Fix a bug, update for current vdiffr

Vignette FOCUS_L failed as I had introduced a bug in the handling of
warnings.

Current vdiffr only runs visual tests if R < 4.1.0, skipping r-devel for now,
see https://github.com/r-lib/vdiffr/commit/630a29d013361fd63fea242f531e2db6aef37919

7 files changed, 17 insertions, 118 deletions

diff --git a/R/mkinfit.R b/R/mkinfit.R
index ec2d3412..154c2a18 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -853,7 +853,7 @@ mkinfit <- function(mkinmod, observed,
 
   if (fit$convergence != 0) {
     convergence_warning = paste0("Optimisation did not converge:\n", fit$message)
-    summary_warnings <- c(warnings, convergence_warning)
+    summary_warnings <- c(summary_warnings, convergence_warning)
     warning(convergence_warning)
   } else {
     if(!quiet) message("Optimisation successfully terminated.\n")
diff --git a/R/summary_DFOP_FOCUS_C.txt b/R/summary_DFOP_FOCUS_C.txt
deleted file mode 100644
index ab64a588..00000000
--- a/R/summary_DFOP_FOCUS_C.txt
+++ /dev/null
@@ -1,82 +0,0 @@
-mkin version used for fitting:    Dummy 0.0 for testing 
-R version used for fitting:       Dummy R version for testing 
-Date of fit:     Dummy date for testing 
-Date of summary: Dummy date for testing 
-
-Equations:
-d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
-           time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))
-           * parent
-
-Model predictions using solution type analytical 
-
-Fitted using test 0 model solutions performed in test time 0 s
-
-Error model: Constant variance 
-
-Error model algorithm: OLS 
-
-Starting values for parameters to be optimised:
-         value   type
-parent_0 85.10  state
-k1        0.10 deparm
-k2        0.01 deparm
-g         0.50 deparm
-
-Starting values for the transformed parameters actually optimised:
-             value lower upper
-parent_0 85.100000  -Inf   Inf
-log_k1   -2.302585  -Inf   Inf
-log_k2   -4.605170  -Inf   Inf
-g_ilr     0.000000  -Inf   Inf
-
-Fixed parameter values:
-None
-
-Results:
-
-       AIC      BIC    logLik
-  29.02372 30.00984 -9.511861
-
-Optimised, transformed parameters with symmetric confidence intervals:
-         Estimate Std. Error   Lower   Upper
-parent_0  85.0000    0.66620 83.1500 86.8500
-log_k1    -0.7775    0.03380 -0.8713 -0.6836
-log_k2    -4.0260    0.13100 -4.3890 -3.6620
-g_ilr      1.2490    0.05811  1.0870  1.4100
-sigma      0.6962    0.16410  0.2406  1.1520
-
-Parameter correlation:
-[1] "Correlation matrix is platform dependent, not tested"
-
-Backtransformed parameters:
-Confidence intervals for internally transformed parameters are asymmetric.
-t-test (unrealistically) based on the assumption of normal distribution
-for estimators of untransformed parameters.
-         Estimate t value    Pr(>t)    Lower    Upper
-parent_0 85.00000 127.600 1.131e-08 83.15000 86.85000
-k1        0.45960  29.580 3.887e-06  0.41840  0.50480
-k2        0.01785   7.636 7.901e-04  0.01241  0.02568
-g         0.85390  83.310 6.221e-08  0.82310  0.88020
-sigma     0.69620   4.243 6.618e-03  0.24060  1.15200
-
-FOCUS Chi2 error levels in percent:
-         err.min n.optim df
-All data   2.661       4  5
-parent     2.661       4  5
-
-Estimated disappearance times:
-        DT50  DT90 DT50_k1 DT50_k2
-parent 1.887 21.25   1.508   38.83
-
-Data:
- time variable observed predicted residual
-    0   parent     85.1    85.003  0.09726
-    1   parent     57.9    58.039 -0.13912
-    3   parent     29.9    30.054 -0.15351
-    7   parent     14.6    13.866  0.73388
-   14   parent      9.7     9.787 -0.08657
-   28   parent      6.6     7.532 -0.93205
-   63   parent      4.0     4.033 -0.03269
-   91   parent      3.9     2.447  1.45348
-  119   parent      0.6     1.484 -0.88424
diff --git a/build.log b/build.log
index 0ed7b19a..b94e6450 100644
--- a/build.log
+++ b/build.log
@@ -2,24 +2,8 @@
 * preparing ‘mkin’:
 * checking DESCRIPTION meta-information ... OK
 * installing the package to build vignettes
-* creating vignettes ... ERROR
---- re-building ‘FOCUS_D.rmd’ using rmarkdown
---- finished re-building ‘FOCUS_D.rmd’
+* creating vignettes ... OK
+* checking for LF line-endings in source and make files and shell scripts
+* checking for empty or unneeded directories
+* building ‘mkin_0.9.50.3.tar.gz’
 
