From 91c5db736a4d3f2290a0cc5698fb4e35ae7bda59 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 18 May 2022 21:26:17 +0200 Subject: Remove outdated comment in FOCUS L vignette, update docs This also adds the first benchmark results obtained on my laptop system --- docs/reference/AIC.mmkin.html | 10 +- docs/reference/CAKE_export.html | 2 +- docs/reference/D24_2014.html | 2 +- docs/reference/DFOP.solution.html | 2 +- docs/reference/Extract.mmkin.html | 6 +- docs/reference/FOCUS_2006_datasets.html | 2 +- docs/reference/FOMC.solution.html | 2 +- docs/reference/HS.solution.html | 2 +- docs/reference/IORE.solution.html | 4 +- docs/reference/NAFTA_SOP_2015.html | 2 +- docs/reference/Rplot001.png | Bin 27711 -> 14083 bytes docs/reference/Rplot002.png | Bin 59119 -> 13699 bytes docs/reference/Rplot003.png | Bin 59152 -> 48687 bytes docs/reference/Rplot004.png | Bin 60094 -> 58906 bytes docs/reference/Rplot005.png | Bin 19451 -> 19452 bytes docs/reference/Rplot006.png | Bin 24295 -> 24269 bytes docs/reference/SFO.solution.html | 2 +- docs/reference/SFORB.solution.html | 2 +- docs/reference/add_err.html | 2 +- docs/reference/aw.html | 2 +- docs/reference/confint.mkinfit.html | 48 +-- docs/reference/create_deg_func.html | 20 +- docs/reference/dimethenamid_2018-1.png | Bin 248143 -> 248255 bytes docs/reference/dimethenamid_2018-2.png | Bin 246117 -> 246153 bytes docs/reference/dimethenamid_2018-3.png | Bin 245058 -> 248013 bytes docs/reference/dimethenamid_2018.html | 92 ++--- docs/reference/endpoints.html | 2 +- docs/reference/experimental_data_for_UBA-1.png | Bin 102904 -> 102928 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/get_deg_func.html | 2 +- docs/reference/ilr.html | 2 +- docs/reference/index.html | 2 +- docs/reference/intervals.saem.mmkin.html | 2 +- docs/reference/loftest-3.png | Bin 76871 -> 76869 bytes docs/reference/loftest-5.png | Bin 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docs/reference/synthetic_data_for_UBA_2014-1.png | Bin 67454 -> 67450 bytes docs/reference/synthetic_data_for_UBA_2014.html | 40 +-- docs/reference/transform_odeparms.html | 2 +- docs/reference/update.mkinfit.html | 4 +- 102 files changed, 570 insertions(+), 568 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html index a049850d..c46824e6 100644 --- a/docs/reference/AIC.mmkin.html +++ b/docs/reference/AIC.mmkin.html @@ -123,6 +123,8 @@ dataframe if there are several fits in the column).

f <- mmkin(c("SFO", "FOMC", "DFOP"), list("FOCUS A" = FOCUS_2006_A, "FOCUS C" = FOCUS_2006_C), cores = 1, quiet = TRUE) +#> Warning: Optimisation did not converge: +#> false convergence (8) # We get a warning because the FOMC model does not converge for the # FOCUS A dataset, as it is well described by SFO @@ -136,17 +138,17 @@ dataframe if there are several fits in the column).

AIC(f[, "FOCUS A"]) #> df AIC #> SFO 3 55.28197 -#> FOMC 4 57.28222 +#> FOMC 4 57.28198 #> DFOP 5 59.28197 AIC(f[, "FOCUS A"], k = 0) # If we do not penalize additional parameters, we get nearly the same #> df AIC #> SFO 3 49.28197 -#> FOMC 4 49.28222 +#> FOMC 4 49.28198 #> DFOP 5 49.28197 BIC(f[, "FOCUS A"]) # Comparing the BIC gives a very similar picture #> df BIC #> SFO 3 55.52030 -#> FOMC 4 57.59999 +#> FOMC 4 57.59975 #> DFOP 5 59.67918 # For FOCUS C, the more complex models fit better @@ -176,7 +178,7 @@ dataframe if there are several fits in the column).

-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/CAKE_export.html b/docs/reference/CAKE_export.html index f16a9e6c..4a0b599b 100644 --- a/docs/reference/CAKE_export.html +++ b/docs/reference/CAKE_export.html @@ -161,7 +161,7 @@ compatible with CAKE.

-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/D24_2014.html b/docs/reference/D24_2014.html index 1c47c7f7..6e2ec0ba 100644 --- a/docs/reference/D24_2014.html +++ b/docs/reference/D24_2014.html @@ -224,7 +224,7 @@ specific pieces of information in the comments.

-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index 86df2efc..41a7d256 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -154,7 +154,7 @@ Version 1.1, 18 December 2014
-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 7193e0f9..e00391e8 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -155,7 +155,7 @@ either a list of mkinfit objects or a single mkinfit object.

) #> $par #> parent_0 log_alpha log_beta sigma -#> 99.666192 2.549850 5.050586 1.890202 +#> 99.666193 2.549849 5.050586 1.890202 #> #> $objective #> [1] 28.58291 @@ -168,7 +168,7 @@ either a list of mkinfit objects or a single mkinfit object.

#> #> $evaluations #> function gradient -#> 25 78 +#> 25 72 #> #> $message #> [1] "both X-convergence and relative convergence (5)" @@ -187,7 +187,7 @@ either a list of mkinfit objects or a single mkinfit object.

