Files in maomlab/BayesPharma
Tools for Bayesian Analysis of Non-Linear Pharmacology Models

.Rbuildignore

.github/.gitignore

.github/workflows/lint.yaml

.github/workflows/pkgdown.yaml

.github/workflows/test-coverage.yaml

.gitignore

.lintr

BayesPharma.Rproj

DESCRIPTION

LICENSE

Makefile

NAMESPACE

R/BayesPharma-bpfit.R R/BayesPharma-package.R R/calculate-log-dose.R R/data.R R/fit-model-cli.R R/globals.R R/helpers-testthat.R R/model-MuSyC-formula.R R/model-MuSyC-function.R R/model-MuSyC-init.R R/model-MuSyC-prior.R R/model-MuSyC-run.R R/model-MuSyC-stanvars.R R/model-MuSyC-utils.R R/model-Pnear-run.R R/model-constant-formula.R R/model-drc.R R/model-growth-formula.R R/model-growth-function.R R/model-growth-init.R R/model-growth-prior.R R/model-growth-run.R R/model-growth-stanvars.R R/model-michaelis_menten-formula.R R/model-michaelis_menten-generate.R R/model-michaelis_menten-init.R R/model-michaelis_menten-prior.R R/model-michaelis_menten-run.R R/model-michaelis_menten-stanvars.R R/model-sigmoid-formula.R R/model-sigmoid-function.R R/model-sigmoid-init.R R/model-sigmoid-prior.R R/model-sigmoid-run.R R/model-sigmoid-stanvars.R R/model-tQ-formula.R R/model-tQ-generate.R R/model-tQ-init.R R/model-tQ-prior.R R/model-tQ-run.R R/model-tQ-stanvars.R R/model-util.R R/plot-density-distirbution.R R/plot-drc.R R/plot-posterior-density.R R/plot-posterior-draws.R R/plot-posterior-predictive-check.R R/plot-prior_posterior_densities.R R/plot-synergy-checkerboard.R R/summary-basic-stats.R README.md

_pkgdown.yml

codecov.yml

data/kor_antag.rda

inst/cli/fit_model

inst/extdata/Pnear/antibody_snugdock/1ahw_rmsd.sc

inst/extdata/Pnear/antibody_snugdock/1jps_rmsd.sc

inst/extdata/Pnear/antibody_snugdock/1mlc_rmsd.sc

inst/extdata/Pnear/antibody_snugdock/1ztx_rmsd.sc

inst/extdata/Pnear/antibody_snugdock/2aep_rmsd.sc

inst/extdata/Pnear/antibody_snugdock/2jel_rmsd.sc

inst/extdata/conductance_KCNQ/Li_CellRes_2021_fig1.xlsx

inst/extdata/enzyme_kinetics/Hettiaratchi_2020.xlsx

man/BayesPharma-package.Rd man/MuSyC_formula.Rd man/MuSyC_genquant.Rd man/MuSyC_hi_to_si.Rd man/MuSyC_init.Rd man/MuSyC_model.Rd man/MuSyC_prior.Rd man/MuSyC_robust.Rd man/MuSyC_si_to_hi.Rd man/MuSyC_stanvar.Rd man/Pnear.Rd man/basic_stats.Rd man/bpfit-class.Rd man/calculate_log_dose.Rd man/cli_init_output_path.Rd man/cli_load_bivariate_formula.Rd man/cli_load_data.Rd man/cli_load_init.Rd man/cli_load_model_fn.Rd man/cli_load_prior.Rd man/cli_load_univariate_formula.Rd man/cli_parse_options.Rd man/constant_formula.Rd man/drc_model.Rd man/eval_init.Rd man/eval_init_one_param.Rd man/expect_gg.Rd man/fit_model_cli.Rd man/get_response_units.Rd man/get_response_variable.Rd man/get_treatment_units.Rd man/get_treatment_variable.Rd man/growth_richards.Rd man/growth_richards_formula.Rd man/growth_richards_init.Rd man/growth_richards_model.Rd man/growth_richards_prior.Rd man/growth_richards_stanvar.Rd man/growth_sigmoid.Rd man/growth_sigmoid_formula.Rd man/growth_sigmoid_init.Rd man/growth_sigmoid_model.Rd man/growth_sigmoid_prior.Rd man/growth_sigmoid_stanvar.Rd man/kor_antag.Rd man/michaelis_menten.Rd man/michaelis_menten_formula.Rd man/michaelis_menten_genquant.Rd man/michaelis_menten_init.Rd man/michaelis_menten_model.Rd man/michaelis_menten_prior.Rd man/michaelis_menten_stanvar.Rd man/plot_density_distribution.Rd man/plot_drc.Rd man/plot_posterior_density.Rd man/plot_posterior_draws.Rd man/plot_pp_check.Rd man/plot_prior_posterior_densities.Rd man/plot_sigmoid_functional_form.Rd man/plot_synergy_checkerboard.Rd man/prepare_init.Rd man/prepare_prior.Rd man/rstan_default_init.Rd man/sigmoid.Rd man/sigmoid_agonist_formula.Rd man/sigmoid_agonist_init.Rd man/sigmoid_agonist_prior.Rd man/sigmoid_antagonist_formula.Rd man/sigmoid_antagonist_init.Rd man/sigmoid_antagonist_prior.Rd man/sigmoid_hill_to_slope.Rd man/sigmoid_model.Rd man/sigmoid_slope_to_hill.Rd man/sigmoid_stanvar.Rd man/tQ_formula.Rd man/tQ_genquant.Rd man/tQ_init.Rd man/tQ_model.Rd man/tQ_model_generate.Rd man/tQ_prior.Rd man/tQ_stanvar.Rd

