anpan_pwy_ranef: Estimate a species-pathway abundance random effects model

In biobakery/anpan: Quantifying Microbial Strain-Host Associations

Estimate a species-pathway abundance random effects model

Description

Fit a model of the form log10_pwy_abd ~ log10_species_abd + (1|pwy) + (0+group|pwy) for a single bug

Usage

anpan_pwy_ranef(
  bug_pwy_dat,
  group_ind = "crc",
  effect_size_threshold = 0.25,
  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
effect_size_threshold	effect size threshold for hit-calling pathway:group effects
group_exp_rate	rate parameter of the exponential distribution prior on group effects
...	other arguments to pass to cmdstanr::sample()

Details

The priors are as follows: A) student_t(3, mean(log10_pwy_abd), 2.5) on the intercept at the mean species abundance. B) half student_t(3, 0, 2.5) on the residual noise C) 0-centered normal priors on pathway specific effects C1) half student_t(5,0,2.5) on the SD of pathway intercepts C2) half standard normal on the SD of group-specific effects.

The pathway index is generated by converting the pwy column to a factor and then to the corresponding integer index.

The group_ind column should be numeric with values in 0,1

The main parameter of interest are the elements of the pwy_effects parameter. The "hit" column is defined by selecting the bug:pwy combinations where 1) 98% posterior intervals for the pwy:group effect exclude 0, 2) the absolute posterior mean exceeds the specified effect size threshold, and 3) the estimated fixed effect of log10_species_abd on log10_pwy_abd is positive.

Value

a list containing the CmdStanMCMC object of the model fit and a summary data frame.

See Also

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

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