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nm-gettersetters.R
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nm-gettersetters.R
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#' @include make_project.R
NULL
#' Get and set path to NONMEM control file
#'
#' @description
#'
#' `r lifecycle::badge("stable")`
#'
#' Similar to [ctl_name()] & [run_in()], this allows you to retrieve and specify
#' the relative path to the control file that will be written by the [run_nm()].
#'
#' @param m An nm object.
#' @param text Optional character. Name of path to control file (see details).
#' Typically, this file does not yet normally exist, but will house the code
#' code for this run.
#'
#' @details Note that `text` can contain an `"{run_id}"` string. E.g.
#' `"Models/run{run_id}.mod"` will use the name `"Models/runm1.mod"` if
#' `run_id(m1)` is `"m1"`.
#'
#' @return `character` with path to NONMEM control file to be copied immediately
#' prior to running (with [run_nm()]).
#'
#' @examples
#'
#' # create example object m1 from package demo files
#' exdir <- system.file("extdata", "examples", "theopp", package = "NMproject")
#' m1 <- new_nm(run_id = "m1",
#' based_on = file.path(exdir, "Models", "ADVAN2.mod"),
#' data_path = file.path(exdir, "SourceData", "THEOPP.csv"))
#'
#'
#' ctl_name(m1)
#' ctl_path(m1)
#'
#' m1 <- m1 %>% ctl_path("Models/nm_{run_id}.ctl")
#' ctl_path(m1)
#'
#'
#' @export
ctl_path <- function(m, text) {
if (missing(text)) {
file.path(run_in(m), ctl_name(m))
} else {
m <- m %>% run_in(dirname(text))
m <- m %>% ctl_name(basename(text))
m
}
}
#' @name nm_getsetters
#' @rdname nm_getsetters
#'
#' @title Functions to access and modify fields of nm objects
#'
#' @description
#'
#' `r lifecycle::badge("stable")`
#'
#' The fields of an object can be viewed by printing the object. Each field has
#' a corresponding function of the same name to access and modify it's value.
#'
#' @param m An nm object.
#' @param text Optional character for replacing field. If present function will
#' modify field (of same name as function) otherwise will return value of
#' field (of same name as function).
#'
#' @details Easiest way to see all fields of an object is to type the object
#' into the console and hit enter. This will display the value of each field.
#'
#' The fundamental structure of all these functions is the same:
#'
#' To access the value of a field:
#' `m %>% fieldname()` or equivalently `fieldname(m)`.
#'
#' To modify the value of a field:
#' `m <- m %>% fieldname("newvalue")`
#'
#' @return The value of the specified field of `m` if `text` is missing.
#' Otherwise an nm object with modified field.
#'
#' @examples
#'
#' # create example object m1 from package demo files
#' exdir <- system.file("extdata", "examples", "theopp", package = "NMproject")
#' m1 <- new_nm(run_id = "m1",
#' based_on = file.path(exdir, "Models", "ADVAN2.mod"),
#' data_path = file.path(exdir, "SourceData", "THEOPP.csv"))
#'
#'
#' run_dir(m1)
#'
#' m1 <- m1 %>% run_dir("{run_id}_dir")
#' run_dir(m1)
#'
#' @export
run_dir <- function(m, text) {
UseMethod("run_dir")
}
#' @export
run_dir.nm_generic <- function(m, text) {
if (missing(text)) {
custom_1d_field(m, "run_dir")
} else {
custom_1d_field(m, "run_dir", text, glue = TRUE)
}
}
#' @export
run_dir.nm_list <- run_dir.nm_generic
#' @rdname nm_getsetters
#' @details Some fields like `cmd` are glue fields. In these cases inserting
#' expressions inside braces in `text` will evaluate the expression (see
#' examples).
