Improve tests

- Reduce significant digits for the objective function output in
mkinfit(..., quiet = FALSE) as R and R-devel gave different output on my
system
- Add makefile target 'devtest' for testing with R-devel, in order
to fix problems showing up with R-devel on Travis

5 files changed, 90 insertions, 49 deletions

diff --git a/GNUmakefile b/GNUmakefile
index 8108704a..1adac4e0 100644
--- a/GNUmakefile
+++ b/GNUmakefile
@@ -10,7 +10,7 @@ WINBIN  := $(PKGSRC)_$(PKGVERS).zip
 # If no alternate bin folder is specified, the default is to use the folder
 # containing the first instance of R on the PATH.
 RBIN ?= $(shell dirname "`which R`")
-#RBIN=/home/jranke/svn/R/r-devel/build/bin
+RDEVBIN=/home/jranke/svn/R/r-devel/build/bin
 
 # Specify package and static documentation directories for subversion on r-forge
 RFSVN ?= $(HOME)/svn/r-forge/kinfit
@@ -78,12 +78,16 @@ test: install
 	"$(RBIN)/Rscript" -e 'devtools::test()' 2>&1 | tee test.log
 	sed -i -e "s/\r.*\r//" test.log
 
+devtest: install
+	"$(RDEVBIN)/Rscript" -e 'devtools::test()' 2>&1 | tee test_dev.log
+	sed -i -e "s/\r.*\r//" test.log
+
 slowtests: install
 	NOT_CRAN=true "$(RBIN)/Rscript" -e 'library(mkin); testthat::test_dir("tests/testthat/slow")' 2>&1 | tee tests_slow.log
 	sed -i -e "s/\r.*\r//" tests_slow.log
 
 vdiffr:
-	/home/jranke/svn/R/r-devel/build/bin/Rscript -e 'vdiffr::manage_cases(filter = "plot|nafta")'
+	"$(RDEVBIN)/Rscript" -e 'vdiffr::manage_cases(filter = "plot|nafta")'
 
 testcheck: test check
 
diff --git a/R/mkinfit.R b/R/mkinfit.R
index 73fe43e0..12df0325 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -637,7 +637,7 @@ mkinfit <- function(mkinmod, observed,
       if (cost < cost.current) {
         assign("cost.current", cost, inherits = TRUE)
         if (!quiet) cat(ifelse(OLS, "Sum of squared residuals", "Negative log-likelihood"),
-                        " at call ", calls, ": ", cost.current, "\n", sep = "")
+                        " at call ", calls, ": ", signif(cost.current, 6), "\n", sep = "")
       }
     }
     return(cost)
diff --git a/man/mmkin.Rd b/man/mmkin.Rd
index 9a74a9cd..e06f6cd1 100644
--- a/man/mmkin.Rd
+++ b/man/mmkin.Rd
@@ -34,8 +34,9 @@ for parallel execution.}
 }
 \value{
 A two-dimensional \code{\link{array}} of \code{\link{mkinfit}}
-objects that can be indexed using the model names for the first index (row index)
-and the dataset names for the second index (column index).
+objects and/or try-errors that can be indexed using the model names for the
+first index (row index) and the dataset names for the second index (column
+index).
