_pkgdown.yaml

---
url: https://openpharma.github.io/crmPack

template:
  bootstrap: 5
  bootswatch: flatly

navbar:
  type: default
  structure:
    left: [intro, reference, articles, tutorials, news, reports]
    right: [search, github]
  components:
    reports:
      text: Reports
      menu:
        - text: Coverage report
          href: coverage-report/
        - text: Unit test report
          href: unit-test-report/
    github:
      icon: fa-github
      aria-label: View on GitHub
      href: https://github.com/openpharma/crmPack
    cran:
      icon: fab fa-r-project
      href: https://cloud.r-project.org/package=crmPack
      aria-label: View on CRAN

articles:
  - title: Articles
    navbar: ~
    contents:
      - trial_definition
      - trial_analysis
      - trial_sanity_checks
      - trial_simulation
      - ordinal-crm
      - rolling-crm
      - simulations
      - knit_print
      - tidy_method
      - migration_from_the_old_crmPack
      - parallel_computing_with_extensions
      - crmPack-jss-paper
      - example

reference:
  - title: Package
    contents:
      - crmPack-package
  - title: Classes
    contents:
      - Validate
      - positive_number
      - CrmPackClass
      - GeneralData
      - Data
      - DataDual
      - DataOrdinal
      - DataParts
      - DataMixture
      - DataDA
      - DataGrouped
      - McmcOptions
      - ModelParamsNormal
      - GeneralModel
      - ModelLogNormal
      - LogisticNormal
      - LogisticLogNormal
      - LogisticLogNormalSub
      - ProbitLogNormal
      - ProbitLogNormalRel
      - LogisticLogNormalGrouped
      - LogisticKadane
      - LogisticKadaneBetaGamma
      - LogisticNormalMixture
      - LogisticNormalFixedMixture
      - LogisticLogNormalMixture
      - DualEndpoint
      - DualEndpointRW
      - DualEndpointBeta
      - DualEndpointEmax
      - ModelPseudo
      - ModelTox
      - ModelEff
      - LogisticIndepBeta
      - Effloglog
      - EffFlexi
      - DALogisticLogNormal
      - TITELogisticLogNormal
      - OneParLogNormalPrior
      - OneParExpPrior
      - FractionalCRM
      - Samples
      - NextBest
      - NextBestMTD
      - NextBestNCRM
      - NextBestNCRMLoss
      - NextBestThreePlusThree
      - NextBestDualEndpoint
      - NextBestMinDist
      - NextBestInfTheory
      - NextBestTD
      - NextBestTDsamples
      - NextBestMaxGain
      - NextBestMaxGainSamples
      - NextBestProbMTDLTE
      - NextBestProbMTDMinDist
      - Increments
      - IncrementsRelative
      - IncrementsRelativeParts
      - IncrementsRelativeDLT
      - IncrementsRelativeDLTCurrent
      - IncrementsDoseLevels
      - IncrementsHSRBeta
      - IncrementsMin
      - IncrementsMaxToxProb
      - Stopping
      - StoppingMissingDose
      - StoppingCohortsNearDose
      - StoppingPatientsNearDose
      - StoppingMinCohorts
      - StoppingMinPatients
      - StoppingTargetProb
      - StoppingMTDdistribution
      - StoppingMTDCV
      - StoppingLowestDoseHSRBeta
      - StoppingTargetBiomarker
      - StoppingSpecificDose
      - StoppingHighestDose
      - StoppingList
      - StoppingAll
      - StoppingAny
      - StoppingTDCIRatio
      - StoppingMaxGainCIRatio
      - StoppingExternal
      - CohortSize
      - CohortSizeRange
      - CohortSizeDLT
      - CohortSizeConst
      - CohortSizeParts
      - CohortSizeMax
      - CohortSizeMin
      - SafetyWindow
      - SafetyWindowSize
      - SafetyWindowConst
      - RuleDesign
      - Design
      - DesignOrdinal
      - RuleDesignOrdinal
      - DualDesign
