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

## Documentation for package ‘packDAMipd’ version 1.1.0

- 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 --

add_entries_sameuse_timepoint | Function to get sum of entries of resource per individual at diff timepoints if same cateogry has listed multiple time for same id of participant , this method comes in handy to get the sum
adl_scoring.df | adl_scoring table
assign_parameters | Function to assign the values of nested parameters from the parameter list

## -- B --

blank.df | 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_equal_columncontents_NAomitted | Function to check the equality of column contents between two data sets with omitting NA
check_equal_sumcolumncontents_NAomitted | Function to check the sum of column contents between two data sets with omitting NA
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
convert_wtpervoldiff_basis | Convert wt per unit volume 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_opioid_liquids_averageMED_long | Function to estimate the cost of liquids when IPD is in long format
costing_opioid_liquids_averageMED_wide | Function to estimate the cost of liquids taken (from IPD)
costing_opioid_patches_averageMED_long | #'########################################################################### Function to estimate the cost of patches when IPD is in long format using a IPD data of long format
costing_opioid_patches_averageMED_wide | Function to estimate the cost of patches taken (from IPD)
costing_opioid_tablets_averageMED_long | Function to estimate the cost of tablets when IPD is in long format
costing_opioid_tablets_averageMED_wide | Function to estimate the cost of tablets taken as an average cost per equivalent dose in the opioid scenario is the morphine equivalent dose (from IPD)
costing_opioid_tablets_MED_wide | Function to estimate the cost of tablets taken (from IPD)
costing_resource_use | Function to estimate the cost of resource use taken (from IPD)
cost_data.df | cost matrix
create_new_dataset | create new dataset while keeping cox regression results and returned coefficients
create_shorttable_from_gtsummary_compare_twogroups_timpoints | Create a table to compare the descriptive analysis (short) from gtsummary of two groups, but at different timepoints
create_table_from_gtsummary_compare_twogroups | Create a table to compare the descriptive analysis from gtsummary of two groups

## -- 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 | ISLR flextable huxtable nlme tm 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_rowwise_sum_multiplecol | Function to get sum of multiple columns of observations
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_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_doses_combination | Convert the combined dose to its individual component numerical value or can be unit/unit
get_doses_combination_units | Convert the combined dose to its individual component numerical value and units
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_single_col_multiple_pattern | Function to get cols for the pattern given
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
init_trace_sjtime | 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
map_resource_use_categories | Function to to read the text form of resource use and replace it with standard texts of resoure use ie. some one can describe GP visit as GP surgery visit, surgery visit or general practioners visit etc. Here all these texts should be given in a excel or csv file and then corresponidng standard form will be read from the file and will be replaced.
markov_model | Definition of Markov model and trace
markov_model_sojourntime | 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_psa | Function to plot CEAC
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_histogram_onetimepoint_twogroups | Function to plot mean and SE for longitudinal observations for twogroups compared
plot_meanSE_longitudinal_twogroups | Function to plot mean and SE for longitudinal observations for twogroups compared
plot_model | E1. Plot a Markov model
plot_nmb_lambda | Plot cost effectiveness acceptability curve
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
promis3a_scoring.df | promis 3a scoring table

## -- 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.df | Parameter table created
trace_data.df | Trace matrix
transition_cost_util | Create the the values of cost and utility while transition
trial_data.df | 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.df | 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_promis3a_scores_IPD | Function to convert promis3a scores to a T score
value_Shows_IPD | Function to estimate the cost of tablets taken (from IPD)

## -- W --

word2num | Function to check the variable null or NA