 }
 \description{
 This function calls \code{\link{mkinfit}} on all combinations of models and
diff --git a/test_dev.log b/test_dev.log
new file mode 100644
index 00000000..b68a7e56
--- /dev/null
+++ b/test_dev.log
@@ -0,0 +1,36 @@
+Loading mkin
+Testing mkin
+✔ |  OK F W S | Context
+
⠏ |   0       | AIC calculation
✔ |   4       | AIC calculation
+
⠏ |   0       | Export dataset for reading into CAKE
✔ |   2       | Export dataset for reading into CAKE
+
⠏ |   0       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠋ |   1       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠹ |   3       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠏ |  10       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
✔ |  14       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8 s]
+
⠏ |   0       | Calculation of FOCUS chi2 error levels
⠙ |   2       | Calculation of FOCUS chi2 error levels
⠸ |   4       | Calculation of FOCUS chi2 error levels
✔ |   4       | Calculation of FOCUS chi2 error levels [0.4 s]
+
⠏ |   0       | Fitting the SFORB model
⠋ |   1       | Fitting the SFORB model
⠼ |   5       | Fitting the SFORB model
✔ |   7       | Fitting the SFORB model [3.0 s]
+
⠏ |   0       | Analytical solutions for coupled models
⠋ |   1       | Analytical solutions for coupled models
⠙ |   2       | Analytical solutions for coupled models
⠹ |   3       | Analytical solutions for coupled models
⠸ |   4       | Analytical solutions for coupled models
⠼ |   5       | Analytical solutions for coupled models
✔ |   5       | Analytical solutions for coupled models [2.9 s]
+
⠏ |   0       | Calculation of Akaike weights
✔ |   5       | Calculation of Akaike weights
+
⠏ |   0       | Confidence intervals and p-values
⠙ |   2       | Confidence intervals and p-values
⠏ |  10       | Confidence intervals and p-values
✔ |  10       | Confidence intervals and p-values [0.9 s]
+
⠏ |   0       | Error model fitting
⠹ |   3       | Error model fitting
⠸ |   4       | Error model fitting
⠼ |   5       | Error model fitting
⠴ |   6       | Error model fitting
⠧ |   8       | Error model fitting
⠏ |  10       | Error model fitting
⠙ |  12       | Error model fitting
⠸ |  13   1   | Error model fitting
⠸ |  13   1   | Error model fitting
⠸ |  13   1   | Error model fitting
⠸ |  13   1   | Error model fitting
⠸ |  14       | Error model fitting
✔ |  14       | Error model fitting [3.7 s]
+
⠏ |   0       | Test fitting the decline of metabolites from their maximum
⠹ |   3       | Test fitting the decline of metabolites from their maximum
⠸ |   4       | Test fitting the decline of metabolites from their maximum
✔ |   4       | Test fitting the decline of metabolites from their maximum [0.2 s]
+
⠏ |   0       | Fitting the logistic model
⠋ |   1       | Fitting the logistic model
✔ |   1       | Fitting the logistic model [0.2 s]
+
⠏ |   0       | Test dataset class mkinds used in gmkin
✔ |   1       | Test dataset class mkinds used in gmkin
+
⠏ |   0       | Special cases of mkinfit calls
⠇ |   9       | Special cases of mkinfit calls
⠏ |  10       | Special cases of mkinfit calls
⠋ |  11       | Special cases of mkinfit calls
⠙ |  12       | Special cases of mkinfit calls
✔ |  12       | Special cases of mkinfit calls [0.6 s]
+
⠏ |   0       | mkinmod model generation and printing
⠧ |   8       | mkinmod model generation and printing
✔ |   8       | mkinmod model generation and printing [0.2 s]
+
⠏ |   0       | Model predictions with mkinpredict
⠋ |   1       | Model predictions with mkinpredict
✔ |   3       | Model predictions with mkinpredict [0.3 s]
+
⠏ |   0       | Evaluations according to 2015 NAFTA guidance
⠙ |   2       | Evaluations according to 2015 NAFTA guidance
⠇ |   9       | Evaluations according to 2015 NAFTA guidance
⠏ |  10       | Evaluations according to 2015 NAFTA guidance
⠴ |  16       | Evaluations according to 2015 NAFTA guidance
