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-rw-r--r--R/mkinfit.R2
-rw-r--r--R/summary_DFOP_FOCUS_C.txt82
-rw-r--r--build.log24
-rw-r--r--test.log22
-rw-r--r--tests/testthat/FOCUS_2006_D.csf2
-rw-r--r--tests/testthat/test_nafta.R2
-rw-r--r--tests/testthat/test_plot.R1
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)

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