pkgdown/index.html

pkgdown/index.md

pkgdown/index.qmd

pkgdown/index_files/libs/bootstrap/bootstrap-icons.css

pkgdown/index_files/libs/bootstrap/bootstrap-icons.woff

pkgdown/index_files/libs/bootstrap/bootstrap.min.css

pkgdown/index_files/libs/bootstrap/bootstrap.min.js

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pkgdown/index_files/libs/quarto-html/tippy.umd.min.js

tests/testdata/ggplot_test_data.rda

tests/testdata/ggplot_test_model.rda

vignettes/.gitignore

vignettes/apply_MuSyC_KCNQ.Rmd

vignettes/apply_MuSyC_KCNQ_files/model-conductance-predictive-1.png

vignettes/apply_MuSyC_KCNQ_files/model-conductance-prior-posterior-1.png

vignettes/apply_MuSyC_KCNQ_files/model-data-subset-1.png

vignettes/apply_MuSyC_KCNQ_files/plot-voltage-by-dose-1.png

vignettes/apply_MuSyC_KCNQ_files/reproduce-fig1-1.png

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vignettes/apply_sigmoid_KOR.Rmd

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vignettes/apply_sigmoid_model_Pnear.Rmd

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vignettes/implement_tidymodels.Rmd

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vignettes/references.bib

vignettes_src/apply_MuSyC_Calbicans_SB.qmd

vignettes_src/apply_MuSyC_KCNQ.Rmd

vignettes_src/apply_MuSyC_KCNQ_ZK-21.qmd

vignettes_src/apply_sigmoid_KOR.Rmd vignettes_src/apply_sigmoid_model_Pnear.Rmd vignettes_src/apply_tQ_model_ChABC_design.Rmd

vignettes_src/apply_tQ_model_Markin2021/apply_tQ_model_Markin2021.qmd

vignettes_src/apply_tQ_model_nSMase2_kinetics.Rmd vignettes_src/derive_MuSyC_model.Rmd

vignettes_src/derive_sigmiod_model.qmd

vignettes_src/derive_tQ_model.Rmd

vignettes_src/implement_distributed_fitting/.gitignore

vignettes_src/implement_distributed_fitting/intermediate_data/.gitignore

vignettes_src/implement_distributed_fitting/product/.gitignore

vignettes_src/implement_distributed_fitting/raw_data/.gitignore

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vignettes_src/manuscript/sections/case_study_kinetics.qmd

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vignettes_src/manuscript/sections/case_study_synergy.qmd

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vignettes_src/references.bib

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maomlab/BayesPharma documentation built on Aug. 24, 2024, 8:45 a.m.

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maomlab/BayesPharma
Tools for Bayesian Analysis of Non-Linear Pharmacology Models

Files in maomlab/BayesPharma
Tools for Bayesian Analysis of Non-Linear Pharmacology Models

R Package Documentation

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maomlab/BayesPharma Tools for Bayesian Analysis of Non-Linear Pharmacology Models

Files in maomlab/BayesPharma Tools for Bayesian Analysis of Non-Linear Pharmacology Models

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maomlab/BayesPharma
Tools for Bayesian Analysis of Non-Linear Pharmacology Models

Files in maomlab/BayesPharma
Tools for Bayesian Analysis of Non-Linear Pharmacology Models