---- re-building ‘FOCUS_L.rmd’ using rmarkdown
-Quitting from lines 80-83 (FOCUS_L.rmd) 
-Error: processing vignette 'FOCUS_L.rmd' failed with diagnostics:
-argument 1 (type 'list') cannot be handled by 'cat'
---- failed re-building ‘FOCUS_L.rmd’
-
---- re-building ‘mkin.rmd’ using rmarkdown
---- finished re-building ‘mkin.rmd’
-
---- re-building ‘twa.rmd’ using rmarkdown
---- finished re-building ‘twa.rmd’
-
-SUMMARY: processing the following file failed:
-  ‘FOCUS_L.rmd’
-
-Error: Vignette re-building failed.
-Execution halted
diff --git a/test.log b/test.log
index c5f0e526..b4e97d72 100644
--- a/test.log
+++ b/test.log
@@ -5,11 +5,11 @@ Testing mkin
 ✔ |   2       | Export dataset for reading into CAKE
 ✔ |  14       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.9 s]
 ✔ |   4       | Calculation of FOCUS chi2 error levels [0.4 s]
-✔ |   7       | Fitting the SFORB model [3.4 s]
-✔ |   5       | Analytical solutions for coupled models [3.2 s]
+✔ |   7       | Fitting the SFORB model [3.5 s]
+✔ |   5       | Analytical solutions for coupled models [3.3 s]
 ✔ |   5       | Calculation of Akaike weights
-✔ |  10       | Confidence intervals and p-values [1.0 s]
-✔ |  14       | Error model fitting [4.1 s]
+✔ |  10       | Confidence intervals and p-values [1.2 s]
+✔ |  14       | Error model fitting [4.0 s]
 ✔ |   4       | Test fitting the decline of metabolites from their maximum [0.3 s]
 ✔ |   1       | Fitting the logistic model [0.2 s]
 ✔ |   1       | Test dataset class mkinds used in gmkin
@@ -17,18 +17,18 @@ Testing mkin
 ✔ |   8       | mkinmod model generation and printing [0.3 s]
 ✔ |   3       | Model predictions with mkinpredict [0.4 s]
 ✔ |  16       | Evaluations according to 2015 NAFTA guidance [1.5 s]
-✔ |   9       | Nonlinear mixed-effects models [7.7 s]
-✔ |  14       | Plotting [1.4 s]
+✔ |   9       | Nonlinear mixed-effects models [8.0 s]
+✔ |  14       | Plotting [1.5 s]
 ✔ |   4       | Residuals extracted from mkinfit models
-✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4 s]
-✔ |   4       | Summary [0.2 s]
+✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5 s]
+✔ |   4       | Summary [0.1 s]
 ✔ |   1       | Summaries of old mkinfit objects
-✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.1 s]
-✔ |   9       | Hypothesis tests [6.6 s]
+✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3 s]
+✔ |   9       | Hypothesis tests [7.0 s]
 ✔ |   4       | Calculation of maximum time weighted average concentrations (TWAs) [2.4 s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 38.2 s
+Duration: 39.7 s
 
 OK:       161
 Failed:   0
diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf
index 7c8340cd..aa9fc233 100644
--- a/tests/testthat/FOCUS_2006_D.csf
+++ b/tests/testthat/FOCUS_2006_D.csf
@@ -5,7 +5,7 @@ Description:
 MeasurementUnits: % AR
 TimeUnits: days
 Comments: Created using mkin::CAKE_export
-Date: 2020-05-29
+Date: 2020-06-15
 Optimiser: IRLS
 
 [Data]
diff --git a/tests/testthat/test_nafta.R b/tests/testthat/test_nafta.R
index 595db999..dad6d84c 100644
--- a/tests/testthat/test_nafta.R
+++ b/tests/testthat/test_nafta.R
@@ -22,7 +22,6 @@ test_that("Test data from Appendix B are correctly evaluated", {
 
   plot_nafta <- function() plot(res)
   if(requireNamespace("vdiffr", quietly = TRUE)) {
-    skip_if(getRversion() > 4.0)
     vdiffr::expect_doppelganger("NAFTA SOP Appendix B", plot_nafta)
   }
 })
@@ -50,7 +49,6 @@ test_that("Test data from Appendix D are correctly evaluated", {
 
   plot_nafta <- function() plot(res)
   if(requireNamespace("vdiffr", quietly = TRUE)) {
-    skip_if(getRversion() > 4.0)
     vdiffr::expect_doppelganger("Plot NAFTA analysis", plot_nafta)
   }
 })
diff --git a/tests/testthat/test_plot.R b/tests/testthat/test_plot.R
index a33de07f..c6a187be 100644
--- a/tests/testthat/test_plot.R
+++ b/tests/testthat/test_plot.R
@@ -21,7 +21,6 @@ test_that("Plotting mkinfit and mmkin objects is reproducible", {
   plot_errmod_fit_obs_1 <- function() plot_err(fit_obs_1, sep_obs = FALSE)
   plot_errmod_fit_tc_1 <- function() plot_err(fit_tc_1, sep_obs = FALSE)
 
-  skip_if(getRversion() > 4.0)
   vdiffr::expect_doppelganger("mkinfit plot for FOCUS C with defaults", plot_default_FOCUS_C_SFO)
   vdiffr::expect_doppelganger("mkinfit plot for FOCUS C with residuals like in gmkin", plot_res_FOCUS_C_SFO)
   vdiffr::expect_doppelganger("plot_res for FOCUS C", plot_res_FOCUS_C_SFO_2)