[R] Obtaining p values from t-test run with a by function

[Stephen Ellison]

Define a wrapper function for the t test that only returns the p-value?

by(mydata$WtBaseline,mydata$Group, function(...) t.test(...)$p.value)

S Ellison
________________________________________
From: R-help [r-help-bounces using r-project.org] on behalf of Sorkin, John [jsorkin using som.umaryland.edu]
Sent: 12 June 2020 22:34
To: r-help using r-project.org (r-help using r-project.org)
Subject: [R] Obtaining p values from t-test run with a by function

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Colleagues,
I am trying to retrieve the p values produced by a Student's t-test run using a by function, but can not do so. I can easily get the p value when I run s Student's t-test without a by function. What is the secret to obtaining results returned from a function run within a by function.

An annotated repeatable example (including data) can be found below.
Thank you,
John


# Test data
mydata <- structure(list(Group = structure(c(2L, 1L, 2L, 2L, 1L, 2L, 1L,
           2L, 2L, 1L, 2L, 1L, 2L), .Label = c("EPA", "P"), class = "factor"),
           WtBaseline = c(76.6, 73.8, 77.6, 91.7, 110.3, 121.7, 82.1,
           82.8, 119, 88.4, 75.7, 71.4, 72.1)), class = "data.frame", row.names = c(NA,-13L))

cat("This is what mydata looks like\n")
mydata

result <- by(mydata$WtBaseline,mydata$Group,t.test)
cat("Student's t-test run using by command\n")
cat("Result has results for both groups, EPA and P\n")
result

cat("I can isolate the collective results for group EPA\n")
result[1]
cat("I can isolate the collective results for group P\n")
result[2]

cat("I cant get the p-values for the gruops")
result[1]$p.value
result[2]$p.value

cat("When run without by function, one can get the p value\n")
xxx <- t.test(WtBaseline~Group,data=mydata)
cat("t-test run without by fundtion\n")
xxx
cat("p value isolated from t-test run without by function\n")
xxx$p.value


John David Sorkin M.D., Ph.D.
Professor of Medicine
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology and Geriatric Medicine
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)


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