From a9427a09abdf7ce9aaeae7c7190f90c8f2e5ef52 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 15 Feb 2021 14:08:13 +0100 Subject: Improve README, introductory vignette and some other docs Also bump version to 1.0.3. --- docs/reference/AIC.mmkin.html | 11 +- docs/reference/CAKE_export.html | 2 +- docs/reference/D24_2014.html | 2 +- docs/reference/DFOP.solution.html | 2 +- docs/reference/Extract.mmkin.html | 4 +- docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html | 2 +- docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html | 2 +- docs/reference/FOCUS_2006_HS_ref_A_to_F.html | 2 +- docs/reference/FOCUS_2006_SFO_ref_A_to_F.html | 2 +- docs/reference/FOCUS_2006_datasets.html | 2 +- docs/reference/FOMC.solution.html | 2 +- docs/reference/HS.solution.html | 2 +- docs/reference/IORE.solution.html | 2 +- docs/reference/NAFTA_SOP_2015-1.png | Bin 62443 -> 61980 bytes docs/reference/NAFTA_SOP_2015.html | 2 +- docs/reference/NAFTA_SOP_Attachment-1.png | Bin 64198 -> 63822 bytes 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@@ -73,7 +73,7 @@ same dataset." /> mkin - 1.0.0 + 1.0.3 @@ -187,8 +187,7 @@ 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 + # We get a warning because the FOMC model does not converge for the # FOCUS A dataset, as it is well described by SFO AIC(f["SFO", "FOCUS A"]) # We get a single number for a single fit @@ -199,15 +198,15 @@ dataframe if there are several fits in the column).

AIC(f[, "FOCUS A"])
#> df AIC #> SFO 3 55.28197 -#> FOMC 4 57.28211 +#> FOMC 4 57.28222 #> 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 49.28211 +#> FOMC 4 49.28222 #> DFOP 5 49.28197
BIC(f[, "FOCUS A"]) # Comparing the BIC gives a very similar picture
#> df BIC #> SFO 3 55.52030 -#> FOMC 4 57.59987 +#> FOMC 4 57.59999 #> DFOP 5 59.67918
# For FOCUS C, the more complex models fit better AIC(f[, "FOCUS C"]) diff --git a/docs/reference/CAKE_export.html b/docs/reference/CAKE_export.html index dcccca1b..05cd04a7 100644 --- a/docs/reference/CAKE_export.html +++ b/docs/reference/CAKE_export.html @@ -73,7 +73,7 @@ specified as well." /> mkin - 1.0.0 + 1.0.3
diff --git a/docs/reference/D24_2014.html b/docs/reference/D24_2014.html index b78e73ef..e2d47f1b 100644 --- a/docs/reference/D24_2014.html +++ b/docs/reference/D24_2014.html @@ -77,7 +77,7 @@ constrained by data protection regulations." /> mkin - 1.0.0 + 1.0.3 diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index cff29301..d04f98cc 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -73,7 +73,7 @@ two exponential decline functions." /> mkin - 1.0.0 + 1.0.3 diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 4e3cbe64..5a99cf1b 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -72,7 +72,7 @@ mkin - 1.0.0 + 1.0.3 @@ -220,7 +220,7 @@ either a list of mkinfit objects or a single mkinfit object.

