# thetatildefun: thetatildefun In SOHPIE: Statistical Approach via Pseudo-Value Information and Estimation

 thetatildefun R Documentation

## thetatildefun

### Description

A function to calculate jackknife pseudo-values

### Usage

``````thetatildefun(thetahatinput, thetahatdropinput, sizegroup)
``````

### Arguments

 `thetahatinput` A network centrality calculated from association matrix for whole sample. `thetahatdropinput` Network centralities calculated from re-estimated association matrices for leave-one-out samples. `sizegroup` Sample size for group.

### Value

A jackknife pseudo-value will be returned.

### Examples

``````
# In this example, the subset of the American Gut Project data will be used.
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]

# 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)

# Now, we estimate (and re-estimate) association matrices
# for each group separately.
asso_matA = asso_mat(OTUdat=OTUtab, group=newindex_grpA)
asso_matB = asso_mat(OTUdat=OTUtab, group=newindex_grpB)

# Calculate the network centrality.
thetahat_grpA = thetahats(asso_matA\$assomat)
thetahat_grpB = thetahats(asso_matB\$assomat)

# Obtain network centrality for the re-estimated association matrices.
thetahat_drop_grpA = sapply(asso_matA\$reest.assomat, thetahats)
thetahat_drop_grpB = sapply(asso_matB\$reest.assomat, thetahats)

# Sample sizes for each group.
n_A <- length(newindex_grpA)
n_B <- length(newindex_grpB)

# Now calculate jackknife pseudo-values for each group.
thetatilde_grpA = thetatildefun(thetahat_grpA, thetahat_drop_grpA, n_A)
thetatilde_grpB = thetatildefun(thetahat_grpB, thetahat_drop_grpB, n_B)

``````

SOHPIE documentation built on Oct. 24, 2023, 1:06 a.m.