From 3a5463672c297b37c3c9135c8b144c48744c05d0 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 31 Mar 2021 19:42:17 +0200 Subject: Bug fix in plot.mkinfit In residual plots, use xlab and xlim if appropriate --- docs/reference/D24_2014.html | 2 +- docs/reference/Extract.mmkin.html | 2 +- docs/reference/Rplot001.png | Bin 27746 -> 1011 bytes docs/reference/Rplot002.png | Bin 59394 -> 16524 bytes docs/reference/Rplot003.png | Bin 15333 -> 15401 bytes docs/reference/Rplot004.png | Bin 10647 -> 10689 bytes docs/reference/Rplot005.png | Bin 19233 -> 19483 bytes docs/reference/Rplot006.png | Bin 24545 -> 24302 bytes docs/reference/Rplot007.png | Bin 24992 -> 25211 bytes docs/reference/add_err-1.png | Bin 108676 -> 109666 bytes docs/reference/add_err-2.png | Bin 63336 -> 63614 bytes docs/reference/add_err-3.png | Bin 58909 -> 59316 bytes docs/reference/add_err.html | 2 +- docs/reference/confint.mkinfit.html | 6 +++--- docs/reference/dimethenamid_2018.html | 2 +- docs/reference/experimental_data_for_UBA-1.png | Bin 102212 -> 102839 bytes docs/reference/experimental_data_for_UBA.html | 2 +- docs/reference/f_time_norm_focus.html | 2 +- docs/reference/focus_soil_moisture.html | 2 +- docs/reference/logLik.mkinfit.html | 2 +- docs/reference/mccall81_245T-1.png | Bin 62537 -> 62564 bytes docs/reference/mccall81_245T.html | 2 +- docs/reference/mixed-1.png | Bin 219866 -> 219876 bytes docs/reference/mixed.html | 2 +- docs/reference/mkinds.html | 2 +- docs/reference/mkindsg.html | 2 +- docs/reference/mkinfit-1.png | Bin 65835 -> 66042 bytes docs/reference/mkinfit.html | 28 ++++++++++++------------- docs/reference/mkinmod.html | 6 +++--- docs/reference/mkinpredict.html | 6 +++--- docs/reference/mkinresplot-1.png | Bin 23819 -> 23907 bytes docs/reference/mkinresplot.html | 2 +- docs/reference/mmkin-1.png | Bin 110459 -> 111569 bytes docs/reference/mmkin-2.png | Bin 107057 -> 108319 bytes docs/reference/mmkin-3.png | Bin 96062 -> 96596 bytes docs/reference/mmkin-4.png | Bin 67191 -> 67345 bytes docs/reference/mmkin-5.png | Bin 64880 -> 65269 bytes docs/reference/mmkin.html | 6 +++--- docs/reference/nlme-1.png | Bin 70133 -> 70276 bytes docs/reference/nlme-2.png | Bin 94031 -> 94239 bytes docs/reference/nlme.html | 2 +- docs/reference/nlme.mmkin-1.png | Bin 124677 -> 124827 bytes docs/reference/nlme.mmkin-2.png | Bin 169523 -> 169698 bytes docs/reference/nlme.mmkin-3.png | Bin 172692 -> 172809 bytes docs/reference/nlme.mmkin.html | 2 +- docs/reference/parms.html | 2 +- docs/reference/plot.mkinfit-1.png | Bin 53151 -> 53333 bytes docs/reference/plot.mkinfit-2.png | Bin 73254 -> 72971 bytes docs/reference/plot.mkinfit-3.png | Bin 67810 -> 67908 bytes docs/reference/plot.mkinfit-4.png | Bin 72295 -> 72505 bytes docs/reference/plot.mkinfit-5.png | Bin 66560 -> 66973 bytes docs/reference/plot.mkinfit-6.png | Bin 72717 -> 72699 bytes docs/reference/plot.mkinfit-7.png | Bin 73553 -> 74240 bytes docs/reference/plot.mkinfit.html | 2 +- docs/reference/plot.mmkin-1.png | Bin 48997 -> 49701 bytes docs/reference/plot.mmkin-2.png | Bin 49376 -> 50025 bytes docs/reference/plot.mmkin-3.png | Bin 46202 -> 46360 bytes docs/reference/plot.mmkin-4.png | Bin 33057 -> 33389 bytes docs/reference/plot.mmkin-5.png | Bin 57372 -> 58129 bytes docs/reference/plot.mmkin.html | 2 +- docs/reference/reexports.html | 2 +- docs/reference/sigma_twocomp-1.png | Bin 43910 -> 43766 bytes docs/reference/sigma_twocomp.html | 2 +- docs/reference/summary.nlme.mmkin.html | 12 +++++------ docs/reference/transform_odeparms.html | 2 +- 65 files changed, 53 insertions(+), 53 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/D24_2014.html b/docs/reference/D24_2014.html index e2d47f1b..c59bfad6 100644 --- a/docs/reference/D24_2014.html +++ b/docs/reference/D24_2014.html @@ -77,7 +77,7 @@ constrained by data protection regulations." /> mkin - 1.0.3 + 1.0.4 diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 5a99cf1b..b1c73ba5 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -72,7 +72,7 @@ mkin - 1.0.3 + 1.0.4 diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png index 1cbcb153..17a35806 100644 Binary files a/docs/reference/Rplot001.png and b/docs/reference/Rplot001.png differ diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png index 745d583d..808f1968 100644 Binary files a/docs/reference/Rplot002.png and b/docs/reference/Rplot002.png differ diff --git a/docs/reference/Rplot003.png b/docs/reference/Rplot003.png index 19198739..97f650e2 100644 Binary files a/docs/reference/Rplot003.png and b/docs/reference/Rplot003.png differ diff --git a/docs/reference/Rplot004.png b/docs/reference/Rplot004.png index 1028a9c4..21ad6783 100644 Binary files a/docs/reference/Rplot004.png and b/docs/reference/Rplot004.png differ diff --git a/docs/reference/Rplot005.png