Define a wrapper function for the t test that only returns the p-value?
by(mydata$WtBaseline,mydata$Group, function(...) t.test(...)$p.value)
S Ellison
________________________________________
From: R-help [r-help-boun...@r-project.org] on behalf of Sorkin, John
[jsor...@som.umaryland.edu]
Sent: 12 June 2020 22:34
To: r-help@r-project.org (r-help@r-project.org)
Subject: [R] Obtaining p values from t-test run with a by function
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EXTERNAL EMAIL
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Colleagues,
I am trying to retrieve the p values produced by a Student's t-test run using a
by function, but can not do so. I can easily get the p value when I run s
Student's t-test without a by function. What is the secret to obtaining results
returned from a function run within a by function.
An annotated repeatable example (including data) can be found below.
Thank you,
John
# Test data
mydata <- structure(list(Group = structure(c(2L, 1L, 2L, 2L, 1L, 2L, 1L,
2L, 2L, 1L, 2L, 1L, 2L), .Label = c("EPA", "P"), class = "factor"),
WtBaseline = c(76.6, 73.8, 77.6, 91.7, 110.3, 121.7, 82.1,
82.8, 119, 88.4, 75.7, 71.4, 72.1)), class = "data.frame", row.names
= c(NA,-13L))
cat("This is what mydata looks like\n")
mydata
result <- by(mydata$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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