-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index 1e0e270e..aeeaf723 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -144,7 +144,7 @@
-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index d507b9c8..7274cadc 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -167,7 +167,7 @@ Technology 24, 1032-1038

-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index d30c4e8a..03b30958 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -155,7 +155,7 @@ Version 1.1, 18 December 2014
-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index fec06e0a..0116760d 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -144,7 +144,7 @@ for Evaluating and Calculating Degradation Kinetics in Environmental Media

print(data.frame(fit.fomc$par, fit.iore$par, fit.iore.deS$par, row.names = paste("model par", 1:4))) #> fit.fomc.par fit.iore.par fit.iore.deS.par -#> model par 1 85.87489063 85.874890 85.874890 +#> model par 1 85.87489063 85.874890 85.874891 #> model par 2 0.05192238 -4.826631 -4.826631 #> model par 3 0.65096665 1.949403 1.949403 #> model par 4 1.85744396 1.857444 1.857444 @@ -170,7 +170,7 @@ for Evaluating and Calculating Degradation Kinetics in Environmental Media

-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html index ab3ae7b8..06b5bd6f 100644 --- a/docs/reference/NAFTA_SOP_2015.html +++ b/docs/reference/NAFTA_SOP_2015.html @@ -178,7 +178,7 @@
-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png index fa5f3834..ca982688 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 3caf465f..de2d61aa 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 88ebd2d4..f8bf10bb 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 7e87d63d..12d337a4 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 76f25647..014bf258 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 48f5bbd8..bc6979e9 100644 Binary files a/docs/reference/Rplot006.png and b/docs/reference/Rplot006.png differ diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index dfae0f69..3607a5ac 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -147,7 +147,7 @@ Version 1.1, 18 December 2014
-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 40ed1338..9b4c391c 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -161,7 +161,7 @@ Version 1.1, 18 December 2014
-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index de773982..3a129533 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -208,7 +208,7 @@ https://jrwb.de/posters/piacenza_2015.pdf

-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/aw.html b/docs/reference/aw.html index 1182ab8c..1694d5f7 100644 --- a/docs/reference/aw.html +++ b/docs/reference/aw.html @@ -151,7 +151,7 @@ Inference: Understanding AIC and BIC in Model Selection.
-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html index 806e94ca..5469f8f8 100644 --- a/docs/reference/confint.mkinfit.html +++ b/docs/reference/confint.mkinfit.html @@ -206,7 +206,7 @@ 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 -#> 4.361 0.964 3.998 +#> 3.409 0.000 3.411 # 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 @@ -214,7 +214,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, c("k_parent_sink", "k_parent_m1", "k_m1_sink", "sigma"), cores = n_cores)) #> Profiling the likelihood #> user system elapsed -#> 1.473 0.118 0.917 +#> 1.317 0.152 0.847 ci_profile #> 2.5% 97.5% #> parent_0 96.456003640 1.027703e+02 @@ -281,7 +281,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, ci_quadratic_transformed_ff <- confint(f_d_2, method = "quadratic") ci_quadratic_transformed_ff #> 2.5% 97.5% -#> parent_0 96.403833578 102.79311649 +#> parent_0 96.403833565 102.79311648 #> k_parent 0.090823771 0.10725430 #> k_m1 0.004012219 0.00689755 #> f_parent_to_m1 0.469118824 0.55959615 @@ -289,7 +289,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, ci_quadratic_untransformed_ff <- confint(f_d_2, method = "quadratic", transformed = FALSE) ci_quadratic_untransformed_ff #> 2.5% 97.5% -#> parent_0 96.403833583 1.027931e+02 +#> parent_0 96.403833570 1.027931e+02 #> k_parent 0.090491913 1.069035e-01 #> k_m1 0.003835485 6.685823e-03 #> f_parent_to_m1 0.469113477 5.598387e-01 @@ -309,17 +309,17 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, #> sigma TRUE FALSE rel_diffs_transformed_ff #> 2.5% 97.5% -#> parent_0 0.0005408690 0.0002217233 -#> k_parent 0.0009598532 0.0009001864 -#> k_m1 