)
#> $par #> parent_0 log_alpha log_beta sigma -#> 99.666193 2.549849 5.050586 1.890202 +#> 99.666192 2.549850 5.050586 1.890202 #> #> $objective #> [1] 28.58291 diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html index d37fa5a5..ba1cb19a 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -76,7 +76,7 @@ in this fit." /> mkin - 1.0.0 + 1.0.3
diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html index d3f7894c..cfb60536 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -76,7 +76,7 @@ in this fit." /> mkin - 1.0.0 + 1.0.3 diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html index a18abad5..c90bcdbb 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -76,7 +76,7 @@ in this fit." /> mkin - 1.0.0 + 1.0.3 diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html index e0fbc498..7b2747dc 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -76,7 +76,7 @@ in this fit." /> mkin - 1.0.0 + 1.0.3 diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index 543e24ad..7a39dcd0 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -72,7 +72,7 @@ mkin - 1.0.0 + 1.0.3 diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index c376227c..9136b882 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -73,7 +73,7 @@ a decreasing rate constant." /> mkin - 1.0.0 + 1.0.3 diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 8a90fec3..e3009bcc 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -73,7 +73,7 @@ between them." /> mkin - 1.0.0 + 1.0.3 diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index 8e6a2792..f1a40d44 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -73,7 +73,7 @@ a concentration dependent rate constant." /> mkin - 1.0.0 + 1.0.3 diff --git a/docs/reference/NAFTA_SOP_2015-1.png b/docs/reference/NAFTA_SOP_2015-1.png index 76d724f0..4f0d7833 100644 Binary files a/docs/reference/NAFTA_SOP_2015-1.png and b/docs/reference/NAFTA_SOP_2015-1.png differ diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html index 301bf684..de9db9eb 100644 --- a/docs/reference/NAFTA_SOP_2015.html +++ b/docs/reference/NAFTA_SOP_2015.html @@ -72,7 +72,7 @@ mkin - 1.0.0 + 1.0.3 diff --git a/docs/reference/NAFTA_SOP_Attachment-1.png b/docs/reference/NAFTA_SOP_Attachment-1.png index eec3dd9b..9417685e 100644 Binary files a/docs/reference/NAFTA_SOP_Attachment-1.png and b/docs/reference/NAFTA_SOP_Attachment-1.png differ diff --git a/docs/reference/NAFTA_SOP_Attachment.html b/docs/reference/NAFTA_SOP_Attachment.html index 03a45bc3..0b063e2c 100644 --- a/docs/reference/NAFTA_SOP_Attachment.html +++ b/docs/reference/NAFTA_SOP_Attachment.html @@ -72,7 +72,7 @@ mkin - 1.0.0 + 1.0.3 @@ -193,7 +193,7 @@ #> Estimate Pr(>t) Lower Upper #> parent_0 9.99e+01 1.41e-26 98.8116 101.0810 #> k1 2.67e-02 5.05e-06 0.0243 0.0295 -#> k2 2.42e-12 5.00e-01 0.0000 Inf +#> k2 2.26e-12 5.00e-01 0.0000 Inf #> g 6.47e-01 3.67e-06 0.6248 0.6677 #> sigma 1.27e+00 8.91e-06 0.8395 1.6929 #> @@ -202,7 +202,7 @@ #> DT50 DT90 DT50_rep #> SFO 67.7 2.25e+02 6.77e+01 #> IORE 58.2 1.07e+03 3.22e+02 -#> DFOP 55.5 5.22e+11 2.86e+11 +#> DFOP 55.5 5.59e+11 3.07e+11 #> #> Representative half-life: #> [1] 321.51
plot(nafta_att_p5a) diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png index 762a3dd4..7f498242 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 d24e35b4..54c31a3f 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 e96adeb3..19198739 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 91058d4b..1028a9c4 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 91058d4b..aa844051 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 74f43dfa..81525882 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 fce3b6ee..10b7455a 100644 Binary files a/docs/reference/Rplot007.png and b/docs/reference/Rplot007.png differ diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 7e4fb237..826a0472 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -72,7 +72,7 @@ mkin - 1.0.0 + 1.0.3
diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 7254c451..b2062e30 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -76,7 +76,7 @@ and no substance in the bound fraction." /> mkin - 1.0.0 + 1.0.3 diff --git a/docs/reference/add_err-1.png b/docs/reference/add_err-1.png index 9d333cbb..9ba106db 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-3.png b/docs/reference/add_err-3.png index 07cf0032..493a761a 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 2009aaf4..6fbecd14 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 - 1.0.0 + 1.0.3 diff --git a/docs/reference/aw.html b/docs/reference/aw.html index 77ee9cef..6399b839 100644 --- a/docs/reference/aw.html +++ b/docs/reference/aw.html @@ -74,7 +74,7 @@ by Burnham and Anderson (2004)." /> mkin - 1.0.0 + 1.0.3 diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html index b71e039a..06e78459 100644 --- a/docs/reference/confint.mkinfit.html +++ b/docs/reference/confint.mkinfit.html @@ -79,7 +79,7 @@ method of Venzon and Moolgavkar (1988)." /> mkin - 1.0.0 + 1.0.3 @@ -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 -#> 4.324 0.980 3.960
# Using more cores does not save much time here, as parent_0 takes up most of the time +#> 4.255 1.029 3.937
# 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 -#> 1.480 0.109 0.905
ci_profile +#> 1.469 0.092 0.911
ci_profile
#> 2.5% 97.5% #> parent_0 96.456003640 1.027703e+02 #> k_parent_sink 0.040762501 5.549764e-02 @@ -349,14 +349,14 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, #> sigma 2.535612399 3.985263e+00
ci_quadratic_transformed_ff <- confint(f_d_2, method = "quadratic") ci_quadratic_transformed_ff
#> 2.5% 97.5% -#> parent_0 96.403833585 102.79311650 +#> parent_0 96.403833578 102.79311649 #> k_parent 0.090823771 0.10725430 #> k_m1 0.004012219 0.00689755 #> f_parent_to_m1 0.469118824 0.55959615 #> sigma 2.396089689 3.85491806
ci_quadratic_untransformed_ff <- confint(f_d_2, method = "quadratic", transformed = FALSE) ci_quadratic_untransformed_ff
#> 2.5% 97.5% -#> parent_0 96.403833589 1.027931e+02 +#> parent_0 96.403833583 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 @@ -374,15 +374,15 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, #> f_parent_to_m1 TRUE FALSE #> sigma TRUE FALSE
rel_diffs_transformed_ff
#> 2.5% 97.5% -#> parent_0 0.0005408689 0.0002217234 +#> parent_0 0.0005408690 0.0002217233 #> k_parent 0.0009598532 0.0009001864 -#> k_m1 0.0307283044 0.0290588365 -#> f_parent_to_m1 0.0046881768 0.0027780063 +#> k_m1 0.0307283041 0.0290588361 +#> f_parent_to_m1 0.0046881769 0.0027780063 #> sigma 0.0550252516 0.0327066836
rel_diffs_untransformed_ff
#> 2.5% 97.5% -#> parent_0 0.0005408689 0.0002217233 -#> k_parent 0.0046102155 0.0023732281 -#> k_m1 0.0146740688 0.0025291817 +#> 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 #> sigma 0.0550252516 0.0327066836
# The profiling for the following fit does not finish in a reasonable time, @@ -396,18 +396,18 @@ 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 94.596126334 106.19944007 -#> k_M1 0.037605408 0.04490759 -#> k_M2 0.008568739 0.01087675 -#> f_parent_to_M1 0.021463787 0.62023881 -#> f_parent_to_M2 0.015166531 0.37975349 -#> k1 0.273897467 0.33388084 -#> k2 0.018614555 0.02250379 -#> g 0.671943606 0.73583278 -#> sigma_low 0.251283766 0.83992113 -#> rsd_high 0.040411014 0.07662005
confint(f_tc_2, "parent_0", method = "quadratic") +#> 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
confint(f_tc_2, "parent_0", method = "quadratic")
#> 2.5% 97.5% -#> parent_0 94.59613 106.1994
# } +#> parent_0 94.59604 106.1995
# }
@@ -182,7 +182,7 @@ replications = 2)
#> Loading required package: rbenchmark
#> test replications elapsed relative user.self sys.self user.child #> 1 analytical 2 0.389 1.000 0.389 0 0 -#> 2 deSolve 2 0.689 1.771 0.688 0 0 +#> 2 deSolve 2 0.690 1.774 0.690 0 0 #> sys.child #> 1 0 #> 2 0
DFOP_SFO <- mkinmod( @@ -193,8 +193,8 @@ 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 0.825 1.000 0.825 0 0 -#> 2 deSolve 2 1.574 1.908 1.573 0 0 +#> 1 analytical 2 0.817 1.000 0.818 0 0 +#> 2 deSolve 2 1.591 1.947 1.591 0 0 #> sys.child #> 1 0 #> 2 0
# } diff --git a/docs/reference/dimethenamid_2018.html b/docs/reference/dimethenamid_2018.html index 435848c2..6845f74f 100644 --- a/docs/reference/dimethenamid_2018.html +++ b/docs/reference/dimethenamid_2018.html @@ -77,7 +77,7 @@ constrained by data protection regulations." /> mkin - 1.0.0 + 1.0.3
diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index e42ca9fe..584079d2 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -78,7 +78,7 @@ advantage that the SFORB model can also be used for metabolites." /> mkin - 1.0.2 + 1.0.3 diff --git a/docs/reference/experimental_data_for_UBA-1.png b/docs/reference/experimental_data_for_UBA-1.png index 22f38cc2..33946ded 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 9333a34f..77f75678 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 - 1.0.0 + 1.0.3 diff --git a/docs/reference/f_time_norm_focus.html b/docs/reference/f_time_norm_focus.html index 6917b4b3..aa494b27 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 - 1.0.0 + 1.0.3 diff --git a/docs/reference/focus_soil_moisture.html b/docs/reference/focus_soil_moisture.html index f0c766da..61f235db 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 - 1.0.0 + 1.0.3 diff --git a/docs/reference/get_deg_func.html b/docs/reference/get_deg_func.html index a0e341c9..44703806 100644 --- a/docs/reference/get_deg_func.html +++ b/docs/reference/get_deg_func.html @@ -72,7 +72,7 @@ mkin - 1.0.0 + 1.0.3 diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index b91ef055..671faf5d 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -73,7 +73,7 @@ transformations." /> mkin - 1.0.0 + 1.0.3 diff --git a/docs/reference/index.html b/docs/reference/index.html index 7b1bc4f1..e21304b9 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -71,7 +71,7 @@ mkin - 1.0.2 + 1.0.3 diff --git a/docs/reference/loftest-3.png b/docs/reference/loftest-3.png index 43e6a00f..6afd084b 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 cf7e5862..43460a65 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 614b8eea..6e72774e 100644 --- a/docs/reference/loftest.html +++ b/docs/reference/loftest.html @@ -75,7 +75,7 @@ lrtest.default from the lmtest package." /> mkin - 1.0.0 + 1.0.3 diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index 8d984e55..9e5b4069 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -76,7 +76,7 @@ the error model." /> mkin - 1.0.0 + 1.0.3 diff --git a/docs/reference/logistic.solution-2.png b/docs/reference/logistic.solution-2.png index 79bf3453..73e6436d 100644 Binary files a/docs/reference/logistic.solution-2.png and b/docs/reference/logistic.solution-2.png differ diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html index 404344a3..d11e1b3c 100644 --- a/docs/reference/logistic.solution.html +++ b/docs/reference/logistic.solution.html @@ -73,7 +73,7 @@ an increasing rate constant, supposedly caused by microbial growth" /> mkin - 1.0.0 + 1.0.3 @@ -240,10 +240,10 @@ Version 1.1, 18 December 2014 plot_sep(m)
summary(m)$bpar
#> Estimate se_notrans t value Pr(>t) Lower -#> parent_0 1.057896e+02 1.9023449703 55.610119 3.768361e-16 1.016451e+02 -#> kmax 6.398190e-02 0.0143201031 4.467978 3.841829e-04 3.929235e-02 +#> parent_0 1.057896e+02 1.9023449590 55.610120 3.768360e-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 0.1718110715 1.317695 1.061044e-01 4.335843e-02 +#> r 2.263946e-01 0.1718110662 1.317695 1.061043e-01 4.335843e-02 #> sigma 5.332935e+00 0.9145907310 5.830952 4.036926e-05 3.340213e+00 #> Upper #> parent_0 109.9341588 diff --git a/docs/reference/lrtest.mkinfit.html b/docs/reference/lrtest.mkinfit.html index e39314d9..d670fb0c 100644 --- a/docs/reference/lrtest.mkinfit.html +++ b/docs/reference/lrtest.mkinfit.html @@ -76,7 +76,7 @@ and can be expressed by fixing the parameters of the other." /> mkin - 1.0.0 + 1.0.3
diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index 2aa5d5f1..4d473893 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -78,7 +78,7 @@ soil section of the FOCUS guidance." /> mkin - 1.0.0 + 1.0.3 diff --git a/docs/reference/mccall81_245T-1.png b/docs/reference/mccall81_245T-1.png index 58ae716a..91fe060e 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 b99138a0..b7dca4a7 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -74,7 +74,7 @@ mkin - 1.0.0 + 1.0.3 @@ -181,30 +181,30 @@ 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 2.1847074888 47.537272 4.472189e-18 +#> T245_0 1.038550e+02 2.1847074945 47.537272 4.472189e-18 #> k_T245 4.337042e-02 0.0018983965 22.845818 2.276911e-13 -#> k_phenol 4.050581e-01 0.2986993400 1.356073 9.756988e-02 -#> k_anisole 6.678742e-03 0.0008021439 8.326114 2.623176e-07 -#> f_T245_to_phenol 6.227599e-01 0.3985340295 1.562627 6.949412e-02 -#> f_phenol_to_anisole 1.000000e+00 0.6718439378 1.488441 7.867787e-02 -#> sigma 2.514628e+00 0.4907558750 5.123989 6.233156e-05 +#> 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 #> Lower Upper -#> T245_0 99.246061370 1.084640e+02 +#> T245_0 99.246061385 1.084640e+02 #> k_T245 0.039631621 4.746194e-02 -#> k_phenol 0.218013878 7.525762e-01 +#> k_phenol 0.218013879 7.525762e-01 #> k_anisole 0.005370739 8.305299e-03 -#> f_T245_to_phenol 0.547559083 6.924813e-01 +#> f_T245_to_phenol 0.547559081 6.924813e-01 #> f_phenol_to_anisole 0.000000000 1.000000e+00 #> sigma 1.706607296 3.322649e+00
endpoints(fit.1)
#> $ff #> T245_phenol T245_sink phenol_anisole phenol_sink -#> 6.227599e-01 3.772401e-01 1.000000e+00 6.894640e-11 +#> 6.227599e-01 3.772401e-01 1.000000e+00 3.773626e-10 #> #> $distimes #> DT50 DT90 #> T245 15.982025 53.09114 #> phenol 1.711229 5.68458 -#> anisole 103.784092 344.76329 +#> anisole 103.784093 344.76329 #>
# formation fraction from phenol to anisol is practically 1. As we cannot # fix formation fractions when using the ilr transformation, we can turn of # the sink in the model generation @@ -215,28 +215,28 @@ quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(fit.2)$bpar
#> Estimate se_notrans t value Pr(>t) Lower -#> T245_0 1.038550e+02 2.1623653027 48.028439 4.993108e-19 99.271020526 -#> k_T245 4.337042e-02 0.0018343666 23.643268 3.573555e-14 0.039650977 -#> k_phenol 4.050582e-01 0.1177237248 3.440752 1.679252e-03 0.218746585 -#> k_anisole 6.678741e-03 0.0006829745 9.778903 1.872894e-08 0.005377083 -#> f_T245_to_phenol 6.227599e-01 0.0342197865 18.198825 2.039410e-12 0.547975628 +#> 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 #> sigma 2.514628e+00 0.3790944250 6.633250 2.875782e-06 1.710983655 #> Upper -#> T245_0 108.43904097 +#> T245_0 108.43904074 #> k_T245 0.04743877 -#> k_phenol 0.75005577 +#> k_phenol 0.75005585 #> k_anisole 0.00829550 -#> f_T245_to_phenol 0.69212306 +#> f_T245_to_phenol 0.69212308 #> sigma 3.31827222
endpoints(fit.1)
#> $ff #> T245_phenol T245_sink phenol_anisole phenol_sink -#> 6.227599e-01 3.772401e-01 1.000000e+00 6.894640e-11 +#> 6.227599e-01 3.772401e-01 1.000000e+00 3.773626e-10 #> #> $distimes #> DT50 DT90 #> T245 15.982025 53.09114 #> phenol 1.711229 5.68458 -#> anisole 103.784092 344.76329 +#> anisole 103.784093 344.76329 #>
plot_sep(fit.2)
# }
diff --git a/docs/reference/mixed-1.png b/docs/reference/mixed-1.png index 05beffc9..28a376f4 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 f5429f8b..23d955e3 100644 --- a/docs/reference/mixed.html +++ b/docs/reference/mixed.html @@ -72,7 +72,7 @@ mkin - 1.0.0 + 1.0.3 @@ -235,18 +235,16 @@ #> Status of individual fits: #> #> dataset -#> model 1 2 3 4 5 6 7 8 -#> DFOP-SFO OK OK OK OK OK C OK OK +#> model 1 2 3 4 5 6 7 8 +#> DFOP-SFO OK OK OK OK OK OK OK OK #> #> OK: No warnings -#> C: Optimisation did not converge: -#> iteration limit reached without convergence (10) #> #> Mean fitted parameters: #> parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 -#> 100.606304 -8.759216 -0.002001 -3.350539 -3.989549 +#> 100.674757 -8.761916 -0.004347 -3.348812 -3.986853 #> g_qlogis -#> -0.090353
plot(f_mixed) +#> -0.087392
plot(f_mixed)
# }
diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index 7eca35de..c82da5dd 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -74,7 +74,7 @@ variable and several dependent variables as columns." /> mkin - 1.0.0 + 1.0.3 diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 5df8972f..15619fba 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -74,7 +74,7 @@ mkinfit." /> mkin - 1.0.0 + 1.0.3 diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index 543ea68d..5111a9e0 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 - 1.0.0 + 1.0.3 diff --git a/docs/reference/mkindsg.html b/docs/reference/mkindsg.html index 74d3a26c..003e5e8f 100644 --- a/docs/reference/mkindsg.html +++ b/docs/reference/mkindsg.html @@ -75,7 +75,7 @@ dataset if no data are supplied." /> mkin - 1.0.0 + 1.0.3 diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 161eadca..f22b4350 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -73,7 +73,7 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006." /> mkin - 1.0.0 + 1.0.3 diff --git a/docs/reference/mkinerrplot.html b/docs/reference/mkinerrplot.html index 2509e4c1..361ce79a 100644 --- a/docs/reference/mkinerrplot.html +++ b/docs/reference/mkinerrplot.html @@ -76,7 +76,7 @@ using the argument show_errplot = TRUE." /> mkin - 1.0.0 + 1.0.3 diff --git a/docs/reference/mkinfit-1.png b/docs/reference/mkinfit-1.png index bbc0ccb6..de2a90a9 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 4d8aeb40..180f2ee7 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -80,7 +80,7 @@ likelihood function." /> mkin - 1.0.0 + 1.0.3 @@ -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: 1.0.0 +
#> mkin version used for fitting: 1.0.3 #> R version used for fitting: 4.0.3 -#> Date of fit: Wed Feb 3 17:28:58 2021 -#> Date of summary: Wed Feb 3 17:28:58 2021 +#> Date of fit: Mon Feb 15 13:43:26 2021 +#> Date of summary: Mon Feb 15 13:43:26 2021 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -476,10 +476,10 @@ doi: 10.3390/environments6 #> #> Parameter correlation: #> parent_0 log_alpha log_beta sigma -#> parent_0 1.000e+00 -1.565e-01 -3.142e-01 4.758e-08 -#> log_alpha -1.565e-01 1.000e+00 9.564e-01 1.007e-07 -#> log_beta -3.142e-01 9.564e-01 1.000e+00 8.568e-08 -#> sigma 4.758e-08 1.007e-07 8.568e-08 1.000e+00 +#> 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 #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. @@ -548,7 +548,7 @@ doi: 10.3390/environments6 #> --- #> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
parms(fit.tc)
#> parent_0 k_parent k_m1 f_parent_to_m1 sigma_low -#> 1.007343e+02 1.005562e-01 5.166712e-03 5.083933e-01 3.049884e-03 +#> 1.007343e+02 1.005562e-01 5.166712e-03 5.083933e-01 3.049883e-03 #> rsd_high #> 7.928118e-02
endpoints(fit.tc)
#> $ff @@ -575,9 +575,9 @@ doi: 10.3390/environments6 solution_type = "analytical")) }
#> test relative elapsed -#> 3 analytical 1.000 0.542 -#> 1 deSolve_compiled 1.812 0.982 -#> 2 eigen 2.234 1.211
# } +#> 3 analytical 1.000 0.550 +#> 1 deSolve_compiled 1.731 0.952 +#> 2 eigen 2.662 1.464
# } # Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO # \dontrun{ @@ -587,22 +587,21 @@ doi: 10.3390/environments6
#> Temporary DLL for differentials generated and loaded
fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_D, quiet = TRUE) # Again, we get a warning and try a more sophisticated error model fit.FOMC_SFO.tc <- mkinfit(FOMC_SFO, FOCUS_D, quiet = TRUE, error_model = "tc") -
#> Warning: Optimisation did not converge: -#> iteration limit reached without convergence (10)
# This model has a higher likelihood, but not significantly so +# This model has a higher likelihood, but not significantly so lrtest(fit.tc, fit.FOMC_SFO.tc)
#> Likelihood ratio test #> #> Model 1: FOMC_SFO with error model tc and fixed parameter(s) m1_0 #> Model 2: SFO_SFO with error model tc and fixed parameter(s) m1_0 #> #Df LogLik Df Chisq Pr(>Chisq) -#> 1 7 -64.870 -#> 2 6 -64.983 -1 0.2259 0.6346
# Also, the missing standard error for log_beta and the t-tests for alpha +#> 1 7 -64.829 +#> 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: NaNs produced
#> Warning: diag(.) had 0 or NA entries; non-finite result is doubtful
#> mkin version used for fitting: 1.0.0 +
#> 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: Wed Feb 3 17:29:09 2021 -#> Date of summary: Wed Feb 3 17:29:09 2021 +#> Date of fit: Mon Feb 15 13:43:38 2021 +#> Date of summary: Mon Feb 15 13:43:38 2021 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -611,12 +610,12 @@ doi: 10.3390/environments6 #> #> Model predictions using solution type deSolve #> -#> Fitted using 4273 model solutions performed in 3.195 s +#> Fitted using 3729 model solutions performed in 2.802 s #> #> Error model: Two-component variance function #> #> Error model algorithm: d_3 -#> Three-step fitting yielded a higher likelihood than direct fitting +#> Direct fitting and three-step fitting yield approximately the same likelihood #> #> Starting values for parameters to be optimised: #> value type @@ -642,72 +641,67 @@ doi: 10.3390/environments6 #> value type #> m1_0 0 state #> -#> -#> Warning(s): -#> Optimisation did not converge: -#> iteration limit reached without convergence (10) -#> #> Results: #> -#> AIC BIC logLik -#> 143.7396 155.2027 -64.86982 +#> AIC BIC logLik +#> 143.658 155.1211 -64.82902 #> #> Optimised, transformed parameters with symmetric confidence intervals: -#> Estimate Std. Error Lower Upper -#> parent_0 1.016e+02 1.90600 97.7400 105.5000 -#> log_k_m1 -5.285e+00 0.09286 -5.4740 -5.0950 -#> f_parent_qlogis 6.482e-04 0.06164 -0.1251 0.1264 -#> log_alpha 5.467e+00 NaN NaN NaN -#> log_beta 7.750e+00 NaN NaN NaN -#> sigma_low 0.000e+00 NaN NaN NaN -#> rsd_high 7.989e-02 NaN NaN NaN +#> 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 +#> 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 +#> rsd_high 0.079210 0.0093280 0.060180 0.098230 #> #> Parameter correlation: -#> parent_0 log_k_m1 f_parent_qlogis log_alpha log_beta -#> parent_0 1.0000000 -0.0002167 -0.6060 NaN NaN -#> log_k_m1 -0.0002167 1.0000000 0.5474 NaN NaN -#> f_parent_qlogis -0.6060320 0.5474423 1.0000 NaN NaN -#> log_alpha NaN NaN NaN 1 NaN -#> log_beta NaN NaN NaN NaN 1 -#> sigma_low NaN NaN NaN NaN NaN -#> rsd_high NaN NaN NaN NaN NaN -#> sigma_low rsd_high -#> parent_0 NaN NaN -#> log_k_m1 NaN NaN -#> f_parent_qlogis NaN NaN -#> log_alpha NaN NaN -#> log_beta NaN NaN -#> sigma_low 1 NaN -#> rsd_high NaN 1 +#> 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 +#> 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 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 +#> log_beta NaN NaN +#> sigma_low 1.000000 -0.652558 +#> rsd_high -0.652558 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 32.5400 7.812e-26 97.740000 1.055e+02 -#> k_m1 5.069e-03 10.0400 1.448e-11 0.004194 6.126e-03 -#> f_parent_to_m1 5.002e-01 20.7300 5.001e-20 0.468800 5.315e-01 -#> alpha 2.367e+02 0.6205 2.697e-01 NA NA -#> beta 2.322e+03 0.6114 2.727e-01 NA NA -#> sigma_low 0.000e+00 NaN NaN NaN NaN -#> rsd_high 7.989e-02 8.6630 4.393e-10 NaN NaN +#> parent_0 1.016e+02 32.7800 6.311e-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 +#> 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 #> #> FOCUS Chi2 error levels in percent: #> err.min n.optim df -#> All data 6.782 5 14 -#> parent 7.142 3 6 -#> m1 4.639 2 8 +#> All data 6.781 5 14 +#> parent 7.141 3 6 +#> m1 4.640 2 8 #> #> Resulting formation fractions: #> ff -#> parent_m1 0.5002 -#> parent_sink 0.4998 +#> parent_m1 0.5004 +#> parent_sink 0.4996 #> #> Estimated disappearance times: -#> DT50 DT90 DT50back -#> parent 6.81 22.7 6.833 -#> m1 136.74 454.2 NA
+#> DT50 DT90 DT50back +#> parent 6.812 22.7 6.834 +#> m1 136.661 454.0 NA
# We can easily use starting parameters from the parent only fit (only for illustration) fit.FOMC = mkinfit("FOMC", FOCUS_2006_D, quiet = TRUE, error_model = "tc") fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_D, quiet = TRUE, diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 43e5cc23..4ce9468a 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -78,7 +78,7 @@ mkinmod." /> mkin - 1.0.0 + 1.0.3
@@ -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/Rtmp1BYo7R/file5c60502538f0.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/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 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: 0x55555caa9ee0>
+#> <environment: 0x55555b0c2760>
# 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/mkinparplot-1.png b/docs/reference/mkinparplot-1.png index dcf3e4b5..c9ed49eb 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 b4d11dcb..c298f5d2 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -73,7 +73,7 @@ mkinfit." /> mkin - 1.0.0 + 1.0.3
@@ -176,7 +176,8 @@ effect, namely to produce a plot.

