CATpmc: Population-mean Cosinor (PMC)

In CATkit: Chronomics Analysis Toolkit (CAT): Periodicity Analysis

Description

When data are collected as a function of time on 3 or more individuals, the population-mean cosinor procedure renders it possible to make inferences concerning a population rhythm, provided the individuals considered represent a random sample from that population. Each individual series is analyzed by the single- or multiple-component single cosinor. The PMC uses takes these results as input. Assuming that the within-individual variances are the same, the PMC estimates the population rhythm parameters by calculating the arithmetic mean of individual MESORs and the vectorial average of individual amplitude-acrophase pairs.

Usage

CATpmc(data, fileName, colNames, VarID=NA, GrpID = NA, alpha = 0.05, 
        header=FALSE, sep="\t", Output=list(Doc=TRUE, Txt=FALSE), 
        functionName="", title="")

Arguments

fileName	(optional) A data file with path; either a data frame (cosinor parameters) or fileName must be provided. "/" is used on Macs in the file pathname; "/" changes to "\" on PCs.
data	(optional) An array of data; either a data frame object or fileName must be provided.
colNames	Specific column names are required by the program: PR, MESOR, Amp, Phi (case insensitive). Must be specified if column headers are absent, or if you wish to rename columns.
GrpID	(optional) a vector of column names (or numbers) referring to factors to be used for grouping populations by levels in each factor (group identifiers). A PMC is performed on the full population, and on each sub-population grouped by factor level, for each GrpID specified; if multiple GrpIDs are specified, corresponding to multiple factors, PMC is also performed on all combinations across all factor levels. If no GrpIDs are specified, only the full population PMC is performed.
VarID	(optional) a single column can be included as a Variable. Each population identified by variable name (value) in the VarID column is compared with each population comparison defined under GrpID. A column would be specified as a VarID if it makes no sense to combine multiple levels (values) for PMC – such as combining temperature with blood pressure, or rhythm parameters related to different trial periods.
alpha	significance level (p) for testing (default = .05).
header	does the file have a header? (default = TRUE); column headers are used as column names unless colNames is used.
sep	is the file tab delimited ("\t") or comma delimited (",") (default = "\t").
Output	Doc=TRUE will output an RTF file; Doc=FALSE will not. Output is always sent to the console.
functionName	a short descriptor, this will be used as a part of the file name for use in identifying output.
title	A longer text descriptor printed out in the header of the result file.

Input Data:

The PMC uses the parameters resulting from a single- or multiple-component single cosinor as input.

Data format: Comma or tab delimited file. There are four required column headers, one optional VarID (variable) column, and any number of (optional) GrpID (factor) columns: PR, MESOR, Amp, Phi, variable, factor1, factor2, ....

Output:

Data Format: An .rtf data file is written to the same file path where the data file is found.

Returned: An output data frame is returned from the function call, and printed to the console.

Author(s)

Cathy Lee Gierke, Germaine Cornelissen-Guillaume

Maintainer: Cathy Lee Gierke <[e-mail]>

References

http://564394709114639785.weebly.com/running-cat-pmc.html

Examples

                # Data is from east Indian subjects:  lipids, smoking, diet, gender, age group
                #        every 6 hours.
                #---------------------  Vignette4    Population-Mean Cosinor  
                # PMC according to behavioral factors and lipids for a population of subjects
                
                #  Normally you would use these lines to read a file for use in CATkit 
                #        (use filePath format for your OS)
                # filePath<-"~/file/path/Installing CAT/Vignette4"          # use for mac
                # filePath<-"c:\file\path\Installing CAT\Vignette4"     # use for PC
                # fileName<-file.path(filePath,'cos02x03.csv')
                
                # this line is used instead of the above since it is part of a package.
                file.copy(system.file("extdata", "cos02x03.csv", package = "CATkit"), 
                    tempdir(), overwrite = TRUE, recursive = FALSE, copy.mode = TRUE, 
                    copy.date = FALSE)
                filePath<-tempdir()
                fileName<-file.path(filePath,'cos02x03.csv')

                #fileName<-system.file("extdata", "cos02x03.csv", package = "CATkit")
                CATpmc(fileName=fileName, VarID=8, GrpID=c(5,10),header=TRUE,
                sep=",",functionName="V8,G5,10", title="Vignette3 V8,G5,10")
                

CATkit documentation built on May 2, 2019, 2:31 p.m.