adl_scoring             adl_scoring table
assign_parameters       Function to assign the values of nested
                        parameters from the parameter list
blank                   Parameter table created
calculate_icer_nmb      Estimation of ICER and NMB
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
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
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
cost_data               cost matrix
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)
create_new_dataset      create new dataset while keeping cox regression
                        results and returned coefficients
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
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
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
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_col_multiple_pattern
                        Function to get cols for the pattern given
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_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
health_state            Definition of health state class or health
                        state constructor
init_trace              Define an all zero trace matrix
keep_results_plot_dsa   Function to do some checks before plotting
                        sensitivity analysis results
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
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)
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
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
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
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
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
value_ADL_scores_IPD    Function to convert ADL scores to a T score
value_Shows_IPD         Function to estimate the cost of tablets taken
                        (from IPD)
value_eq5d3L_IPD        Function to add EQ5D3L scores to IPD data
value_eq5d5L_IPD        Function to add EQ5D5L scores to IPD data
word2num                Function to check the variable null or NA