phenol = mkinsub("SFO", to = c("anisole")), 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) +
#> Warning: Observations with value of zero were removed from the data
#> Warning: Optimisation did not converge: +#> false convergence (8)
mkinparplot(fit)
# }
diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 1f0be544..b20a8c96 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -73,7 +73,7 @@ plot.mkinfit." /> mkin - 1.0.0 + 1.0.3 diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 035a21f9..25e26419 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 - 1.0.0 + 1.0.3 @@ -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 4.0 0.020 -#> 3 deSolve 44.6 0.223
+#> 1 eigen 4.4 0.022 +#> 3 deSolve 47.0 0.235
# \dontrun{ # Predict from a fitted model f <- mkinfit(SFO_SFO, FOCUS_2006_C, quiet = TRUE) diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index 69517f36..04ff15b8 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -75,7 +75,7 @@ argument show_residuals = TRUE." /> mkin - 1.0.0 + 1.0.3
diff --git a/docs/reference/mmkin-1.png b/docs/reference/mmkin-1.png index cce02aed..0db3379f 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 4f2529fa..024a9892 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 fb5d4470..a23d7cb9 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 4f11753e..89975db5 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 5d653de9..a2f34983 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 77f815da..c9800fe7 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -75,7 +75,7 @@ datasets specified in its first two arguments." /> mkin - 1.0.0 + 1.0.3 @@ -234,19 +234,19 @@ plotting.

