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Last data update: 2014.03.03

R: Match IDs from Clinical and Actigraph Data

fda.matchid

R Documentation

Match IDs from Clinical and Actigraph Data

Description

A function used to match actigraphy data and clinical covariates by subject IDs and return a list of the data combined by IDs. Only the subjects with both actigraphy and covariate data will be returned by this function.

Usage

fda.matchid(mat, acov, type, grouplab)

Arguments

`mat`	A data frame with the rows being the time and the columns being the activity, with the column names being the subjects.
`acov`	A two column data frame that contains only subject IDs and a covariate of interest, respectively.
`type`	A string specifying either `"contin"` for continuous and `"factor"` for categorical covariates.
`grouplab`	A vector of names of the categories if `type is TRUE`.

Details

Note: Only the subjects with both actigraphy and covariate data will be returned by this function.

Value

A list consisting of two components as follows:

`mat`	A matrix where rows represent the time, columns are the samples, and the column names are the subjects.
`cov`	A two column matrix that contains the actigraphy data and clinical covariates.

Author(s)

William D. Shannon, Tao Li, Hong Xian, Jia Wang, Elena Deych, Carlos Gonzalez

Examples

	data(act_29pt)
	data(clinic_29pt_ahi)
	
	colnames(act_29pt) <- sub("X", "", colnames(act_29pt)) 
	data <- as.matrix(act_29pt[,-1])
	
	### Example 1: Continuous Covariate
	matchida  <- fda.matchid(data, clinic_29pt_ahi, "contin")
	
	
	### Example 2: Categorical Covariate
	ahi <- clinic_29pt_ahi
	
	ahi$ahicat <- as.factor(ifelse(ahi$AHI >= 0 & ahi$AHI <= 5, 1, 
	       ifelse(ahi$AHI > 5 & ahi$AHI <= 15, 2,
	       ifelse(ahi$AHI > 15 & ahi$AHI <= 30, 3,
	       ifelse(ahi$AHI > 30, 4, 0)))))
	
	matchidb  <- fda.matchid(data, ahi[,-2], "factor", 
		c("normal", "mild", "moderate", "severe"))

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(Actigraphy)
Loading required package: fda
Loading required package: splines
Loading required package: Matrix

Attaching package: 'fda'

The following object is masked from 'package:graphics':

    matplot

> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/Actigraphy/fda.matchid.Rd_%03d_medium.png", width=480, height=480)
> ### Name: fda.matchid
> ### Title: Match IDs from Clinical and Actigraph Data
> ### Aliases: fda.matchid
> 
> ### ** Examples
> 
> 	data(act_29pt)
> 	data(clinic_29pt_ahi)
> 	
> 	colnames(act_29pt) <- sub("X", "", colnames(act_29pt)) 
> 	data <- as.matrix(act_29pt[,-1])
> 	
> 	### Example 1: Continuous Covariate
> 	matchida  <- fda.matchid(data, clinic_29pt_ahi, "contin")
> 	
> 	
> 	### Example 2: Categorical Covariate
> 	ahi <- clinic_29pt_ahi
> 	
> 	ahi$ahicat <- as.factor(ifelse(ahi$AHI >= 0 & ahi$AHI <= 5, 1, 
+ 	       ifelse(ahi$AHI > 5 & ahi$AHI <= 15, 2,
+ 	       ifelse(ahi$AHI > 15 & ahi$AHI <= 30, 3,
+ 	       ifelse(ahi$AHI > 30, 4, 0)))))
> 	
> 	matchidb  <- fda.matchid(data, ahi[,-2], "factor", 
+ 		c("normal", "mild", "moderate", "severe"))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>