b/docs/reference/Rplot005.png index aa844051..4828f5b2 100644 Binary files a/docs/reference/Rplot005.png and b/docs/reference/Rplot005.png differ diff --git a/docs/reference/Rplot006.png b/docs/reference/Rplot006.png index 81525882..4aed2c87 100644 Binary files a/docs/reference/Rplot006.png and b/docs/reference/Rplot006.png differ diff --git a/docs/reference/Rplot007.png b/docs/reference/Rplot007.png index 10b7455a..3405a171 100644 Binary files a/docs/reference/Rplot007.png and b/docs/reference/Rplot007.png differ diff --git a/docs/reference/add_err-1.png b/docs/reference/add_err-1.png index 9ba106db..70118923 100644 Binary files a/docs/reference/add_err-1.png and b/docs/reference/add_err-1.png differ diff --git a/docs/reference/add_err-2.png b/docs/reference/add_err-2.png index 3088c40e..69b820c2 100644 Binary files a/docs/reference/add_err-2.png and b/docs/reference/add_err-2.png differ diff --git a/docs/reference/add_err-3.png b/docs/reference/add_err-3.png index 493a761a..1de78fa7 100644 Binary files a/docs/reference/add_err-3.png and b/docs/reference/add_err-3.png differ diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 6fbecd14..18ca517e 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -74,7 +74,7 @@ may depend on the predicted value and is specified as a standard deviation." /> mkin - 1.0.3 + 1.0.4 diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html index 06e78459..e81e0c7b 100644 --- a/docs/reference/confint.mkinfit.html +++ b/docs/reference/confint.mkinfit.html @@ -79,7 +79,7 @@ method of Venzon and Moolgavkar (1988)." /> mkin - 1.0.3 + 1.0.4 @@ -285,13 +285,13 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, f_d_1 <- mkinfit(SFO_SFO, subset(FOCUS_2006_D, value != 0), quiet = TRUE) system.time(ci_profile <- confint(f_d_1, method = "profile", cores = 1, quiet = TRUE))
#> user system elapsed -#> 4.255 1.029 3.937
# Using more cores does not save much time here, as parent_0 takes up most of the time +#> 3.871 0.000 3.871
# Using more cores does not save much time here, as parent_0 takes up most of the time # If we additionally exclude parent_0 (the confidence of which is often of # minor interest), we get a nice performance improvement if we use at least 4 cores system.time(ci_profile_no_parent_0 <- confint(f_d_1, method = "profile", c("k_parent_sink", "k_parent_m1", "k_m1_sink", "sigma"), cores = n_cores))
#> Profiling the likelihood
#> user system elapsed -#> 1.469 0.092 0.911
ci_profile +#> 1.484 0.116 0.923
ci_profile
#> 2.5% 97.5% #> parent_0 96.456003640 1.027703e+02 #> k_parent_sink 0.040762501 5.549764e-02 diff --git a/docs/reference/dimethenamid_2018.html b/docs/reference/dimethenamid_2018.html index 6845f74f..3b6ae721 100644 --- a/docs/reference/dimethenamid_2018.html +++ b/docs/reference/dimethenamid_2018.html @@ -77,7 +77,7 @@ constrained by data protection regulations." /> mkin - 1.0.3 + 1.0.4
diff --git a/docs/reference/experimental_data_for_UBA-1.png b/docs/reference/experimental_data_for_UBA-1.png index 33946ded..5527c07f 100644 Binary files a/docs/reference/experimental_data_for_UBA-1.png and b/docs/reference/experimental_data_for_UBA-1.png differ diff --git a/docs/reference/experimental_data_for_UBA.html b/docs/reference/experimental_data_for_UBA.html index 77f75678..4da8d6c3 100644 --- a/docs/reference/experimental_data_for_UBA.html +++ b/docs/reference/experimental_data_for_UBA.html @@ -100,7 +100,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl mkin - 1.0.3 + 1.0.4 diff --git a/docs/reference/f_time_norm_focus.html b/docs/reference/f_time_norm_focus.html index aa494b27..a0899ac8 100644 --- a/docs/reference/f_time_norm_focus.html +++ b/docs/reference/f_time_norm_focus.html @@ -73,7 +73,7 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)." /> mkin - 1.0.3 + 1.0.4 diff --git a/docs/reference/focus_soil_moisture.html b/docs/reference/focus_soil_moisture.html index 61f235db..bbacc554 100644 --- a/docs/reference/focus_soil_moisture.html +++ b/docs/reference/focus_soil_moisture.html @@ -73,7 +73,7 @@ corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5." /> mkin - 1.0.3 + 1.0.4 diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index 9e5b4069..83fb4e48 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -76,7 +76,7 @@ the error model." /> mkin - 1.0.3 + 1.0.4 diff --git a/docs/reference/mccall81_245T-1.png b/docs/reference/mccall81_245T-1.png index 91fe060e..478462ae 100644 Binary files a/docs/reference/mccall81_245T-1.png and b/docs/reference/mccall81_245T-1.png differ diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index b7dca4a7..4f8d3fa0 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -74,7 +74,7 @@ mkin - 1.0.3 + 1.0.4 diff --git a/docs/reference/mixed-1.png b/docs/reference/mixed-1.png index 28a376f4..b9454c86 100644 Binary files