time_default
#> user system elapsed -#> 4.634 0.317 1.280
time_1 +#> 4.630 0.415 1.717
time_1
#> user system elapsed -#> 5.249 0.016 5.267
+#> 5.694 0.000 5.694
endpoints(fits.0[["SFO_lin", 2]])
#> $ff #> parent_M1 parent_sink M1_M2 M1_sink -#> 0.7340478 0.2659522 0.7505687 0.2494313 +#> 0.7340481 0.2659519 0.7505683 0.2494317 #> #> $distimes #> DT50 DT90 #> parent 0.877769 2.915885 -#> M1 2.325746 7.725960 -#> M2 33.720083 112.015691 +#> M1 2.325744 7.725956 +#> M2 33.720100 112.015749 #>
# plot.mkinfit handles rows or columns of mmkin result objects plot(fits.0[1, ]) @@ -273,12 +273,10 @@ plotting.

#> dataset #> model A B C D #> SFO OK OK OK OK -#> FOMC C OK OK OK +#> FOMC OK OK OK OK #> DFOP OK OK OK OK #> -#> OK: No warnings -#> C: Optimisation did not converge: -#> false convergence (8)
# We get false convergence for the FOMC fit to FOCUS_2006_A because this +#> OK: No warnings
# We get false convergence for the FOMC fit to FOCUS_2006_A because this # dataset is really SFO, and the FOMC fit is overparameterised stopCluster(cl) # } diff --git a/docs/reference/nafta-1.png b/docs/reference/nafta-1.png index 76d724f0..4f0d7833 100644 Binary files a/docs/reference/nafta-1.png and b/docs/reference/nafta-1.png differ diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html index c6c1b173..29e03251 100644 --- a/docs/reference/nafta.html +++ b/docs/reference/nafta.html @@ -76,7 +76,7 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP." /> mkin - 1.0.0 + 1.0.3
diff --git a/docs/reference/nlme-1.png b/docs/reference/nlme-1.png index 82b952f7..728cc557 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 6bc121d1..e8167455 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 f9e68b7f..7b0c6a97 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 - 1.0.0 + 1.0.3 diff --git a/docs/reference/nlme.mmkin-1.png b/docs/reference/nlme.mmkin-1.png index 546a3731..9186c135 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 7b5b4ab0..d395fe02 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 7c04df4b..40518a59 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 2e4f6337..189e34ef 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 - 1.0.0 + 1.0.3 @@ -157,7 +157,7 @@ have been obtained by fitting the same model to a list of datasets.

