Decision Analysis Modelling Package with Parameters Estimation Ability from Individual Patient Level Data

Documentation for package ‘packDAMipd’ version 0.2.2

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-- A --

adl_scoring	adl_scoring table
assign_parameters	Function to assign the values of nested parameters from the parameter list

-- B --

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Parameter table created

-- C --

calculate_icer_nmb	Estimation of ICER and NMB
checks_markov_pick_method	Checks the input to run the Markov cycles and picks correct method
checks_plot_dsa	Function to do some checks before plotting sensitivity analysis results
check_link_glm	Function to find the keyword for family of distribution in glm
check_list_markov_models	check the list of Markov models
check_null_na	Function to check the variable null or NA
check_trans_prob	Check the transition probabilities for numeric values and unity row sum
check_treatment_arm	Function to return treatment arm
check_values_states	Check if the values of health states are provided
combine_markov	Join Markov model objects
combine_state	Join health states
convert_freq_diff_basis	Convert frequency medication to given basis
convert_to_given_timeperiod	Convert period to given basis
convert_volume_basis	Convert volume to given basis
convert_weight_diff_basis	Convert unit strength to given basis
convert_wtpertimediff_basis	Convert weight per time to given basis
costing_AandE_admission	Function to estimate the cost of inpatient admission but taken from GP records where code or description known
costing_inpatient_daycase_admission	Function to estimate the cost of inpatient admission but taken from GP records where HRG code or description known
costing_resource_use	Function to estimate the cost of resource use taken (from IPD)
cost_data	cost matrix
create_new_dataset	create new dataset while keeping cox regression results and returned coefficients

-- D --

define_parameters	Function to return a list of parameters given
define_parameters_psa	Define parameter lists for deterministic sensitivity analysis
define_parameters_sens_anal	Define parameter lists for deterministic sensitivity analysis
define_transition_table	Define the table for transition
do_psa	Function to do probabilistic sensitivity analysis
do_sensitivity_analysis	Function to do deterministic sensitivity analysis

-- E --

encode_codes_data	Function to get the codes and the corresponding entries
eval_assign_trans_prob	Attribute parameters to probabilities of transition matrix
eval_assign_values_states	Attribute values in health states

-- F --

find_glm_distribution	Function to find the keyword for family of distribution in glm
find_keyword_rand_generation	Function to find the keyword for generating random numbers the distribution
find_keyword_regression_method	Function to find the keyword for regression methods
find_parameters_btn_operators	Function to return parameters with in a expression containing operators
find_required_parameter_combs	Function to find the parameters that determine the probability distribution
find_survreg_distribution	Function to find the keyword for survreg distribution
form_expression_glm	Form expression to use with glm()
form_expression_lm	Form expression to use with lm()
form_expression_mixed_model_lme4	Form expression to use with mixed models

-- G --

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_age_details	Function to get the details of the age column
get_colnames_codedvalues	Function to keep the column name, coded values and non response code into a dataframe
get_col_multiple_pattern	Function to get cols for the pattern given
get_cost_AandE_code	Function to extract the unit hospital inpatient admission by matching code
get_cost_AandE_description	Function to extract the unit cost by descirption of AandE att matching description
get_cost_ip_dc_description	Function to extract the unit hospital inpatient admission by matching description
get_cost_ip_dc_hrg	Function to extract the unit hospital inpatient admission by matching HRG code
get_eq5d_details	Function to get the details of the EQ5D column
get_extension_file	Function to get extension of a file name
get_gender_details	Function to get the details of the gender column
get_mean_sd_age	Function to return mean age from a data frame
get_mortality_from_file	Get the mortality rate values from reading a file
get_name_value_probdistrb_def	Function to return the two parameters from a given expression separated by comma,
get_outcome_details	Function to get the details of the outcome column
get_parameter_def_distribution	Get the definition of given parameter distribution defined in a file
get_parameter_direct	Get the parameter values from reading a file
get_parameter_estimated_regression	Get the parameter values using the provided statistical regression methods
get_parameter_read	Get the parameter values from reading a file
get_slope_intercept	help function to keep slope and intercept portion ready in mixed model expression
get_slope_intercept_cross	help function to keep slope and intercept portion ready in mixed model expression
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
get_trial_arm_details	Function to get the details of the trial arm
get_var_state	Get the attribute for the health state