a/docs/reference/mixed-1.png and b/docs/reference/mixed-1.png differ diff --git a/docs/reference/mixed.html b/docs/reference/mixed.html index 23d955e3..b4f8db16 100644 --- a/docs/reference/mixed.html +++ b/docs/reference/mixed.html @@ -72,7 +72,7 @@ mkin - 1.0.3 + 1.0.4 diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index 5111a9e0..fe89012c 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -75,7 +75,7 @@ provided by this package come as mkinds objects nevertheless." /> mkin - 1.0.3 + 1.0.4 diff --git a/docs/reference/mkindsg.html b/docs/reference/mkindsg.html index 003e5e8f..a9686e4c 100644 --- a/docs/reference/mkindsg.html +++ b/docs/reference/mkindsg.html @@ -75,7 +75,7 @@ dataset if no data are supplied." /> mkin - 1.0.3 + 1.0.4 diff --git a/docs/reference/mkinfit-1.png b/docs/reference/mkinfit-1.png index de2a90a9..e1d0f2f4 100644 Binary files a/docs/reference/mkinfit-1.png and b/docs/reference/mkinfit-1.png differ diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 180f2ee7..2c162e49 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -80,7 +80,7 @@ likelihood function." /> mkin - 1.0.3 + 1.0.4 @@ -431,10 +431,10 @@ doi: 10.3390/environments6 # Use shorthand notation for parent only degradation fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit) -
#> mkin version used for fitting: 1.0.3 -#> R version used for fitting: 4.0.3 -#> Date of fit: Mon Feb 15 13:43:26 2021 -#> Date of summary: Mon Feb 15 13:43:26 2021 +
#> mkin version used for fitting: 1.0.4 +#> R version used for fitting: 4.0.4 +#> Date of fit: Wed Mar 31 19:15:41 2021 +#> Date of summary: Wed Mar 31 19:15:41 2021 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -574,10 +574,10 @@ doi: 10.3390/environments6 analytical = mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE, error_model = "tc", solution_type = "analytical")) } -
#> test relative elapsed -#> 3 analytical 1.000 0.550 -#> 1 deSolve_compiled 1.731 0.952 -#> 2 eigen 2.662 1.464
# } +
#> Loading required package: rbenchmark
#> test relative elapsed +#> 3 analytical 1.000 0.547 +#> 1 deSolve_compiled 1.717 0.939 +#> 2 eigen 2.644 1.446
# } # Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO # \dontrun{ @@ -598,10 +598,10 @@ doi: 10.3390/environments6 #> 2 6 -64.983 -1 0.3075 0.5792
# Also, the missing standard error for log_beta and the t-tests for alpha # and beta indicate overparameterisation summary(fit.FOMC_SFO.tc, data = FALSE) -
#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: diag(.) had 0 or NA entries; non-finite result is doubtful
#> mkin version used for fitting: 1.0.3 -#> R version used for fitting: 4.0.3 -#> Date of fit: Mon Feb 15 13:43:38 2021 -#> Date of summary: Mon Feb 15 13:43:38 2021 +
#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: diag(.) had 0 or NA entries; non-finite result is doubtful
#> mkin version used for fitting: 1.0.4 +#> R version used for fitting: 4.0.4 +#> Date of fit: Wed Mar 31 19:15:53 2021 +#> Date of summary: Wed Mar 31 19:15:53 2021 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -610,7 +610,7 @@ doi: 10.3390/environments6 #> #> Model predictions using solution type deSolve #> -#> Fitted using 3729 model solutions performed in 2.802 s +#> Fitted using 3729 model solutions performed in 2.798 s #> #> Error model: Two-component variance function #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 4ce9468a..1e8ad60d 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -78,7 +78,7 @@ mkinmod." /> mkin - 1.0.3 + 1.0.4
@@ -348,7 +348,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media

parent = mkinsub("SFO", "m1", full_name = "Test compound"), m1 = mkinsub("SFO", full_name = "Metabolite M1"), name = "SFO_SFO", dll_dir = DLL_dir, unload = TRUE, overwrite = TRUE) -
#> Copied DLL from /tmp/RtmpiJ2M4Z/filee097a4a94a921.so to /home/jranke/.local/share/mkin/SFO_SFO.so
# Now we can save the model and restore it in a new session +
#> Copied DLL from /tmp/Rtmp17EVw2/file269cfd5cc541a9.so to /home/jranke/.local/share/mkin/SFO_SFO.so
# Now we can save the model and restore it in a new session saveRDS(SFO_SFO.2, file = "~/SFO_SFO.rds") # Terminate the R session here if you would like to check, and then do library(mkin) @@ -397,7 +397,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media

#> }) #> return(predicted) #> } -#> <environment: 0x55555b0c2760>
+#> <environment: 0x55555c17ae90>
# If we have several parallel metabolites # (compare tests/testthat/test_synthetic_data_for_UBA_2014.R) m_synth_DFOP_par <- mkinmod( diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 25e26419..5775ba62 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -74,7 +74,7 @@ kinetic parameters and initial values for the state variables." /> mkin - 1.0.3 + 1.0.4
@@ -410,8 +410,8 @@ as these always return mapped output.

