From ffc12f79fdb283bc59f073208c883b84271be121 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 15 May 2015 14:04:49 +0200 Subject: Make mkinmod quiet in tests --- R/mkinmod.R | 8 ++++---- man/mkinmod.Rd | 5 ++++- tests/testthat/test_FOCUS_D_UBA_expertise.R | 4 ++-- tests/testthat/test_FOCUS_chi2_error_level.R | 2 +- tests/testthat/test_mkinpredict_SFO_SFO.R | 4 ++-- tests/testthat/test_schaefer07_complex_case.R | 2 +- tests/testthat/test_synthetic_data_for_UBA_2014.R | 4 ++-- 7 files changed, 16 insertions(+), 13 deletions(-) diff --git a/R/mkinmod.R b/R/mkinmod.R index 149d2beb..e865fa27 100644 --- a/R/mkinmod.R +++ b/R/mkinmod.R @@ -16,7 +16,7 @@ # You should have received a copy of the GNU General Public License along with # this program. If not, see }}} -mkinmod <- function(..., use_of_ff = "min", speclist = NULL) +mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE) { if (is.null(speclist)) spec <- list(...) else spec <- speclist @@ -272,8 +272,8 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL) model$coefmat <- m }#}}} - # Create a function compiled from C code if possible #{{{ - if (requireNamespace("ccSolve", quietly = TRUE)) { + # Create a function compiled from C code if more than one observed variable and ccSolve is available #{{{ + if (length(obs_vars) > 1 & requireNamespace("ccSolve", quietly = TRUE)) { diffs.C <- paste(diffs, collapse = ";\n") diffs.C <- paste0(diffs.C, ";") for (i in seq_along(diffs)) { @@ -297,7 +297,7 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL) } if (sum(sapply(spec, function(x) x$type %in% c("SFO", "FOMC", "DFOP", "SFORB"))) == length(spec)) { - message("Compiling differential equation model from auto-generated C code...") + if (!quiet) message("Compiling differential equation model from auto-generated C code...") model$compiled <- ccSolve::compile.ode(diffs.C, language = "C", parms = parms, declaration = "double time = *t;") diff --git a/man/mkinmod.Rd b/man/mkinmod.Rd index f73b78da..4de4c98a 100644 --- a/man/mkinmod.Rd +++ b/man/mkinmod.Rd @@ -13,7 +13,7 @@ in the FOCUS and NAFTA guidance documents are used. } \usage{ -mkinmod(..., use_of_ff = "min", speclist = NULL) +mkinmod(..., use_of_ff = "min", speclist = NULL, quiet = FALSE) } \arguments{ \item{...}{ @@ -42,6 +42,9 @@ mkinmod(..., use_of_ff = "min", speclist = NULL) The specification of the observed variables and their submodel types and pathways can be given as a single list using this argument. Default is NULL. } + \item{quiet}{ + Should messages be suppressed? + } } \value{ A list of class \code{mkinmod} for use with \code{\link{mkinfit}}, containing diff --git a/tests/testthat/test_FOCUS_D_UBA_expertise.R b/tests/testthat/test_FOCUS_D_UBA_expertise.R index ce1e0a5a..b12834e5 100644 --- a/tests/testthat/test_FOCUS_D_UBA_expertise.R +++ b/tests/testthat/test_FOCUS_D_UBA_expertise.R @@ -19,10 +19,10 @@ context("Results for FOCUS D established in expertise for UBA (Ranke 2014)") SFO_SFO <- mkinmod(parent = list(type = "SFO", to = "m1"), - m1 = list(type = "SFO")) + m1 = list(type = "SFO"), quiet = TRUE) SFO_SFO.ff <- mkinmod(parent = list(type = "SFO", to = "m1"), m1 = list(type = "SFO"), - use_of_ff = "max") + use_of_ff = "max", quiet = TRUE) fit.default <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE) fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE) diff --git a/tests/testthat/test_FOCUS_chi2_error_level.R b/tests/testthat/test_FOCUS_chi2_error_level.R index 65e1ada7..2db2f4e6 100644 --- a/tests/testthat/test_FOCUS_chi2_error_level.R +++ b/tests/testthat/test_FOCUS_chi2_error_level.R @@ -22,7 +22,7 @@ context("Calculation of FOCUS chi2 error levels") SFO_SFO.ff <- mkinmod(parent = list(type = "SFO", to = "m1"), m1 = list(type = "SFO"), - use_of_ff = "max") + use_of_ff = "max", quiet = TRUE) test_that("Chi2 error levels for FOCUS D are as in mkin 0.9-33", { diff --git a/tests/testthat/test_mkinpredict_SFO_SFO.R b/tests/testthat/test_mkinpredict_SFO_SFO.R index 1238bb28..b7004f64 100644 --- a/tests/testthat/test_mkinpredict_SFO_SFO.R +++ b/tests/testthat/test_mkinpredict_SFO_SFO.R @@ -28,9 +28,9 @@ test_that("Variants of model predictions for SFO_SFO model give equivalent resul # and relative tolerance is thus not met tol = 0.01 SFO_SFO.1 <- mkinmod(parent = list(type = "SFO", to = "m1"), - m1 = list(type = "SFO"), use_of_ff = "min") + m1 = list(type = "SFO"), use_of_ff = "min", quiet = TRUE) SFO_SFO.2 <- mkinmod(parent = list(type = "SFO", to = "m1"), - m1 = list(type = "SFO"), use_of_ff = "max") + m1 = list(type = "SFO"), use_of_ff = "max", quiet = TRUE) ot = seq(0, 100, by = 1) r.1.e <- subset(mkinpredict(SFO_SFO.1, diff --git a/tests/testthat/test_schaefer07_complex_case.R b/tests/testthat/test_schaefer07_complex_case.R index 1ef5106e..1b51e5d2 100644 --- a/tests/testthat/test_schaefer07_complex_case.R +++ b/tests/testthat/test_schaefer07_complex_case.R @@ -25,7 +25,7 @@ schaefer07_complex_model <- mkinmod( A1 = list(type = "SFO", to = "A2"), B1 = list(type = "SFO"), C1 = list(type = "SFO"), - A2 = list(type = "SFO"), use_of_ff = "max") + A2 = list(type = "SFO"), use_of_ff = "max", quiet = TRUE) schaefer07_long <- mkin_wide_to_long(schaefer07_complex_case, time = "time") diff --git a/tests/testthat/test_synthetic_data_for_UBA_2014.R b/tests/testthat/test_synthetic_data_for_UBA_2014.R index 2bf01075..25f841b1 100644 --- a/tests/testthat/test_synthetic_data_for_UBA_2014.R +++ b/tests/testthat/test_synthetic_data_for_UBA_2014.R @@ -21,12 +21,12 @@ context("Results for synthetic data established in expertise for UBA (Ranke 2014 m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"), M1 = list(type = "SFO", to = "M2"), - M2 = list(type = "SFO"), use_of_ff = "max") + M2 = list(type = "SFO"), use_of_ff = "max", quiet = TRUE) m_synth_DFOP_par <- mkinmod(parent = list(type = "DFOP", to = c("M1", "M2")), M1 = list(type = "SFO"), - M2 = list(type = "SFO"), use_of_ff = "max") + M2 = list(type = "SFO"), use_of_ff = "max", quiet = TRUE) fit_SFO_lin_a <- mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data, -- cgit v1.2.1