#' @examples
#'
#' ## set cmd field of m1
#' m1 <- m1 %>% cmd("execute {ctl_name} -dir={run_dir}")
#'
#' m1 %>% cmd()
#' ## displays "execute runm1.mod -dir=m1"
#'
#' ## can also view field when viewing object
#' m1
#' @export
cmd <- function(m, text) {
if (missing(text)) {
custom_1d_field(m, "cmd")
} else {
clean_text <- text[grepl("\\-clean\\=", text)]
if (length(clean_text)) {
clean_number <- gsub(".*\\-clean\\=([0-9]+).*", "\\1", clean_text)
clean_number <- as.numeric(clean_number)
if (clean_number > 2) {
warning("use of -clean flag more than 2 is not recommended with NMproject.
NMproject uses files in the NM_run directories instead of files copied back to main directory.
see ?ls_tempfiles for post run clean up options")
}
}
custom_1d_field(m, "cmd", text, glue = TRUE)
}
}
#' @rdname nm_getsetters
#' @export
type <- function(m, text) {
if (missing(text)) {
custom_1d_field(m, "type")
} else {
m <- custom_1d_field(m, "type", text)
if (text %in% "nmfe") {
m <- m %>%
run_in(file.path(run_in(m), "{run_dir}")) %>%
lst_path("{gsub(\"mod\", \"lst\", ctl_name)}")
}
m
}
}
#' @rdname nm_getsetters
#' @export
parent_run_id <- function(m, text) {
if (missing(text)) custom_1d_field(m, "parent_run_id") else custom_1d_field(m, "parent_run_id", as.character(text))
}
#' @rdname nm_getsetters
#' @export
parent_run_in <- function(m, text) {
if (missing(text)) custom_1d_field(m, "parent_run_in") else custom_1d_field(m, "parent_run_in", as.character(text))
}
#' @rdname nm_getsetters
#' @export
parent_ctl_name <- function(m, text) {
if (missing(text)) custom_1d_field(m, "parent_ctl_name") else custom_1d_field(m, "parent_ctl_name", as.character(text))
}
#' @rdname nm_getsetters
#' @export
parent_results_dir <- function(m, text) {
if (missing(text)) custom_1d_field(m, "parent_results_dir") else custom_1d_field(m, "parent_results_dir", as.character(text))
}
#' @rdname nm_getsetters
#' @export
unique_id <- function(m, text) {
if (missing(text)) custom_1d_field(m, "unique_id") else custom_1d_field(m, "unique_id", text, glue = TRUE)
}
#' @rdname nm_getsetters
#' @export
ctl_name <- function(m, text) {
if (missing(text)) custom_1d_field(m, "ctl_name") else custom_1d_field(m, "ctl_name", text, glue = TRUE)
}
#' @rdname nm_getsetters
#' @export
results_dir <- function(m, text) {
if (missing(text)) custom_1d_field(m, "results_dir") else custom_1d_field(m, "results_dir", text, glue = TRUE)
}
#' @rdname nm_getsetters
#' @export
run_in <- function(m, text) {
UseMethod("run_in")
}
#' @export
run_in.nm_generic <- function(m, text) {
if (missing(text)) {
custom_1d_field(m, "run_in")
} else {
m <- custom_1d_field(m, "run_in", text)
## additional code to ensure data_path is redone
data_path <- data_path(m)
m <- m %>% data_path(data_path) ## reset data path
m
}
}
#' @export
run_in.nm_list <- Vectorize_nm_list(run_in.nm_generic, pre_glue = TRUE)
#' @rdname nm_getsetters
#' @param update_ctl Should NONMEM code be updated to reflect the new run_id.
#' Assumes `text` is not missing. Default = FALSE.