#> test relative elapsed #> 2 deSolve_compiled 1.0 0.005 #> 4 analytical 1.0 0.005 -#> 1 eigen 4.4 0.022 -#> 3 deSolve 47.0 0.235
+#> 1 eigen 4.0 0.020 +#> 3 deSolve 46.2 0.231
# \dontrun{ # Predict from a fitted model f <- mkinfit(SFO_SFO, FOCUS_2006_C, quiet = TRUE) diff --git a/docs/reference/mkinresplot-1.png b/docs/reference/mkinresplot-1.png index ffd34f6f..963aa5b7 100644 Binary files a/docs/reference/mkinresplot-1.png and b/docs/reference/mkinresplot-1.png differ diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index 04ff15b8..fe3150e7 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -75,7 +75,7 @@ argument show_residuals = TRUE." /> mkin - 1.0.3 + 1.0.4
diff --git a/docs/reference/mmkin-1.png b/docs/reference/mmkin-1.png index 0db3379f..26586ab9 100644 Binary files a/docs/reference/mmkin-1.png and b/docs/reference/mmkin-1.png differ diff --git a/docs/reference/mmkin-2.png b/docs/reference/mmkin-2.png index 024a9892..dbcdd8ee 100644 Binary files a/docs/reference/mmkin-2.png and b/docs/reference/mmkin-2.png differ diff --git a/docs/reference/mmkin-3.png b/docs/reference/mmkin-3.png index a23d7cb9..80245fc6 100644 Binary files a/docs/reference/mmkin-3.png and b/docs/reference/mmkin-3.png differ diff --git a/docs/reference/mmkin-4.png b/docs/reference/mmkin-4.png index 89975db5..328aa564 100644 Binary files a/docs/reference/mmkin-4.png and b/docs/reference/mmkin-4.png differ diff --git a/docs/reference/mmkin-5.png b/docs/reference/mmkin-5.png index a2f34983..9ce5e919 100644 Binary files a/docs/reference/mmkin-5.png and b/docs/reference/mmkin-5.png differ diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index c9800fe7..c73d14bf 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -75,7 +75,7 @@ datasets specified in its first two arguments." /> mkin - 1.0.3 + 1.0.4 @@ -234,9 +234,9 @@ plotting.

time_default
#> user system elapsed -#> 4.630 0.415 1.717
time_1 +#> 5.387 0.413 1.864
time_1
#> user system elapsed -#> 5.694 0.000 5.694
+#> 5.786 0.008 5.794
endpoints(fits.0[["SFO_lin", 2]])
#> $ff #> parent_M1 parent_sink M1_M2 M1_sink diff --git a/docs/reference/nlme-1.png b/docs/reference/nlme-1.png index 728cc557..cca4ce0a 100644 Binary files a/docs/reference/nlme-1.png and b/docs/reference/nlme-1.png differ diff --git a/docs/reference/nlme-2.png b/docs/reference/nlme-2.png index e8167455..c0d8e857 100644 Binary files a/docs/reference/nlme-2.png and b/docs/reference/nlme-2.png differ diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html index 7b0c6a97..c6b43aab 100644 --- a/docs/reference/nlme.html +++ b/docs/reference/nlme.html @@ -75,7 +75,7 @@ datasets. They are used internally by the nlme.mmkin() method." /> mkin - 1.0.3 + 1.0.4
diff --git a/docs/reference/nlme.mmkin-1.png b/docs/reference/nlme.mmkin-1.png index 9186c135..90ede880 100644 Binary files a/docs/reference/nlme.mmkin-1.png and b/docs/reference/nlme.mmkin-1.png differ diff --git a/docs/reference/nlme.mmkin-2.png b/docs/reference/nlme.mmkin-2.png index d395fe02..0d140fd1 100644 Binary files a/docs/reference/nlme.mmkin-2.png and b/docs/reference/nlme.mmkin-2.png differ diff --git a/docs/reference/nlme.mmkin-3.png b/docs/reference/nlme.mmkin-3.png index 40518a59..8a60b52b 100644 Binary files a/docs/reference/nlme.mmkin-3.png and b/docs/reference/nlme.mmkin-3.png differ diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html index 189e34ef..03448606 100644 --- a/docs/reference/nlme.mmkin.html +++ b/docs/reference/nlme.mmkin.html @@ -74,7 +74,7 @@ have been obtained by fitting the same model to a list of datasets." /> mkin - 1.0.3 + 1.0.4 diff --git a/docs/reference/parms.html b/docs/reference/parms.html index e45d6a5c..b4346b13 100644 --- a/docs/reference/parms.html +++ b/docs/reference/parms.html @@ -74,7 +74,7 @@ considering the error structure that was assumed for the fit." /> mkin - 1.0.3 + 1.0.4 diff --git a/docs/reference/plot.mkinfit-1.png b/docs/reference/plot.mkinfit-1.png index e5da9f1c..54e5c46f 100644 Binary files a/docs/reference/plot.mkinfit-1.png and b/docs/reference/plot.mkinfit-1.png differ diff --git a/docs/reference/plot.mkinfit-2.png b/docs/reference/plot.mkinfit-2.png index a11d1680..ff8418a3 100644 Binary files a/docs/reference/plot.mkinfit-2.png and b/docs/reference/plot.mkinfit-2.png differ diff --git a/docs/reference/plot.mkinfit-3.png b/docs/reference/plot.mkinfit-3.png index c976d4b1..54f2b981 100644 Binary files a/docs/reference/plot.mkinfit-3.png and b/docs/reference/plot.mkinfit-3.png differ diff --git a/docs/reference/plot.mkinfit-4.png b/docs/reference/plot.mkinfit-4.png