heemod: Models for Health Economic Evaluation

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Health Economic Evaluation Modelling. Markov models (decision trees, homogeneous and non-homogeneous) for health economic evaluation. Model comparison, sensitivity and probabilistic analysis.

Author
Antoine Filipovic-Pierucci [aut, cre], Kevin Zarca [aut], Matthew Wiener [ctb], Zdenek Kabat [ctb], Vojtech Filipec [ctb]
Date of publication
2016-11-29 12:43:51
Maintainer
Antoine Filipovic-Pierucci <pierucci@gmail.com>
License
GPL (>= 3)
Version
0.7.1
URLs

View on CRAN

Man pages

acceptability_curve
Acceptability Curve from Probabilistic Analysis
as_expr_list
Convert Lazy Dots to Expression List
check_matrix
Check Markov Model Transition Matrix
check_names
Check Names
check_states
Check Model States for Consistency
check_strategy_index
Check Strategy Index
clean_factors
Convert Data Frame Factor Variables to Character
cluster
Run 'heemod' on a Cluster
combine_models
Combine Multiple Models
compute_counts
Compute Count of Individual in Each State per Cycle
compute_icer
Compute ICER
compute_values
Compute State Values per Cycle
create_demographic_table
Read a Demographic Table
create_df_from_tabular
Load Data From a Folder Into an Environment
create_matrix_from_tabular
Create a Transition Matrix From Tabular Input
create_model_from_tabular
Create a 'heemod' Model From Tabular Files Info
create_model_list_from_tabular
Read Models Specified by Files
create_options_from_tabular
Create Model Options From a Tabular Input
create_parameters_from_tabular
Create a Parameter Definition From Tabular Input
create_states_from_tabular
Create State Definitions From Tabular Input
define_correlation
Define a Correlation Structure for Probabilistic Uncertainty...
define_dsa
Define a Sensitivity Analysis
define_multinom
Define That Parameters Belong to the Same Multinomial...
define_parameters
Define Markov Model Parameters
define_psa
Define Parameters Distribution for Probabilistic Analysis
define_state
Define a Markov Model State
define_state_list
Define Markov Model State List
define_strategy
Define a Markov Model
define_transition
Define Transition Matrix for Markov Model
density
Probability Density Functions for Probabilistic Uncertainty...
discount
Discount a Quantity Over Time
discount_hack
Hack to Work Around a Discounting Issue
eval_matrix
Evaluate Markov Model Transition Matrix
eval_models_from_tabular
Evaluate Models From a Tabular Source
eval_parameters
Evaluate Markov model parameters
eval_resample
Evaluate Resampling Definition
eval_state_list
Evaluate Markov Model States
eval_strategy
Evaluate Strategy
eval_strategy_newdata
Iteratively Evaluate a Markov Model With New Parameter Values
expand_state
Expand Time-Dependant States into Tunnel States
file-checkers
Check File Type
filter_blanks
Remove Blank Rows From Table
gather_model_info
Gather Information for Running a Model From Tabular Data
get_code
Display the Code to Generate an Object
get_counts
Get State Membership Counts
get_frontier
Return Efficiency Frontier
get_matrix
Get Markov Model Transition Matrix
get_matrix_order
Return Markov Model Transition Matrix Order
get_parameter_names
Return parameters names
get_state_names
Get State Names
get_state_number
Return Number of State
get_state_value_names
Return Names of State Values
get_values
Get Strategy Values
heemod
heemod: Health Economic Evaluation MODelling
heemod_scale
Normalize Cost and Effect
insert
Insert Elements in Vector
interp_heemod
Interpolate Lazy Dots
is.wholenumber
Check Wholenumbers
list_all_same
Check if All the Elements of a List Are the Same
look_up
Look Up Values in a Data Frame
make_names
Make Syntactically Valid Names
modify
Modify Object
parse_multi_spec
Specify Inputs for Multiple Models From a Single File
plot.dsa
Plot Sensitivity Analysis
plot.psa
Plot Results of Probabilistic Analysis
plot.run_model
Plot Results of a Markov Model
plur
Returns "s" if x > 1
probability
Convenience Functions to Compute Probabilities
read_file
Read the accepted file formats for tabular input
run_dsa
Run Sensitivity Analysis
run_model
Run one or more Markov Model
run_model_tabular
Run Analyses From Files
run_psa
Run Probabilistic Uncertainty Analysis
safe-conversion
Safely Convert From Characters to Numbers
save_outputs
Save Model Outputs
summary.run_model
Summarise Markov Model Results
update-model
Run Model on New Data
who-mortality
Use WHO Mortality Rate
wtd_summary
Weighted Summary

