John Sorkin
2015-Dec-28 21:54 UTC
[R] error using by(goop[, c("a", "b", "c")], goop[, "Arm"], mySD) was Re: by gives no results, gives warning that data are non-numeric, but the data appears to be numeric.
I am trying to use the by function to get the SD of each column of a data
frame, stratified by ARM. Using a suggestion provided by both William Dunlap and
Rolf Turner, I have written the code below which fails with the error:
Error in match.fun(FUN) : 'sqrt(var(x))' is not a function, character
or symbol
code:
mySD <- function(x) {sapply(x,sqrt(var(x)))}
class(mySD)
by(goop[,c("a","b","c")],goop[,"Arm"],mySD)
Below I include code which will create goop (thank you Bill for suggesting I use
dput), which will run will recreate mmy error. Any thoughts on why the by
function fails and how to fix it would be appreciated.
Thank you,
John
goop <- structure(c(180L, 153L, 149L, 218L, 217L, 147L, 141L, 141L, 174L,
162L, 163L, 206L, 168L, 227L, 142L, 179L, 270L, 206L, 243L,
134L,
131L, 222L, 142L, 119L, 149L, 190L, 196L, 145L, 185L, 235L,
165L,
246L, 152L, 186L, 222L, 248L, 125L, 149L, 233L, 145L, 154L,
231L,
146L, 161L, 150L, 133L, 115L, 145L, 180L, 202L, 158L, 210L,
153L,
136L, 265L, 255L, 199L, 131L, 110L, 169L, 147L, 133L, 108L,
203L,
185L, 153L, 154L, 207L, 167L, 233L, 135L, 127L, 197L, 245L,
124L,
125L, 146L, 139L, 158L, 211L, 183L, 169L, 137L, 114L, 176L,
143L,
156L, 209L, 163L, 194L, 151L, 238L, 253L, 293L, 208L, 147L,
186L,
179L, 150L, 203L, 112L, 185L, 156L, 127L, 132L, 243L, 177L,
242L,
144L, 140L, 194L, 249L, 109L, 91L, 10163L, 10987L, 19882L,
19899L,
20104L, 20105L, 20167L, 20318L, 20338L, 20392L, 20453L,
20454L,
20467L, 20500L, 20682L, 20687L, 20692L, 20744L, 20750L,
20751L,
20806L, 20848L, 20856L, 20959L, 21023L, 21048L, 21114L,
21134L,
21135L, 21320L, 21329L, 21349L, 21353L, 21521L, 21663L,
21784L,
22031L, 22081L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 2L,
2L,
2L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 2L,
1L,
2L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L), .Dim = c(38L, 5L),
.Dimnames = list(
NULL, c("a", "b", "c",
"ID", "Arm")), na.action = structure(37, class =
"omit"))
goop
mySD <- function(x) {sapply(x,sqrt(var(x)))}
class(mySD)
by(goop[,c("a","b","c")],goop[,"Arm"],mySD)
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)
Confidentiality Statement:
This email message, including any attachments, is for the sole use of the
intended recipient(s) and may contain confidential and privileged information.
Any unauthorized use, disclosure or distribution is prohibited. If you are not
the intended recipient, please contact the sender by reply email and destroy all
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ruipbarradas at sapo.pt
2015-Dec-28 22:10 UTC
[R] error using by(goop[, c("a", "b", "c")], goop[, "Arm"], mySD) was Re: by gives no results, gives warning that data are non-numeric, but the data appears to be numeric.
Hello,
Try the following.
mySD <- function(x) {sapply(x, function(y) sqrt(var(y)))}
Hope this helps,
Rui Barradas
?
Citando John Sorkin <jsorkin at grecc.umaryland.edu>:
> I am? trying to use the by function to get the SD of each column of
> a data frame, stratified by ARM. Using a suggestion provided by both
> William Dunlap and Rolf Turner, I have written the code below which
> fails with the error:
> Error in match.fun(FUN) :? ?'sqrt(var(x))' is not a function,
> character or symbol
>
> code:
> mySD <- function(x) {sapply(x,sqrt(var(x)))}
> class(mySD)
>
by(goop[,c("a","b","c")],goop[,"Arm"],mySD)
>
> Below I include code which will create goop (thank you Bill for
> suggesting I use dput), which will run will recreate mmy error. Any
> thoughts on why the by function fails and how to fix it would be
> appreciated.