index c8bc00fe..7a7bfc6c 100644 Binary files a/docs/reference/plot.mkinfit-4.png and b/docs/reference/plot.mkinfit-4.png differ diff --git a/docs/reference/plot.mkinfit-5.png b/docs/reference/plot.mkinfit-5.png index 6631aa68..6a6741e7 100644 Binary files a/docs/reference/plot.mkinfit-5.png and b/docs/reference/plot.mkinfit-5.png differ diff --git a/docs/reference/plot.mkinfit-6.png b/docs/reference/plot.mkinfit-6.png index 946b20c5..c4d0b9c7 100644 Binary files a/docs/reference/plot.mkinfit-6.png and b/docs/reference/plot.mkinfit-6.png differ diff --git a/docs/reference/plot.mkinfit-7.png b/docs/reference/plot.mkinfit-7.png index 10807ea8..802b00ef 100644 Binary files a/docs/reference/plot.mkinfit-7.png and b/docs/reference/plot.mkinfit-7.png differ diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index b80c672d..ff6da93e 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -74,7 +74,7 @@ observed data together with the solution of the fitted model." /> mkin - 1.0.3 + 1.0.4 diff --git a/docs/reference/plot.mmkin-1.png b/docs/reference/plot.mmkin-1.png index 647dfb8a..d06d683c 100644 Binary files a/docs/reference/plot.mmkin-1.png and b/docs/reference/plot.mmkin-1.png differ diff --git a/docs/reference/plot.mmkin-2.png b/docs/reference/plot.mmkin-2.png index 1bc1c9db..d3678aca 100644 Binary files a/docs/reference/plot.mmkin-2.png and b/docs/reference/plot.mmkin-2.png differ diff --git a/docs/reference/plot.mmkin-3.png b/docs/reference/plot.mmkin-3.png index 50d6ffac..f84d5782 100644 Binary files a/docs/reference/plot.mmkin-3.png and b/docs/reference/plot.mmkin-3.png differ diff --git a/docs/reference/plot.mmkin-4.png b/docs/reference/plot.mmkin-4.png index e049fa16..9919dacb 100644 Binary files a/docs/reference/plot.mmkin-4.png and b/docs/reference/plot.mmkin-4.png differ diff --git a/docs/reference/plot.mmkin-5.png b/docs/reference/plot.mmkin-5.png index 2421995b..945b863f 100644 Binary files a/docs/reference/plot.mmkin-5.png and b/docs/reference/plot.mmkin-5.png differ diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index 20f9033d..3348e050 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -76,7 +76,7 @@ the fit of at least one model to the same dataset is shown." /> mkin - 1.0.3 + 1.0.4 diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html index 864c4ff9..c6d716a1 100644 --- a/docs/reference/reexports.html +++ b/docs/reference/reexports.html @@ -79,7 +79,7 @@ below to see their documentation. mkin - 1.0.3 + 1.0.4 diff --git a/docs/reference/sigma_twocomp-1.png b/docs/reference/sigma_twocomp-1.png index 6e61684e..fddb86a7 100644 Binary files a/docs/reference/sigma_twocomp-1.png and b/docs/reference/sigma_twocomp-1.png differ diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html index 397582f0..1b4e45e4 100644 --- a/docs/reference/sigma_twocomp.html +++ b/docs/reference/sigma_twocomp.html @@ -73,7 +73,7 @@ dependence of the measured value \(y\):" /> mkin - 1.0.3 + 1.0.4 diff --git a/docs/reference/summary.nlme.mmkin.html b/docs/reference/summary.nlme.mmkin.html index d6840425..8df9011d 100644 --- a/docs/reference/summary.nlme.mmkin.html +++ b/docs/reference/summary.nlme.mmkin.html @@ -76,7 +76,7 @@ endpoints such as formation fractions and DT50 values. Optionally mkin - 1.0.3 + 1.0.4 @@ -265,10 +265,10 @@ José Pinheiro and Douglas Bates for the components inherited from nlme

#> iteration limit reached without convergence (10)
f_nlme <- nlme(f_mmkin)
#> Warning: Iteration 4, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)
summary(f_nlme, data = TRUE)
#> nlme version used for fitting: 3.1.152 -#> mkin version used for pre-fitting: 1.0.3 -#> R version used for fitting: 4.0.3 -#> Date of fit: Mon Feb 15 13:46:13 2021 -#> Date of summary: Mon Feb 15 13:46:13 2021 +#> mkin version used for pre-fitting: 1.0.4 +#> R version used for fitting: 4.0.4 +#> Date of fit: Wed Mar 31 19:18:24 2021 +#> Date of summary: Wed Mar 31 19:18:24 2021 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -278,7 +278,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme

#> #> Model predictions using solution type analytical #> -#> Fitted in 0.553 s using 4 iterations +#> Fitted in 0.537 s using 4 iterations #> #> Variance model: Two-component variance function #> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index c3c756f6..bbaad91e 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -77,7 +77,7 @@ the ilr transformation is used." /> mkin - 1.0.3 + 1.0.4