Files in this package

heemod
heemod/COPYING
heemod/inst
heemod/inst/examples
heemod/inst/examples/example_eval_strategy_newdata.R
heemod/inst/examples/example_define_state.R
heemod/inst/examples/example_define_strategy.R
heemod/inst/examples/example_transform.R
heemod/inst/examples/example_define_resample.R
heemod/inst/examples/example_define_transition.R
heemod/inst/examples/example_plot.run_model.R
heemod/inst/examples/example_look_up.R
heemod/inst/examples/example_update.R
heemod/inst/examples/example_run_model.R
heemod/inst/examples/example_define_parameters.R
heemod/inst/examples/example_run_psa.R
heemod/inst/examples/example_eval_strategy.R
heemod/inst/examples/example_run_dsa.R
heemod/inst/examples/example_eval_parameters.R
heemod/inst/shiny
heemod/inst/shiny/main
heemod/inst/shiny/main/rsconnect
heemod/inst/shiny/main/rsconnect/shinyapps.io
heemod/inst/shiny/main/rsconnect/shinyapps.io/pierucci
heemod/inst/shiny/main/rsconnect/shinyapps.io/pierucci/main.dcf
heemod/inst/media
heemod/inst/media/logo.png
heemod/inst/tmp
heemod/inst/tmp/benchmark.R
heemod/inst/tmp/j-multiple.Rmd
heemod/inst/doc
heemod/inst/doc/a-introduction.html
heemod/inst/doc/a-introduction.R
heemod/inst/doc/i-reproduction.R
heemod/inst/doc/d-non-homogeneous.html
heemod/inst/doc/c-homogeneous.html
heemod/inst/doc/b-time-dependency.html
heemod/inst/doc/f-sensitivity.R
heemod/inst/doc/g-heterogeneity.Rmd
heemod/inst/doc/e-probabilistic.Rmd
heemod/inst/doc/b-time-dependency.Rmd
heemod/inst/doc/c-homogeneous.R
heemod/inst/doc/c-homogeneous.Rmd
heemod/inst/doc/i-reproduction.Rmd
heemod/inst/doc/h-tabular.Rmd
heemod/inst/doc/d-non-homogeneous.R
heemod/inst/doc/b-time-dependency.R
heemod/inst/doc/g-heterogeneity.R
heemod/inst/doc/e-probabilistic.html
heemod/inst/doc/d-non-homogeneous.Rmd
heemod/inst/doc/h-tabular.html
heemod/inst/doc/f-sensitivity.html
heemod/inst/doc/i-reproduction.html
heemod/inst/doc/f-sensitivity.Rmd
heemod/inst/doc/e-probabilistic.R
heemod/inst/doc/h-tabular.R
heemod/inst/doc/a-introduction.Rmd
heemod/inst/doc/g-heterogeneity.html
heemod/inst/tabular
heemod/inst/tabular/thr
heemod/inst/tabular/thr/THR_transition_probs.csv
heemod/inst/tabular/thr/THR_demographic_table.csv
heemod/inst/tabular/thr/THR_options.csv
heemod/inst/tabular/thr/output
heemod/inst/tabular/thr/output/psa_values.csv
heemod/inst/tabular/thr/output/cycle_values.csv
heemod/inst/tabular/thr/output/psa.png
heemod/inst/tabular/thr/output/state_counts.csv
heemod/inst/tabular/thr/output/icer_by_group.csv
heemod/inst/tabular/thr/output/dsa.png
heemod/inst/tabular/thr/output/acceptability.pdf
heemod/inst/tabular/thr/output/dsa.pdf
heemod/inst/tabular/thr/output/dsa_diff.png
heemod/inst/tabular/thr/output/dsa_diff.pdf
heemod/inst/tabular/thr/output/state_count_plot.pdf
heemod/inst/tabular/thr/output/acceptability.png
heemod/inst/tabular/thr/output/psa.pdf
heemod/inst/tabular/thr/output/dsa.csv
heemod/inst/tabular/thr/output/state_count_plot.png
heemod/inst/tabular/thr/THR_options_2core.csv
heemod/inst/tabular/thr/REFERENCE.csv
heemod/inst/tabular/thr/input_dataframes
heemod/inst/tabular/thr/input_dataframes/mr_table.xlsx
heemod/inst/tabular/thr/THR_states.csv
heemod/inst/tabular/thr/THR_parameters.csv
heemod/inst/tabular/thr/REFERENCE_2core.csv