0.0307283041 0.0290588361 -#> f_parent_to_m1 0.0046881769 0.0027780063 +#> parent_0 0.0005408691 0.0002217232 +#> k_parent 0.0009598534 0.0009001862 +#> k_m1 0.0307283050 0.0290588375 +#> f_parent_to_m1 0.0046881765 0.0027780058 #> sigma 0.0550252516 0.0327066836 rel_diffs_untransformed_ff #> 2.5% 97.5% -#> parent_0 0.0005408689 0.0002217232 -#> k_parent 0.0046102156 0.0023732281 -#> k_m1 0.0146740690 0.0025291820 -#> f_parent_to_m1 0.0046995211 0.0023457712 +#> parent_0 0.0005408691 0.0002217231 +#> k_parent 0.0046102157 0.0023732283 +#> k_m1 0.0146740682 0.0025291807 +#> f_parent_to_m1 0.0046995207 0.0023457708 #> sigma 0.0550252516 0.0327066836 # The profiling for the following fit does not finish in a reasonable time, @@ -333,19 +333,19 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, error_model_algorithm = "direct", quiet = TRUE) confint(f_tc_2, method = "quadratic") #> 2.5% 97.5% -#> parent_0 94.596039609 106.19954892 -#> k_M1 0.037605368 0.04490762 -#> k_M2 0.008568731 0.01087676 -#> f_parent_to_M1 0.021462489 0.62023882 -#> f_parent_to_M2 0.015165617 0.37975348 -#> k1 0.273897348 0.33388101 -#> k2 0.018614554 0.02250378 -#> g 0.671943411 0.73583305 -#> sigma_low 0.251283495 0.83992077 -#> rsd_high 0.040411024 0.07662008 +#> parent_0 94.596210088 106.19935874 +#> k_M1 0.037605436 0.04490756 +#> k_M2 0.008568746 0.01087674 +#> f_parent_to_M1 0.021466645 0.62023879 +#> f_parent_to_M2 0.015168549 0.37975352 +#> k1 0.273897574 0.33388069 +#> k2 0.018614555 0.02250379 +#> g 0.671943815 0.73583258 +#> sigma_low 0.251283808 0.83992121 +#> rsd_high 0.040411010 0.07662004 confint(f_tc_2, "parent_0", method = "quadratic") #> 2.5% 97.5% -#> parent_0 94.59604 106.1995 +#> parent_0 94.59621 106.1994 # } @@ -361,7 +361,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/create_deg_func.html b/docs/reference/create_deg_func.html index 2516edff..36b054fe 100644 --- a/docs/reference/create_deg_func.html +++ b/docs/reference/create_deg_func.html @@ -114,31 +114,21 @@ # \dontrun{ fit_2 <- mkinfit(SFO_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE) if (require(rbenchmark)) - benchmark( + benchmark( analytical = mkinfit(SFO_SFO, FOCUS_D, solution_type = "analytical", quiet = TRUE), deSolve = mkinfit(SFO_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE), replications = 2) #> Loading required package: rbenchmark -#> test replications elapsed relative user.self sys.self user.child -#> 1 analytical 2 0.394 1.000 0.393 0 0 -#> 2 deSolve 2 0.678 1.721 0.677 0 0 -#> sys.child -#> 1 0 -#> 2 0 +#> Warning: there is no package called ‘rbenchmark’ DFOP_SFO <- mkinmod( parent = mkinsub("DFOP", "m1"), m1 = mkinsub("SFO")) #> Temporary DLL for differentials generated and loaded - benchmark( + benchmark( analytical = mkinfit(DFOP_SFO, FOCUS_D, solution_type = "analytical", quiet = TRUE), deSolve = mkinfit(DFOP_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE), replications = 2) -#> test replications elapsed relative user.self sys.self user.child -#> 1 analytical 2 0.829 1.000 0.829 0 0 -#> 2 deSolve 2 1.559 1.881 1.559 0 0 -#> sys.child -#> 1 0 -#> 2 0 +#> Error in benchmark(analytical = mkinfit(DFOP_SFO, FOCUS_D, solution_type = "analytical", quiet = TRUE), deSolve = mkinfit(DFOP_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE), replications = 2): could not find function "benchmark" # } @@ -154,7 +144,7 @@
-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/dimethenamid_2018-1.png b/docs/reference/dimethenamid_2018-1.png index 4300b0c0..6e5d357d 100644 Binary files a/docs/reference/dimethenamid_2018-1.png and b/docs/reference/dimethenamid_2018-1.png differ diff --git a/docs/reference/dimethenamid_2018-2.png b/docs/reference/dimethenamid_2018-2.png index 36db063c..cf5f03f7 100644 Binary files a/docs/reference/dimethenamid_2018-2.png and b/docs/reference/dimethenamid_2018-2.png differ diff --git a/docs/reference/dimethenamid_2018-3.png b/docs/reference/dimethenamid_2018-3.png index efb89bdb..339aaef6 100644 Binary files a/docs/reference/dimethenamid_2018-3.png and b/docs/reference/dimethenamid_2018-3.png differ diff --git a/docs/reference/dimethenamid_2018.html b/docs/reference/dimethenamid_2018.html index d2ed8647..a3cfc271 100644 --- a/docs/reference/dimethenamid_2018.html +++ b/docs/reference/dimethenamid_2018.html @@ -202,9 +202,9 @@ specific pieces of information in the comments.

