if (helper_skip()) { context("Test reader parameters") reader_help <- reader_helpers() #------------------- read_mlx18_res start -------------------------------------- test_that("read_mlx18_res: params: path, x; result: data.table", { skip_on_os("windows") ipath <- file.path(reader_help$wd, "predictions.txt") names. <- names(reader_help$conf$data) x <- reader_help$conf$data[names.] expect_error(read_mlx18_res(ipath, x[["predictions"]])) }) test_that("read_mlx18_res: params: path is wrong, subfolder is not empty, file exists, endpoint; result: identical structure", { skip_on_os("windows") ipath <- file.path(reader_help$wd, "predictions.txt") names. <- names(reader_help$conf$data) x <- reader_help$conf$data[names.] x$predictions$endpoint <- "pred" expect_error(read_mlx18_res(ipath, x$predictions)) }) test_that("read_mlx18_res: params: path is wrong, subfolder is not empty, file exists; result: identical structure", { skip_on_os("windows") ipath <- file.path(system.file(package = "ggPMX"), "testdata", "theophylline", "predictions.txt") names. <- names(reader_help$conf$data) x <- reader_help$conf$data[names.] x$predictions$subfolder <- "Monolix" x$predictions$file <- "predictions.txt" expect_null(read_mlx18_res(ipath, x$predictions)) }) test_that("read_mlx18_res: params: newnames, path is wrong, subfolder is not empty, file exists; result: identical structure", { skip_on_os("windows") ipath <- file.path(system.file(package = "ggPMX"), "testdata", "theophylline", "predictions.txt") names. <- names(reader_help$conf$data) x <- reader_help$conf$data[names.] x$predictions$subfolder <- "Monolix" x$predictions$file <- "predictions.txt" x$predictions$newnames <- list( ID = "id", TIME = "time", PRED = "poppred", NPDE = "npde", IPRED = "mlx_ipred", IWRES = "mlx_iwres" ) r <- read_mlx18_res(ipath, x$predictions) expect_identical(r, NULL) }) test_that("read_mlx18_res: params: pattern, path is wrong, subfolder is not empty, file exists; result: identical structure", { skip_on_os("windows") ipath <- file.path(system.file(package = "ggPMX"), "testdata", "theophylline", "finegrid.txt") names. <- names(reader_help$conf$data) x <- reader_help$conf$data[names.] x$finegrid$names <- list( ID = "ID", time = "time", popPred = "popPred", "indPred_mean*" = "indPred_mean*", indPred_mode = "indPred_mode", V6 = "V6" ) x$finegrid$subfolder <- "Monolix" x$finegrid$file <- "finegrid.txt" x$finegrid$id <- "ID" x$finegrid$pattern <- "_obsVsPred" r <- read_mlx18_res(ipath, x$finegrid) expect_identical(r, NULL) }) test_that("read_mlx18_res: 11params: path is wrong, subfolder is not empty, file exists; result: identical structure", { skip_on_os("windows") ipath <- file.path(system.file(package = "ggPMX"), "testdata", "theophylline", "finegrid.txt") names. <- names(reader_help$conf$data) x <- reader_help$conf$data[names.] x$finegrid$names <- list( ID = "ID", time = "time", popPred = "popPred", "indPred_mean*" = "indPred_mean*", indPred_mode = "indPred_mode", V6 = "V6" ) x$finegrid$subfolder <- "Monolix" x$finegrid$file <- "finegrid.txt" x$finegrid$id <- "ID" expect_s3_class(read_mlx18_res(ipath, x$finegrid), c("data.table", "data.frame")) }) test_that("read_mlx18_res: params: path, occ = OCC and its in file; result: error", { skip_on_os("windows") my.file <- tempfile() fwrite( data.frame( "IDS" = c(1, 1, 1), "time" = c(0, 0.5, 1), "y1" = c(2000, 0, 0), "OCC" = c(0, 130, 228), "meanPred" = c(1, 0, 0), "indPred_mean*" = c(87, 87, 87), "indPred_mode" = c(125.3, 412.5, 658.63), "popWRes" = c(0.00, 0.52, 0.69), "meanWRes" = c(0.15, 0.21, 0.42), "indWRes_mean*" = c(0.15, 0.21, 0.42), "indWRes_mode" = c(121, 132, 145), "NPDE" = c(121, 132, 145), "OCC" = c(1, 0, 1) ), my.file ) names. <- names(reader_help$conf$data) x <- reader_help$conf$data[names.] x$predictions$file <- basename(my.file) x$predictions$id <- "ID" expect_error(read_mlx18_res(dirname(my.file), x$predictions, occ = "OCC")) }) test_that("read_mlx18_res: params: path is NULL, x; result: error", { skip_on_os("windows") ipath <- NULL names. <- names(reader_help$conf$data) x <- reader_help$conf$data[names.] expect_error(read_mlx18_res(ipath, x$predictions)) }) test_that("read_mlx18_res: params: path, x is NULL; result: error", { skip_on_os("windows") ipath <- file.path(reader_help$wd, "predictions.txt") x <- NULL expect_error(read_mlx18_res(ipath, x)) }) ##------------------- read_mlx18_res end----------------------------------------- #------------------- read_mlx_pred start --------------------------------------- test_that("read_mlx_pred: params: path, x; result: identical class", { ipath <- file.path(reader_help$wd, "predictions.txt") names. <- names(reader_help$conf$data) x <- reader_help$conf$data[names.] r <- read_mlx_pred(ipath, x$predictions) expect_true(inherits(r, "data.frame")) }) test_that("read_mlx_pred: params: path, x$id is ID; result: identical class", { ipath <- file.path(reader_help$wd, "predictions.txt") names. <- names(reader_help$conf$data) x <- reader_help$conf$data[names.] x$id <- "ID" r <- read_mlx_pred(ipath, x$predictions) expect_true(inherits(r, "data.frame")) }) test_that("read_mlx_pred: params: path, occ = OCC and its in file; result: identical class", { my.file <- tempfile() write.csv( data.frame( "IDS" = c(1, 1, 1), "time" = c(0, 0.5, 1), "y1" = c(2000, 0, 0), "popPred" = c(0, 130, 228), "meanPred" = c(1, 0, 0), "indPred_mean*" = c(87, 87, 87), "indPred_mode" = c(125.3, 412.5, 658.63), "popWRes" = c(0.00, 0.52, 0.69), "meanWRes" = c(0.15, 0.21, 0.42), "indWRes_mean*" = c(0.15, 0.21, 0.42), "indWRes_mode" = c(121, 132, 145), "NPDE" = c(121, 132, 145), "OCC" = c(1, 0, 1) ), my.file ) names. <- names(reader_help$conf$data) x <- reader_help$conf$data[names.] x$id <- "IDS" r <- read_mlx_pred(my.file, x$predictions, occ = "OCC") expect_true(inherits(r, "data.frame")) }) test_that("read_mlx_pred: params: path, occ = OCC but not such column in file; result: error", { my.file <- tempfile() write.csv( data.frame( "IDS" = c(1, 1, 1), "time" = c(0, 0.5, 1), "y1" = c(2000, 0, 0), "popPred" = c(0, 130, 228), "meanPred" = c(1, 0, 0), "indPred_mean*" = c(87, 87, 87), "indPred_mode" = c(125.3, 412.5, 658.63), "popWRes" = c(0.00, 0.52, 0.69), "meanWRes" = c(0.15, 0.21, 0.42), "indWRes_mean*" = c(0.15, 0.21, 0.42), "indWRes_mode" = c(121, 132, 145), "NPDE" = c(121, 132, 145) ), my.file ) names. <- names(reader_help$conf$data) x <- reader_help$conf$data[names.] x$id <- "IDS" expect_error(read_mlx_pred(my.file, x$predictions, occ = "OCC")) }) test_that("read_mlx_pred: params: path, x is NULL; result: error", { ipath <- file.path(reader_help$wd, "predictions.txt") x <- NULL expect_error(read_mlx_pred(ipath, x$predictions)) }) test_that("read_mlx_pred: params: path is NULL, x; result: error", { ipath <- NULL names. <- names(reader_help$conf$data) x <- reader_help$conf$data[names.] expect_error(read_mlx_pred(ipath, x$predictions)) }) #------------------- read_mlx_pred end------------------------------------------ #------------------- read_mlx18_pred start ------------------------------------- test_that("read_mlx18_pred: params: path, x; result: identical structure", { ipath <- file.path(reader_help$wd, "predictions.txt") names. <- names(reader_help$conf$data) x <- reader_help$conf$data[names.] r <- read_mlx18_pred(ipath, x$predictions) expect_identical( names(r), c("ID", "TIME", "PRED", "NPDE", "IPRED", "IWRES") ) }) test_that("read_mlx18_pred: params: path is wrong, subfolder is not empty, file exists; result: identical structure", { ipath <- file.path(system.file(package = "ggPMX"), "testdata", "theophylline", "predictions.txt") names. <- names(reader_help$conf$data) x <- reader_help$conf$data[names.] x$predictions$subfolder <- "Monolix" x$predictions$file <- "predictions.txt" r <- read_mlx18_pred(ipath, x$predictions) expect_identical( names(r), c("ID", "TIME", "PRED", "NPDE", "IPRED", "IWRES") ) }) test_that("read_mlx18_pred: params:path is wrong, subfolder is not empty, file doesn't exist; result: NULL", { ipath <- file.path(system.file(package = "ggPMX"), "testdata", "predictions.txt") names. <- names(reader_help$conf$data) x <- reader_help$conf$data[names.] x$predictions$subfolder <- "theophylline" x$predictions$file <- "predictions.txt" r <- read_mlx18_pred(ipath, x$predictions) expect_identical( r, NULL ) }) test_that("read_mlx18_pred: params: residuals; result: error", { ipath <- file.path(reader_help$wd, "predictions.txt") names. <- names(reader_help$conf$data) x <- reader_help$conf$data[names.] x$predictions$residuals <- x$finegrid x$predictions$endpoint <- pmx_endpoint( code = "236", file.code = "2" ) x$predictions$id <- "ID" expect_error(read_mlx18_pred(ipath, x$predictions)) }) #------------------- read_mlx18_pred end---------------------------------------- #------------------- read_mlx_par_est start ------------------------------------ test_that("read_mlx_par_est: params: path, x; result: identical class and structure", { ipath <- file.path(reader_help$wd, "estimates.txt") x <- NULL x$sep <- ";" r <- read_mlx_par_est(ipath, x) expect_identical(c("PARAM", "VALUE", "SE", "RSE", "PVALUE"), names(r)) expect_true(inherits(r, "data.frame")) }) test_that("read_mlx_par_est: params: path is NULL, x; result: error", { ipath <- NULL x <- NULL x$sep <- ";" expect_error( read_mlx_par_est(ipath, x) ) }) test_that("read_mlx_par_est: params: path, x is '' ; result: error", { ipath <- file.path(reader_help$wd, "estimates.txt") x <- NULL x$sep <- "" expect_error(read_mlx_par_est(ipath, x)) }) #------------------- read_mlx_par_est end--------------------------------------- }