heemod/inst/tabular/test
heemod/inst/tabular/test/THR_test_transition_probs_2.csv
heemod/inst/tabular/test/test_diff_mod_name
heemod/inst/tabular/test/test_diff_mod_name/THR_transition_probs.csv
heemod/inst/tabular/test/test_diff_mod_name/REFERENCE.csv
heemod/inst/tabular/test/test_diff_mod_name/THR_states.csv
heemod/inst/tabular/test/test_no_overwrite
heemod/inst/tabular/test/test_no_overwrite/THR_transition_probs.csv
heemod/inst/tabular/test/test_no_overwrite/THR_demographic_table.csv
heemod/inst/tabular/test/test_no_overwrite/THR_options.csv
heemod/inst/tabular/test/test_no_overwrite/output
heemod/inst/tabular/test/test_no_overwrite/output/state_count_plot_standard.png
heemod/inst/tabular/test/test_no_overwrite/REFERENCE.csv
heemod/inst/tabular/test/test_no_overwrite/input_dataframes
heemod/inst/tabular/test/test_no_overwrite/input_dataframes/mr_table.xlsx
heemod/inst/tabular/test/test_no_overwrite/THR_states.csv
heemod/inst/tabular/test/test_no_overwrite/THR_parameters.csv
heemod/inst/tabular/test/testing_CSV_file_with_comment_col.csv
heemod/inst/tabular/test/wrong_ext.tab
heemod/inst/tabular/test/THR_options.csv
heemod/inst/tabular/test/THR_test_states.csv
heemod/inst/tabular/test/edited_ref.csv
heemod/inst/tabular/test/THR_test_transition_probs.csv
heemod/inst/tabular/test/testing_XLS_file_with_comment_col.xls
heemod/inst/tabular/test/testing_XLSX_file_with_comment_col.xlsx
heemod/inst/tabular/test/THR_test_transition_probs_bad.csv
heemod/inst/tabular/test/test_no_output_dir
heemod/inst/tabular/test/test_no_output_dir/THR_transition_probs.csv
heemod/inst/tabular/test/test_no_output_dir/THR_demographic_table.csv
heemod/inst/tabular/test/test_no_output_dir/THR_options.csv
heemod/inst/tabular/test/test_no_output_dir/REFERENCE.csv
heemod/inst/tabular/test/test_no_output_dir/input_dataframes
heemod/inst/tabular/test/test_no_output_dir/input_dataframes/mr_table.xlsx
heemod/inst/tabular/test/test_no_output_dir/THR_states.csv
heemod/inst/tabular/test/test_no_output_dir/THR_parameters.csv
heemod/inst/tabular/test/bad_REFERENCE.csv
heemod/inst/tabular/test/toedit_REFERENCE.csv
heemod/tests
heemod/tests/testthat.R
heemod/tests/testthat
heemod/tests/testthat/test_parallel.R
heemod/tests/testthat/Rplots.pdf
heemod/tests/testthat/test_states.R
heemod/tests/testthat/test_look_up.R
heemod/tests/testthat/test_parameters.R
heemod/tests/testthat/test_run_model.R
heemod/tests/testthat/test_sensitivity.R
heemod/tests/testthat/test_transform.R
heemod/tests/testthat/test_gho.R
heemod/tests/testthat/test_expand.R
heemod/tests/testthat/test_tabular_input.R
heemod/tests/testthat/test_get_code.R
heemod/tests/testthat/test_model.R
heemod/tests/testthat/test_probabilistic.R
heemod/tests/testthat/test_matrix.R
heemod/tests/testthat/test_heterogeneity.R
heemod/NAMESPACE
heemod/NEWS.md
heemod/R
heemod/R/strategy_define.R
heemod/R/get_code.R
heemod/R/utils.R
heemod/R/combine.R
heemod/R/covariance.R
heemod/R/resamp_print.R
heemod/R/look_up.R
heemod/R/efficiency_frontier.R
heemod/R/theme_ggplot.R
heemod/R/sysdata.rda
heemod/R/resamp_define.R
heemod/R/param_print.R
heemod/R/run_model_summary.R
heemod/R/run_model_define.R
heemod/R/acceptability_curve.R
heemod/R/update.R
heemod/R/heemod.R
heemod/R/gho_mortality.R