#' @export
run_id <- function(m, text, update_ctl = FALSE) {
UseMethod("run_id")
}
#' @export
run_id.nm_generic <- function(m, text, update_ctl = FALSE) {
if (missing(text)) {
# if(is_single_na(m)) return(NA_character_)
if (length(m[["run_id"]]) > 0) {
return(m[["run_id"]])
} else {
return(NA_character_)
}
}
m[["job_info"]] <- NA_character_ ## wipe job info
# m[["paUseMethod()rent_run_id"]] <- m[["run_id"]]
m[["run_id"]] <- as.character(text)
## Do all glueing first.
for (field in names(m$glue_fields)) {
m <- replace_tag(m, field)
}
## why was this here?
if (update_ctl) {
if ("ctl_contents" %in% names(m)) m <- m %>% ctl_contents(m[["ctl_contents"]]) ## update ctl_contents object
}
m
}
#' @export
run_id.nm_list <- Vectorize_nm_list(run_id.nm_generic)
#' @rdname nm_getsetters
#' @export
result_files <- function(m, text) {
UseMethod("result_files")
}
#' @export
result_files.nm_generic <- function(m, text) {
if (missing(text)) {
return(m[["result_files"]])
}
m[["result_files"]] <- unique(c(m[["result_files"]], text))
m
}
#' @export
result_files.nm_list <- Vectorize_nm_list(result_files.nm_generic, SIMPLIFY = FALSE)
#' @name nm_getsetters_execution
#' @rdname nm_getsetters_execution
#'
#' @title Execution related functions to access and modify fields of nm objects
#'
#' @description
#'
#' `r lifecycle::badge("stable")`
#'
#' The fields of an object can be viewed by printing the object. Each field has
#' a corresponding function of the same name to access and modify it's value.
#'
#' @param m An nm object.
#' @param text Optional character for replacing field. If present function will
#' modify field (of same name as function) otherwise will return value of
#' field (of same name as function).
#'
#' @details Easiest way to see all fields of an object is to type the object
#' into the console and hit enter. This will display the value of each field.
#' some fields like `cmd` are glue fields. In these cases inserting
#' expressions inside braces in `text` will evaluate the expression
#'
#' The fundamental structure of all these functions is the same:
#'
#' To access the value of a field:
#' `m %>% fieldname()` or equivalently `fieldname(m)`
#'
#' To modify the value of a field:
#' `m <- m %>% fieldname("newvalue")`
#'
#' @examples
#'
#' # create example object m1 from package demo files
#' exdir <- system.file("extdata", "examples", "theopp", package = "NMproject")
#' m1 <- new_nm(run_id = "m1",
#' based_on = file.path(exdir, "Models", "ADVAN2.mod"),
#' data_path = file.path(exdir, "SourceData", "THEOPP.csv"))
#'
#' m1 <- m1 %>% cmd("execute -parafile={parafile} {ctl_name} -dir={run_dir} -nodes={cores}")
#'
#' m1 <- m1 %>% cores(8) %>% parafile("mpilinux8.pnm")
#'
#' cmd(m1)
#' cores(m1)
#'
#'
#' @export
cores <- function(m, text) {
if (missing(text)) custom_1d_field(m, "cores") else custom_1d_field(m, "cores", text)
}
#' @rdname nm_getsetters_execution
#' @export
parafile <- function(m, text) {
if (missing(text)) {
custom_1d_field(m, "parafile")
} else {
custom_1d_field(m, "parafile", normalizePath(text, winslash = "/", mustWork = FALSE))
}
}
#' @rdname nm_getsetters_execution
#' @export
walltime <- function(m, text) {
if (missing(text)) custom_1d_field(m, "walltime") else custom_1d_field(m, "walltime", text)
}
#' @rdname nm_getsetters_execution
#' @export
executed <- function(m, text) {
if (missing(text)) custom_1d_field(m, "executed") else custom_1d_field(m, "executed", text)
}
#' @rdname nm_getsetters
#' @details The function `lst_path()` sets the expected location of the lst file
#' and all output files relative to the `run_in` location.
#' @export
lst_path <- function(m, text) {
if (missing(text)) custom_1d_field(m, "lst_path") else custom_1d_field(m, "lst_path", text, glue = TRUE)
}
#' Get path to run_dir
#'
#' @description
#'
#' `r lifecycle::badge("stable")`
#'
#' The function [run_dir()] gives the directory name, whereas this function gets
#' the (relative) path of [run_dir()].
