readCyclopsData: Read Cyclops data from file

In Cyclops: Cyclic Coordinate Descent for Logistic, Poisson and Survival Analysis

Read Cyclops data from file

Description

readCyclopsData reads a Cyclops-formatted text file.

Usage

readCyclopsData(fileName, modelType)

Arguments

fileName	Name of text file to be read. If fileName does not contain an absolute path,
modelType	character string: Valid types are listed below.

Details

This function reads a Cyclops-formatted text file and returns a Cyclops data object. The first line of the file may start with '‘⁠#⁠’', indicating that it contains header options. Valid header options are:

⁠ row_label⁠	(assume file contains a numeric column of unique row identifiers)
⁠ stratum_label⁠	(assume file contains a numeric column of stratum identifiers)
⁠ weight⁠	(assume file contains a column of row-specific model weights, currently unused)
⁠ offset⁠	(assume file contains a dense column of linear predictor offsets)
⁠ bbr_outcome⁠	(assume logistic outcomes are encoded -1/+1 following BBR)
⁠ log_offset⁠	(assume file contains a dense column of values x_i for which log(x_i) is the offset)
⁠ add_intercept⁠	(automatically include an intercept column of all 1s for each entry)
⁠ indicator_only⁠	(assume all covariates 0/1-valued and only covariate name is given)
⁠ sparse⁠	(force all BBR formatted covariates to be represented as sparse, instead of
	sparse-indicator, columns .. really only for debugging)
⁠ dense⁠	(force all BBR formatted covariates to be represented as dense columns.. really
	only for debugging)

Successive lines of the file are white-space delimited and follow the format:

	[Row ID] {Stratum ID} [Weight] <Outcome> {Censored} {Offset} <BBR covariates>

• ⁠[optional]⁠

• ⁠<required>⁠

• ⁠{required or optional depending on model}⁠

Bayesian binary regression (BBR) covariates are white-space delimited and generally in a sparse ‘⁠<name>:<value>⁠’ format, where ‘⁠name⁠’ must (currently) be numeric and ‘⁠value⁠’ is non-zero. If option ‘⁠indicator_only⁠’ is specified, then format is simply ‘⁠<name>⁠’. ‘⁠Row ID⁠’ and ‘⁠Stratum ID⁠’ must be numeric, and rows must be sorted such that equal ‘⁠Stratum ID⁠’ are consecutive. ‘⁠Stratum ID⁠’ is required for ‘⁠clr⁠’ and ‘⁠sccs⁠’ models. ‘⁠Censored⁠’ is required for a ‘⁠cox⁠’ model. ‘⁠Offset⁠’ is (currently) required for a ‘⁠sccs⁠’ model.

Value

A list that contains a Cyclops model data object pointer and an operation duration

Models

Currently supported model types are:

⁠ "ls"⁠	Least squares
⁠ "pr"⁠	Poisson regression
⁠ "lr"⁠	Logistic regression
⁠ "clr"⁠	Conditional logistic regression
⁠ "cpr"⁠	Conditional Poisson regression
⁠ "sccs"⁠	Self-controlled case series
⁠ "cox"⁠	Cox proportional hazards regression
⁠ "fgr"⁠	Fine-Gray proportional subdistribution hazards regression

Examples

## Not run: 
dataPtr = readCyclopsData(system.file("extdata/infert_ccd.txt", package="Cyclops"), "clr")

## End(Not run)

Cyclops documentation built on June 22, 2024, 10:24 a.m.