heemod/R/matrix_plot.R
heemod/R/sensitivity_define.R
heemod/R/param_eval.R
heemod/R/newdata.R
heemod/R/resamp_eval.R
heemod/R/deprecated.R
heemod/R/density.R
heemod/R/sensitivity_eval.R
heemod/R/cluster.R
heemod/R/tabular_input.R
heemod/R/states_define.R
heemod/R/param_define.R
heemod/R/states_print.R
heemod/R/expand.R
heemod/R/transform.R
heemod/R/strategy_eval.R
heemod/R/matrix_eval.R
heemod/R/strategy_print.R
heemod/R/matrix_define.R
heemod/R/states_eval.R
heemod/R/zzz.R
heemod/R/sensitivity_print.R
heemod/vignettes
heemod/vignettes/g-heterogeneity.Rmd
heemod/vignettes/e-probabilistic.Rmd
heemod/vignettes/b-time-dependency.Rmd
heemod/vignettes/c-homogeneous.Rmd
heemod/vignettes/i-reproduction.Rmd
heemod/vignettes/h-tabular.Rmd
heemod/vignettes/d-non-homogeneous.Rmd
heemod/vignettes/f-sensitivity.Rmd
heemod/vignettes/a-introduction.Rmd
heemod/README.md
heemod/MD5
heemod/build
heemod/build/vignette.rds
heemod/DESCRIPTION
heemod/man
heemod/man/combine_models.Rd
heemod/man/create_states_from_tabular.Rd
heemod/man/eval_models_from_tabular.Rd
heemod/man/run_model_tabular.Rd
heemod/man/get_counts.Rd
heemod/man/safe-conversion.Rd
heemod/man/modify.Rd
heemod/man/get_values.Rd
heemod/man/eval_state_list.Rd
heemod/man/acceptability_curve.Rd
heemod/man/discount.Rd
heemod/man/plot.dsa.Rd
heemod/man/get_state_names.Rd
heemod/man/wtd_summary.Rd
heemod/man/as_expr_list.Rd
heemod/man/gather_model_info.Rd
heemod/man/check_states.Rd
heemod/man/get_frontier.Rd
heemod/man/save_outputs.Rd
heemod/man/create_options_from_tabular.Rd
heemod/man/compute_icer.Rd
heemod/man/filter_blanks.Rd
heemod/man/interp_heemod.Rd
heemod/man/check_names.Rd
heemod/man/run_model.Rd
heemod/man/is.wholenumber.Rd
heemod/man/define_transition.Rd
heemod/man/who-mortality.Rd
heemod/man/define_psa.Rd
heemod/man/define_multinom.Rd
heemod/man/cluster.Rd
heemod/man/eval_parameters.Rd
heemod/man/get_code.Rd
heemod/man/compute_values.Rd
heemod/man/expand_state.Rd
heemod/man/create_model_list_from_tabular.Rd
heemod/man/check_matrix.Rd
heemod/man/heemod.Rd
heemod/man/heemod_scale.Rd
heemod/man/update-model.Rd
heemod/man/read_file.Rd
heemod/man/run_psa.Rd
heemod/man/define_state_list.Rd
heemod/man/create_df_from_tabular.Rd
heemod/man/define_correlation.Rd
heemod/man/eval_resample.Rd
heemod/man/summary.run_model.Rd
heemod/man/get_parameter_names.Rd
heemod/man/create_matrix_from_tabular.Rd
heemod/man/insert.Rd
heemod/man/look_up.Rd
heemod/man/get_state_value_names.Rd
heemod/man/plur.Rd
heemod/man/clean_factors.Rd
heemod/man/plot.run_model.Rd
heemod/man/eval_strategy.Rd
heemod/man/probability.Rd
heemod/man/define_dsa.Rd
heemod/man/create_demographic_table.Rd
heemod/man/get_matrix.Rd
heemod/man/define_state.Rd
heemod/man/compute_counts.Rd
heemod/man/get_matrix_order.Rd
heemod/man/discount_hack.Rd
heemod/man/eval_strategy_newdata.Rd
heemod/man/file-checkers.Rd
heemod/man/plot.psa.Rd
heemod/man/create_parameters_from_tabular.Rd
heemod/man/create_model_from_tabular.Rd
heemod/man/eval_matrix.Rd
heemod/man/define_strategy.Rd
heemod/man/parse_multi_spec.Rd
heemod/man/run_dsa.Rd
heemod/man/get_state_number.Rd
heemod/man/define_parameters.Rd
heemod/man/make_names.Rd
heemod/man/density.Rd
heemod/man/check_strategy_index.Rd
heemod/man/list_all_same.Rd