#'
#' @param m An nm object.
#'
#' @return A path to the `run_dir` field of `m`.
#'
#' @seealso [nm_getsetters()].
#'
#' @examples
#'
#' # create example object m1 from package demo files
#' exdir <- system.file("extdata", "examples", "theopp", package = "NMproject")
#' m1 <- new_nm(run_id = "m1",
#' based_on = file.path(exdir, "Models", "ADVAN2.mod"),
#' data_path = file.path(exdir, "SourceData", "THEOPP.csv"))
#'
#' run_dir_path(m1)
#'
#' @export
run_dir_path <- function(m) file.path(run_in(m), run_dir(m))
#' Use file to set control file contents in nm object
#'
#' @description
#'
#' `r lifecycle::badge("stable")`
#'
#' This function is mostly called by the `new_nm()` and will not generally be
#' used directly by users. The function populates/modifies the `ctl_contents`
#' field of an nm object, with the contents of an already existing control file.
#'
#' @param m An nm object.
#' @param ctl_ob Path to control file.
#' @param update_numbering Logical. Should table numbers and author fields be updated.
#' @param update_dollar_data Logical. Should $DATA in control file be updated.
#' @param ... Additional arguments.
#'
#' @return An nm object with modified `ctl_contents` field.
#'
#' @keywords internal
#'
#' @export
based_on <- function(m, ctl_ob, update_numbering = TRUE, update_dollar_data = TRUE, ...) {
UseMethod("based_on")
}
#' @export
based_on.nm_generic <- function(m, ctl_ob, update_numbering = TRUE, update_dollar_data = TRUE, ...) {
if (missing(ctl_ob)) {
if (length(m[["ctl_contents"]]) > 0) {
return(m[["ctl_contents"]])
} else {
return(NA_character_)
}
}
# if(inherits(try(ctl_list2(ctl_ob)), "try-error")) browser()
## if NA just set field as NA
if (is_single_na(ctl_ob)) {
m[["ctl_contents"]] <- NA_character_
return(m)
}
ctl <- ctl_list2(ctl_ob)
if (update_numbering) {
for (i in which(names(ctl) %in% "TABLE")) {
ctl[[i]] <- gsub(paste0("(FILE\\s*=\\s*\\S*tab)\\S*\\b"), paste0("\\1", run_id(m)), ctl[[i]])
}
ctl[[1]] <- gsub("^(\\s*;;\\s*[0-9]*\\.\\s*Based on:).*", paste("\\1", parent_run_id(m)), ctl[[1]])
ctl[[1]] <- gsub("^(\\s*;;\\s*\\w*\\.\\s*Author:).*", paste("\\1", Sys.info()["user"]), ctl[[1]])
}
m[["ctl_contents"]] <- ctl
## set as ctl_orig only if ctl_orig doesn't exist
# if(!"ctl_orig" %in% names(m)) m[["ctl_orig"]] <- ctl
if (is_single_na(m[["ctl_orig"]])) m[["ctl_orig"]] <- ctl
## overwrite the data_path field if it's blank
data_path <- data_path(m)
if (is.na(data_path) & "DATA" %in% names(ctl)) { # & !from_staging){
## NOTE: this assumes run is from same run_in(m) directory
data_name <- gsub("^ *\\$DATA\\s*([^ ]+).*$", "\\1", ctl$DATA)[1]
data_path <- normalizePath(file.path(run_in(m), data_name), mustWork = FALSE)
if (file.exists(data_path)) {
## issue - run_in might not exist
## remove dir/.. segments
while (grepl("\\.\\.", data_path)) {
data_path <- gsub(
paste0("[^", .Platform$file.sep, "\\.]+", .Platform$file.sep, "\\.\\.", .Platform$file.sep),
"",
data_path
)
}
data_path <- relative_path(data_path, getwd())
m[["data_path"]] <- data_path
}
}
if (!is.na(data_path) & update_dollar_data) {
m <- m %>% fill_dollar_data(data_path)
}
m
}
#' @export
based_on.nm_list <- Vectorize_nm_list(based_on.nm_generic, SIMPLIFY = FALSE, replace_arg = "ctl_ob", pre_glue = TRUE)
#' Get/set control file contents
#'
#' This function is an alias for [based_on()].
