anpan_pwy_ranef_batch: Fit the pathway random effects model for multiple bugs

In biobakery/anpan: Quantifying Microbial Strain-Host Associations

Fit the pathway random effects model for multiple bugs

Description

Fit the pathway random effects model for multiple bugs

Usage

anpan_pwy_ranef_batch(
  bug_pwy_dat,
  group_ind = "crc",
  out_dir = NULL,
  group_exp_rate = 3,
  ...
)

Arguments

bug_pwy_dat	a data frame with a row for each observation and columns "pwy", "log10_species_abd", "log10_pwy_abd", and a group indicator column named according to the group_ind argument
group_ind	a character giving the name of the column for the 0/1 group indicator variable in bug_pwy_dat
out_dir	output directory
group_exp_rate	rate parameter of the exponential distribution prior on group effects
...	other arguments to pass to cmdstanr::sample()

Details

In addition to the column requirements of anpan_pwy_ranef(), the input data frame bug_pwy_dat here must also contain a variable called "bug" which gives a unique identifier for each bug.

Value

a tibble of row-binded anpan_pwy_ranef results

See Also

plot_pwy_ranef() , plot_pwy_ranef_intervals(), cmdstanr::CmdStanMCMC

Examples

## Not run: 
library(tidyverse)
library(anpan)

set.seed(123)
input_dat = tibble(bug = rep(paste0("bug", 1:5), each = 200),
                   pwy = rep(paste0('pwy', 1:5), times = 200),
                   log10_species_abd = rnorm(1000),
                   log10_pwy_abd = rnorm(1000, mean = .8*log10_species_abd),
                   group = sample(c(0,1), size = 1000, replace = TRUE))
 # ^ the pathway and and group are NOT related in any pathway.

res = anpan_pwy_ranef_batch(input_dat, group_ind = "group")

# Examine the summary
pwy_group_res = res |>
  dplyr::select(bug, summary_df) |>             # select the two main columns
  tidyr::unnest(c(summary_df)) |>               # unnest
  dplyr::filter(grepl("^pwy_eff", variable)) |> # get just the pwy:group terms
  dplyr::arrange(-abs(mean))                    # sort by decreasing effect size

print(pwy_group_res)

pwy_group_res |> filter(hit)
# ^ Here, there are no hits because we simulated with no dependence

## End(Not run)

biobakery/anpan documentation built on Aug. 14, 2024, 8:19 a.m.