heemod: Models for Health Economic Evaluation

Health Economic Evaluation Modelling: decision trees and cohort simulations. Provides a simple and consistent interface for Markov models specification, comparison, sensitivity and probabilistic analysis, input of survival models, etc. Models with time varying properties (non-homogeneous Markov models and semi-Markov models) are supported.

AuthorAntoine Filipovic-Pierucci [aut, cre], Kevin Zarca [aut], Matthew Wiener [ctb], Zdenek Kabat [ctb], Vojtech Filipec [ctb]
Date of publication2017-02-11 00:16:59
MaintainerAntoine Filipovic-Pierucci <pierucci@gmail.com>
LicenseGPL (>= 3)
Version0.8.0
https://github.com/pierucci/heemod
https://pierucci.org

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

combine_probs: Combine Probabilities

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_inflow: Define Inflow for a BIA

define_multinom: Define That Parameters Belong to the Same Multinomial...

define_parameters: Define Markov Model Parameters

define_part_surv: Define Partitioned Survival

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_survival: Define a Survival Distribution

define_transition: Define Transition Matrix for Markov Model

discount: Discount a Quantity Over Time

discount_hack: Hack to Work Around a Discounting Issue

dispatch_strategy: Dispatch Values According to Strategy

dispatch_strategy_hack: Hack to Automate Use of Strategy Name

distributions: Probability Density Functions for Probabilistic Uncertainty...

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

eval_transition: Evaluate Markov Model Transition Matrix

expand_state: Expand Time-Dependant States into Tunnel States

export_savi: Export PSA Results for SAVI

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_order: Return Markov Model Transition Matrix Order

