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Diffstat (limited to 'inst')
| -rw-r--r-- | inst/WORDLIST | 310 | ||||
| -rw-r--r-- | inst/rmarkdown/templates/hierarchical_kinetics/skeleton/.skeleton.Rmd.swp | bin | 20480 -> 0 bytes | |||
| -rw-r--r-- | inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd | 18 | ||||
| -rw-r--r-- | inst/testdata/active_substance_medium_source_year.xlsx | bin | 0 -> 29924 bytes |
4 files changed, 219 insertions, 109 deletions
diff --git a/inst/WORDLIST b/inst/WORDLIST index 895550ba..8b3aae37 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -1,118 +1,241 @@ AAM +AR Agric +Alterra +Anova +BBA +BMC +Backtransform +Backtransformed +BayerCropScience +Beltman +Berater +BerliOS +Boesten +Borstel +CFuncList +CMD +ChangeLog +Colors +Crauste +DAR +DCP +DFOP +DI +DM +DMTA +DMTAP +DT +Defauls +DegKin +Dimethenamid +EFSA +Ethofumesate +Eurofins +FIM +FME +FO +FOMC +FOrum +Filzmoser +Flaach +Fragoulis +Fth +Gandrillon +Geosci +Glyphosate +Grenzach +Guillemin +Götz +HS +Hellas +Hierarchichal +Hron +IKF +ILR +IORE +IRLS +Imazamox +Isofetamid +JCZ +JSE +Janina +KP +Kalibera +Karel +Karline +KinGUI +KinGUII +KineticEval +Kronacher +Kullback +LME +LOD +LOQ +LR +Leibler +Levenberg +Lorenzato +MWHC +Marquardt +MatLab +Math +Meinecke +Mikolasch +ModelMaker +Modellierungssoftware +Moolgavkar +Multimodel +NAFTA +NLHM +Nambsheim +Nonlinear +Nvim +ORCID +OpenBlas +PEC +Pawitan +PestDF +Petzoldt +Piacenza +Pinheiro +Pol +Privatdozent +Projektnummer +Prüfung +RAR +RCC +RUnit +Rainbird +Rmd +Rocke +Rprofile +Rtools +SAEM +SFO +SFORB +Sanco +Schäfer +Soetaert +Staudenmaier +Str +Syngenta +Sys +TWAs +TeX +Technometrics +Tessella +Thifensulfuron +Topfit +Trichlorophenoxyacetic +UBA +USe +Umweltbundesamt +Validierung +Venzon +Vrona +Wageningen +Wissenschaftlicher +Workgroup +Wyhlen +Wöltjen als anova -AR autogenerated autogeneration aw +backends backtransform -Backtransform backtransformation backtransformed -BayerCropScience -Berater -BerliOS +biexponential bpar bparms -bremen calulations +centering cf -CFuncList cfunction -ChangeLog +ci +clearpage cloneable -CMD -codecov -Colors +coauthor +colum +conf confint const cran csf cutoff -Defauls -DegKin -degparms +cyantraniliprole +cyhalothrin deSolve -DFOP -DI +degparms +detectCores dichlorophenoxyacetic diethylether +dimethenamid +dir distimes -DM +dll +dmta doi +dontrun ds -DT -EFSA +efsa eigen errmin errmod errplot +erythropoiesis ethofumesate -Ethofumesate etics -Eurofins -Filzmoser -FME -FOMC -FOrum +eu +europa fourstep frac -Fragoulis +func gcc -Geosci github glyphosate -Glyphosate gmkin -Grenzach +gq hessians -Hron -HS -IKF +hierarchichal +identifiabiliy +illparms ilr -ILR imazamox -Imazamox ini +init inital -IORE +intersoil irls -IRLS isofetamid -Isofetamid jrwb -Karel -Karline -KineticEval kinfit -KinGUI -KinGUII knitr -KP -Kronacher -Kullback -Leibler -Levenberg +lin linux +llhist +llmin +llquant +lme lmtest -LOD +lod loftest logLik +loglik logratio -LOQ -Lorenzato -LR lrtest lsoda -Marquardt -Math -MatLab +maxabs maxitmodFit md -Meinecke -Mikolasch +mesotrione +mhmkin mkinds +mkindsg +mkinerrmin mkinerrplot mkinfit mkinmod @@ -120,100 +243,79 @@ mkinparplot mkinpredict mkinresplot mmkin -Modellierungssoftware -ModelMaker -Moolgavkar -Multimodel +multicompartment +multistart nafta -NAFTA +nd nlme nlminb nls nobs nonlinear -Nonlinear +nq numDeriv -Nvim obs -ODEs -oftentimes -ORCID +odeparms +optim overparameterisation overparameterised +pF parms -Pawitan -PEC -PestDF +parplot pfm piacenza -Piacenza pkgbuild -Privatdozent -Projektnummer -Prüfung +posix +racemic radiolabel radiolabels -Rainbird -RAR -RCC +rda +rel reparameterisation res resplot reweight reweighting rl -Rocke +rmarkdown +rmd +rnw roxygen -Rprofile rsd -Rtools -RUnit -Sanco -Schäfer +saem +saemix sep -SFO -SFORB -Soetaert -speclist -Str -Syngenta -Sys +shapiro tb tc -Technometrics -Tessella +testdata testthat tex textrm texttt +th thifensulfuron -Thifensulfuron threestep -Topfit +tinytex +tlmgr +tol topright trichloroanisole trichlorophenol trichlorophenoxyacetic -Trichlorophenoxyacetic twa -TWAs twocomp twostep -UBA ulticompartment -Umweltbundesamt uncompiled und unixoid -USe -Validierung var -Venzon -Vrona +vspace winbuilder -Wissenschaftlicher workgroup -Workgroup -Wyhlen +xlab +xlim +ylab ylim zu diff --git a/inst/rmarkdown/templates/hierarchical_kinetics/skeleton/.skeleton.Rmd.swp b/inst/rmarkdown/templates/hierarchical_kinetics/skeleton/.skeleton.Rmd.swp Binary files differdeleted file mode 100644 index 2c5bfed8..00000000 --- a/inst/rmarkdown/templates/hierarchical_kinetics/skeleton/.skeleton.Rmd.swp +++ /dev/null diff --git a/inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd index 0baf866a..f61413ba 100644 --- a/inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd +++ b/inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd @@ -122,7 +122,7 @@ From the refined fits, the most suitable model is selected using the AIC. ```{r parent-best, dependson = "parent-mhmkin"} aic_parent <- AIC(parent_mhmkin_refined) -min_aic <- which(aic_parent == min(aic_parent), arr.ind = TRUE) +min_aic <- which(aic_parent == min(aic_parent, na.rm = TRUE), arr.ind = TRUE) best_degmod_parent <- rownames(aic_parent)[min_aic[1]] best_errmod_parent <- colnames(aic_parent)[min_aic[2]] anova(parent_mhmkin_refined) |> kable(digits = 1) @@ -157,11 +157,12 @@ models for both of them is fitted. ```{r parent-best-pH} parent_best_pH_1 <- update(parent_best, covariates = covariates, - covariate_models = list(log_k_lambda_free ~ pH)) + covariate_models = list(log_k_lambda_free ~ pH), center_covariates = "median") parent_best_pH_2 <- update(parent_best, covariates = covariates, - covariate_models = list(log_k_lambda_bound_free ~ pH)) + covariate_models = list(log_k_lambda_bound_free ~ pH), center_covariates = "median") parent_best_pH_3 <- update(parent_best, covariates = covariates, - covariate_models = list(log_k_lambda_free ~ pH, log_k_lambda_bound_free ~ pH)) + covariate_models = list(log_k_lambda_free ~ pH, log_k_lambda_bound_free ~ pH), + center_covariates = "median") ``` The resulting models are compared. @@ -244,6 +245,7 @@ model that was identified for the parent degradation, are attempted below. path_1 <- mhmkin(list(sforb_sep_const, sforb_sep_tc), no_random_effect = c("lambda_free_0", "log_k_lambda_free_bound"), covariates = covariates, covariate_models = list(log_k_lambda_bound_free ~ pH), + center_covariates = "median", cluster = cl_path) ``` @@ -294,7 +296,13 @@ The pathway endpoints corresponding to the median pH in the tested soils are shown below. ```{r dependson = "parent-best-pH"} -endpoints(parent_best_pH_2) +endpoints(path_1_refined) +``` + +We can also show endpoints corresponding to a user defined pH value. + +```{r dependson = "parent-best-pH"} +endpoints(path_1_refined, covariates = c(pH = 7)) ``` ```{r} diff --git a/inst/testdata/active_substance_medium_source_year.xlsx b/inst/testdata/active_substance_medium_source_year.xlsx Binary files differnew file mode 100644 index 00000000..a11f0dc5 --- /dev/null +++ b/inst/testdata/active_substance_medium_source_year.xlsx |