✔ |  16       | Evaluations according to 2015 NAFTA guidance [1.4 s]
+
⠏ |   0       | Nonlinear mixed-effects models
⠋ |   1       | Nonlinear mixed-effects models
⠙ |   2       | Nonlinear mixed-effects models
⠸ |   4       | Nonlinear mixed-effects models
⠼ |   5       | Nonlinear mixed-effects models
⠴ |   6       | Nonlinear mixed-effects models
⠧ |   8       | Nonlinear mixed-effects models
⠇ |   9       | Nonlinear mixed-effects models
✔ |   9       | Nonlinear mixed-effects models [7.0 s]
+
⠏ |   0       | Plotting
⠋ |   1       | Plotting
⠸ |   4       | Plotting
⠦ |   7       | Plotting
⠇ |   9       | Plotting
⠙ |  12       | Plotting
✔ |  14       | Plotting [1.3 s]
+
⠏ |   0       | Residuals extracted from mkinfit models
✔ |   4       | Residuals extracted from mkinfit models
+
⠏ |   0       | Complex test case from Schaefer et al. (2007) Piacenza paper
⠋ |   1       | Complex test case from Schaefer et al. (2007) Piacenza paper
✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [1.3 s]
+
⠏ |   0       | Summary
✔ |   4       | Summary
+
⠏ |   0       | Summaries of old mkinfit objects
✔ |   1       | Summaries of old mkinfit objects
+
⠏ |   0       | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠋ |   1       | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠹ |   3       | Results for synthetic data established in expertise for UBA (Ranke 2014)
✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.0 s]
+
⠏ |   0       | Hypothesis tests
⠼ |   5       | Hypothesis tests
⠴ |   6       | Hypothesis tests
⠧ |   8       | Hypothesis tests
⠇ |   9       | Hypothesis tests
✔ |   9       | Hypothesis tests [7.1 s]
+
⠏ |   0       | Calculation of maximum time weighted average concentrations (TWAs)
⠋ |   1       | Calculation of maximum time weighted average concentrations (TWAs)
⠙ |   2       | Calculation of maximum time weighted average concentrations (TWAs)
⠹ |   3       | Calculation of maximum time weighted average concentrations (TWAs)
⠸ |   4       | Calculation of maximum time weighted average concentrations (TWAs)
✔ |   4       | Calculation of maximum time weighted average concentrations (TWAs) [2.2 s]
+
+══ Results ═════════════════════════════════════════════════════════════════════
+Duration: 35.7 s
+
+OK:       161
+Failed:   0
+Warnings: 0
+Skipped:  0
diff --git a/tests/testthat/DFOP_FOCUS_C_messages.txt b/tests/testthat/DFOP_FOCUS_C_messages.txt
index 6aa73e01..b5a83146 100644
--- a/tests/testthat/DFOP_FOCUS_C_messages.txt
+++ b/tests/testthat/DFOP_FOCUS_C_messages.txt
@@ -3,146 +3,146 @@ parent_0   log_k1     log_k2     g_ilr
 Sum of squared residuals at call 1: 7391.39
   85.10000   -2.30259   -4.60517    0.00000 
   85.10000   -2.30259   -4.60517    0.00000 
-Sum of squared residuals at call 3: 7391.389
+Sum of squared residuals at call 3: 7391.39
   85.10000   -2.30259   -4.60517    0.00000 
-Sum of squared residuals at call 4: 7391.389
+Sum of squared residuals at call 4: 7391.39
  8.51000e+01 -2.30259e+00 -4.60517e+00  1.49012e-08 
  85.063710  -1.773280  -4.250366   0.769827 
-Sum of squared residuals at call 6: 2000.127
+Sum of squared residuals at call 6: 2000.13
  85.063752  -1.773280  -4.250366   0.769827 
  85.063710  -1.773322  -4.250366   0.769827 
  85.063710  -1.773280  -4.250408   0.769827 
  85.063710  -1.773280  -4.250366   0.769785 
  85.035419  -0.960852  -4.115460   1.336361 
-Sum of squared residuals at call 11: 32.97798
+Sum of squared residuals at call 11: 32.978
  85.035421  -0.960852  -4.115460   1.336361 
  85.035419  -0.960853  -4.115460   1.336361 
  85.035419  -0.960852  -4.115460   1.336361 
  85.035419  -0.960852  -4.115460   1.336361 
  85.037040  -0.256064  -4.273512   0.644775 
  85.032855  -0.782283  -4.127513   1.312494 
-Sum of squared residuals at call 17: 5.348133
+Sum of squared residuals at call 17: 5.34813
  85.032856  -0.782283  -4.127513   1.312494 
-Sum of squared residuals at call 18: 5.348132