data = "auto", fixed = lapply(as.list(names(mean_degparms(model))), function(el) eval(parse(text = paste(el, 1, sep = "~")))), - random = pdDiag(fixed), + random = pdDiag(fixed), groups, start = mean_degparms(model, random = TRUE), correlation = NULL, @@ -290,7 +290,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as anova(f_nlme_sfo, f_nlme_dfop)
#> Model df AIC BIC logLik Test L.Ratio p-value #> f_nlme_sfo 1 5 625.0539 637.5529 -307.5269 -#> f_nlme_dfop 2 9 495.1270 517.6253 -238.5635 1 vs 2 137.9268 <.0001
print(f_nlme_dfop) +#> f_nlme_dfop 2 9 495.1270 517.6253 -238.5635 1 vs 2 137.9269 <.0001
print(f_nlme_dfop)
#> Kinetic nonlinear mixed-effects model fit by maximum likelihood #> #> Structural model: @@ -318,7 +318,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
endpoints(f_nlme_dfop)
#> $distimes #> DT50 DT90 DT50back DT50_k1 DT50_k2 -#> parent 10.79857 100.7937 30.34192 4.193937 43.85442 +#> parent 10.79857 100.7937 30.34193 4.193938 43.85443 #>
ds_2 <- lapply(experimental_data_for_UBA_2019[6:10], function(x) x$data[c("name", "time", "value")]) @@ -350,8 +350,8 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
anova(f_nlme_dfop_sfo, f_nlme_sfo_sfo)
#> Model df AIC BIC logLik Test L.Ratio p-value -#> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9274 -#> f_nlme_sfo_sfo 2 9 1085.1821 1113.4043 -533.5910 1 vs 2 249.3274 <.0001
+#> f_nlme_dfop_sfo 1 13 843.8548 884.6201 -408.9274 +#> f_nlme_sfo_sfo 2 9 1085.1821 1113.4043 -533.5910 1 vs 2 249.3273 <.0001
endpoints(f_nlme_sfo_sfo)
#> $ff #> parent_sink parent_A1 A1_sink @@ -364,12 +364,12 @@ methods that will automatically work on 'nlme.mmkin' objects, such as #>
endpoints(f_nlme_dfop_sfo)
#> $ff #> parent_A1 parent_sink -#> 0.2768574 0.7231426 +#> 0.2768575 0.7231425 #> #> $distimes #> DT50 DT90 DT50back DT50_k1 DT50_k2 -#> parent 11.07091 104.6320 31.49738 4.462384 46.20825 -#> A1 162.30523 539.1663 NA NA NA +#> parent 11.07091 104.6320 31.49737 4.462384 46.20825 +#> A1 162.30492 539.1653 NA NA NA #>
if (length(findFunction("varConstProp")) > 0) { # tc error model for nlme available # Attempts to fit metabolite kinetics with the tc error model are possible, @@ -396,7 +396,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as #> Fixed effects: #> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) #> parent_0 log_k1 log_k2 g_qlogis -#> 94.04775 -1.82340 -4.16715 0.05685 +#> 94.04774 -1.82340 -4.16716 0.05686 #> #> Random effects: #> Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) @@ -410,7 +410,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as #> Formula: ~fitted(.) #> Parameter estimates: #> const prop -#> 2.23224114 0.01262341
+#> 2.23223147 0.01262395
f_2_obs <- update(f_2, error_model = "obs") f_nlme_sfo_sfo_obs <- nlme(f_2_obs["SFO-SFO", ]) print(f_nlme_sfo_sfo_obs) @@ -442,7 +442,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as #> Formula: ~1 | name #> Parameter estimates: #> parent A1 -#> 1.0000000 0.2050003
f_nlme_dfop_sfo_obs <- nlme(f_2_obs["DFOP-SFO", ], +#> 1.0000000 0.2049995
f_nlme_dfop_sfo_obs <- nlme(f_2_obs["DFOP-SFO", ], control = list(pnlsMaxIter = 120, tolerance = 5e-4)) f_2_tc <- update(f_2, error_model = "tc") @@ -452,8 +452,8 @@ methods that will automatically work on 'nlme.mmkin' objects, such as anova(f_nlme_dfop_sfo, f_nlme_dfop_sfo_obs)
#> Model df AIC BIC logLik Test L.Ratio -#> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9274 -#> f_nlme_dfop_sfo_obs 2 14 817.5338 861.4350 -394.7669 1 vs 2 28.32089 +#> f_nlme_dfop_sfo 1 13 843.8548 884.6201 -408.9274 +#> f_nlme_dfop_sfo_obs 2 14 817.5338 861.4350 -394.7669 1 vs 2 28.32093 #> p-value #> f_nlme_dfop_sfo #> f_nlme_dfop_sfo_obs <.0001
diff --git a/docs/reference/nobs.mkinfit.html b/docs/reference/nobs.mkinfit.html index dff8a285..6b9948c3 100644 --- a/docs/reference/nobs.mkinfit.html +++ b/docs/reference/nobs.mkinfit.html @@ -72,7 +72,7 @@ mkin - 1.0.0 + 1.0.3
diff --git a/docs/reference/parms.html b/docs/reference/parms.html index ab5888fa..e45d6a5c 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 - 1.0.0 + 1.0.3 @@ -219,10 +219,10 @@ such matrices is returned.

#> #> $DFOP #> Dataset 7 -#> parent_0 91.058971597 +#> parent_0 91.058971589 #> k1 0.044946770 #> k2 0.002868336 -#> g 0.526942414 +#> g 0.526942415 #> sigma 2.221302196 #>
parms(fits)
#> $SFO @@ -233,17 +233,17 @@ such matrices is returned.

#> #> $FOMC #> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 -#> parent_0 95.558575 92.6837649 90.719787 98.383939 94.8481458 +#> parent_0 95.558575 92.6837649 90.719787 98.383939 94.8481459 #> alpha 1.338667 0.4967832 1.639099 1.074460 0.2805272 #> beta 13.033315 14.1451255 5.007077 4.397126 6.9052224 #> sigma 1.847671 1.9167519 1.066063 3.146056 1.6222778 #> #> $DFOP #> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 -#> parent_0 96.55213663 91.058971597 90.34509493 98.14858820 94.311323733 +#> parent_0 96.55213663 91.058971589 90.34509493 98.14858820 94.311323734 #> k1 0.21954588 0.044946770 0.41232288 0.31697588 0.080663857 #> k2 0.02957934 0.002868336 0.07581766 0.03260384 0.003425417 -#> g 0.44845068 0.526942414 0.66091967 0.65322767 0.342652880 +#> g 0.44845068 0.526942415 0.66091967 0.65322767 0.342652880 #> sigma 1.35690468 2.221302196 1.34169076 2.87159846 1.942067831 #>
parms(fits, transformed = TRUE)
#> $SFO diff --git a/docs/reference/plot.mixed.mmkin.html b/docs/reference/plot.mixed.mmkin.html index 46303c44..4b72a308 100644 --- a/docs/reference/plot.mixed.mmkin.html +++ b/docs/reference/plot.mixed.mmkin.html @@ -72,7 +72,7 @@ mkin - 1.0.2 + 1.0.3
diff --git a/docs/reference/plot.mkinfit-2.png b/docs/reference/plot.mkinfit-2.png index 376c812f..a11d1680 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-5.png b/docs/reference/plot.mkinfit-5.png index bc44de88..6631aa68 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 eb8cbd92..946b20c5 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 92a664f4..10807ea8 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 1be0f9af..b80c672d 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 - 1.0.0 + 1.0.3 diff --git a/docs/reference/plot.mmkin-1.png b/docs/reference/plot.mmkin-1.png index f12b7907..647dfb8a 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 e3127554..1bc1c9db 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 5448976e..50d6ffac 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 9a25fc50..e049fa16 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 82b422b5..2421995b 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 4e9836ec..20f9033d 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 - 1.0.0 + 1.0.3 diff --git a/docs/reference/plot.nafta.html b/docs/reference/plot.nafta.html index 29cc984a..544ee5eb 100644 --- a/docs/reference/plot.nafta.html +++ b/docs/reference/plot.nafta.html @@ -73,7 +73,7 @@ function (SFO, then IORE, then DFOP)." /> mkin - 1.0.0 + 1.0.3 diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html index 2bfeb582..864c4ff9 100644 --- a/docs/reference/reexports.html +++ b/docs/reference/reexports.html @@ -79,7 +79,7 @@ below to see their documentation. mkin - 1.0.0 + 1.0.3 diff --git a/docs/reference/residuals.mkinfit.html b/docs/reference/residuals.mkinfit.html index db7c1a40..c5c2dcaf 100644 --- a/docs/reference/residuals.mkinfit.html +++ b/docs/reference/residuals.mkinfit.html @@ -72,7 +72,7 @@ mkin - 1.0.0 + 1.0.3 @@ -175,7 +175,7 @@ standard deviation obtained from the fitted error model?

