zGPS_tool: Perform zGPS analysis on real data.

In umich-biostatistics/zGPS.AO: Zero Inflated Gamma Poisson Shrinker with Adverse Event Ontology

Description

Perform zGPS analysis on real data.

Usage

zGPS_tool(grp_data, pair_data, merge_list, min_freq = 15, min_size = 20)

Arguments

grp_data	a data.frame containing the following 2 columns: AE_NAME: The name of the Adverse Event (AE) GROUP_NAME: The AE group of the AE
pair_data	a data.frame containing the following 3 columns: ID: The unique identifier of the report VAX_TYPE: The vaccines appeared in the report AE_NAME: The AEs appeared in the report Please notice that this data reflects all the vaccine-AE combinations. If n1 AEs and n2 vaccines are mentioned in one reports, then n1*n2 pairs should be generated in the data.
merge_list,	a list with nesting lists, indicating which vaccines are of interest and which vaccines are to be merged. For example, if you are interested in vaccines FLU3 and FLU4, and you want to merge them into one vaccine FLU, you would like to add list(c('FLU3','FLU4'),'FLU') in this list
min_freq	a non-negative integer indicating the criteria for scarce AEs. If an AE appears less than 'min_freq' times in the data.frame pair_data, it will be labeled as scarce and be ignored in the study. It can be set to 0.
min_size	a positive integer indicating the criteria for small AE groups. If an AE group contains less than 'min_size' AEs, it will be label as a small AE group, and be ignored from the study.

Value

An object of S3 class zGPS. It contains a big data.frame 'big_data' containing the following columns:

• y: The weighted count of the vaccine-AE cell

• E: The baseline frequency of the vaccine-AE cell

• vaccine: The vaccine type

• AE_grp: The AE group

• AE: The Adverse Event (AE)

• s: The group level RR for this vaccine

• r: The over dispersion parameter for this AE group

• p: The zero component probability of this vaccine-AE_grp combination

• beta: The log mean parameter for this vaccine-AE_grp combination

• lambda_hat: The individual AE RR (Bayes Estimator)

It also contains the input arguments 'pair_data', 'grp_lst', and the 'merge_list'. It has another list 'resample_results', which is for the bootstrap.

umich-biostatistics/zGPS.AO documentation built on Sept. 26, 2021, 5:21 p.m.