      - TDsamplesDesign
      - TDDesign
      - DesignGrouped
  - title: Internal Helper Functions
    contents:
      - h_blind_plot_data
      - h_convert_ordinal_data
      - h_convert_ordinal_model
      - h_convert_ordinal_samples
      - h_doses_unique_per_cohort
      - h_all_equivalent
      - h_plot_data_df
      - h_plot_data_cohort_lines
      - h_check_fun_formals
      - h_slots
      - h_format_number
      - h_rapply
      - h_null_if_na
      - h_is_positive_definite
      - h_test_named_numeric
      - h_in_range
      - h_find_interval
      - h_validate_combine_results
      - h_jags_add_dummy
      - h_jags_join_models
      - h_jags_get_model_inits
      - h_jags_get_data
      - h_jags_write_model
      - h_jags_extract_samples
      - h_model_dual_endpoint_sigma2W
      - h_model_dual_endpoint_rho
      - h_model_dual_endpoint_sigma2betaW
      - h_model_dual_endpoint_beta
      - h_info_theory_dist
      - h_next_best_mg_ci
      - h_next_best_mg_doses_at_grid
      - h_next_best_eligible_doses
      - h_next_best_ncrm_loss_plot
      - h_next_best_tdsamples_plot
      - h_next_best_td_plot
      - h_next_best_mg_plot
      - h_next_best_mgsamples_plot
      - h_obtain_dose_grid_range
      - h_covr_helpers
      - h_default_if_empty
      - h_unpack_stopit
      - h_calc_report_label_percentage
      - h_validate_common_data_slots
      - h_summarize_add_stats
      - h_determine_dlts
  - title: Internal Validation Functions
    contents:
      - v_general_data
      - v_data
      - v_data_dual
      - v_data_parts
      - v_data_mixture
      - v_data_da
      - v_mcmc_options
      - v_model_params_normal
      - v_general_model
      - v_model_logistic_kadane
      - v_model_logistic_kadane_beta_gamma
      - v_model_logistic_normal_mix
      - v_model_logistic_normal_fixed_mix
      - v_model_logistic_log_normal_mix
      - v_model_dual_endpoint
      - v_model_dual_endpoint_rw
      - v_model_dual_endpoint_beta
      - v_model_dual_endpoint_emax
      - v_model_logistic_indep_beta
      - v_model_eff_log_log
      - v_model_eff_flexi
      - v_model_da_logistic_log_normal
      - v_model_tite_logistic_log_normal
      - v_model_one_par_exp_normal_prior
      - v_model_one_par_exp_prior
      - v_samples
      - v_next_best_mtd
      - v_next_best_ncrm
      - v_next_best_ncrm_loss
      - v_next_best_dual_endpoint
      - v_next_best_min_dist
      - v_next_best_inf_theory
      - v_next_best_td
      - v_next_best_td_samples
      - v_next_best_max_gain_samples
      - v_next_best_prob_mtd_lte
      - v_next_best_prob_mtd_min_dist
      - v_increments_relative
      - v_increments_relative_parts
      - v_increments_relative_dlt
      - v_increments_dose_levels
      - v_increments_hsr_beta
      - v_increments_min
      - v_increments_maxtoxprob
      - v_starting_dose
      - v_stopping_cohorts_near_dose
      - v_stopping_min_cohorts
      - v_stopping_min_patients
      - v_stopping_target_prob
      - v_stopping_mtd_distribution
      - v_stopping_mtd_cv
      - v_stopping_target_biomarker
      - v_stopping_list
      - v_stopping_all
      - v_stopping_tdci_ratio
      - v_cohort_size_range
      - v_cohort_size_dlt
      - v_cohort_size_const
      - v_cohort_size_parts
      - v_cohort_size_max
      - v_safety_window_size
      - v_safety_window_const
      - v_rule_design
      - v_general_simulations
      - v_pseudo_simulations
  - title: Custom Checkmate Assertions
    contents:
      - assert_probabilities
      - assert_probability
      - assert_probability_range
