toxboot: Main function to sample, fit, and write results to mongoDB

Description Usage Arguments Details See Also

View source: R/toxboot.R

Description

toxboot is the main function that performs the bootstrap sampling, fitting, and writing to the database

Usage

1
2
toxboot(dat, m4id, boot_method, replicates = 100, concvals = F,
  destination = "memory")

Arguments

dat

A data.table. Required columns are: logc: numeric, contains concentrations resp: numeric, normalized response values paired with concentrations m3id: numeric, value unique to each row corresponding to an individual concentration and response m4id: numeric, value unique to an aeid/spid pair. Multiple m3ids per m4id aeid: numeric, assay id spid: character, sample ID bmad: numeric, baseline mad. Unique to an aeid.

m4id

numeric length 1, m4id to bootstrap. Choice of m4id will determine which rows are selected, and therefore the values of logc, resp, m3id, aeid, spid, and bmad.

boot_method

parameter passed to toxbootReplicates to determine sampling method

replicates

number of bootstrap samples. Default 100

concvals

logical, default is FALSE. If TRUE, dose response samples written to the database as well.

destination

string length 1, options are "mongo", "mysql", "file", "memory"

Details

toxboot is the workhorse function of this package. This function will typically be wrapped in a mclapply to perform in parallel using toxbootmc. The dose response data is passed to toxbootReplicates. The returned matrix is passed to tcpl::tcplFit.

There are multiple options for saving the results, based on the value of destination.

The fitted results are assembled into a bson object using rmongodb and written to the mongoDB.

See Also

toxbootReplicates


toxboot documentation built on May 29, 2017, 10:53 p.m.