From 6e559ef8680053873a8da51a000f6c2f2d28d719 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 11 Apr 2022 08:53:38 +0200 Subject: Update static docs --- docs/reference/CAKE_export.html | 4 ++-- docs/reference/Rplot001.png | Bin 90922 -> 27711 bytes docs/reference/Rplot002.png | Bin 90653 -> 59119 bytes docs/reference/Rplot003.png | Bin 20189 -> 59152 bytes docs/reference/Rplot004.png | Bin 19212 -> 60094 bytes docs/reference/dimethenamid_2018-1.png | Bin 254862 -> 248143 bytes docs/reference/dimethenamid_2018-2.png | Bin 254236 -> 246117 bytes docs/reference/dimethenamid_2018-3.png | Bin 7629 -> 245058 bytes docs/reference/dimethenamid_2018.html | 18 +++++++++++------- docs/reference/mean_degparms.html | 12 +++++++++++- docs/reference/plot.mixed.mmkin-2.png | Bin 174398 -> 173322 bytes docs/reference/plot.mixed.mmkin-3.png | Bin 173804 -> 172513 bytes docs/reference/plot.mixed.mmkin-4.png | Bin 176780 -> 175535 bytes docs/reference/plot.mixed.mmkin.html | 4 ++++ 14 files changed, 28 insertions(+), 10 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/CAKE_export.html b/docs/reference/CAKE_export.html index 44297d1b..f16a9e6c 100644 --- a/docs/reference/CAKE_export.html +++ b/docs/reference/CAKE_export.html @@ -96,11 +96,11 @@ specified as well.

filename = "CAKE_export.csf", path = ".", overwrite = FALSE, - study = "Codlemone aerobic soil degradation", + study = "Degradinol aerobic soil degradation", description = "", time_unit = "days", res_unit = "% AR", - comment = "Created using mkin::CAKE_export", + comment = "", date = Sys.Date(), optimiser = "IRLS" ) diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png index 26efcdd2..fa5f3834 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 065f21f6..3caf465f 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 50a52a1c..88ebd2d4 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 0f3d8214..7e87d63d 100644 Binary files a/docs/reference/Rplot004.png and b/docs/reference/Rplot004.png differ diff --git a/docs/reference/dimethenamid_2018-1.png b/docs/reference/dimethenamid_2018-1.png index be59fc90..4300b0c0 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 0bbb14d8..36db063c 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 71087e85..efb89bdb 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 85e954ac..d2ed8647 100644 --- a/docs/reference/dimethenamid_2018.html +++ b/docs/reference/dimethenamid_2018.html @@ -186,20 +186,25 @@ specific pieces of information in the comments.

# between these variants plot(mixed(dmta_sfo_sfo3p_tc), test_log_parms = TRUE) -# Therefore we use nonlinear mixed-effects models +# We can also specify a default value for the failing +# log parameters, to mimic FOCUS guidance +plot(mixed(dmta_sfo_sfo3p_tc), test_log_parms = TRUE, + default_log_parms = log(2)/1000) + +# As these attempts are not satisfying, we use nonlinear mixed-effects models # f_dmta_nlme_tc <- nlme(dmta_sfo_sfo3p_tc) # nlme reaches maxIter = 50 without convergence f_dmta_saem_tc <- saem(dmta_sfo_sfo3p_tc) # I am commenting out the convergence plot as rendering them -# with pkgdown fails (at least without further tweaks to the +# with pkgdown fails (at least without further tweaks to the # graphics device used) #saemix::plot(f_dmta_saem_tc$so, plot.type = "convergence") 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: Wed Mar 16 14:32:04 2022 -#> Date of summary: Wed Mar 16 14:32:04 2022 +#> Date of fit: Sat Apr 9 18:03:34 2022 +#> Date of summary: Sat Apr 9 18:03:34 2022 #> #> Equations: #> d_DMTA/dt = - k_DMTA * DMTA @@ -212,7 +217,7 @@ specific pieces of information in the comments.

#> #> Model predictions using solution type deSolve #> -#> Fitted in 927.963 s +#> Fitted in 787.836 s #> Using 300, 100 iterations and 9 chains #> #> Variance model: Two-component variance function @@ -300,8 +305,7 @@ specific pieces of information in the comments.

# covariance.model = diag(c(0, rep(1, 7)))) # saemix::plot(f_dmta_saem_tc_2$so, plot.type = "convergence") # This does not perform better judged by AIC and BIC -saemix::compare.saemix(f_dmta_saem_tc$so, f_dmta_saem_tc_2$so) -#> Error in saemix::compare.saemix(f_dmta_saem_tc$so, f_dmta_saem_tc_2$so): object 'f_dmta_saem_tc_2' not found +# saemix::compare.saemix(f_dmta_saem_tc$so, f_dmta_saem_tc_2$so) # } diff --git a/docs/reference/mean_degparms.html b/docs/reference/mean_degparms.html index aaeb44ea..efe91b6f 100644 --- a/docs/reference/mean_degparms.html +++ b/docs/reference/mean_degparms.html @@ -87,7 +87,13 @@
- 
mean_degparms(object, random = FALSE, test_log_parms = FALSE, conf.level = 0.6)
+ 
mean_degparms(
+  object,
+  random = FALSE,
+  test_log_parms = FALSE,
+  conf.level = 0.6,
+  default_log_parms = NA
+)
@@ -103,6 +109,10 @@ rate constants) pass the t-test for significant difference from zero.

conf.level

Possibility to adjust the required confidence level for parameter that are tested if requested by 'test_log_parms'.

+
default_log_parms
+

If set to a numeric value, this is used +as a default value for the tested log parameters that failed the +t-test.

Value

diff --git a/docs/reference/plot.mixed.mmkin-2.png b/docs/reference/plot.mixed.mmkin-2.png index 67c9b8ab..8678c166 100644 Binary files a/docs/reference/plot.mixed.mmkin-2.png and b/docs/reference/plot.mixed.mmkin-2.png differ diff --git a/docs/reference/plot.mixed.mmkin-3.png b/docs/reference/plot.mixed.mmkin-3.png index 0840c7da..9bd01852 100644 Binary files a/docs/reference/plot.mixed.mmkin-3.png and b/docs/reference/plot.mixed.mmkin-3.png differ diff --git a/docs/reference/plot.mixed.mmkin-4.png b/docs/reference/plot.mixed.mmkin-4.png index a78087bb..d2fa1ae1 100644 Binary files a/docs/reference/plot.mixed.mmkin-4.png and b/docs/reference/plot.mixed.mmkin-4.png differ diff --git a/docs/reference/plot.mixed.mmkin.html b/docs/reference/plot.mixed.mmkin.html index b405b84a..52971427 100644 --- a/docs/reference/plot.mixed.mmkin.html +++ b/docs/reference/plot.mixed.mmkin.html @@ -99,6 +99,7 @@ pred_over = NULL, test_log_parms = FALSE, conf.level = 0.6, + default_log_parms = NA, ymax = "auto", maxabs = "auto", ncol.legend = ifelse(length(i) <= 3, length(i) + 1, ifelse(length(i) <= 8, 3, 4)), @@ -143,6 +144,9 @@ from mkinpredict with a compatible mean_degparms in the case of an mixed.mmkin object

+
default_log_parms
+

Passed to mean_degparms in the case of an +mixed.mmkin object

ymax

Vector of maximum y axis values

maxabs
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