
Statistical modelling for individual taxa across multiple ranks
Source:R/taxatree_models.R
taxatree_models.Rd
taxatree_models
runs tax_model
on every taxon at multiple taxonomic
ranks (you choose which ranks with the plural ranks
argument).
It returns the results as a named nested list of models
attached to a psExtra object.
One list per rank, one model per taxon at each rank.
The result can then be used with taxatree_models2stats
to extract a
dataframe of statistics for use with taxatree_plots
.
Usage
taxatree_models(
ps,
ranks = NULL,
type = "lm",
variables = NULL,
formula = NULL,
use_future = FALSE,
checkVars = TRUE,
checkNA = "warning",
verbose = "rank",
trans = "identity",
trans_args = list(),
...
)
Arguments
- ps
phyloseq object or psExtra
- ranks
vector of rank names at which to aggregate taxa for modelling
- type
name of regression modelling function, or the function itself
- variables
vector of variable names, to be used as model formula right hand side. If variables is a list, not a vector, a model is fit for each entry in list.
- formula
Right hand side of a formula, as a formula object or character string. Or a list of these. (alternative to variables argument, do not provide both)
- use_future
if TRUE parallel processing with future is possible, see details of ?tax_model.
- checkVars
check variance of variables?
- checkNA
check variables for NAs?
- verbose
message about progress: "rank" only notifies which rank is being processed; TRUE notifies you about each taxon being processed; FALSE for no messages.
- trans
name of tax_transform transformation to apply to aggregated taxa before fitting statistical models
- trans_args
named list of any additional arguments to tax_transform e.g. list(zero_replace = "halfmin")
- ...
extra arguments are passed directly to modelling function
See also
tax_model
for more details and examples
taxatree_plots
for how to plot the output of taxatree_models