Make mkinmod quiet in tests

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 <http://www.gnu.org/licenses/> }}}

 

-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,