summary(f_dmta_saem_tc) #> saemix version used for fitting: 3.0 #> mkin version used for pre-fitting: 1.1.0 -#> R version used for fitting: 4.1.3 -#> Date of fit: Sat Apr 9 18:03:34 2022 -#> Date of summary: Sat Apr 9 18:03:34 2022 +#> R version used for fitting: 4.2.0 +#> Date of fit: Wed May 18 20:37:14 2022 +#> Date of summary: Wed May 18 20:37:14 2022 #> #> Equations: #> d_DMTA/dt = - k_DMTA * DMTA @@ -217,7 +217,7 @@ specific pieces of information in the comments.

#> #> Model predictions using solution type deSolve #> -#> Fitted in 787.836 s +#> Fitted in 1660.941 s #> Using 300, 100 iterations and 9 chains #> #> Variance model: Two-component variance function @@ -239,65 +239,65 @@ specific pieces of information in the comments.

#> #> Optimised parameters: #> est. lower upper -#> DMTA_0 88.5943 84.3961 92.7925 -#> log_k_DMTA -3.0466 -3.5609 -2.5322 -#> log_k_M23 -4.0684 -4.9340 -3.2029 -#> log_k_M27 -3.8628 -4.2627 -3.4628 -#> log_k_M31 -3.9803 -4.4804 -3.4801 -#> f_DMTA_ilr_1 0.1304 -0.2186 0.4795 -#> f_DMTA_ilr_2 0.1490 -0.2559 0.5540 -#> f_DMTA_ilr_3 -1.3970 -1.6976 -1.0964 +#> DMTA_0 88.3098 84.1383 92.4813 +#> log_k_DMTA -3.0510 -3.5659 -2.5361 +#> log_k_M23 -4.0567 -4.9178 -3.1955 +#> log_k_M27 -3.8592 -4.2571 -3.4614 +#> log_k_M31 -3.9685 -4.4683 -3.4686 +#> f_DMTA_ilr_1 0.1382 -0.2120 0.4885 +#> f_DMTA_ilr_2 0.1429 -0.2616 0.5473 +#> f_DMTA_ilr_3 -1.3889 -1.6943 -1.0836 #> #> Correlation: #> DMTA_0 l__DMTA lg__M23 lg__M27 lg__M31 f_DMTA__1 f_DMTA__2 -#> log_k_DMTA 0.0309 -#> log_k_M23 -0.0231 -0.0031 -#> log_k_M27 -0.0381 -0.0048 0.0039 -#> log_k_M31 -0.0251 -0.0031 0.0021 0.0830 -#> f_DMTA_ilr_1 -0.0046 -0.0006 0.0417 -0.0437 0.0328 -#> f_DMTA_ilr_2 -0.0008 -0.0002 0.0214 -0.0270 -0.0909 -0.0361 -#> f_DMTA_ilr_3 -0.1832 -0.0135 0.0434 0.0804 0.0395 -0.0070 0.0059 +#> log_k_DMTA 0.0315 +#> log_k_M23 -0.0237 -0.0031 +#> log_k_M27 -0.0392 -0.0048 0.0040 +#> log_k_M31 -0.0257 -0.0032 0.0022 0.0821 +#> f_DMTA_ilr_1 -0.0048 -0.0007 0.0415 -0.0435 0.0333 +#> f_DMTA_ilr_2 -0.0007 -0.0002 0.0214 -0.0270 -0.0900 -0.0372 +#> f_DMTA_ilr_3 -0.1861 -0.0136 0.0431 0.0797 0.0382 -0.0072 0.0066 #> #> Random effects: #> est. lower upper -#> SD.DMTA_0 3.3651 -0.9655 7.6956 -#> SD.log_k_DMTA 0.6415 0.2774 1.0055 -#> SD.log_k_M23 1.0176 0.3809 1.6543 -#> SD.log_k_M27 0.4538 0.1522 0.7554 -#> SD.log_k_M31 0.5684 0.1905 0.9464 -#> SD.f_DMTA_ilr_1 0.4111 0.1524 0.6699 -#> SD.f_DMTA_ilr_2 0.4788 0.1808 0.7768 -#> SD.f_DMTA_ilr_3 0.3501 0.1316 0.5685 +#> SD.DMTA_0 3.2733 -1.1098 7.6564 +#> SD.log_k_DMTA 0.6422 0.2777 1.0066 +#> SD.log_k_M23 1.0131 0.3797 1.6465 +#> SD.log_k_M27 0.4511 0.1510 0.7513 +#> SD.log_k_M31 0.5695 0.1923 0.9466 +#> SD.f_DMTA_ilr_1 0.4123 0.1526 0.6720 +#> SD.f_DMTA_ilr_2 0.4780 0.1804 0.7757 +#> SD.f_DMTA_ilr_3 0.3559 0.1344 0.5775 #> #> Variance model: #> est. lower upper -#> a.1 0.9349 0.8395 1.0302 -#> b.1 0.1344 0.1176 0.1512 +#> a.1 0.9255 0.8288 1.0221 +#> b.1 0.1365 0.1191 0.1538 #> #> Backtransformed parameters: #> est. lower upper -#> DMTA_0 88.59431 84.396147 92.79246 -#> k_DMTA 0.04752 0.028413 0.07948 -#> k_M23 0.01710 0.007198 0.04064 -#> k_M27 0.02101 0.014084 0.03134 -#> k_M31 0.01868 0.011329 0.03080 -#> f_DMTA_to_M23 0.14498 NA NA -#> f_DMTA_to_M27 0.12056 NA NA -#> f_DMTA_to_M31 0.11015 NA NA +#> DMTA_0 88.30980 84.138334 92.48126 +#> k_DMTA 0.04731 0.028272 0.07918 +#> k_M23 0.01731 0.007315 0.04095 +#> k_M27 0.02108 0.014164 0.03139 +#> k_M31 0.01890 0.011467 0.03116 +#> f_DMTA_to_M23 0.14626 NA NA +#> f_DMTA_to_M27 0.12029 NA NA +#> f_DMTA_to_M31 0.11135 NA NA #> #> Resulting formation fractions: #> ff -#> DMTA_M23 0.1450 -#> DMTA_M27 0.1206 -#> DMTA_M31 0.1101 -#> DMTA_sink 0.6243 +#> DMTA_M23 0.1463 +#> DMTA_M27 0.1203 +#> DMTA_M31 0.1113 +#> DMTA_sink 0.6221 #> #> Estimated disappearance times: #> DT50 DT90 -#> DMTA 14.59 48.45 -#> M23 40.52 134.62 -#> M27 32.99 109.60 -#> M31 37.11 123.26 +#> DMTA 14.65 48.67 +#> M23 40.05 133.05 +#> M27 32.88 109.21 +#> M31 36.67 121.81 # As the confidence interval for the random effects of DMTA_0 # includes zero, we could try an alternative model without # such random effects @@ -321,7 +321,7 @@ specific pieces of information in the comments.