#> [1] 0.09726374 -0.13912142 -0.15351210 0.73388322 -0.08657004 -0.93204702 #> [7] -0.03269080 1.45347823 -0.88423697
residuals(f, standardized = TRUE)
#> [1] 0.13969917 -0.19981904 -0.22048826 1.05407091 -0.12433989 -1.33869208 -#> [7] -0.04695354 2.08761977 -1.27002287
+#> [7] -0.04695355 2.08761977 -1.27002287 @@ -186,15 +186,15 @@
endpoints(fit)
#> $ff #> parent_A1 parent_B1 parent_C1 parent_sink A1_A2 A1_sink -#> 0.3809620 0.1954665 0.4235715 0.0000000 0.4479662 0.5520338 +#> 0.3809620 0.1954667 0.4235713 0.0000000 0.4479619 0.5520381 #> #> $distimes #> DT50 DT90 #> parent 13.95078 46.34350 -#> A1 49.75343 165.27731 -#> B1 37.26912 123.80533 -#> C1 11.23131 37.30959 -#> A2 28.50569 94.69386 +#> A1 49.75342 165.27728 +#> B1 37.26908 123.80520 +#> C1 11.23131 37.30961 +#> A2 28.50624 94.69567 #>
# } # Compare with the results obtained in the original publication print(schaefer07_complex_results) diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html index 46ca562a..397582f0 100644 --- a/docs/reference/sigma_twocomp.html +++ b/docs/reference/sigma_twocomp.html @@ -73,7 +73,7 @@ dependence of the measured value \(y\):" /> mkin - 1.0.0 + 1.0.3
@@ -188,6 +188,10 @@ Additive, Multiplicative, and Mixed Analytical Errors. Clinical Chemistry 24(11), 1895-1898.

Rocke, David M. and Lorenzato, Stefan (1995) A two-component model 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 +.

Examples

times <- c(0, 1, 3, 7, 14, 28, 60, 90, 120)
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 7be427bf..67a50216 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -76,7 +76,7 @@ values." />
       
       
         mkin
-        1.0.0
+        1.0.3
       
     

 
@@ -236,17 +236,17 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
     
Examples

     

   summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
-
#> mkin version used for fitting:    1.0.0 
+
#> mkin version used for fitting:    1.0.3 
 #> R version used for fitting:       4.0.3 
-#> Date of fit:     Wed Feb  3 17:32:02 2021 
-#> Date of summary: Wed Feb  3 17:32:02 2021 
+#> Date of fit:     Mon Feb 15 13:46:11 2021 
+#> Date of summary: Mon Feb 15 13:46:11 2021 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 131 model solutions performed in 0.028 s
+#> Fitted using 131 model solutions performed in 0.029 s
 #> 
 #> Error model: Constant variance 
 #> 
diff --git a/docs/reference/summary.nlme.mmkin.html b/docs/reference/summary.nlme.mmkin.html
index bc60b53e..d6840425 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
-        1.0.0
+        1.0.3
       
     

 
@@ -264,11 +264,11 @@ José Pinheiro and Douglas Bates for the components inherited from nlme

 
#> Warning: Optimisation did not converge:
 #> 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:      3.1.151 
-#> mkin version used for pre-fitting:  1.0.0 
+
#> 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:     Wed Feb  3 17:32:05 2021 
-#> Date of summary: Wed Feb  3 17:32:05 2021 
+#> Date of fit:     Mon Feb 15 13:46:13 2021 
+#> Date of summary: Mon Feb 15 13:46:13 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 0.526 s using 4 iterations
+#> Fitted in 0.553 s using 4 iterations
 #> 
 #> Variance model: Two-component variance function 
 #> 
@@ -307,19 +307,19 @@ José Pinheiro and Douglas Bates for the components inherited from nlme

 #>  Formula: list(parent_0 ~ 1, log_k_parent ~ 1)
 #>  Level: ds
 #>  Structure: Diagonal
-#>         parent_0 log_k_parent Residual
-#> StdDev: 6.91e-05       0.5863        1
+#>          parent_0 log_k_parent Residual
+#> StdDev: 6.924e-05       0.5863        1
 #> 
 #> Variance function:
 #>  Structure: Constant plus proportion of variance covariate
 #>  Formula: ~fitted(.) 
 #>  Parameter estimates:
 #>        const         prop 
-#> 0.0001206605 0.0789967776 
+#> 0.0001208853 0.0789968036 
 #> 
 #> Backtransformed parameters with asymmetric confidence intervals:
 #>              lower      est.     upper
-#> parent_0 99.370883 101.59243 103.81398
+#> parent_0 99.370882 101.59243 103.81398
 #> k_parent  0.006923   0.01168   0.01972
 #> 
 #> Estimated disappearance times:
@@ -330,68 +330,68 @@ José Pinheiro and Douglas Bates for the components inherited from nlme

