stderrs_specific_var {SOHPIE}

stderrs_specific_var

Description

A function to retrieve a vector of standard error of coefficient estimates (betahats) of each taxa for one specific variable.

Usage

stderrs_specific_var(stderrstab, varname)

Arguments

stderrstab

A table that includes standard error of betahat for a specific variable.

varname

Specify the name of the variable of interest.

Value

A vector of standard error of betahats for a single variable from the model.

Examples

data(combinedamgut) # A complete data containing columns with taxa and clinical covariates.

# Note: The line below will use a toy example with the first 30 out of 138 taxa.
OTUtab = combinedamgut[ , 8:37]
# Clinical/demographic covariates (phenotypic data):
# Note: All of these covariates will be included in the regression, so
# please make sure that phenodat includes the variables that will be analyzed only.
phenodat = combinedamgut[, 1:7] # first column is ID, so not using it.
# Obtain indices of each grouping factor
# In this example, a variable indicating the status of living with a dog was chosen (i.e. bin_dog).
# Accordingly, Groups A and B imply living without and with a dog, respectively.
 newindex_grpA = which(combinedamgut$bin_dog == 0)
 newindex_grpB = which(combinedamgut$bin_dog == 1)

SOHPIEres <- SOHPIE_DNA(OTUdat = OTUtab, clindat = phenodat,
groupA = newindex_grpA, groupB = newindex_grpB, c = 0.5)

# stderrs() function will return standard error of betahats only.
stderrstab <- stderrs(SOHPIEres)

# stderrs_specific_var() will return standard error of coefficient estimates of
# a single variable of interest.
stderrs_specific_var(stderrstab = stderrstab, varname = "bin_dog")