+00 8.2592E+01 1.5502E+02 5.2430E+00 8.5705E+00 5.1937E-02 5.1937E-02 5.2102E-02 1.5778E-02 3.6324E-02 1.0829E+00 - 6.8100E+02 2.1633E+00 7.1523E+01 1.5502E+02 9.8997E+00 8.5705E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 - 6.8200E+02 2.1633E+00 7.1523E+01 1.5502E+02 9.8997E+00 8.5705E+00 1.3477E-01 1.3477E-01 1.2016E-01 1.2674E-01 -6.5752E-03 -4.9332E-01 - 6.8300E+02 2.1633E+00 7.1523E+01 1.5502E+02 9.8997E+00 8.5705E+00 2.9649E-01 2.9649E-01 3.6903E-01 2.7516E-01 9.3873E-02 7.9345E-01 - 6.8400E+02 2.1633E+00 7.1523E+01 1.5502E+02 9.8997E+00 8.5705E+00 3.1138E-01 3.1138E-01 3.8870E-01 2.8359E-01 1.0511E-01 8.9563E-01 - 6.8500E+02 2.1633E+00 7.1523E+01 1.5502E+02 9.8997E+00 8.5705E+00 2.5881E-01 2.5881E-01 1.9279E-01 2.2747E-01 -3.4677E-02 -9.0720E-01 - 6.8600E+02 2.1633E+00 7.1523E+01 1.5502E+02 9.8997E+00 8.5705E+00 1.6188E-01 1.6188E-01 1.9117E-01 1.3175E-01 5.9417E-02 9.0899E-01 - 6.8700E+02 2.1633E+00 7.1523E+01 1.5502E+02 9.8997E+00 8.5705E+00 7.6820E-02 7.6820E-02 8.7244E-02 5.5048E-02 3.2196E-02 7.1369E-01 - 6.9200E+02 2.1633E+00 1.2042E+02 1.5502E+02 2.2662E+01 8.5705E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 - 6.9400E+02 2.1633E+00 1.2042E+02 1.5502E+02 2.2662E+01 8.5705E+00 1.1990E-01 1.1990E-01 1.2057E-01 1.8931E-01 -6.8738E-02 -4.2760E-01 - 6.9500E+02 2.1633E+00 1.2042E+02 1.5502E+02 2.2662E+01 8.5705E+00 1.8683E-01 1.8683E-01 2.0807E-01 2.8932E-01 -8.1249E-02 -3.0184E-01 - 6.9600E+02 2.1633E+00 1.2042E+02 1.5502E+02 2.2662E+01 8.5705E+00 1.6069E-01 1.6069E-01 1.1653E-01 2.4133E-01 -1.2480E-01 -1.1404E+00 - 6.9700E+02 2.1633E+00 1.2042E+02 1.5502E+02 2.2662E+01 8.5705E+00 1.0118E-01 1.0118E-01 9.7987E-02 1.4415E-01 -4.6164E-02 -5.2426E-01 - 7.0200E+02 2.1633E+00 6.3676E+01 1.5502E+02 1.8614E+01 8.5705E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 - 7.0300E+02 2.1633E+00 6.3676E+01 1.5502E+02 1.8614E+01 8.5705E+00 6.4318E-02 6.4318E-02 6.8493E-02 5.4296E-02 1.4197E-02 2.6277E-01 - 7.0400E+02 2.1633E+00 6.3676E+01 1.5502E+02 1.8614E+01 8.5705E+00 2.6245E-01 2.6245E-01 2.9452E-01 2.2799E-01 6.6528E-02 5.6013E-01 - 7.0500E+02 2.1633E+00 6.3676E+01 1.5502E+02 1.8614E+01 8.5705E+00 3.1616E-01 3.1616E-01 3.8954E-01 2.8889E-01 1.0065E-01 8.5652E-01 - 7.0600E+02 2.1633E+00 6.3676E+01 1.5502E+02 1.8614E+01 8.5705E+00 2.5300E-01 2.5300E-01 1.8790E-01 2.5536E-01 -6.7464E-02 -1.0446E+00 - 7.0700E+02 2.1633E+00 6.3676E+01 1.5502E+02 1.8614E+01 8.5705E+00 1.2525E-01 1.2525E-01 1.3172E-01 1.5747E-01 -2.5749E-02 -3.1662E-01 - 7.1200E+02 2.1633E+00 4.4267E+01 1.5502E+02 1.2967E+01 8.5705E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 - 7.1300E+02 2.1633E+00 4.4267E+01 1.5502E+02 1.2967E+01 8.5705E+00 1.5330E-01 1.5330E-01 1.8039E-01 9.0643E-02 8.9747E-02 1.1829E+00 - 7.1400E+02 2.1633E+00 4.4267E+01 1.5502E+02 1.2967E+01 8.5705E+00 4.1544E-01 4.1544E-01 4.5544E-01 2.5958E-01 1.9586E-01 1.0102E+00 - 7.1500E+02 2.1633E+00 4.4267E+01 1.5502E+02 1.2967E+01 8.5705E+00 4.3409E-01 4.3409E-01 5.3140E-01 