-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index f764b742..883c9e5d 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -178,7 +178,7 @@ HS and DFOP, as well as from Eigenvalues b1 and b2 of any SFORB models

-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/experimental_data_for_UBA-1.png b/docs/reference/experimental_data_for_UBA-1.png index b7b4d63b..50c09278 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 e87105b6..69a8baf4 100644 --- a/docs/reference/experimental_data_for_UBA.html +++ b/docs/reference/experimental_data_for_UBA.html @@ -238,7 +238,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/f_time_norm_focus.html b/docs/reference/f_time_norm_focus.html index eb0e6f73..27da5718 100644 --- a/docs/reference/f_time_norm_focus.html +++ b/docs/reference/f_time_norm_focus.html @@ -194,7 +194,7 @@ Version 1.1, 18 December 2014
-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/focus_soil_moisture.html b/docs/reference/focus_soil_moisture.html index 9189ef76..6b64ba73 100644 --- a/docs/reference/focus_soil_moisture.html +++ b/docs/reference/focus_soil_moisture.html @@ -133,7 +133,7 @@ Version 2.2, May 2014 -

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/get_deg_func.html b/docs/reference/get_deg_func.html index 130e786a..c63a968c 100644 --- a/docs/reference/get_deg_func.html +++ b/docs/reference/get_deg_func.html @@ -108,7 +108,7 @@ nlme.mmkin

-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index d0cb6372..58ae56b0 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -170,7 +170,7 @@ Compositional Data Using Robust Methods. Math Geosci 40 233-248

-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/index.html b/docs/reference/index.html index 90387a56..4d657918 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -429,7 +429,7 @@ kinetic models fitted with mkinfit

-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/intervals.saem.mmkin.html b/docs/reference/intervals.saem.mmkin.html index ddc565b3..ae621adc 100644 --- a/docs/reference/intervals.saem.mmkin.html +++ b/docs/reference/intervals.saem.mmkin.html @@ -123,7 +123,7 @@ class attribute

-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/loftest-3.png b/docs/reference/loftest-3.png index d897c363..a1a65a61 100644 Binary files a/docs/reference/loftest-3.png and b/docs/reference/loftest-3.png differ diff --git a/docs/reference/loftest-5.png b/docs/reference/loftest-5.png index 0847bbec..c441f2ed 100644 Binary files a/docs/reference/loftest-5.png and b/docs/reference/loftest-5.png differ diff --git a/docs/reference/loftest.html b/docs/reference/loftest.html index a96e6932..ee9b37e4 100644 --- a/docs/reference/loftest.html +++ b/docs/reference/loftest.html @@ -302,7 +302,7 @@ of replicate samples.

-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index c41950a3..9c34d890 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -162,7 +162,7 @@ and the fitted error model parameters.

-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html index ed6e29dc..b09d3a69 100644 --- a/docs/reference/logistic.solution.html +++ b/docs/reference/logistic.solution.html @@ -176,20 +176,20 @@ Version 1.1, 18 December 2014 summary(m)$bpar #> Estimate se_notrans t value Pr(>t) Lower -#> parent_0 1.057896e+02 1.9023449590 55.610120 3.768360e-16 1.016451e+02 +#> parent_0 1.057896e+02 1.9023449649 55.610120 3.768361e-16 1.016451e+02 #> kmax 6.398190e-02 0.0143201029 4.467978 3.841828e-04 3.929235e-02 -#> k0 1.612775e-04 0.0005866813 0.274898 3.940351e-01 5.846688e-08 -#> r 2.263946e-01 0.1718110662 1.317695 1.061043e-01 4.335843e-02 +#> k0 1.612775e-04 0.0005866813 0.274898 3.940351e-01 5.846685e-08 +#> r 2.263946e-01 0.1718110773 1.317695 1.061044e-01 4.335843e-02 #> sigma 5.332935e+00 0.9145907310 5.830952 4.036926e-05 3.340213e+00 #> Upper #> parent_0 109.9341588 #> kmax 0.1041853 -#> k0 0.4448749 -#> r 1.1821120 +#> k0 0.4448750 +#> r 1.1821121 #> sigma 7.3256566 endpoints(m)$distimes #> DT50 DT90 DT50_k0 DT50_kmax -#> parent 36.86533 62.41511 4297.853 10.83349 +#> parent 36.86533 62.41511 4297.854 10.83349 @@ -205,7 +205,7 @@ Version 1.1, 18 December 2014
-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/lrtest.mkinfit.html b/docs/reference/lrtest.mkinfit.html index 6adc1245..bc8dab67 100644 --- a/docs/reference/lrtest.mkinfit.html +++ b/docs/reference/lrtest.mkinfit.html @@ -191,7 +191,7 @@ lower number of fitted parameters (null hypothesis).

-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index 29b17d1a..69da881b 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -179,7 +179,7 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 9b698e64..97ac647e 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -117,7 +117,7 @@

Source

McCall P, Vrona SA, Kelley SS (1981) Fate of uniformly carbon-14 ring labelled 2,4,5-Trichlorophenoxyacetic acid and 2,4-dichlorophenoxyacetic acid. J Agric Chem 29, 100-107 - doi: 10.1021/jf00103a026