-- H --

health_state

Definition of health state class or health state constructor

-- I --

init_trace

Define an all zero trace matrix

-- K --

keep_results_plot_dsa

Function to do some checks before plotting sensitivity analysis results

-- L --

list_paramwise_psa_result	Function to list probabilistic sensitivity analysis results parameterwise
load_trial_data	Function to load the file containing trial data and return it

-- M --

map_eq5d5Lto3L_VanHout	Function to map EQ5D5L scores to EQ5D3L scores and then add to IPD data
markov_model	Definition of Markov model and trace
microcosting_liquids_long	Function to estimate the cost of liquids when IPD is in long format
microcosting_liquids_wide	Function to estimate the cost of liquids 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
microcosting_patches_wide	Function to estimate the cost of patches taken (from IPD)
microcosting_tablets_long	Function to estimate the cost of tablets when IPD is in long format
microcosting_tablets_wide	Function to estimate the cost of tablets taken (from IPD)

-- P --

plot_ceac	Plot cost effectiveness acceptability curve
plot_dsa	Function to plot results of sensitivity analysis do_sensitivity_analysis()
plot_dsa_difference	Function to do some checks before plotting sensitivity analysis results
plot_dsa_icer_range	Function to do some checks before plotting sensitivity analysis results
plot_dsa_nmb_range	Function to do some checks before plotting sensitivity analysis results
plot_dsa_others_range	Function to do some checks before plotting sensitivity analysis results
plot_efficiency_frontier	Plot efficiency frontier
plot_model	E1. Plot a Markov model
plot_prediction_parametric_survival	Plot the predicted survival curves for covariates keeping the others fixed
plot_return_residual_cox	Plotting and return the residuals after cox proportional hazard model
plot_return_residual_survival	Plotting and return the residuals after survival model
plot_return_survival_curve	Plotting survival function for all covariates using survfit
plot_survival_cox_covariates	Plotting survival function for all covariates calculated from cox regression results and returned coefficients
populate_transition_matrix	Populate transition matrix
predict_coxph	Predict risk/hazard function for cox ph regression

-- R --

report_sensitivity_analysis	Function to report deterministic sensitivity analysis
return0_if_not_null_na	Function to return 0 if the param is not null or NA trimming the white spaces
return_equal_liststring_col	Function to get the subset of data compared to a string after trimming the white spaces
return_equal_liststring_listcol	Function to get the subset of data compared to a string after trimming the white spaces
return_equal_str_col	Function to get the subset of data compared to a string after trimming the white spaces

-- S --

set_var_state	Set the attribute for the health state
strategy	Definition of strategy - or arm
summary_plot_psa	Function to summarise and plot probabilistic sensitivity analysis

-- T --

table_param	Parameter table created
trace_data	Trace matrix
transition_cost_util	Create the the values of cost and utility while transition
trial_data	Example trial data

-- U --

use_coxph_survival	########################################################################### Get the parameter values using the survival analysis using cox proportional hazard
use_fh2_survival	############################################################################ Get the parameter values using the survival analysis using FH2 method
use_fh_survival	########################################################################### Get the parameter values using the survival analysis method FH
use_generalised_linear_mixed_model	Function for generalised linear mixed model
use_generalised_linear_model	############################################################################ Get the parameter values using logistic regression
use_km_survival	########################################################################### Get the parameter values using the Kaplan-Meier survival analysis
use_linear_mixed_model	Function for mixed effect regression
use_linear_regression	########################################################################### Get the parameter values using the linear regression
use_parametric_survival	########################################################################### Get the parameter values using the survival analysis parametric survival
use_seemingly_unrelated_regression	Bivariate regression for correlated observations
use_survival_analysis	############################################################################ Get the parameter values using the survival analysis
utility_data	utility matrix

-- V --

value_ADL_scores_IPD	Function to convert ADL scores to a T score
value_eq5d3L_IPD	Function to add EQ5D3L scores to IPD data
value_eq5d5L_IPD	Function to add EQ5D5L scores to IPD data
value_Shows_IPD	Function to estimate the cost of tablets taken (from IPD)

-- W --

word2num

Function to check the variable null or NA