      - assert_length
      - assert_range
      - check_probabilities
      - check_probability
      - check_probability_range
      - check_length
      - check_range
      - test_probabilities
      - test_probability
      - test_probability_range
      - test_length
      - test_range
      - expect_probabilities
      - expect_probability
      - expect_probability_range
      - expect_range
  - title: Methods
    contents:
      - plot-Data
      - plot-DataDual
      - plot-DataDA
      - update-Data
      - update-DataParts
      - update-DataDual
      - update-DataDA
      - update-DataOrdinal
      - getEff
      - getEff-DataDual
      - ngrid
      - ngrid-Data
      - dose_grid_range
      - dose_grid_range-Data
      - saveSample
      - saveSample-McmcOptions
      - size
      - size-McmcOptions
      - size-Samples
      - size-CohortSizeRange
      - size-CohortSizeDLT
      - size-CohortSizeMax
      - size-CohortSizeMin
      - size-CohortSizeConst
      - size-CohortSizeParts
      - doseFunction
      - doseFunction-GeneralModel
      - doseFunction-ModelPseudo
      - dose
      - dose-LogisticNormal
      - dose-LogisticLogNormal
      - dose-LogisticLogNormalSub
      - dose-ProbitLogNormal
      - dose-ProbitLogNormalRel
      - dose-LogisticKadane
      - dose-LogisticKadaneBetaGamma
      - dose-LogisticNormalMixture
      - dose-LogisticNormalFixedMixture
      - dose-LogisticLogNormalMixture
      - dose-DualEndpoint
      - dose-LogisticIndepBeta
      - dose-LogisticIndepBeta-noSamples
      - dose-Effloglog-noSamples
      - dose-EffFlexi
      - dose-OneParLogNormalPrior
      - dose-OneParExpPrior
      - probFunction
      - probFunction-GeneralModel
      - probFunction-ModelTox
      - prob
      - prob-LogisticNormal
      - prob-LogisticLogNormal
      - prob-LogisticLogNormalSub
      - prob-ProbitLogNormal
      - prob-ProbitLogNormalRel
      - prob-LogisticKadane
      - prob-LogisticKadaneBetaGamma
      - prob-LogisticIndepBeta
      - prob-LogisticNormalMixture
      - prob-LogisticNormalFixedMixture
      - prob-LogisticLogNormalMixture
      - prob-DualEndpoint
      - prob-LogisticIndepBeta-noSamples
      - prob-OneParLogNormalPrior
      - prob-OneParExpPrior
      - efficacyFunction
      - efficacyFunction-ModelEff
      - efficacy
      - efficacy-Effloglog
      - efficacy-Effloglog-noSamples
      - efficacy-EffFlexi
      - biomarker
      - biomarker-DualEndpoint
      - gain
      - gain-ModelTox-ModelEff
      - gain-ModelTox-Effloglog-noSamples
      - update-ModelPseudo
      - mcmc-GeneralData
      - mcmc-GeneralData-DualEndpointBeta
      - mcmc-GeneralData-OneParExpPrior
      - names-Samples
      - nextBest
      - nextBest-NextBestMTD
      - nextBest-NextBestNCRM
      - nextBest-NextBestNCRM-DataParts
      - nextBest-NextBestNCRMLoss
      - nextBest-NextBestThreePlusThree
      - nextBest-NextBestDualEndpoint
      - nextBest-NextBestMinDist
      - nextBest-NextBestInfTheory
      - nextBest-NextBestTDsamples
      - nextBest-NextBestTD
      - nextBest-NextBestMaxGain
      - nextBest-NextBestMaxGainSamples
      - nextBest-NextBestProbMTDLTE
      - nextBest-NextBestProbMTDMinDist
      - stopTrial-StoppingMissingDose
      - stopTrial-StoppingLowestDoseHSRBeta
      - stopTrial-StoppingMTDCV
      - maxDose
      - maxDose-IncrementsRelative
      - maxDose-IncrementsRelativeDLT
      - maxDose-IncrementsRelativeDLTCurrent
      - maxDose-IncrementsRelativeParts
      - maxDose-IncrementsDoseLevels
      - maxDose-IncrementsHSRBeta