-- cgit v1.2.3 From c74b79c983fe9fc872bac1262040e82f16049477 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 21 Apr 2021 13:11:47 +0200 Subject: Version 1.0.4 published yesterday --- DESCRIPTION | 2 +- NEWS.md | 2 + R/mmkin.R | 5 +- check.log | 8 +- docs/news/index.html | 1 + docs/pkgdown.yml | 2 +- docs/reference/Rplot001.png | Bin 1011 -> 27637 bytes docs/reference/Rplot002.png | Bin 16524 -> 59394 bytes docs/reference/Rplot003.png | Bin 15401 -> 33192 bytes docs/reference/Rplot004.png | Bin 10689 -> 23509 bytes docs/reference/Rplot005.png | Bin 19483 -> 23509 bytes docs/reference/Rplot006.png | Bin 24302 -> 22129 bytes docs/reference/mmkin-1.png | Bin 111569 -> 110844 bytes docs/reference/mmkin-2.png | Bin 108319 -> 107612 bytes docs/reference/mmkin-3.png | Bin 96596 -> 96248 bytes docs/reference/mmkin-4.png | Bin 67345 -> 66653 bytes docs/reference/mmkin-5.png | Bin 65269 -> 65046 bytes docs/reference/mmkin.html | 9 +- docs/reference/nlme-1.png | Bin 70276 -> 70244 bytes docs/reference/plot.mixed.mmkin-1.png | Bin 85433 -> 84976 bytes man/mmkin.Rd | 5 +- test.log | 43 +++++---- ...ot-for-focus-c-with-residuals-like-in-gmkin.svg | 42 ++++----- .../mkinfit-plot-for-focus-c-with-sep-true.svg | 42 ++++----- tests/figs/plotting/plot-res-for-focus-c.svg | 42 ++++----- tests/figs/plotting/plot-res-for-focus-d.svg | 98 ++++++++++----------- 26 files changed, 158 insertions(+), 143 deletions(-) (limited to 'docs/reference') diff --git a/DESCRIPTION b/DESCRIPTION index 176c3039..f5b7f070 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data Version: 1.0.4 -Date: 2021-02-24 +Date: 2021-04-20 Authors@R: c( person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de", diff --git a/NEWS.md b/NEWS.md index 9d03fa3d..88509b66 100644 --- a/NEWS.md +++ b/NEWS.md @@ -4,6 +4,8 @@ - 'plot.mkinfit': Use xlab and xlim for the residual plot if show_residuals is TRUE +- 'mmkin': Use cores = 1 per default on Windows to make it easier for first time users + # mkin 1.0.3 (2021-02-15) - Review and update README, the 'Introduction to mkin' vignette and some of the help pages diff --git a/R/mmkin.R b/R/mmkin.R index 030fb27b..fe04129e 100644 --- a/R/mmkin.R +++ b/R/mmkin.R @@ -13,7 +13,8 @@ #' is only used when the \code{cluster} argument is \code{NULL}. On Windows #' machines, cores > 1 is not supported, you need to use the \code{cluster} #' argument to use multiple logical processors. Per default, all cores -#' detected by [parallel::detectCores()] are used. +#' detected by [parallel::detectCores()] are used, except on Windows where +#' the default is 1. #' @param cluster A cluster as returned by \code{\link{makeCluster}} to be used #' for parallel execution. #' @param \dots Further arguments that will be passed to \code{\link{mkinfit}}. @@ -75,7 +76,7 @@ #' #' @export mmkin mmkin <- function(models = c("SFO", "FOMC", "DFOP"), datasets, - cores = parallel::detectCores(), cluster = NULL, ...) + cores = if (Sys.info()["sysname"] == "Windows") 1 else parallel::detectCores(), cluster = NULL, ...) { call <- match.call() parent_models_available = c("SFO", "FOMC", "DFOP", "HS", "SFORB", "IORE", "logistic") diff --git a/check.log b/check.log index 0d04e05e..b848a900 100644 --- a/check.log +++ b/check.log @@ -1,5 +1,5 @@ * using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’ -* using R version 4.0.4 (2021-02-15) +* using R version 4.0.5 (2021-03-31) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using options ‘--no-tests --as-cran’ @@ -43,7 +43,9 @@ The Date field is over a month old. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK -* checking R code for possible problems ... OK +* checking R code for possible problems ... NOTE +mmkin: possible error in Sys.info("sysname"): unused argument + ("sysname") * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK @@ -69,7 +71,7 @@ The Date field is over a month old. * checking for detritus in the temp directory ... OK * DONE -Status: 1 NOTE +Status: 2 NOTEs See ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’ for details. diff --git a/docs/news/index.html b/docs/news/index.html index fae6503a..2905c120 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -147,6 +147,7 @@
