[R] Repeated measures

[Chuck Cleland]

Tom Backer Johnsen wrote:
> I am having a hard time understanding how to perform a "repeated 
> measures" type of ANOVA with R.  When reading the document found here:
> 
> http://cran.r-project.org/doc/contrib/Lemon-kickstart/kr_repms.html
> 
> I find that there is a reference to a function make.rm () that is 
> supposed to rearrange a "one row per person" type of frame to a "one 
> row per observation" type of frame.  But that function does not seem 
> to be there.  Nor does the help.search suggest anything.  Is that 
> function buried in some package?

  I'm not able to find that function.  Perhaps that document is out of date.

> Is there  some simple documentation that might be useful somewhere? 
> Starting with a really simple problem (one group, two observations)?

  Here is an example showing the use of reshape() and analysis via aov()
and lme() in the nlme package.

tolerance <-
read.table("http://www.ats.ucla.edu/stat/Splus/examples/alda/tolerance1.txt",
            sep=",", header=TRUE)

tolerance.long <- reshape(tolerance,
                          varying = list(c("tol11","tol12","tol13",
                                           "tol14", "tol15")),
                          v.names = c("tol"), timevar = "time",
                          times = 11:15, direction = "long")

tolerance.aov <- aov(tol ~ as.factor(time) * male + Error(id),
                     data = tolerance.long)

summary(tolerance.aov)

Error: id
     Df   Sum Sq  Mean Sq
male  1 0.085168 0.085168

Error: Within
                     Df  Sum Sq Mean Sq F value  Pr(>F)
as.factor(time)       4  2.8326  0.7081  3.0538 0.02236 *
male                  1  0.3024  0.3024  1.3039 0.25745
as.factor(time):male  4  0.1869  0.0467  0.2015 0.93670
Residuals            69 16.0002  0.2319
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

library(nlme)

tolerance.lme <- lme(tol ~ as.factor(time) * male, random = ~ 1 | id,
                     data = tolerance.long)

anova(tolerance.lme)
                     numDF denDF  F-value p-value
(Intercept)              1    56 353.9049  <.0001
as.factor(time)          4    56   5.1309  0.0014
male                     1    14   0.6071  0.4488
as.factor(time):male     4    56   0.3386  0.8508

  RSiteSearch("repeated measures") points to other examples, functions,
and documentation.

> Tom
> 
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> and provide commented, minimal, self-contained, reproducible code.

-- 
Chuck Cleland, Ph.D.
NDRI, Inc.
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