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"# packDAMipd"

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install.packages('packDAMipd')

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1.1.0

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GPL-3

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Maintainer

Sheeja Manchira Krishnan

Last Published

March 24th, 2024

Functions in packDAMipd (1.1.0)

checks_markov_pick_method

Checks the input to run the Markov cycles and picks correct method
check_values_states

Check if the values of health states are provided
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
check_estimate_substitute_proper_params

####################################################################### Function to get the expression, analyse it for what distribution it is, then check if it has all parameters requires, if not estimate the required parameters from given parameters, and substitute it for actual expression that can be used with R stats package
check_null_na

Function to check the variable null or NA
check_list_markov_models

check the list of Markov models
convert_wtpertimediff_basis

Convert weight per time to given basis
convert_weight_diff_basis

Convert unit strength to given basis
check_link_glm

Function to find the keyword for family of distribution in glm
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
adl_scoring.df

adl_scoring table
check_estimate_required_params

Function to check if the parameters are sufficient to define a distribution and if not see if we can estimate the parameters from the given parameters, e.g. for gamma distribution, shape and rate can be estimated from mean and sd
combine_state

Join health states
convert_freq_diff_basis

Convert frequency medication to given basis
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)
define_parameters_psa

Define parameter lists for deterministic sensitivity analysis
convert_wtpervoldiff_basis

Convert wt per unit volume to given basis
check_trans_prob

Check the transition probabilities for numeric values and unity row sum
check_treatment_arm

Function to return treatment arm
cost_data.df

cost matrix
convert_to_given_timeperiod

Convert period to given basis
convert_volume_basis

Convert volume to given basis
find_keyword_regression_method

Function to find the keyword for regression methods
costing_resource_use

Function to estimate the cost of resource use taken (from IPD)
do_diagnostic_linear_regression

Do the diagnostic test for lm model assumption
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)
combine_markov

Join Markov model objects
find_survreg_distribution

Function to find the keyword for survreg distribution
blank.df

Parameter table created
define_parameters_sens_anal

ISLR flextable huxtable nlme tm Define parameter lists for deterministic sensitivity analysis
assign_parameters

Function to assign the values of nested parameters from the parameter list
checks_plot_dsa

Function to do some checks before plotting sensitivity analysis results
do_psa

Function to do probabilistic sensitivity analysis
find_parameters_btn_operators

Function to return parameters with in a expression containing operators
form_expression_glm

Form expression to use with glm()
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_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_MED_wide

Function to estimate the cost of tablets taken (from IPD)
define_transition_table

Define the table for transition
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
do_diagnostic_glm

Do the diagnostic test for glm model assumption
form_expression_lm

Form expression to use with lm()
generate_wt_time_units

Function to get the weight and time units
costing_opioid_tablets_averageMED_long

Function to estimate the cost of tablets when IPD is in long format
generate_wt_vol_units

Function to get the weight and volume units
get_extension_file

Function to get extension of a file name
get_eq5d_details

Function to get the details of the EQ5D column
get_mean_sd_age

Function to return mean age from a data frame
get_gender_details

Function to get the details of the gender column
get_slope_intercept

help function to keep slope and intercept portion ready in mixed model expression
plot_dsa_icer_range

Function to do some checks before plotting sensitivity analysis results
get_slope_intercept_nested

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
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.
get_timepoint_details

Function to get the details of the time point column
plot_model

E1. Plot a Markov model
form_expression_mixed_model_lme4

Form expression to use with mixed models
markov_model

Definition of Markov model and trace
define_parameters

Function to return a list of parameters given
get_doses_combination

Convert the combined dose to its individual component numerical value or can be unit/unit
find_glm_distribution

Function to find the keyword for family of distribution in glm
create_table_from_gtsummary_compare_twogroups

Create a table to compare the descriptive analysis from gtsummary of two groups
find_keyword_rand_generation

Function to find the keyword for generating random numbers the distribution
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
markov_model_sojourntime

Definition of Markov model and trace
get_doses_combination_units

Convert the combined dose to its individual component numerical value and units
microcosting_liquids_long

Function to estimate the cost of liquids when IPD is in long format
get_cost_AandE_code

Function to extract the unit hospital inpatient admission by matching code
plot_dsa_nmb_range

Function to do some checks before plotting sensitivity analysis results
return0_if_not_null_na

Function to return 0 if the param is not null or NA trimming the white spaces
eval_assign_values_states

Attribute values in health states
eval_assign_trans_prob

Attribute parameters to probabilities of transition matrix
plot_dsa_others_range

Function to do some checks before plotting sensitivity analysis results
get_cost_AandE_description

Function to extract the unit cost by descirption of AandE att matching description
plot_ceac_psa

Function to plot CEAC
plot_efficiency_frontier

Plot efficiency frontier
get_parameter_estimated_regression

Get the parameter values using the provided statistical regression methods
microcosting_tablets_wide