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index df454e62..3f97ea94 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -10,7 +10,7 @@ articles: web_only/NAFTA_examples: NAFTA_examples.html web_only/benchmarks: benchmarks.html web_only/compiled_models: compiled_models.html -last_built: 2021-03-31T17:15Z +last_built: 2021-04-20T14:34Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png index 17a35806..49fb9af1 100644 Binary files a/docs/reference/Rplot001.png and b/docs/reference/Rplot001.png differ diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png index 808f1968..745d583d 100644 Binary files a/docs/reference/Rplot002.png and b/docs/reference/Rplot002.png differ diff --git a/docs/reference/Rplot003.png b/docs/reference/Rplot003.png index 97f650e2..eba202e9 100644 Binary files a/docs/reference/Rplot003.png and b/docs/reference/Rplot003.png differ diff --git a/docs/reference/Rplot004.png b/docs/reference/Rplot004.png index 21ad6783..a4f878c8 100644 Binary files a/docs/reference/Rplot004.png and b/docs/reference/Rplot004.png differ diff --git a/docs/reference/Rplot005.png b/docs/reference/Rplot005.png index 4828f5b2..a4f878c8 100644 Binary files a/docs/reference/Rplot005.png and b/docs/reference/Rplot005.png differ diff --git a/docs/reference/Rplot006.png b/docs/reference/Rplot006.png index 4aed2c87..ff8a5d83 100644 Binary files a/docs/reference/Rplot006.png and b/docs/reference/Rplot006.png differ diff --git a/docs/reference/mmkin-1.png b/docs/reference/mmkin-1.png index 26586ab9..f6bb2131 100644 Binary files a/docs/reference/mmkin-1.png and b/docs/reference/mmkin-1.png differ diff --git a/docs/reference/mmkin-2.png b/docs/reference/mmkin-2.png index dbcdd8ee..50102a3d 100644 Binary files a/docs/reference/mmkin-2.png and b/docs/reference/mmkin-2.png differ diff --git a/docs/reference/mmkin-3.png b/docs/reference/mmkin-3.png index 80245fc6..9aa7f0db 100644 Binary files a/docs/reference/mmkin-3.png and b/docs/reference/mmkin-3.png differ diff --git a/docs/reference/mmkin-4.png b/docs/reference/mmkin-4.png index 328aa564..f4f413d1 100644 Binary files a/docs/reference/mmkin-4.png and b/docs/reference/mmkin-4.png differ diff --git a/docs/reference/mmkin-5.png b/docs/reference/mmkin-5.png index 9ce5e919..48ab2c50 100644 Binary files a/docs/reference/mmkin-5.png and b/docs/reference/mmkin-5.png differ diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index c73d14bf..caba300e 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -155,7 +155,7 @@ datasets specified in its first two arguments.

mmkin(
   models = c("SFO", "FOMC", "DFOP"),
   datasets,
-  cores = parallel::detectCores(),
+  cores = if (Sys.info()["sysname"] == "Windows") 1 else parallel::detectCores(),
   cluster = NULL,
   ...
 )
@@ -183,7 +183,8 @@ data for mkinfit.

 is only used when the cluster argument is NULL. On Windows
 machines, cores > 1 is not supported, you need to use the cluster
 argument to use multiple logical processors. Per default, all cores
-detected by parallel::detectCores() are used.

+detected by parallel::detectCores() are used, except on Windows where
+the default is 1.

     
     
       cluster
@@ -234,9 +235,9 @@ plotting.
time_default
#> user system elapsed -#> 5.387 0.413 1.864
time_1 +#> 4.656 0.403 1.734
time_1
#> user system elapsed -#> 5.786 0.008 5.794
+#> 5.627 0.004 5.631
endpoints(fits.0[["SFO_lin", 2]])
#> $ff #> parent_M1 parent_sink M1_M2 M1_sink diff --git a/docs/reference/nlme-1.png b/docs/reference/nlme-1.png index cca4ce0a..c41adc27 100644 Binary files a/docs/reference/nlme-1.png and b/docs/reference/nlme-1.png differ diff --git a/docs/reference/plot.mixed.mmkin-1.png b/docs/reference/plot.mixed.mmkin-1.png index 2224d96e..65660abe 100644 Binary files a/docs/reference/plot.mixed.mmkin-1.png and b/docs/reference/plot.mixed.mmkin-1.png differ diff --git a/man/mmkin.Rd b/man/mmkin.Rd index 170ce8df..309761dd 100644 --- a/man/mmkin.Rd +++ b/man/mmkin.Rd @@ -9,7 +9,7 @@ more datasets} mmkin( models = c("SFO", "FOMC", "DFOP"), datasets, - cores = parallel::detectCores(), + cores = if (Sys.info()["sysname"] == "Windows") 1 else parallel::detectCores(), cluster = NULL, ... ) @@ -28,7 +28,8 @@ data for \code{\link{mkinfit}}.} is only used when the \code{cluster} argument is \code{NULL}. On Windows machines, cores > 1 is not supported, you need to use the \code{cluster} argument to use multiple logical processors. Per default, all cores -detected by \code{\link[parallel:detectCores]{parallel::detectCores()}} are used.} +detected by \code{\link[parallel:detectCores]{parallel::detectCores()}} are used, except on Windows where +the default is 1.} \item{cluster}{A cluster as returned by \code{\link{makeCluster}} to be used for parallel execution.