get_parameter_names: Return parameters names

get_probs_from_surv: Extract Transition Probabilities from a Survival Model

get_state_names: Get State Names

get_state_number: Return Number of State

get_state_value_names: Return Names of State Values

get_transition: Get Markov Model Transition Matrix

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

rescale_discount_rate: Rescale Discount Rate

run_dsa: Run Sensitivity Analysis

run_model: Run 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

Functions

acceptability_curve Man page
as_expr_list Man page
as_integer_safe Man page
as_numeric_safe Man page
beta Man page
beta Man page
binomial Man page
check_matrix Man page
check_names Man page
check_states Man page
check_strategy_index Man page
clean_factors Man page
close_cluster Man page
cluster Man page
combine_models Man page
combine_probs Man page
compute_counts Man page
compute_icer Man page
compute_values Man page
create_demographic_table Man page
create_df_from_tabular Man page
create_matrix_from_tabular Man page
create_model_from_tabular Man page
create_model_list_from_tabular Man page
create_options_from_tabular Man page
create_parameters_from_tabular Man page
create_states_from_tabular Man page
define_correlation Man page
define_correlation_ Man page
define_distribution Man page
define_dsa Man page
define_dsa_ Man page
define_inflow Man page
define_multinom Man page
define_parameters Man page
define_parameters_ Man page
define_part_surv Man page
define_part_surv_ Man page
define_psa Man page
define_psa_ Man page
define_state Man page
define_state_ Man page
define_state_list Man page
define_state_list_ Man page
define_strategy Man page
define_strategy_ Man page
define_survival Man page
define_transition Man page
define_transition_ Man page
discount Man page
discount_hack Man page
dispatch_strategy Man page
dispatch_strategy_hack Man page
distributions Man page
eval_models_from_tabular Man page
eval_parameters Man page
eval_resample Man page
eval_state_list Man page
eval_strategy Man page
eval_strategy_newdata Man page
eval_transition Man page
expand_state Man page
expand_state.uneval_matrix Man page
expand_state.uneval_state_list Man page
export_savi Man page
filter_blanks Man page
gamma Man page
gather_model_info Man page
get_code Man page
get_code.run_model Man page
get_code.state Man page
get_code.uneval_matrix Man page
get_code.uneval_model Man page
get_code.uneval_parameters Man page
get_code.uneval_state_list Man page
get_counts Man page
get_counts.combined_model Man page
get_counts.eval_strategy Man page
get_counts.list Man page
get_counts.run_model Man page
get_counts.updated_model Man page
get_frontier Man page
get_matrix_order Man page
get_parameter_names Man page
get_probs_from_surv Man page
get_probs_from_surv Man page
get_probs_from_surv_ Man page
get_probs_from_surv_.flexsurvreg Man page
get_probs_from_surv_.surv_dist Man page
get_state_names Man page
get_state_number Man page
get_state_value_names Man page
get_transition Man page
get_values Man page
get_values.combined_model Man page
get_values.eval_strategy Man page
get_values.list Man page
get_values.run_model Man page
get_values.updated_model Man page
get_who_mr Man page
get_who_mr_ Man page
heemod Man page
heemod-package Man page
heemod_scale Man page
insert Man page
interp_heemod Man page
interp_heemod.default Man page
interp_heemod.part_surv Man page
interp_heemod.state Man page
interp_heemod.uneval_matrix Man page
interp_heemod.uneval_state_list Man page
is_csv Man page
is.wholenumber Man page
is_xls Man page
is_xlsx Man page
list_all_same Man page
logitnormal Man page
lognormal Man page
look_up Man page
make_names Man page
modify Man page
modify.state Man page
modify.uneval_matrix Man page
modify.uneval_parameters Man page
modify.uneval_state_list Man page
multinomial Man page
normal Man page
or_to_prob Man page
parse_multi_spec Man page
plot.dsa Man page
plot.psa Man page
plot.run_model Man page
plot.uneval_matrix Man page
plot.updated_model Man page
plur Man page
plur_y Man page
poisson Man page
probability Man page
prob_to_prob Man page
rate_to_prob Man page
read_file Man page
rescale_discount_rate Man page
rescale_prob Man page
rr_to_prob Man page
run_dsa Man page
run_model Man page
run_model_ Man page
run_model_tabular Man page
run_psa Man page
safe-conversion Man page
safe_convert Man page
save_outputs Man page
scale.combined_model Man page
scale.dsa Man page
scale.psa Man page
scale.run_model Man page
status_cluster Man page
summary.run_model Man page
triangle Man page
triangle Man page
update-model Man page
update.run_model Man page
use_cluster Man page
who-mortality Man page
wtd_summary Man page

Files

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/j-survival.Rmd
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/j-survival.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/j-survival.html
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_1missing.csv
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/example_multinom_params.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/survival_spec_1.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/REFERENCE_1probmissing.csv
heemod/inst/tabular/test/survival_spec_error_2.csv
heemod/inst/tabular/test/survival_spec_error_1.csv
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/survival_spec_2.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_survival.R
heemod/tests/testthat/test_transform.R
heemod/tests/testthat/test_gho.R
heemod/tests/testthat/test_expand.R
heemod/tests/testthat/test_efficiency_frontier.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/tests/testthat/test_dmhee.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/part_surv.R heemod/R/density.R heemod/R/sensitivity_eval.R heemod/R/evpi.R heemod/R/cluster.R heemod/R/tabular_input.R heemod/R/survival.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/dispatch_strategy.R heemod/R/states_eval.R heemod/R/zzz.R heemod/R/sensitivity_print.R
heemod/vignettes
heemod/vignettes/j-survival.Rmd
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/eval_transition.Rd heemod/man/discount.Rd heemod/man/plot.dsa.Rd heemod/man/get_state_names.Rd heemod/man/wtd_summary.Rd heemod/man/export_savi.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/define_part_surv.Rd heemod/man/read_file.Rd heemod/man/define_survival.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/combine_probs.Rd heemod/man/distributions.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/define_state.Rd heemod/man/dispatch_strategy_hack.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/define_inflow.Rd heemod/man/plot.psa.Rd heemod/man/create_parameters_from_tabular.Rd heemod/man/rescale_discount_rate.Rd heemod/man/create_model_from_tabular.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/get_transition.Rd heemod/man/make_names.Rd heemod/man/dispatch_strategy.Rd heemod/man/get_probs_from_surv.Rd heemod/man/check_strategy_index.Rd heemod/man/list_all_same.Rd

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