Man pages for packDAMipd
Decision Analysis Modelling Package with Parameters Estimation Ability from Individual Patient Level Data
| adl_scoring | adl_scoring table |
| assign_parameters | Function to assign the values of nested parameters from the... |
| blank | Parameter table created |
| calculate_icer_nmb | Estimation of ICER and NMB |
| check_estimate_required_params | Function to check if the parameters are sufficient to define... |
| check_estimate_substitute_proper_params | #######################################################################... |
| check_link_glm | Function to find the keyword for family of distribution in... |
| check_list_markov_models | check the list of Markov models |
| check_null_na | Function to check the variable null or NA |
| checks_markov_pick_method | Checks the input to run the Markov cycles and picks correct... |
| checks_plot_dsa | Function to do some checks before plotting sensitivity... |
| check_trans_prob | Check the transition probabilities for numeric values and... |
| 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 |
| cost_data | cost matrix |
| costing_AandE_admission | Function to estimate the cost of inpatient admission but... |
| costing_inpatient_daycase_admission | Function to estimate the cost of inpatient admission but... |
| costing_resource_use | Function to estimate the cost of resource use taken (from... |
| create_new_dataset | create new dataset while keeping cox regression results and... |
| 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_diagnostic_glm | Do the diagnostic test for glm model assumption |
| do_diagnostic_linear_regression | Do the diagnostic test for lm model assumption |
| 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... |
| find_keyword_rand_generation | Function to find the keyword for generating random numbers... |
| 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... |
| find_required_parameter_combs | Function to find the parameters that determine the... |
| 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... |
| get_cost_AandE_code | Function to extract the unit hospital inpatient admission by... |
| get_cost_AandE_description | Function to extract the unit cost by descirption of AandE att... |
| get_cost_ip_dc_description | Function to extract the unit hospital inpatient admission by... |
| get_cost_ip_dc_hrg | Function to extract the unit hospital inpatient admission by... |
| 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... |
| 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... |
| get_parameter_direct | Get the parameter values from reading a file |
| get_parameter_estimated_regression | Get the parameter values using the provided statistical... |
| get_parameter_read | Get the parameter values from reading a file |
| get_slope_intercept | help function to keep slope and intercept portion ready in... |
| get_slope_intercept_cross | help function to keep slope and intercept portion ready in... |
| get_slope_intercept_nested | help function to keep slope and intercept portion ready in... |
| 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... |
| list_paramwise_psa_result | Function to list probabilistic sensitivity analysis results... |
| load_trial_data | Function to load the file containing trial data and return it |
| make_string_covariates | Make a string of covariates using addition sign |
| map_eq5d5Lto3L_VanHout | Function to map EQ5D5L scores to EQ5D3L scores and then add... |
| markov_model | Definition of Markov model and trace |
| microcosting_liquids_long | Function to estimate the cost of liquids when IPD is in long... |
| microcosting_liquids_wide | Function to estimate the cost of liquids taken (from IPD) |
| microcosting_patches_long | #'###########################################################################... |
| 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... |
| 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... |
| plot_dsa_difference | Function to do some checks before plotting sensitivity... |
| plot_dsa_icer_range | Function to do some checks before plotting sensitivity... |
| plot_dsa_nmb_range | Function to do some checks before plotting sensitivity... |
| plot_dsa_others_range | Function to do some checks before plotting sensitivity... |
| 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... |
| plot_return_residual_cox | Plotting and return the residuals after cox proportional... |
| 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... |
| populate_transition_matrix | Populate transition matrix |
| predict_coxph | Predict risk/hazard function for cox ph regression |
| prediction_regression | Do the prediction for 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... |
| return_equal_liststring_col | Function to get the subset of data compared to a string after... |
| return_equal_liststring_listcol | Function to get the subset of data compared to a string after... |
| return_equal_str_col | Function to get the subset of data compared to a string after... |
| 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... |
| 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 | ###########################################################################... |
| use_fh2_survival | ############################################################################... |
| use_fh_survival | ###########################################################################... |
| use_generalised_linear_mixed_model | Function for generalised linear mixed model |
| use_generalised_linear_model | ############################################################################... |
| use_km_survival | ###########################################################################... |
| use_linear_mixed_model | Function for mixed effect regression |
| use_linear_regression | ###########################################################################... |
| use_parametric_survival | ###########################################################################... |
| use_seemingly_unrelated_regression | Bivariate regression for correlated observations |
| use_survival_analysis | ############################################################################... |
| utility_data | utility matrix |
| 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) |
| word2num | Function to check the variable null or NA |