Function to estimate the cost of tablets taken (from IPD)
get_parameter_direct

Get the parameter values from reading a file
return_equal_liststring_col

Function to get the subset of data compared to a string after trimming the white spaces
make_string_covariates

Make a string of covariates using addition sign
get_single_col_multiple_pattern

Function to get cols for the pattern given
plot_survival_cox_covariates

Plotting survival function for all covariates calculated from cox regression results and returned coefficients
get_parameter_read

Get the parameter values from reading a file
map_eq5d5Lto3L_VanHout

Function to map EQ5D5L scores to EQ5D3L scores and then add to IPD data
plot_nmb_lambda

Plot cost effectiveness acceptability curve
get_trial_arm_details

Function to get the details of the trial arm
get_var_state

Get the attribute for the health state
use_seemingly_unrelated_regression

Bivariate regression for correlated observations
encode_codes_data

Function to get the codes and the corresponding entries
do_sensitivity_analysis

Function to do deterministic sensitivity analysis
find_required_parameter_combs

Function to find the parameters that determine the probability distribution
get_mortality_from_file

Get the mortality rate values from reading a file
get_cost_ip_dc_hrg

Function to extract the unit hospital inpatient admission by matching HRG code
find_rowwise_sum_multiplecol

Function to get sum of multiple columns of observations
get_cost_ip_dc_description

Function to extract the unit hospital inpatient admission by matching description
return_equal_liststring_listcol

Function to get the subset of data compared to a string after trimming the white spaces
transition_cost_util

Create the the values of cost and utility while transition
return_equal_str_col

Function to get the subset of data compared to a string after trimming the white spaces
trace_data.df

Trace matrix
get_name_value_probdistrb_def

Function to return the two parameters from a given expression separated by comma,
use_survival_analysis

############################################################################ Get the parameter values using the survival analysis
predict_coxph

Predict risk/hazard function for cox ph regression
plot_return_residual_survival

Plotting and return the residuals after survival model
microcosting_patches_wide

Function to estimate the cost of patches taken (from IPD)
plot_return_survival_curve

Plotting survival function for all covariates using survfit
microcosting_tablets_long

Function to estimate the cost of tablets when IPD is in long format
populate_transition_matrix

Populate transition matrix
init_trace

Define an all zero trace matrix
health_state

Definition of health state class or health state constructor
init_trace_sjtime

Define an all zero trace matrix
prediction_regression

Do the prediction for regression
summary_plot_psa

Function to summarise and plot probabilistic sensitivity analysis
value_eq5d3L_IPD

Function to add EQ5D3L scores to IPD data
value_Shows_IPD

Function to estimate the cost of tablets taken (from IPD)
set_var_state

Set the attribute for the health state
strategy

Definition of strategy - or arm
use_linear_regression

########################################################################### Get the parameter values using the linear regression
use_parametric_survival

########################################################################### Get the parameter values using the survival analysis parametric survival
list_paramwise_psa_result

Function to list probabilistic sensitivity analysis results parameterwise
plot_dsa

Function to plot results of sensitivity analysis do_sensitivity_analysis()
load_trial_data

Function to load the file containing trial data and return it
microcosting_liquids_wide

Function to estimate the cost of liquids taken (from IPD)
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
keep_results_plot_dsa

Function to do some checks before plotting sensitivity analysis results
trial_data.df

Example trial data
microcosting_patches_long

#'########################################################################### Function to estimate the cost of patches when IPD is in long format using a IPD data of long format
plot_dsa_difference

Function to do some checks before plotting sensitivity analysis results
plot_return_residual_cox

Plotting and return the residuals after cox proportional hazard model
plot_prediction_parametric_survival

Plot the predicted survival curves for covariates keeping the others fixed
use_generalised_linear_mixed_model

Function for generalised linear mixed model
table_param.df

Parameter table created
report_sensitivity_analysis

Function to report deterministic sensitivity analysis
use_fh2_survival

############################################################################ Get the parameter values using the survival analysis using FH2 method
promis3a_scoring.df

promis 3a scoring table
use_fh_survival

########################################################################### Get the parameter values using the survival analysis method FH
use_coxph_survival

########################################################################### Get the parameter values using the survival analysis using cox proportional hazard
value_ADL_scores_IPD

Function to convert ADL scores to a T score
use_km_survival

########################################################################### Get the parameter values using the Kaplan-Meier survival analysis
utility_data.df

utility matrix
use_linear_mixed_model

Function for mixed effect regression
value_eq5d5L_IPD

Function to add EQ5D5L scores to IPD data
word2num

Function to check the variable null or NA
use_generalised_linear_model

############################################################################ Get the parameter values using logistic regression
value_promis3a_scores_IPD

Function to convert promis3a scores to a T score
calculate_icer_nmb

Estimation of ICER and NMB
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