} diff --git a/test.log b/test.log index b49088e5..a8b42364 100644 --- a/test.log +++ b/test.log @@ -1,27 +1,33 @@ -Loading mkin +ℹ Loading mkin Loading required package: parallel -Testing mkin +ℹ Testing mkin ✔ | OK F W S | Context ✔ | 5 | AIC calculation -✔ | 2 | Export dataset for reading into CAKE -✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [1.0 s] -✔ | 4 | Calculation of FOCUS chi2 error levels [0.5 s] -✔ | 7 | Fitting the SFORB model [3.5 s] -✔ | 5 | Analytical solutions for coupled models [3.1 s] +✔ | 5 | Analytical solutions for coupled models [3.2 s] ✔ | 5 | Calculation of Akaike weights -✔ | 12 | Confidence intervals and p-values [1.0 s] -✔ | 14 | Error model fitting [4.2 s] +✔ | 2 | Export dataset for reading into CAKE +✔ | 12 | Confidence intervals and p-values [1.3 s] +✔ | 14 | Error model fitting [4.3 s] ✔ | 5 | Time step normalisation +✔ | 4 | Calculation of FOCUS chi2 error levels [0.5 s] +✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.7 s] ✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3 s] ✔ | 1 | Fitting the logistic model [0.2 s] ✔ | 5 | Nonlinear mixed-effects models [0.1 s] ✔ | 2 | Test dataset classes mkinds and mkindsg -✔ | 1 | mkinfit features [0.3 s] ✔ | 10 | Special cases of mkinfit calls [0.3 s] +✔ | 1 | mkinfit features [0.3 s] ✔ | 8 | mkinmod model generation and printing [0.2 s] -✔ | 3 | Model predictions with mkinpredict [0.4 s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.6 s] -✔ | 9 | Nonlinear mixed-effects models [7.9 s] +✔ | 3 | Model predictions with mkinpredict [0.3 s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.7 s] +✖ | 7 1 | Nonlinear mixed-effects models [1.9 s] +──────────────────────────────────────────────────────────────────────────────── +Error (test_nlme.R:116:3): nlme_function works correctly in other cases +Error: unused argument ("sysname") +Backtrace: + 1. mkin::mmkin("SFO", ds_me_sfo_5, quiet = TRUE) test_nlme.R:116:2 + 2. parallel::mclapply(...) /home/jranke/git/mkin/R/mmkin.R:118:4 +──────────────────────────────────────────────────────────────────────────────── ✖ | 10 4 | Plotting [1.7 s] ──────────────────────────────────────────────────────────────────────────────── Failure (test_plot.R:20:3): Plotting mkinfit, mmkin and mixed model objects is reproducible @@ -42,13 +48,14 @@ Figures don't match: plot-res-for-focus-d.svg ──────────────────────────────────────────────────────────────────────────────── ✔ | 4 | Residuals extracted from mkinfit models ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5 s] -✔ | 4 | Summary [0.1 s] +✔ | 7 | Fitting the SFORB model [3.6 s] ✔ | 1 | Summaries of old mkinfit objects +✔ | 4 | Summary [0.1 s] ✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2 s] -✔ | 9 | Hypothesis tests [8.3 s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.5 s] +✔ | 9 | Hypothesis tests [8.1 s] +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.4 s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 41.0 s +Duration: 35.2 s -[ FAIL 4 | WARN 0 | SKIP 0 | PASS 170 ] +[ FAIL 5 | WARN 0 | SKIP 0 | PASS 168 ] diff --git a/tests/figs/plotting/mkinfit-plot-for-focus-c-with-residuals-like-in-gmkin.svg b/tests/figs/plotting/mkinfit-plot-for-focus-c-with-residuals-like-in-gmkin.svg index a84e170d..bef1556f 100644 --- a/tests/figs/plotting/mkinfit-plot-for-focus-c-with-residuals-like-in-gmkin.svg +++ b/tests/figs/plotting/mkinfit-plot-for-focus-c-with-residuals-like-in-gmkin.svg @@ -75,21 +75,21 @@ - + - - - - - - + + + + + + 0 -20 -40 -60 -80 -100 -120 +20 +40 +60 +80 +100 +120 @@ -115,14 +115,14 @@ - - - - - - - - + + + + + + + + diff --git a/tests/figs/plotting/mkinfit-plot-for-focus-c-with-sep-true.svg b/tests/figs/plotting/mkinfit-plot-for-focus-c-with-sep-true.svg index 9b16c583..54f0e961 100644 --- a/tests/figs/plotting/mkinfit-plot-for-focus-c-with-sep-true.svg +++ b/tests/figs/plotting/mkinfit-plot-for-focus-c-with-sep-true.svg @@ -86,21 +86,21 @@ - + - - - - - - + + + + + + 0 -20 -40 -60 -80 -100 -120 +20 +40 +60 +80 +100 +120 @@ -126,14 +126,14 @@ - - - - - - - - + + + + + + + + diff --git a/tests/figs/plotting/plot-res-for-focus-c.svg b/tests/figs/plotting/plot-res-for-focus-c.svg index 226d9014..3e6de1ce 100644 --- a/tests/figs/plotting/plot-res-for-focus-c.svg +++ b/tests/figs/plotting/plot-res-for-focus-c.svg @@ -75,21 +75,21 @@ - + - - - - - - + + + + + + 0 -20 -40 -60 -80 -100 -120 +20 +40 +60 +80 +100 +120 @@ -115,14 +115,14 @@ - - - - - - - - + + + + + + + + diff --git a/tests/figs/plotting/plot-res-for-focus-d.svg b/tests/figs/plotting/plot-res-for-focus-d.svg index 6504365c..222d85f6 100644 --- a/tests/figs/plotting/plot-res-for-focus-d.svg +++ b/tests/figs/plotting/plot-res-for-focus-d.svg @@ -110,21 +110,21 @@ - + - - - - - - + + + + + + 0 -20 -40 -60 -80 -100 -120 +20 +40 +60 +80 +100 +120 @@ -151,42 +151,42 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + -- cgit v1.2.3