+Sum of squared residuals at call 18: 5.34813
  85.032855  -0.782283  -4.127513   1.312494 
-Sum of squared residuals at call 19: 5.348131
+Sum of squared residuals at call 19: 5.34813
  85.032855  -0.782283  -4.127513   1.312494 
  85.032855  -0.782283  -4.127513   1.312494 
-Sum of squared residuals at call 21: 5.348131
+Sum of squared residuals at call 21: 5.34813
   85.02325   -0.74968   -4.05900    1.14891 
  85.031268  -0.790907  -4.114802   1.268157 
-Sum of squared residuals at call 23: 4.704445
+Sum of squared residuals at call 23: 4.70444
  85.031266  -0.790907  -4.114802   1.268157 
-Sum of squared residuals at call 24: 4.704444
+Sum of squared residuals at call 24: 4.70444
  85.031268  -0.790907  -4.114802   1.268157 
  85.031268  -0.790907  -4.114800   1.268157 
-Sum of squared residuals at call 26: 4.704433
+Sum of squared residuals at call 26: 4.70443
  85.031268  -0.790907  -4.114802   1.268158 
  85.030010  -0.780151  -4.069435   1.262797 
-Sum of squared residuals at call 28: 4.421625
+Sum of squared residuals at call 28: 4.42162
  85.030012  -0.780151  -4.069435   1.262797 
  85.030010  -0.780151  -4.069435   1.262797 
-Sum of squared residuals at call 30: 4.421624
+Sum of squared residuals at call 30: 4.42162
  85.030010  -0.780151  -4.069435   1.262797 
  85.030010  -0.780151  -4.069435   1.262797 
  85.028777  -0.790084  -4.023945   1.256918 
  85.029639  -0.785735  -4.054587   1.260236 
-Sum of squared residuals at call 34: 4.414346
+Sum of squared residuals at call 34: 4.41435
  85.029641  -0.785735  -4.054587   1.260236 
  85.029639  -0.785735  -4.054587   1.260236 
-Sum of squared residuals at call 36: 4.414346
+Sum of squared residuals at call 36: 4.41435
  85.029639  -0.785735  -4.054588   1.260236 
  85.029639  -0.785735  -4.054587   1.260236 
  85.028119  -0.777813  -4.042219   1.253890 
-Sum of squared residuals at call 39: 4.372463
+Sum of squared residuals at call 39: 4.37246
  85.028121  -0.777813  -4.042219   1.253890 
  85.028119  -0.777813  -4.042219   1.253890 
-Sum of squared residuals at call 41: 4.372462
+Sum of squared residuals at call 41: 4.37246
  85.028119  -0.777813  -4.042219   1.253890 
  85.028119  -0.777813  -4.042219   1.253890 
  85.024185  -0.776514  -4.029420   1.245094 
  85.026297  -0.777842  -4.036021   1.249634 
-Sum of squared residuals at call 45: 4.369313
+Sum of squared residuals at call 45: 4.36931
  85.026298  -0.777842  -4.036021   1.249634 
  85.026297  -0.777842  -4.036021   1.249634 
-Sum of squared residuals at call 47: 4.369313
+Sum of squared residuals at call 47: 4.36931
  85.026297  -0.777842  -4.036022   1.249634 
  85.026297  -0.777842  -4.036021   1.249634 
-Sum of squared residuals at call 49: 4.369313
+Sum of squared residuals at call 49: 4.36931
  85.022674  -0.778681  -4.029670   1.252015 
-Sum of squared residuals at call 50: 4.365062
+Sum of squared residuals at call 50: 4.36506
  85.022676  -0.778681  -4.029670   1.252015 
  85.022674  -0.778681  -4.029670   1.252015 
  85.022674  -0.778681  -4.029670   1.252015 
-Sum of squared residuals at call 53: 4.365062
+Sum of squared residuals at call 53: 4.36506
  85.022674  -0.778681  -4.029670   1.252015 
  85.016327  -0.776316  -4.027611   1.248897 
-Sum of squared residuals at call 55: 4.364078
+Sum of squared residuals at call 55: 4.36408
  85.016328  -0.776316  -4.027611   1.248897 
-Sum of squared residuals at call 56: 4.364078
+Sum of squared residuals at call 56: 4.36408
  85.016327  -0.776316  -4.027611   1.248897 
-Sum of squared residuals at call 57: 4.364077
+Sum of squared residuals at call 57: 4.36408
  85.016327  -0.776316  -4.027611   1.248897 
  85.016327  -0.776316  -4.027611   1.248897 
  85.008939  -0.777792  -4.026307   1.247720 
-Sum of squared residuals at call 60: 4.364052
+Sum of squared residuals at call 60: 4.36405
  85.008938  -0.777792  -4.026307   1.247720 