#'
#' @param ... Arguments to be passed to [based_on()].
#' @return An nm object with modified `ctl_contents` field.
#'
#' @examples
#'
#' # create example object m1 from package demo files
#' exdir <- system.file("extdata", "examples", "theopp", package = "NMproject")
#' m1 <- new_nm(run_id = "m1",
#' based_on = file.path(exdir, "Models", "ADVAN2.mod"),
#' data_path = file.path(exdir, "SourceData", "THEOPP.csv"))
#'
#' m1 %>% ctl_contents()
#'
#' @export
ctl_contents <- function(...) based_on(...)
## minimal version of ctl_contents (just sets ctl_contents without mods)
ctl_contents_simple <- function(m, ctl_ob, ...) {
ctl_contents(m, ctl_ob, update_numbering = FALSE, update_dollar_data = FALSE, ...)
}
#' Interface for getting and setting your own simple fields in nm objects
#'
#' @description
#'
#' `r lifecycle::badge("stable")`
#'
#' @param m An nm object.
#' @param ... Arguments to get/set fields.
#'
#' @return If `...` contains an assignment, an nm object with modified field,
#' otherwise returns the field value.
#'
#' @examples
#'
#' # create example object m1 from package demo files
#' exdir <- system.file("extdata", "examples", "theopp", package = "NMproject")
#' m1 <- new_nm(run_id = "m1",
#' based_on = file.path(exdir, "Models", "ADVAN2.mod"),
#' data_path = file.path(exdir, "SourceData", "THEOPP.csv"))
#'
#' m1 <- m1 %>% simple_field(stars = 3)
#' m1 %>% simple_field(stars)
#' m1 ## see that stars is a field of the nm object.
#'
#' @export
simple_field <- function(m, ...) {
dots_exp <- rlang::enexprs(...)
if (identical(names(dots_exp), "")) {
get_simple_field(m, ...)
} else {
set_simple_field(m, ...)
}
}
set_simple_field <- function(m, ...) {
dots <- list(...)
fields <- names(dots)
for (i in seq_along(dots)) {
m <- m %>% custom_1d_field(field = fields[i], replace = dots[[i]])
}
m
}
get_simple_field <- function(m, field) {
field <- rlang::enquo(field)
field <- rlang::quo_name(field)
m %>% custom_1d_field(field = field)
}
custom_1d_field <- function(m, field, replace, glue = FALSE) {
UseMethod("custom_1d_field")
}
custom_1d_field.nm_generic <- function(m, field, replace, glue = FALSE) {
if (missing(replace)) {
if (length(m[[field]]) > 0) {
return(m[[field]])
} else {
return(NA_character_)
}
}
## Only update if there is a change
if (field %in% names(m)) {
if (glue) old_glue_field <- m$glue_fields[[field]] else old_glue_field <- m[[field]]
if (identical(replace, old_glue_field)) {
return(m)
}
}
if (glue) {
m$glue_fields[[field]] <- replace
m[[field]] <- replace
## glue the field
if (!is.na(replace)) m <- replace_tags(m, field)
} else {
m[[field]] <- replace
}
## reglue all other glueable fields
for (other_col in names(m$glue_fields)[!names(m$glue_fields) %in% field]) {
m <- replace_tags(m, other_col)
}
m
}
custom_1d_field.nm_list <- Vectorize_nm_list(custom_1d_field.nm_generic, replace_arg = "replace")