run_rr: Summary measures base on epiR

In xiangpin/MetaMicrobiome: An R package for meta-analysis and visualization of Microbiome.

Description

Computes summary measures of risk and a chi-squared test for difference in the observed proportions from count data presented in a 2 by 2 table with high low vector. With multiple strata the function returns crude and Mantel-Haenszel adjusted measures of association and chi-squared tests of homogeneity(based on [epiR]{epi.2by2}.

Usage

run_rr(var_high_low, metadavector, prefix = "Group",
  grouptype = "Case", method = "cohort.count", conf.level = 0.95,
  score = "OR.strata.score", ...)

Arguments

var_high_low	list or vector, the list of vectors with high/low versus the threshold
metadavector	dataframe, metada dataframe contained the group information.
prefix	character, the header names of the metada data frame, default is 'Group'.
grouptype	character, the positive group names, default is "Case".
method	characer, a character string indicating the study design on which the tabular data has been based. Options are cohort.count, cohort.time, case.control, or cross.sectional, default is cohort.count. See epi.2by2 for details.
conf.level	numeric, magnitude of the returned confidence intervals. Must be a single number between 0 and 1. See epi.2by2 for details.
score	character, Wald and score confidence intervals for the effect value for each strata, default is OR.strata.score, See epi.2by2 for details .
...	Additional arguments passed to epi.2by2.

Details

TODO

Value

the summary measures of risk and a chi-squared test

Author(s)

Shuangbin Xu

xiangpin/MetaMicrobiome documentation built on May 26, 2019, 2:34 a.m.