+ doi:10.1021/jf00103a026

@@ -128,19 +128,20 @@ #> Temporary DLL for differentials generated and loaded # \dontrun{ fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE) +#> Warning: Observations with value of zero were removed from the data summary(fit.1)$bpar #> Estimate se_notrans t value Pr(>t) -#> T245_0 1.038550e+02 2.1847074945 47.537272 4.472189e-18 +#> T245_0 1.038550e+02 2.1847074929 47.537272 4.472189e-18 #> k_T245 4.337042e-02 0.0018983965 22.845818 2.276911e-13 -#> k_phenol 4.050581e-01 0.2986993563 1.356073 9.756989e-02 -#> k_anisole 6.678742e-03 0.0008021439 8.326114 2.623177e-07 -#> f_T245_to_phenol 6.227599e-01 0.3985340558 1.562627 6.949413e-02 -#> f_phenol_to_anisole 1.000000e+00 0.6718439825 1.488441 7.867789e-02 -#> sigma 2.514628e+00 0.4907558883 5.123989 6.233157e-05 +#> k_phenol 4.050581e-01 0.2986993439 1.356073 9.756988e-02 +#> k_anisole 6.678742e-03 0.0008021439 8.326114 2.623176e-07 +#> f_T245_to_phenol 6.227599e-01 0.3985340365 1.562627 6.949413e-02 +#> f_phenol_to_anisole 1.000000e+00 0.6718439498 1.488441 7.867788e-02 +#> sigma 2.514628e+00 0.4907558786 5.123989 6.233156e-05 #> Lower Upper -#> T245_0 99.246061385 1.084640e+02 +#> T245_0 99.246061401 1.084640e+02 #> k_T245 0.039631621 4.746194e-02 -#> k_phenol 0.218013879 7.525762e-01 +#> k_phenol 0.218013878 7.525762e-01 #> k_anisole 0.005370739 8.305299e-03 #> f_T245_to_phenol 0.547559081 6.924813e-01 #> f_phenol_to_anisole 0.000000000 1.000000e+00 @@ -148,13 +149,13 @@ endpoints(fit.1) #> $ff #> T245_phenol T245_sink phenol_anisole phenol_sink -#> 6.227599e-01 3.772401e-01 1.000000e+00 3.773626e-10 +#> 6.227599e-01 3.772401e-01 1.000000e+00 3.195366e-10 #> #> $distimes #> DT50 DT90 #> T245 15.982025 53.09114 #> phenol 1.711229 5.68458 -#> anisole 103.784093 344.76329 +#> anisole 103.784092 344.76329 #> # formation fraction from phenol to anisol is practically 1. As we cannot # fix formation fractions when using the ilr transformation, we can turn of @@ -165,31 +166,32 @@ #> Temporary DLL for differentials generated and loaded fit.2 <- mkinfit(SFO_SFO_SFO_2, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE) +#> Warning: Observations with value of zero were removed from the data summary(fit.2)$bpar #> Estimate se_notrans t value Pr(>t) Lower -#> T245_0 1.038550e+02 2.1623653066 48.028439 4.993108e-19 99.271020284 -#> k_T245 4.337042e-02 0.0018343666 23.643268 3.573556e-14 0.039650976 -#> k_phenol 4.050582e-01 0.1177237473 3.440752 1.679254e-03 0.218746587 -#> k_anisole 6.678742e-03 0.0006829745 9.778903 1.872894e-08 0.005377083 -#> f_T245_to_phenol 6.227599e-01 0.0342197875 18.198824 2.039411e-12 0.547975637 +#> T245_0 1.038550e+02 2.1623653038 48.028439 4.993108e-19 99.271020197 +#> k_T245 4.337042e-02 0.0018343667 23.643268 3.573556e-14 0.039650977 +#> k_phenol 4.050583e-01 0.1177237899 3.440751 1.679257e-03 0.218746592 +#> k_anisole 6.678741e-03 0.0006829745 9.778903 1.872895e-08 0.005377082 +#> f_T245_to_phenol 6.227599e-01 0.0342197865 18.198824 2.039410e-12 0.547975622 #> sigma 2.514628e+00 0.3790944250 6.633250 2.875782e-06 1.710983655 #> Upper -#> T245_0 108.43904074 -#> k_T245 0.04743877 -#> k_phenol 0.75005585 -#> k_anisole 0.00829550 -#> f_T245_to_phenol 0.69212308 -#> sigma 3.31827222 +#> T245_0 1.084390e+02 +#> k_T245 4.743877e-02 +#> k_phenol 7.500560e-01 +#> k_anisole 8.295499e-03 +#> f_T245_to_phenol 6.921231e-01 +#> sigma 3.318272e+00 endpoints(fit.1) #> $ff #> T245_phenol T245_sink phenol_anisole phenol_sink -#> 6.227599e-01 3.772401e-01 1.000000e+00 3.773626e-10 +#> 6.227599e-01 3.772401e-01 1.000000e+00 3.195366e-10 #> #> $distimes #> DT50 DT90 #> T245 15.982025 53.09114 #> phenol 1.711229 5.68458 -#> anisole 103.784093 344.76329 +#> anisole 103.784092 344.76329 #> plot_sep(fit.2) @@ -208,7 +210,7 @@
-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/mean_degparms.html b/docs/reference/mean_degparms.html index efe91b6f..bea9f2d8 100644 --- a/docs/reference/mean_degparms.html +++ b/docs/reference/mean_degparms.html @@ -134,7 +134,7 @@ nlme for the case of a single grouping variable ds.

-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/mixed-1.png b/docs/reference/mixed-1.png index 54b81b70..fe7e6c47 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 af73f22a..dfc7a731 100644 --- a/docs/reference/mixed.html +++ b/docs/reference/mixed.html @@ -177,9 +177,9 @@ single dataframe which is convenient for plotting

#> #> Mean fitted parameters: #> parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 -#> 100.674757 -8.761916 -0.004347 -3.348812 -3.986853 +#> 100.674757 -8.762456 -0.004347 -3.348812 -3.986853 #> g_qlogis -#> -0.087392 +#> -0.087391 plot(f_mixed) # } @@ -197,7 +197,7 @@ single dataframe which is convenient for plotting

-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index ed0abedd..ba00a80a 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -157,7 +157,7 @@ observed values called "value".

-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 37c84761..0cb9ebca 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -139,7 +139,7 @@ column of observed values.

-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index 73a14840..bef3be93 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -145,9 +145,9 @@ and value in order to be compatible with mkinfit

Public methods

-

+

Method new()

Create a new mkinds object

Usage

@@ -175,7 +175,7 @@ and value in order to be compatible with mkinfit

-

+

Method clone()

The objects of this class are cloneable with this method.