 #>    ds   name time observed predicted  residual    std standardized
 #>  ds 1 parent    0    104.1   101.592   2.50757 8.0255     0.312451
 #>  ds 1 parent    0    105.0   101.592   3.40757 8.0255     0.424594
-#>  ds 1 parent    1     98.5   100.796  -2.29571 7.9625    -0.288314
+#>  ds 1 parent    1     98.5   100.796  -2.29571 7.9625    -0.288313
 #>  ds 1 parent    1     96.1   100.796  -4.69571 7.9625    -0.589725
 #>  ds 1 parent    3    101.9    99.221   2.67904 7.8381     0.341796
-#>  ds 1 parent    3     85.2    99.221 -14.02096 7.8381    -1.788813
+#>  ds 1 parent    3     85.2    99.221 -14.02096 7.8381    -1.788812
 #>  ds 1 parent    7     99.1    96.145   2.95512 7.5951     0.389081
 #>  ds 1 parent    7     93.0    96.145  -3.14488 7.5951    -0.414065
-#>  ds 1 parent   14     88.1    90.989  -2.88944 7.1879    -0.401988
+#>  ds 1 parent   14     88.1    90.989  -2.88944 7.1879    -0.401987
 #>  ds 1 parent   14     84.1    90.989  -6.88944 7.1879    -0.958480
 #>  ds 1 parent   28     80.2    81.493  -1.29305 6.4377    -0.200857
-#>  ds 1 parent   28     91.3    81.493   9.80695 6.4377     1.523365
+#>  ds 1 parent   28     91.3    81.493   9.80695 6.4377     1.523364
 #>  ds 1 parent   60     65.1    63.344   1.75642 5.0039     0.351008
 #>  ds 1 parent   60     65.8    63.344   2.45642 5.0039     0.490898
-#>  ds 1 parent   90     47.8    50.018  -2.21764 3.9512    -0.561253
+#>  ds 1 parent   90     47.8    50.018  -2.21764 3.9512    -0.561252
 #>  ds 1 parent   90     53.5    50.018   3.48236 3.9512     0.881335
 #>  ds 1 parent  120     37.6    39.495  -1.89515 3.1200    -0.607423
 #>  ds 1 parent  120     39.3    39.495  -0.19515 3.1200    -0.062549
-#>  ds 2 parent    0    107.9   101.592   6.30757 8.0255     0.785944
+#>  ds 2 parent    0    107.9   101.592   6.30757 8.0255     0.785943
 #>  ds 2 parent    0    102.1   101.592   0.50757 8.0255     0.063245
-#>  ds 2 parent    1    103.8   100.058   3.74159 7.9043     0.473362
-#>  ds 2 parent    1    108.6   100.058   8.54159 7.9043     1.080627
+#>  ds 2 parent    1    103.8   100.058   3.74159 7.9043     0.473361
+#>  ds 2 parent    1    108.6   100.058   8.54159 7.9043     1.080626
 #>  ds 2 parent    3     91.0    97.060  -6.05952 7.6674    -0.790297
 #>  ds 2 parent    3     84.9    97.060 -12.15952 7.6674    -1.585874
-#>  ds 2 parent    7     79.3    91.329 -12.02867 7.2147    -1.667252
-#>  ds 2 parent    7    100.9    91.329   9.57133 7.2147     1.326648
+#>  ds 2 parent    7     79.3    91.329 -12.02867 7.2147    -1.667251
+#>  ds 2 parent    7    100.9    91.329   9.57133 7.2147     1.326647
 #>  ds 2 parent   14     77.3    82.102  -4.80185 6.4858    -0.740366
 #>  ds 2 parent   14     83.5    82.102   1.39815 6.4858     0.215571
 #>  ds 2 parent   28     66.8    66.351   0.44945 5.2415     0.085748
 #>  ds 2 parent   28     63.3    66.351  -3.05055 5.2415    -0.582002
 #>  ds 2 parent   60     40.8    40.775   0.02474 3.2211     0.007679
-#>  ds 2 parent   60     44.8    40.775   4.02474 3.2211     1.249486
+#>  ds 2 parent   60     44.8    40.775   4.02474 3.2211     1.249485
 #>  ds 2 parent   90     27.8    25.832   1.96762 2.0407     0.964198
 #>  ds 2 parent   90     27.0    25.832   1.16762 2.0407     0.572171
-#>  ds 2 parent  120     15.2    16.366  -1.16561 1.2928    -0.901596
+#>  ds 2 parent  120     15.2    16.366  -1.16561 1.2928    -0.901595
 #>  ds 2 parent  120     15.5    16.366  -0.86561 1.2928    -0.669547
 #>  ds 3 parent    0     97.7   101.592  -3.89243 8.0255    -0.485009
-#>  ds 3 parent    0     88.2   101.592 -13.39243 8.0255    -1.668740
-#>  ds 3 parent    1    109.9    99.218  10.68196 7.8379     1.362859
+#>  ds 3 parent    0     88.2   101.592 -13.39243 8.0255    -1.668739
+#>  ds 3 parent    1    109.9    99.218  10.68196 7.8379     1.362858
 #>  ds 3 parent    1     97.8    99.218  -1.41804 7.8379    -0.180921
 #>  ds 3 parent    3    100.5    94.634   5.86555 7.4758     0.784603
 #>  ds 3 parent    3     77.4    94.634 -17.23445 7.4758    -2.305360
-#>  ds 3 parent    7     78.3    86.093  -7.79273 6.8010    -1.145813
-#>  ds 3 parent    7     90.3    86.093   4.20727 6.8010     0.618621
-#>  ds 3 parent   14     76.0    72.958   3.04222 5.7634     0.527849
-#>  ds 3 parent   14     79.1    72.958   6.14222 5.7634     1.065723
+#>  ds 3 parent    7     78.3    86.093  -7.79273 6.8011    -1.145813
+#>  ds 3 parent    7     90.3    86.093   4.20727 6.8011     0.618620
+#>  ds 3 parent   14     76.0    72.958   3.04222 5.7634     0.527848
+#>  ds 3 parent   14     79.1    72.958   6.14222 5.7634     1.065722
 #>  ds 3 parent   28     46.0    52.394  -6.39404 4.1390    -1.544842
 #>  ds 3 parent   28     53.4    52.394   1.00596 4.1390     0.243046
 #>  ds 3 parent   60     25.1    24.582   0.51786 1.9419     0.266676
-#>  ds 3 parent   60     21.4    24.582  -3.18214 1.9419    -1.638665
-#>  ds 3 parent   90     11.0    12.092  -1.09202 0.9552    -1.143200
-#>  ds 3 parent   90     14.2    12.092   2.10798 0.9552     2.206777
+#>  ds 3 parent   60     21.4    24.582  -3.18214 1.9419    -1.638664
+#>  ds 3 parent   90     11.0    12.092  -1.09202 0.9552    -1.143199
+#>  ds 3 parent   90     14.2    12.092   2.10798 0.9552     2.206776
 #>  ds 3 parent  120      5.8     5.948  -0.14810 0.4699    -0.315178
 #>  ds 3 parent  120      6.1     5.948   0.15190 0.4699     0.323282
 #>  ds 4 parent    0     95.3   101.592  -6.29243 8.0255    -0.784057
-#>  ds 4 parent    0    102.0   101.592   0.40757 8.0255     0.050785
+#>  ds 4 parent    0    102.0   101.592   0.40757 8.0255     0.050784
 #>  ds 4 parent    1    104.4   101.125   3.27549 7.9885     0.410025
 #>  ds 4 parent    1    105.4   101.125   4.27549 7.9885     0.535205
 #>  ds 4 parent    3    113.7   100.195  13.50487 7.9151     1.706218
-#>  ds 4 parent    3     82.3   100.195 -17.89513 7.9151    -2.260887
+#>  ds 4 parent    3     82.3   100.195 -17.89513 7.9151    -2.260886
 #>  ds 4 parent    7     98.1    98.362  -0.26190 7.7703    -0.033706
 #>  ds 4 parent    7     87.8    98.362 -10.56190 7.7703    -1.359270
 #>  ds 4 parent   14     97.9    95.234   2.66590 7.5232     0.354357
-#>  ds 4 parent   14    104.8    95.234   9.56590 7.5232     1.271522
+#>  ds 4 parent   14    104.8    95.234   9.56590 7.5232     1.271521
 #>  ds 4 parent   28     85.0    89.274  -4.27372 7.0523    -0.606001
 #>  ds 4 parent   28     77.2    89.274 -12.07372 7.0523    -1.712017
 #>  ds 4 parent   60     82.2    77.013   5.18661 6.0838     0.852526
@@ -400,18 +400,18 @@ José Pinheiro and Douglas Bates for the components inherited from nlme

 #>  ds 4 parent   90     61.7    67.053  -5.35308 5.2970    -1.010591
 #>  ds 4 parent  120     60.0    58.381   1.61905 4.6119     0.351058
 #>  ds 4 parent  120     56.4    58.381  -1.98095 4.6119    -0.429530
-#>  ds 5 parent    0     92.6   101.592  -8.99243 8.0255    -1.120486
+#>  ds 5 parent    0     92.6   101.592  -8.99243 8.0255    -1.120485
 #>  ds 5 parent    0    116.5   101.592  14.90757 8.0255     1.857531
 #>  ds 5 parent    1    108.0    99.914   8.08560 7.8929     1.024413
-#>  ds 5 parent    1    104.9    99.914   4.98560 7.8929     0.631656
+#>  ds 5 parent    1    104.9    99.914   4.98560 7.8929     0.631655
 #>  ds 5 parent    3    100.5    96.641   3.85898 7.6343     0.505477
-#>  ds 5 parent    3     89.5    96.641  -7.14102 7.6343    -0.935383
+#>  ds 5 parent    3     89.5    96.641  -7.14102 7.6343    -0.935382
 #>  ds 5 parent    7     91.7    90.412   1.28752 7.1423     0.180267
-#>  ds 5 parent    7     95.1    90.412   4.68752 7.1423     0.656305
-#>  ds 5 parent   14     82.2    80.463   1.73715 6.3563     0.273296
+#>  ds 5 parent    7     95.1    90.412   4.68752 7.1423     0.656304
+#>  ds 5 parent   14     82.2    80.463   1.73715 6.3563     0.273295
 #>  ds 5 parent   14     84.5    80.463   4.03715 6.3563     0.635141
 #>  ds 5 parent   28     60.5    63.728  -3.22788 5.0343    -0.641178
-#>  ds 5 parent   28     72.8    63.728   9.07212 5.0343     1.802063
+#>  ds 5 parent   28     72.8    63.728   9.07212 5.0343     1.802062
 #>  ds 5 parent   60     38.3    37.399   0.90061 2.9544     0.304835
 #>  ds 5 parent   60     40.7    37.399   3.30061 2.9544     1.117174
 #>  ds 5 parent   90     22.5    22.692  -0.19165 1.7926    -0.106913
diff --git a/docs/reference/synthetic_data_for_UBA_2014-1.png b/docs/reference/synthetic_data_for_UBA_2014-1.png
index 4f11753e..89975db5 100644
Binary files a/docs/reference/synthetic_data_for_UBA_2014-1.png and b/docs/reference/synthetic_data_for_UBA_2014-1.png differ
diff --git a/docs/reference/synthetic_data_for_UBA_2014.html b/docs/reference/synthetic_data_for_UBA_2014.html
index af8bdcb2..c37b986e 100644
--- a/docs/reference/synthetic_data_for_UBA_2014.html
+++ b/docs/reference/synthetic_data_for_UBA_2014.html
@@ -87,7 +87,7 @@ Compare also the code in the example section to see the degradation models." />
       
       
         mkin
-        1.0.0
+        1.0.3
       
     

