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

## Documentation for package ‘packDAMipd’ version 0.2.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D E F G H I K L M P R S T U V W

## -- A --

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

## -- B --

blank | 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