Usage

@@ -220,7 +220,7 @@ and value in order to be compatible with mkinfit

-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/mkindsg.html b/docs/reference/mkindsg.html index 7f4ff290..ceee4f37 100644 --- a/docs/reference/mkindsg.html +++ b/docs/reference/mkindsg.html @@ -142,9 +142,9 @@ or covariates like soil pH).

Public methods

-

+

Method new()

Create a new mkindsg object

Usage

@@ -172,7 +172,7 @@ or covariates like soil pH).

-

+

Method clone()

The objects of this class are cloneable with this method.

Usage

@@ -406,7 +406,7 @@ or covariates like soil pH).

-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index dc2cdab8..b6051ab8 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -139,6 +139,7 @@ Document Reference Sanco/10058/2005 version 2.0, 434 pp, #> Temporary DLL for differentials generated and loaded fit_FOCUS_D = mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE) +#> Warning: Observations with value of zero were removed from the data round(mkinerrmin(fit_FOCUS_D), 4) #> err.min n.optim df #> All data 0.0640 4 15 @@ -167,7 +168,7 @@ Document Reference Sanco/10058/2005 version 2.0, 434 pp,
-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/mkinerrplot-1.png b/docs/reference/mkinerrplot-1.png index 49bb1c0e..852da18d 100644 Binary files a/docs/reference/mkinerrplot-1.png and b/docs/reference/mkinerrplot-1.png differ diff --git a/docs/reference/mkinerrplot.html b/docs/reference/mkinerrplot.html index 95206b61..4b78f6eb 100644 --- a/docs/reference/mkinerrplot.html +++ b/docs/reference/mkinerrplot.html @@ -164,6 +164,7 @@ lines of the mkinfit object.

model <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO")) #> Temporary DLL for differentials generated and loaded fit <- mkinfit(model, FOCUS_2006_D, error_model = "tc", quiet = TRUE) +#> Warning: Observations with value of zero were removed from the data mkinerrplot(fit) # } @@ -182,7 +183,7 @@ lines of the mkinfit object.

-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index c006ddab..e5bf1203 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -307,7 +307,7 @@ internal rate transformation.

for measurement error in analytical chemistry. Technometrics 37(2), 176-184.

Ranke J and Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical Degradation Data. Environments 6(12) 124 -doi: 10.3390/environments6120124 +doi:10.3390/environments6120124 .

