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packDAMipd

"packDAMipd" is a package that allows to do decision analysis using Markov model. It allows estimating incremental cost effectiveness ratio and net monetary benefit for the strategies that you are trying to compare. For the Markov modelling, the parameters like transition probabilities, costs and qualys can be given either directly, or in a data file or the package will estimate the parameter using regression models. In such instances, the individual patient level data should be provided. This also allows estimating the qalys using a package in CRAN "valueEQ5D". Moreover to cost effectiveness analysis, the package can also be used to estimate the sensitivity analysis, both deterministic and probabilistic sensitivity analysis.

Usage

See the User Guide Vignette for examples on using the package.

For a simple toy model please see toy_model.R

Installation

You can install the released version from CRAN with the command:

install.packages("packDAMipd")

Alternatively, the latest release can be installed from www.github.com/sheejamk/packDAMipd

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Install

install.packages('packDAMipd')

Monthly Downloads

60

Version

0.2.0

License

GPL-3

Issues

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Repository

https://github.com/sheejamk/packDAMipd

Maintainer

Sheeja Manchira Krishnan

Last Published

February 19th, 2021

Functions in packDAMipd (0.2.0)

Function to find the keyword for family of distribution in glm

eval_assign_trans_prob

Attribute parameters to probabilities of transition matrix

check_list_markov_models

check the list of Markov models

check_values_states

Check if the values of health states are provided

check_treatment_arm

Function to return treatment arm

encode_codes_data

Function to get the codes and the corresponding entries

get_age_details

Function to get the details of the age column

convert_wtpertimediff_basis

Convert weight per time to given basis

convert_freq_diff_basis

Convert frequency medication to given basis

Parameter table created

convert_to_given_timeperiod

Convert period to given basis

use_generalised_linear_mixed_model

Function for generalised linear mixed model

adl_scoring table

assign_parameters

Function to assign the values of nested parameters from the parameter list

get_slope_intercept_cross

help function to keep slope and intercept portion ready in mixed model expression

convert_weight_diff_basis

Convert unit strength to given basis

value_ADL_scores_IPD

Function to convert ADL scores to a T score

calculate_icer_nmb

Estimation of ICER and NMB

convert_volume_basis

Convert volume to given basis

define_parameters_sens_anal

Define parameter lists for deterministic sensitivity analysis

Join Markov model objects

get_mean_sd_age

Function to return mean age from a data frame

get_slope_intercept

help function to keep slope and intercept portion ready in mixed model expression

Join health states

check_estimate_required_params

Function to check if the parameters are sufficient to define a distribution and if not see if we can estimate the parameters from the given parameters, e.g. for gamma distribution, shape and rate can be estimated from mean and sd

costing_inpatient_daycase_admission

Function to estimate the cost of inpatient admission but taken from GP records where HRG code or description known

get_outcome_details

Function to get the details of the outcome column

eval_assign_values_states

Attribute values in health states

get_col_multiple_pattern

Function to get cols for the pattern given

plot_dsa_nmb_range

Function to do some checks before plotting sensitivity analysis results

costing_AandE_admission

Function to estimate the cost of inpatient admission but taken from GP records where code or description known

define_transition_table

Define the table for transition

get_extension_file

Function to get extension of a file name

do_diagnostic_glm

Do the diagnostic test for glm model assumption

form_expression_lm

Form expression to use with lm()

form_expression_mixed_model_lme4

Form expression to use with mixed models

define_parameters

Function to return a list of parameters given

checks_markov_pick_method

Checks the input to run the Markov cycles and picks correct method

find_glm_distribution

Function to find the keyword for family of distribution in glm

checks_plot_dsa

Function to do some checks before plotting sensitivity analysis results

check_estimate_substitute_proper_params

####################################################################### Function to get the expression, analyse it for what distribution it is, then check if it has all parameters requires, if not estimate the required parameters from given parameters, and substitute it for actual expression that can be used with R stats package

Function to check the variable null or NA

define_parameters_psa

Define parameter lists for deterministic sensitivity analysis

get_name_value_probdistrb_def

Function to return the two parameters from a given expression separated by comma,

check_trans_prob

Check the transition probabilities for numeric values and unity row sum

costing_resource_use

Function to estimate the cost of resource use taken (from IPD)