 
@@ -297,10 +297,10 @@ Compare also the code in the example section to see the degradation models." />
                  quiet = TRUE)
   plot_sep(fit)
 
  summary(fit)
-
#> mkin version used for fitting:    1.0.0 
+
#> mkin version used for fitting:    1.0.3 
 #> R version used for fitting:       4.0.3 
-#> Date of fit:     Wed Feb  3 17:32:06 2021 
-#> Date of summary: Wed Feb  3 17:32:06 2021 
+#> Date of fit:     Mon Feb 15 13:46:15 2021 
+#> Date of summary: Mon Feb 15 13:46:15 2021 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -309,7 +309,7 @@ Compare also the code in the example section to see the degradation models." />
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 822 model solutions performed in 0.645 s
+#> Fitted using 833 model solutions performed in 0.665 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -361,15 +361,15 @@ Compare also the code in the example section to see the degradation models." />
 #> log_k_M2         2.819e-02    7.166e-02 -3.929e-01  1.000e+00      -2.658e-01
 #> f_parent_qlogis -4.624e-01   -5.682e-01  7.478e-01 -2.658e-01       1.000e+00
 #> f_M1_qlogis      1.614e-01    4.102e-01 -8.109e-01  5.419e-01      -8.605e-01
-#> sigma           -7.941e-08   -9.143e-09 -1.268e-08  5.947e-08       5.657e-08
+#> sigma           -2.900e-08   -8.030e-09 -2.741e-08  3.938e-08      -2.681e-08
 #>                 f_M1_qlogis      sigma
-#> parent_0          1.614e-01 -7.941e-08
-#> log_k_parent      4.102e-01 -9.143e-09
-#> log_k_M1         -8.109e-01 -1.268e-08
-#> log_k_M2          5.419e-01  5.947e-08
-#> f_parent_qlogis  -8.605e-01  5.657e-08
-#> f_M1_qlogis       1.000e+00 -2.382e-10
-#> sigma            -2.382e-10  1.000e+00
+#> parent_0          1.614e-01 -2.900e-08
+#> log_k_parent      4.102e-01 -8.030e-09
+#> log_k_M1         -8.109e-01 -2.741e-08
+#> log_k_M2          5.419e-01  3.938e-08
+#> f_parent_qlogis  -8.605e-01 -2.681e-08
+#> f_M1_qlogis       1.000e+00  4.971e-08
+#> sigma             4.971e-08  1.000e+00
 #> 
 #> Backtransformed parameters:
 #> Confidence intervals for internally transformed parameters are asymmetric.
@@ -416,7 +416,7 @@ Compare also the code in the example section to see the degradation models." />
 #>     7   parent      0.3  5.772e-01 -0.27717
 #>    14   parent      3.5  3.264e-03  3.49674
 #>    28   parent      3.2  1.045e-07  3.20000
-#>    90   parent      0.6  9.532e-10  0.60000
+#>    90   parent      0.6  9.530e-10  0.60000
 #>   120   parent      3.5 -5.940e-10  3.50000
 #>     1       M1     36.4  3.479e+01  1.61088
 #>     1       M1     37.4  3.479e+01  2.61088
@@ -427,7 +427,7 @@ Compare also the code in the example section to see the degradation models." />
 #>    14       M1      5.8  1.995e+00  3.80469
 #>    14       M1      1.2  1.995e+00 -0.79531
 #>    60       M1      0.5  2.111e-06  0.50000
-#>    90       M1      3.2 -9.671e-10  3.20000
+#>    90       M1      3.2 -9.670e-10  3.20000
 #>   120       M1      1.5  7.670e-10  1.50000
 #>   120       M1      0.6  7.670e-10  0.60000
 #>     1       M2      4.8  4.455e+00  0.34517
diff --git a/docs/reference/test_data_from_UBA_2014-1.png b/docs/reference/test_data_from_UBA_2014-1.png
index 168103ee..7bf0bd0f 100644
Binary files a/docs/reference/test_data_from_UBA_2014-1.png and b/docs/reference/test_data_from_UBA_2014-1.png differ
diff --git a/docs/reference/test_data_from_UBA_2014-2.png b/docs/reference/test_data_from_UBA_2014-2.png
index 68288aed..fc1f77e0 100644
Binary files a/docs/reference/test_data_from_UBA_2014-2.png and b/docs/reference/test_data_from_UBA_2014-2.png differ
diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html
index eeaef9e0..c0056d45 100644
--- a/docs/reference/test_data_from_UBA_2014.html
+++ b/docs/reference/test_data_from_UBA_2014.html
@@ -73,7 +73,7 @@
       
       
         mkin
-        1.0.0
+        1.0.3
       
     

 
@@ -203,25 +203,25 @@
 
#> Warning: Observations with value of zero were removed from the data
  plot_sep(f_soil, lpos = c("topright", "topright", "topright", "bottomright"))
 
  summary(f_soil)$bpar
 
#>                   Estimate  se_notrans    t value       Pr(>t)        Lower
-#> parent_0       76.55425649 0.859186399 89.1008710 1.113861e-26 74.755959406
+#> parent_0       76.55425650 0.859186399 89.1008710 1.113861e-26 74.755959418
 #> k_parent        0.12081956 0.004601918 26.2541722 1.077359e-16  0.111561575
-#> k_M1            0.84258614 0.806159820  1.0451850 1.545267e-01  0.113779670
-#> k_M2            0.04210880 0.017083035  2.4649483 1.170188e-02  0.018013857
-#> k_M3            0.01122918 0.007245855  1.5497385 6.885052e-02  0.002909431
-#> f_parent_to_M1  0.32240200 0.240783909  1.3389682 9.819073e-02           NA
-#> f_parent_to_M2  0.16099855 0.033691953  4.7785463 6.531137e-05           NA
-#> f_M1_to_M3      0.27921507 0.269423745  1.0363417 1.565266e-01  0.022978220
-#> f_M2_to_M3      0.55641253 0.595119954  0.9349586 1.807707e-01  0.008002509
+#> k_M1            0.84258615 0.806160102  1.0451846 1.545268e-01  0.113779609
+#> k_M2            0.04210880 0.017083034  2.4649483 1.170188e-02  0.018013857
+#> k_M3            0.01122918 0.007245856  1.5497385 6.885052e-02  0.002909431
+#> f_parent_to_M1  0.32240200 0.240783943  1.3389680 9.819076e-02           NA
+#> f_parent_to_M2  0.16099855 0.033691952  4.7785464 6.531136e-05           NA
+#> f_M1_to_M3      0.27921507 0.269423780  1.0363416 1.565267e-01  0.022978205
+#> f_M2_to_M3      0.55641252 0.595119966  0.9349586 1.807707e-01  0.008002509
 #> sigma           1.14005399 0.149696423  7.6157731 1.727024e-07  0.826735778
 #>                      Upper
-#> parent_0       78.35255357
+#> parent_0       78.35255358
 #> k_parent        0.13084582
-#> k_M1            6.23970352
+#> k_M1            6.23970702
 #> k_M2            0.09843260
 #> k_M3            0.04333992
 #> f_parent_to_M1          NA
 #> f_parent_to_M2          NA
-#> f_M1_to_M3      0.86450768
+#> f_M1_to_M3      0.86450775
 #> f_M2_to_M3      0.99489895
 #> sigma           1.45337221
  mkinerrmin(f_soil)
 
#>             err.min n.optim df
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index e2cb876b..c3c756f6 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -77,7 +77,7 @@ the ilr transformation is used." />
       
       
         mkin
-        1.0.1
+        1.0.3
       
     

 
@@ -259,13 +259,13 @@ This is no problem for the internal use in mkinfit.fit.2.s <- summary(fit.2)
 print(fit.2.s$par, 3)
 
#>               Estimate Std. Error    Lower    Upper
-#> parent_0      99.59849    1.57022 96.40385 1.03e+02
+#> parent_0      99.59848    1.57022 96.40384 1.03e+02
 #> k_parent_sink  0.04792    0.00365  0.04049 5.54e-02
 #> k_parent_m1    0.05078    0.00205  0.04661 5.49e-02
 #> k_m1_sink      0.00526    0.00070  0.00384 6.69e-03
 #> sigma          3.12550    0.35852  2.39609 3.85e+00
print(fit.2.s$bpar, 3)
 
#>               Estimate se_notrans t value   Pr(>t)    Lower    Upper
-#> parent_0      99.59849    1.57022   63.43 2.30e-36 96.40385 1.03e+02
+#> parent_0      99.59848    1.57022   63.43 2.30e-36 96.40384 1.03e+02
 #> k_parent_sink  0.04792    0.00365   13.11 6.13e-15  0.04049 5.54e-02
 #> k_parent_m1    0.05078    0.00205   24.80 3.27e-23  0.04661 5.49e-02
 #> k_m1_sink      0.00526    0.00070    7.51 6.16e-09  0.00384 6.69e-03
diff --git a/docs/reference/update.mkinfit.html b/docs/reference/update.mkinfit.html
index f7149d84..09050e53 100644
--- a/docs/reference/update.mkinfit.html
+++ b/docs/reference/update.mkinfit.html
@@ -75,7 +75,7 @@ override these starting values." />
       
       
         mkin
-        1.0.0
+        1.0.3
       
     

 
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