@@ -330,16 +330,16 @@ doi: fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit) #> mkin version used for fitting: 1.1.0 -#> R version used for fitting: 4.1.2 -#> Date of fit: Mon Mar 7 13:11:56 2022 -#> Date of summary: Mon Mar 7 13:11:56 2022 +#> R version used for fitting: 4.2.0 +#> Date of fit: Wed May 18 20:37:57 2022 +#> Date of summary: Wed May 18 20:37:57 2022 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 222 model solutions performed in 0.045 s +#> Fitted using 222 model solutions performed in 0.041 s #> #> Error model: Constant variance #> @@ -374,10 +374,10 @@ doi: #> #> Parameter correlation: #> parent_0 log_alpha log_beta sigma -#> parent_0 1.000e+00 -1.565e-01 -3.142e-01 4.772e-08 -#> log_alpha -1.565e-01 1.000e+00 9.564e-01 1.005e-07 -#> log_beta -3.142e-01 9.564e-01 1.000e+00 8.541e-08 -#> sigma 4.772e-08 1.005e-07 8.541e-08 1.000e+00 +#> parent_0 1.000e+00 -1.565e-01 -3.142e-01 4.770e-08 +#> log_alpha -1.565e-01 1.000e+00 9.564e-01 9.974e-08 +#> log_beta -3.142e-01 9.564e-01 1.000e+00 8.468e-08 +#> sigma 4.770e-08 9.974e-08 8.468e-08 1.000e+00 #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. @@ -462,7 +462,7 @@ doi: #> $distimes #> DT50 DT90 #> parent 6.89313 22.89848 -#> m1 134.15634 445.65772 +#> m1 134.15634 445.65770 #> # We can show a quick (only one replication) benchmark for this case, as we @@ -471,7 +471,7 @@ doi: # benchmark vignette # \dontrun{ if(require(rbenchmark)) { - benchmark(replications = 1, order = "relative", columns = c("test", "relative", "elapsed"), + benchmark(replications = 1, order = "relative", columns = c("test", "relative", "elapsed"), deSolve_compiled = mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE, error_model = "tc", solution_type = "deSolve", use_compiled = TRUE), eigen = mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE, error_model = "tc", @@ -479,10 +479,8 @@ doi: analytical = mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE, error_model = "tc", solution_type = "analytical")) } -#> test relative elapsed -#> 3 analytical 1.000 0.573 -#> 1 deSolve_compiled 1.642 0.941 -#> 2 eigen 2.517 1.442 +#> Loading required package: rbenchmark +#> Warning: there is no package called ‘rbenchmark’ # } # Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO @@ -506,10 +504,13 @@ doi: # 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: 1.1.0 -#> R version used for fitting: 4.1.2 -#> Date of fit: Mon Mar 7 13:12:07 2022 -#> Date of summary: Mon Mar 7 13:12:07 2022 +#> R version used for fitting: 4.2.0 +#> Date of fit: Wed May 18 20:38:07 2022 +#> Date of summary: Wed May 18 20:38:07 2022 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -518,12 +519,12 @@ doi: #> #> Model predictions using solution type deSolve #> -#> Fitted using 3729 model solutions performed in 2.67 s +#> Fitted using 3924 model solutions performed in 7.107 s #> #> Error model: Two-component variance function #> #> Error model algorithm: d_3 -#> Direct fitting and three-step fitting yield approximately the same likelihood +#> Three-step fitting yielded a higher likelihood than direct fitting #> #> Starting values for parameters to be optimised: #> value type @@ -558,7 +559,7 @@ doi: #> Estimate Std. Error Lower Upper #> parent_0 101.600000 2.6400000 96.240000 107.000000 #> log_k_m1 -5.284000 0.0929100 -5.474000 -5.095000 -#> f_parent_qlogis 0.001426 0.0767000 -0.155000 0.157800 +#> f_parent_qlogis 0.001426 0.0766900 -0.155000 0.157800 #> log_alpha 5.522000 0.0077320 5.506000 5.538000 #> log_beta 7.806000 NaN NaN NaN #> sigma_low 0.002488 0.0002431 0.001992 0.002984 @@ -566,31 +567,31 @@ doi: #> #> Parameter correlation: #> parent_0 log_k_m1 f_parent_qlogis log_alpha log_beta -#> parent_0 1.000000 -0.095226 -0.76678 0.70544 NaN -#> log_k_m1 -0.095226 1.000000 0.51432 -0.14387 NaN -#> f_parent_qlogis -0.766780 0.514321 1.00000 -0.61396 NaN -#> log_alpha 0.705444 -0.143872 -0.61396 1.00000 NaN +#> parent_0 1.000000 -0.095145 -0.76674 0.70541 NaN +#> log_k_m1 -0.095145 1.000000 0.51428 -0.14381 NaN +#> f_parent_qlogis -0.766743 0.514278 1.00000 -0.61392 NaN +#> log_alpha 0.705413 -0.143809 -0.61392 1.00000 NaN #> log_beta NaN NaN NaN NaN 1 -#> sigma_low 0.016073 0.001586 0.01548 5.87007 NaN -#> rsd_high 0.006626 -0.011700 -0.05357 0.04849 NaN +#> sigma_low 0.016077 0.001586 0.01548 5.87034 NaN +#> rsd_high 0.006617 -0.011694 -0.05356 0.04848 NaN #> sigma_low rsd_high -#> parent_0 0.016073 0.006626 -#> log_k_m1 0.001586 -0.011700 -#> f_parent_qlogis 0.015476 -0.053566 -#> log_alpha 5.870075 0.048487 +#> parent_0 0.016077 0.006617 +#> log_k_m1 0.001586 -0.011694 +#> f_parent_qlogis 0.015476 -0.053560 +#> log_alpha 5.870339 0.048481 #> log_beta NaN NaN -#> sigma_low 1.000000 -0.652558 -#> rsd_high -0.652558 1.000000 +#> sigma_low 1.000000 -0.652555 +#> rsd_high -0.652555 1.000000 #> #> 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 1.016e+02 32.7800 6.311e-26 9.624e+01 1.070e+02 +#> parent_0 1.016e+02 32.7800 6.312e-26 9.624e+01 1.070e+02 #> k_m1 5.072e-03 10.1200 1.216e-11 4.196e-03 6.130e-03 -#> f_parent_to_m1 5.004e-01 20.8300 4.317e-20 4.613e-01 5.394e-01 -#> alpha 2.502e+02 0.5624 2.889e-01 2.463e+02 2.542e+02 +#> f_parent_to_m1 5.004e-01 20.8300 4.318e-20 4.613e-01 5.394e-01 +#> alpha 2.502e+02 0.5624 2.890e-01 2.463e+02 2.542e+02 #> beta 2.455e+03 0.5549 2.915e-01 NA NA #> sigma_low 2.488e-03 0.4843 3.158e-01 1.992e-03 2.984e-03 #> rsd_high 7.921e-02 8.4300 8.001e-10 6.018e-02 9.823e-02 @@ -630,7 +631,7 @@ doi:
-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 72a9ea52..3a29b39b 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -258,6 +258,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media

# \dontrun{ fit_sfo_sfo <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, solution_type = "deSolve") +#> Warning: Observations with value of zero were removed from the data # Now supplying compound names used for plotting, and write to user defined location # We need to choose a path outside the session tempdir because this gets removed @@ -267,13 +268,14 @@ 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/Rtmp1TiIZY/file1180516cafe4a2.so to /home/jranke/.local/share/mkin/SFO_SFO.so +#> Copied DLL from /tmp/RtmpkcKjUM/file8dd657f864c2.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) SFO_SFO.3 <- readRDS("~/SFO_SFO.rds") fit_sfo_sfo <- mkinfit(SFO_SFO.3, FOCUS_2006_D, quiet = TRUE, solution_type = "deSolve") +#> Warning: Observations with value of zero were removed from the data # Show details of creating the C function SFO_SFO <- mkinmod( @@ -319,7 +321,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media

#> }) #> return(predicted) #> } -#> <environment: 0x55555f6c4cd8> +#> <environment: 0x55cc1a5f8ad8> # If we have several parallel metabolites # (compare tests/testthat/test_synthetic_data_for_UBA_2014.R) @@ -348,7 +350,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media

-

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+

Site built with pkgdown 2.0.3.

diff --git a/docs/reference/mkinparplot-1.png b/docs/reference/mkinparplot-1.png index fff98391..69d9ac75 100644 Binary files a/docs/reference/mkinparplot-1.png and b/docs/reference/mkinparplot-1.png differ diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index 2e787240..b9eda413 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -117,6 +117,7 @@ effect, namely to produce a plot.

anisole = mkinsub("SFO"), use_of_ff = "max") #> Temporary DLL for differentials generated and loaded fit <- mkinfit(model, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE) +#> Warning: Observations with value of zero were removed from the data mkinparplot(fit) # } @@ -134,7 +135,7 @@ effect, namely to produce a plot.

-

Site built with pkgdown 2.0.2.

+

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diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 79599787..cad5b35f 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -120,7 +120,7 @@ plot.mkinfit.">