      - maxDose-IncrementsMin
      - maxDose-IncrementsMaxToxProb
  - title: Functions
    contents:
      - enable_logging
      - disable_logging
      - is_logging_enabled
      - log_trace
      - dapply
      - knit_print
  - title: Classes
    contents:
      - CohortSizeOrdinal-class
      - IncrementsOrdinal-class
      - DADesign-class
      - DADesign
      - DASimulations-class
      - DASimulations
      - DualResponsesDesign-class
      - DualResponsesDesign
      - DualResponsesSamplesDesign-class
      - DualResponsesSamplesDesign
      - DualSimulations-class
      - DualSimulations
      - DualSimulationsSummary-class
      - GeneralSimulations-class
      - GeneralSimulations
      - GeneralSimulationsSummary-class
      - IncrementsMaxToxProb-class
      - LogisticLogNormalOrdinal-class
      - MinimalInformative
      - NextBestOrdinal-class
      - PseudoDualFlexiSimulations-class
      - PseudoDualFlexiSimulations
      - PseudoDualSimulations-class
      - PseudoDualSimulations
      - PseudoDualSimulationsSummary-class
      - PseudoSimulations-class
      - PseudoSimulations
      - PseudoSimulationsSummary-class
      - Quantiles2LogisticNormal
      - Report
      - Simulations-class
      - Simulations
      - SimulationsSummary-class
      - StoppingOrdinal-class
      - approximate
      - assertions
      - assert_equal
      - check_equal
      - check_format
      - assert_format
      - test_format
      - crmPackExample
      - crmPackHelp
      - examine
      - fit
      - fitGain
      - fitPEM
      - get,Samples,character-method
      - h_get_min_inf_beta
      - logit
      - match_within_tolerance
      - maxSize
      - minSize
      - or-Stopping-Stopping
      - or-Stopping-StoppingAny
      - or-StoppingAny-Stopping
      - plot,Data,ModelTox-method
      - plot,DataDual,ModelEff-method
      - plot,DualSimulations,missing-method
      - plot,DualSimulationsSummary,missing-method
      - plot,GeneralSimulations,missing-method
      - plot,GeneralSimulationsSummary,missing-method
      - plot,PseudoDualFlexiSimulations,missing-method
      - plot,PseudoDualSimulations,missing-method
      - plot,PseudoDualSimulationsSummary,missing-method
      - plot,PseudoSimulationsSummary,missing-method
      - plot,Samples,DALogisticLogNormal-method
      - plot,Samples,DualEndpoint-method
      - plot,Samples,GeneralModel-method
      - plot,Samples,ModelEff-method
      - plot,Samples,ModelTox-method
      - plot,SimulationsSummary,missing-method
      - plotDualResponses
      - plotGain
      - plot.gtable
      - probit
      - set_seed
      - show,DualSimulationsSummary-method
      - show,GeneralSimulationsSummary-method
      - show,PseudoDualSimulationsSummary-method
      - show,PseudoSimulationsSummary-method
      - show,SimulationsSummary-method
      - simulate,DADesign-method
      - simulate,Design-method
      - simulate,DualDesign-method
      - simulate,DualResponsesDesign-method
      - simulate,DualResponsesSamplesDesign-method
      - simulate,RuleDesign-method
      - simulate,TDDesign-method
      - simulate,TDsamplesDesign-method
      - simulate-DesignGrouped
      - summary,DualSimulations-method
      - summary,GeneralSimulations-method
      - summary,PseudoDualFlexiSimulations-method
      - summary,PseudoDualSimulations-method
      - summary,Simulations-method
      - summary,PseudoSimulations-method
      - tidy
      - windowLength
      - "&,Stopping,Stopping-method"
      - "&,Stopping,StoppingAll-method"
      - "&,StoppingAll,Stopping-method"