2.8938E-01 2.4202E-01 1.4944E+00 - 7.1600E+02 2.1633E+00 4.4267E+01 1.5502E+02 1.2967E+01 8.5705E+00 3.0800E-01 3.0800E-01 3.1196E-01 2.4237E-01 6.9594E-02 2.1560E-02 - 7.1700E+02 2.1633E+00 4.4267E+01 1.5502E+02 1.2967E+01 8.5705E+00 1.3012E-01 1.3012E-01 1.4115E-01 1.4132E-01 -1.7391E-04 -7.0655E-02 - 7.2200E+02 2.1633E+00 1.2829E+02 1.5502E+02 6.9895E+00 8.5705E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 - 7.2400E+02 2.1633E+00 1.2829E+02 1.5502E+02 6.9895E+00 8.5705E+00 1.1683E-01 1.1683E-01 1.5180E-01 1.9157E-01 -3.9771E-02 1.9369E-01 - 7.2500E+02 2.1633E+00 1.2829E+02 1.5502E+02 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1.5502E+02 2.7918E+01 8.5705E+00 1.2696E+00 1.2696E+00 6.9625E-01 1.7169E+00 -1.0206E+00 -1.1654E+00 - 1.4950E+03 2.1633E+00 1.0149E+02 1.5502E+02 2.7918E+01 8.5705E+00 1.9092E+00 1.9092E+00 1.8122E+00 2.6177E+00 -8.0554E-01 -3.2492E-01 - 1.4960E+03 2.1633E+00 1.0149E+02 1.5502E+02 2.7918E+01 8.5705E+00 2.0466E+00 2.0466E+00 2.4193E+00 2.8838E+00 -4.6448E-01 1.2683E-01 - 1.4970E+03 2.1633E+00 1.0149E+02 1.5502E+02 2.7918E+01 8.5705E+00 1.6722E+00 1.6722E+00 1.3850E+00 2.4756E+00 -1.0906E+00 -7.8705E-01 - 1.4980E+03 2.1633E+00 1.0149E+02 1.5502E+02 2.7918E+01 8.5705E+00 8.3669E-01 8.3669E-01 6.1468E-01 1.4230E+00 -8.0829E-01 -1.0661E+00 - 1.4990E+03 2.1633E+00 1.0149E+02 1.5502E+02 2.7918E+01 8.5705E+00 2.5571E-01 2.5571E-01 2.4103E-01 5.6783E-01 -3.2680E-01 -5.9772E-01 - 1.5000E+03 2.1633E+00 1.0149E+02 1.5502E+02 2.7918E+01 8.5705E+00 1.1693E-01 1.1693E-01 9.7516E-02 3.1218E-01 -2.1466E-01 -4.8371E-01 - 1.5010E+03 2.1633E+00 1.0149E+02 1.5502E+02 2.7918E+01 8.5705E+00 6.7513E-02 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e82a1a36..5b76480d 100644 --- a/tests/testthat/test_NMdata_utils.R +++ b/tests/testthat/test_NMdata_utils.R @@ -1,19 +1,20 @@ context("NMdata Utils") NMdataConf(reset=TRUE) -NMdata_filepath <- function(...) { - system.file(..., package = "NMdata") -} +## NMdata_filepath <- function(...) { +## ## system.file(..., package = "NMdata") +## file.path("testData/nonmem/",..., package = "NMdata") +## } test_that("basic",{ NMdataConf(reset=T) - file.lst.1 <- system.file("examples/nonmem/xgxr001.lst" ,package="NMdata") + file.lst.1 <- "testData/nonmem/xgxr001.lst" res1 <- NMscanData(file=file.lst.1, quiet=T, order.columns = F, merge.by.row=FALSE, check.time = FALSE) - file.lst.2 <- NMdata_filepath("examples/nonmem/xgxr002.lst") + file.lst.2 <- "testData/nonmem/xgxr002.lst" res2 <- NMscanData(file=file.lst.2, check.time = FALSE, merge.by.row=FALSE,quiet=TRUE) diff --git a/tests/testthat/test_NMorderColumns.R b/tests/testthat/test_NMorderColumns.R index dc97f501..dcd10327 100644 --- a/tests/testthat/test_NMorderColumns.R +++ b/tests/testthat/test_NMorderColumns.R @@ -2,9 +2,10 @@ context("NMorderColumns") test_that("last NULL",{ - fileRef <- "testReference/NMorderColumns_1.rds" + fileRef <- "testReference/NMorderColumns_01.rds" - pk <- readRDS(file=system.file("examples/data/xgxr2.rds",package="NMdata")) + ## pk <- readRDS(file=system.file("examples/data/xgxr2.rds",package="NMdata")) + pk <- readRDS(file="testData/data/xgxr2.rds")|> setDT() pk1 <- NMorderColumns(pk) pk2 <- NMorderColumns(pk,last=c("FLAG",NULL)) @@ -20,3 +21,28 @@ test_that("last NULL",{ ,fileRef) }) + +test_that("Non-numeric DATE and TIME",{ + + fileRef <- "testReference/NMorderColumns_02.rds" + + pk <- readRDS(file="testData/data/xgxr2.rds") + setDT(pk) + + pk[,time.tz:=as.POSIXct("2000/01/01",tz="UTC")+TIME*3600] +## pk[,DATE:=as.character(as.Date(time.tz),format="%y/%m/%d")] + ## pk[,TIME:=as.character(time.tz,format="%H:%M:%S")] + + pk[,DATE:=format(as.Date(time.tz),format="%y/%m/%d")] + pk[,TIME:=format(time.tz,format="%H:%M:%S")] + + + pk1 <- NMorderColumns(pk) + + dtres <- data.table(colnames(pk),colnames(pk1)) + + expect_equal_to_reference( + dtres + ,fileRef) +readRDS(fileRef) +}) diff --git a/tests/testthat/test_NMscanData.R b/tests/testthat/test_NMscanData.R index ccf4a0d2..7137bdf0 100644 --- a/tests/testthat/test_NMscanData.R +++ b/tests/testthat/test_NMscanData.R @@ -552,7 +552,9 @@ test_that("input.txt/output.txt - unset modelname",{ res1[,(cols.differ):=NULL] res1dir[,(cols.differ):=NULL] - expect_equal(res1[,!("model")],res1dir[,!("model")]) + expect_equal(unNMdata(res1[,!("model")]),unNMdata(res1dir[,!("model")])) + ## NMinfo(res1,"tables") + ## NMinfo(res1dir,"tables") NMdataConf(as.fun=NULL) }) @@ -983,13 +985,12 @@ test_that("csv vs rds vs fst",{ test_that("inside lappy",{ ### there are issues running NMdata functions in lapply - probably due to getArgs - lsts <- c( "testData/nonmem/xgxr014.lst", "testData/nonmem/xgxr032.lst") - res1 <- NMscanData(lsts[1],as.fun="data.table") - res2 <- NMscanData(lsts[2],as.fun="data.table") + res1 <- NMscanData(lsts[1],as.fun="data.table",check.time=FALSE,quiet=TRUE) + res2 <- NMscanData(lsts[2],as.fun="data.table",check.time=FALSE,quiet=TRUE) - res.all <- rbindlist(lapply(lsts,NMscanData,as.fun="data.table"),fill=T ) + res.all <- rbindlist(lapply(lsts,NMscanData,as.fun="data.table",check.time=FALSE,quiet=TRUE),fill=T ) dims1 <- dims( diff --git a/tests/testthat/test_NMscanInput.R b/tests/testthat/test_NMscanInput.R index c8adb29b..98d73f70 100644 --- a/tests/testthat/test_NMscanInput.R +++ b/tests/testthat/test_NMscanInput.R @@ -141,12 +141,13 @@ test_that("Including meta data",{ test_that("CYCLE=DROP",{ fileRef <- "testReference/NMscanInput_07.rds" - file.lst <- system.file("examples/nonmem/xgxr002.lst",package="NMdata") + ### file.lst <- system.file("examples/nonmem/xgxr002.lst",package="NMdata") + file.lst <- "testData/nonmem/xgxr002.lst" ## res <- NMscanInput(file=file.lst,applyFilters = T,as.fun="none") ### using as.data.table for as.fun is not recommended but still allowed res <- - NMscanInput(file=file.lst,applyFilters = T,as.fun="data.table") + NMscanInput(file=file.lst,apply.filters = T,as.fun="data.table") fix.time(res) nm1 <- NMinfo(res) @@ -201,7 +202,8 @@ test_that("Missing control stream",{ test_that("apply.filters=F and recover.rows=FALSE",{ fileRef <- "testReference/NMscanInput_11.rds" - file.lst <- system.file("examples/nonmem/xgxr002.lst",package="NMdata") + ##file.lst <- system.file("examples/nonmem/xgxr002.lst",package="NMdata") +file.lst <- "testData/nonmem/xgxr002.lst" ## res <- NMscanInput(file=file.lst,applyFilters = T,as.fun="none") ### using as.data.table for as.fun is not recommended but still allowed diff --git a/tests/testthat/test_NMscanTables.R b/tests/testthat/test_NMscanTables.R index 7848b37d..70f3dcd3 100644 --- a/tests/testthat/test_NMscanTables.R +++ b/tests/testthat/test_NMscanTables.R @@ -22,7 +22,8 @@ test_that("Multiple output table formats",{ if(F){ res.dt readRDS(fileRef) - } + NMinfo(readRDS(fileRef),"tables") + } ## test that we have data.tables from using as.fun=none expect_true(all(unlist(lapply(res.dt,is.data.table)))) diff --git a/tests/testthat/test_NMwriteData.R b/tests/testthat/test_NMwriteData.R index 04a32975..dff5e806 100644 --- a/tests/testthat/test_NMwriteData.R +++ b/tests/testthat/test_NMwriteData.R @@ -79,7 +79,8 @@ test_that("Dropping a column in Nonmem",{ test_that("A comma in a character",{ - pk <- readRDS(file=system.file("examples/data/xgxr2.rds",package="NMdata")) + ## pk <- readRDS(file=system.file("examples/data/xgxr2.rds",package="NMdata")) + pk <- readRDS(file="testData/data/xgxr2.rds") |> setDT() ## dropping a character column pk[,CYCLE:=paste0(as.character(CYCLE),",0")] @@ -88,7 +89,7 @@ test_that("A comma in a character",{ expect_error( NMwriteData(pk,file="testOutput/NMwriteDataTmp.csv", ,formats=NULL - ,nm.drop="CYCLE") + ,nm.drop="CYCLE") ) }) @@ -96,7 +97,7 @@ test_that("A comma in a character",{ test_that("Identical column names",{ - pk <- readRDS(file=system.file("examples/data/xgxr2.rds",package="NMdata")) + pk <- readRDS(file="testData/data/xgxr2.rds") |> setDT() pk <- cbind(pk[,.(CYCLE)],pk) expect_warning(NMwriteData(pk,file="testOutput/NMwriteDataTmp.csv" ,write.rds=F,write.csv=F @@ -300,3 +301,41 @@ test_that("save csv and fst",{ } ) + + +test_that("Non-numeric DATE and TIME",{ + + + fileRef <- "testReference/NMwriteData_13.rds" + outfile <- "testOutput/NMwriteData_13.csv" + + pk <- readRDS(file="testData/data/xgxr2.rds") |> setDT() + + ## pk <- fix.input(pk) + + pk[,time.tz:=as.POSIXct("2000/01/01",tz="UTC")+TIME*3600] + ## pk[,DATE:=as.character(as.Date(time.tz),format="%y/%m/%d")] + pk[,DATE:=format(as.Date(time.tz),format="%y/%m/%d")] + ## pk[,TIME:=as.character(time.tz,format="%H:%M:%S")] + pk[,TIME:=format(time.tz,format="%H:%M:%S")] + + + pk <- NMorderColumns(pk) + + nmcode <- NMwriteData(pk,file=outfile + ,script="DATE and TIME as char",formats=cc(csv), + args.stamp=list(time="2021-11-21 11:00:00")) + + res <- NMreadCsv(fnExtension(outfile,"csv"),as.fun="data.table") + + + expect_equal_to_reference( + res + ,fileRef,version=2) + + if(F){ + ref <- readRDS(fileRef) + compareCols(res,ref) +} + +})