Definition of health state class or health state constructor

get_gender_details

Function to get the details of the gender column

get_trial_arm_details

Function to get the details of the trial arm

find_keyword_rand_generation

Function to find the keyword for generating random numbers the distribution

plot_efficiency_frontier

Plot efficiency frontier

return_equal_liststring_col

Function to get the subset of data compared to a string after trimming the white spaces

do_diagnostic_linear_regression

Do the diagnostic test for lm model assumption

E1. Plot a Markov model

generate_wt_time_units

Function to get the weight and time units

generate_wt_vol_units

Function to get the weight and volume units

get_cost_ip_dc_hrg

Function to extract the unit hospital inpatient admission by matching HRG code

Get the attribute for the health state

return_equal_liststring_listcol

Function to get the subset of data compared to a string after trimming the white spaces

transition_cost_util

Create the the values of cost and utility while transition

plot_prediction_parametric_survival

Plot the predicted survival curves for covariates keeping the others fixed

get_parameter_estimated_regression

Get the parameter values using the provided statistical regression methods

Plot cost effectiveness acceptability curve

list_paramwise_psa_result

Function to list probabilistic sensitivity analysis results parameterwise

Function to plot results of sensitivity analysis do_sensitivity_analysis()

keep_results_plot_dsa

Function to do some checks before plotting sensitivity analysis results

get_eq5d_details

Function to get the details of the EQ5D column

find_keyword_regression_method

Function to find the keyword for regression methods

get_parameter_read

Get the parameter values from reading a file

Example trial data

plot_return_residual_cox

Plotting and return the residuals after cox proportional hazard model

use_parametric_survival

########################################################################### Get the parameter values using the survival analysis parametric survival

find_survreg_distribution

Function to find the keyword for survreg distribution

value_eq5d3L_IPD

Function to add EQ5D3L scores to IPD data

create_new_dataset

create new dataset while keeping cox regression results and returned coefficients

Function to do probabilistic sensitivity analysis

use_linear_mixed_model

Function for mixed effect regression

return_equal_str_col

Function to get the subset of data compared to a string after trimming the white spaces

use_linear_regression

########################################################################### Get the parameter values using the linear regression

Set the attribute for the health state

find_parameters_btn_operators

Function to return parameters with in a expression containing operators

do_sensitivity_analysis

Function to do deterministic sensitivity analysis

find_required_parameter_combs

Function to find the parameters that determine the probability distribution

get_cost_AandE_description

Function to extract the unit cost by descirption of AandE att matching description

get_colnames_codedvalues

Function to keep the column name, coded values and non response code into a dataframe

form_expression_glm

Form expression to use with glm()

get_parameter_def_distribution

Get the definition of given parameter distribution defined in a file

load_trial_data

Function to load the file containing trial data and return it

get_parameter_direct

Get the parameter values from reading a file

get_cost_AandE_code

Function to extract the unit hospital inpatient admission by matching code

make_string_covariates

Make a string of covariates using addition sign

plot_dsa_difference

Function to do some checks before plotting sensitivity analysis results

get_cost_ip_dc_description

Function to extract the unit hospital inpatient admission by matching description

get_slope_intercept_nested

help function to keep slope and intercept portion ready in mixed model expression

get_timepoint_details

Function to get the details of the time point column

map_eq5d5Lto3L_VanHout

Function to map EQ5D5L scores to EQ5D3L scores and then add to IPD data

get_mortality_from_file

Get the mortality rate values from reading a file

microcosting_liquids_long

Function to estimate the cost of liquids when IPD is in long format

plot_survival_cox_covariates

Plotting survival function for all covariates calculated from cox regression results and returned coefficients

Define an all zero trace matrix

Definition of strategy - or arm

microcosting_liquids_wide

Function to estimate the cost of liquids taken (from IPD)

plot_dsa_icer_range

Function to do some checks before plotting sensitivity analysis results

use_generalised_linear_model

############################################################################ Get the parameter values using logistic regression

populate_transition_matrix

Populate transition matrix

use_seemingly_unrelated_regression

Bivariate regression for correlated observations

microcosting_tablets_long

Function to estimate the cost of tablets when IPD is in long format

report_sensitivity_analysis

Function to report deterministic sensitivity analysis

use_coxph_survival

########################################################################### Get the parameter values using the survival analysis using cox proportional hazard

summary_plot_psa

Function to summarise and plot probabilistic sensitivity analysis

Definition of Markov model and trace

use_fh2_survival

############################################################################ Get the parameter values using the survival analysis using FH2 method

plot_dsa_others_range

Function to do some checks before plotting sensitivity analysis results

microcosting_patches_wide

Function to estimate the cost of patches taken (from IPD)

microcosting_patches_long

#'########################################################################### Function to estimate the cost of patches when IPD is in long format using a IPD data of long format

plot_return_residual_survival

Plotting and return the residuals after survival model

plot_return_survival_curve

Plotting survival function for all covariates using survfit

Predict risk/hazard function for cox ph regression

value_Shows_IPD

Function to estimate the cost of tablets taken (from IPD)

use_km_survival

########################################################################### Get the parameter values using the Kaplan-Meier survival analysis

return0_if_not_null_na

Function to return 0 if the param is not null or NA trimming the white spaces

microcosting_tablets_wide

Function to estimate the cost of tablets taken (from IPD)

prediction_regression

Do the prediction for regression

use_fh_survival

########################################################################### Get the parameter values using the survival analysis method FH

Parameter table created

Function to check the variable null or NA

value_eq5d5L_IPD

Function to add EQ5D5L scores to IPD data

use_survival_analysis

############################################################################ Get the parameter values using the survival analysis