-Sum of squared residuals at call 61: 4.364052
+Sum of squared residuals at call 61: 4.36405
  85.008939  -0.777792  -4.026307   1.247720 
-Sum of squared residuals at call 62: 4.364052
+Sum of squared residuals at call 62: 4.36405
  85.008939  -0.777792  -4.026307   1.247720 
  85.008939  -0.777792  -4.026307   1.247720 
-Sum of squared residuals at call 64: 4.364052
+Sum of squared residuals at call 64: 4.36405
  85.005185  -0.777308  -4.026004   1.248453 
-Sum of squared residuals at call 65: 4.362751
+Sum of squared residuals at call 65: 4.36275
  85.005186  -0.777308  -4.026004   1.248453 
  85.005185  -0.777308  -4.026004   1.248453 
-Sum of squared residuals at call 67: 4.362751
+Sum of squared residuals at call 67: 4.36275
  85.005185  -0.777308  -4.026005   1.248453 
  85.005185  -0.777308  -4.026004   1.248453 
  85.001344  -0.777605  -4.025878   1.248775 
-Sum of squared residuals at call 70: 4.362721
+Sum of squared residuals at call 70: 4.36272
  85.001345  -0.777605  -4.025878   1.248775 
-Sum of squared residuals at call 71: 4.362721
+Sum of squared residuals at call 71: 4.36272
  85.001344  -0.777605  -4.025878   1.248775 
-Sum of squared residuals at call 72: 4.362721
+Sum of squared residuals at call 72: 4.36272
  85.001344  -0.777605  -4.025878   1.248775 
  85.001344  -0.777605  -4.025878   1.248775 
  85.003200  -0.777473  -4.025700   1.248643 
-Sum of squared residuals at call 75: 4.362715
+Sum of squared residuals at call 75: 4.36271
  85.003201  -0.777473  -4.025700   1.248643 
  85.003200  -0.777473  -4.025700   1.248643 
-Sum of squared residuals at call 77: 4.362715
+Sum of squared residuals at call 77: 4.36271
  85.003200  -0.777473  -4.025700   1.248643 
  85.003200  -0.777473  -4.025700   1.248643 
  85.003200  -0.777473  -4.025700   1.248643 
  85.003200  -0.777473  -4.025700   1.248643 
  85.002495  -0.777491  -4.025911   1.248679 
-Sum of squared residuals at call 82: 4.362715
+Sum of squared residuals at call 82: 4.36271
  85.002496  -0.777491  -4.025911   1.248679 
-Sum of squared residuals at call 83: 4.362715
+Sum of squared residuals at call 83: 4.36271
  85.002494  -0.777491  -4.025911   1.248679 
   85.00249   -0.77749   -4.02591    1.24868 
  85.002495  -0.777491  -4.025911   1.248679 
-Sum of squared residuals at call 86: 4.362715
+Sum of squared residuals at call 86: 4.36271
  85.002495  -0.777491  -4.025911   1.248679 
  85.002495  -0.777491  -4.025911   1.248679 
  85.002495  -0.777491  -4.025911   1.248679 
  85.002495  -0.777491  -4.025911   1.248679 
  85.002737  -0.777492  -4.025821   1.248672 
-Sum of squared residuals at call 91: 4.362714
+Sum of squared residuals at call 91: 4.36271
  85.002739  -0.777492  -4.025821   1.248672 
  85.002736  -0.777492  -4.025821   1.248672 
-Sum of squared residuals at call 93: 4.362714
+Sum of squared residuals at call 93: 4.36271
  85.002737  -0.777492  -4.025821   1.248672 
-Sum of squared residuals at call 94: 4.362714
+Sum of squared residuals at call 94: 4.36271
  85.002737  -0.777492  -4.025821   1.248672 
  85.002737  -0.777492  -4.025821   1.248672 
  85.002737  -0.777492  -4.025821   1.248672 
  85.002737  -0.777492  -4.025821   1.248672 
  85.002737  -0.777492  -4.025821   1.248672 
  85.002731  -0.777491  -4.025817   1.248670 
-Sum of squared residuals at call 100: 4.362714
+Sum of squared residuals at call 100: 4.36271
  85.002752  -0.777491  -4.025817   1.248670 
  85.002710  -0.777491  -4.025817   1.248670 
   85.00273   -0.77749   -4.02582    1.24867 
@@ -152,7 +152,7 @@ Sum of squared residuals at call 100: 4.362714
  85.002731  -0.777491  -4.025817   1.248671 
  85.002731  -0.777491  -4.025817   1.248669 
  85.002737  -0.777491  -4.025819   1.248671 
-Sum of squared residuals at call 109: 4.362714
+Sum of squared residuals at call 109: 4.36271
  85.002758  -0.777491  -4.025819   1.248671 
  85.002716  -0.777491  -4.025819   1.248671 
   85.00274   -0.77749   -4.02582    1.24867