>
> Thank you,
> John
>
> goop <- structure(c(180L, 153L, 149L, 218L, 217L, 147L, 141L, 141L,
174L,
> ? ? ? ? ? ? ? ? ? ?162L, 163L, 206L, 168L, 227L, 142L, 179L, 270L,
> 206L, 243L, 134L,
> ? ? ? ? ? ? ? ? ? ?131L, 222L, 142L, 119L, 149L, 190L, 196L, 145L,
> 185L, 235L, 165L,
> ? ? ? ? ? ? ? ? ? ?246L, 152L, 186L, 222L, 248L, 125L, 149L, 233L,
> 145L, 154L, 231L,
> ? ? ? ? ? ? ? ? ? ?146L, 161L, 150L, 133L, 115L, 145L, 180L, 202L,
> 158L, 210L, 153L,
> ? ? ? ? ? ? ? ? ? ?136L, 265L, 255L, 199L, 131L, 110L, 169L, 147L,
> 133L, 108L, 203L,
> ? ? ? ? ? ? ? ? ? ?185L, 153L, 154L, 207L, 167L, 233L, 135L, 127L,
> 197L, 245L, 124L,
> ? ? ? ? ? ? ? ? ? ?125L, 146L, 139L, 158L, 211L, 183L, 169L, 137L,
> 114L, 176L, 143L,
> ? ? ? ? ? ? ? ? ? ?156L, 209L, 163L, 194L, 151L, 238L, 253L, 293L,
> 208L, 147L, 186L,
> ? ? ? ? ? ? ? ? ? ?179L, 150L, 203L, 112L, 185L, 156L, 127L, 132L,
> 243L, 177L, 242L,
> ? ? ? ? ? ? ? ? ? ?144L, 140L, 194L, 249L, 109L, 91L, 10163L,
> 10987L, 19882L, 19899L,
> ? ? ? ? ? ? ? ? ? ?20104L, 20105L, 20167L, 20318L, 20338L, 20392L,
> 20453L, 20454L,
> ? ? ? ? ? ? ? ? ? ?20467L, 20500L, 20682L, 20687L, 20692L, 20744L,
> 20750L, 20751L,
> ? ? ? ? ? ? ? ? ? ?20806L, 20848L, 20856L, 20959L, 21023L, 21048L,
> 21114L, 21134L,
> ? ? ? ? ? ? ? ? ? ?21135L, 21320L, 21329L, 21349L, 21353L, 21521L,
> 21663L, 21784L,
> ? ? ? ? ? ? ? ? ? ?22031L, 22081L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 2L,
> 1L, 1L, 2L, 2L,
> ? ? ? ? ? ? ? ? ? ?2L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 2L,
> 1L, 1L, 2L, 1L,
> ? ? ? ? ? ? ? ? ? ?2L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L), .Dim =
> c(38L, 5L), .Dimnames = list(
> ? ? ? ? ? ? ? ? ? ? ?NULL, c("a", "b", "c",
"ID", "Arm")), na.action
> = structure(37, class = "omit"))
> goop
> mySD <- function(x) {sapply(x,sqrt(var(x)))}
> class(mySD)
>
by(goop[,c("a","b","c")],goop[,"Arm"],mySD)
>
> 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)
>
> Confidentiality Statement:
> This email message, including any attachments, is for ...{{dropped:18}}
William Dunlap
2015-Dec-28 23:27 UTC
[R] error using by(goop[, c("a", "b", "c")], goop[, "Arm"], mySD) was Re: by gives no results, gives warning that data are non-numeric, but the data appears to be numeric.
sapply's FUN argument must be a function (or a character string naming
a function) and sqrt(var(x)) evaluates to a number, not a function.
mySD <- function(x) {sapply(x,function(x)sqrt(var(x)))}
would work, but I like to make it
mySD <- function(x) {sapply(x,function(xi)sqrt(var(xi)))}
to make it clear to the user that the 'x's in the first function
have 2 different meanings.
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Mon, Dec 28, 2015 at 1:54 PM, John Sorkin <jsorkin at
grecc.umaryland.edu>
wrote:
>
> I am trying to use the by function to get the SD of each column of a data
> frame, stratified by ARM. Using a suggestion provided by both William
> Dunlap and Rolf Turner, I have written the code below which fails with the
> error:
> Error in match.fun(FUN) : 'sqrt(var(x))' is not a function,
character or
> symbol
>
>
> code:
> mySD <- function(x) {sapply(x,sqrt(var(x)))}
> class(mySD)
>
by(goop[,c("a","b","c")],goop[,"Arm"],mySD)
>
> Below I include code which will create goop (thank you Bill for suggesting
> I use dput), which will run will recreate mmy error. Any thoughts on why
> the by function fails and how to fix it would be appreciated.
>
> Thank you,
> John
>
> goop <- structure(c(180L, 153L, 149L, 218L, 217L, 147L, 141L, 141L,
174L,
> 162L, 163L, 206L, 168L, 227L, 142L, 179L, 270L, 206L,
> 243L, 134L,
> 131L, 222L, 142L, 119L, 149L, 190L, 196L, 145L, 185L,
> 235L, 165L,
> 246L, 152L, 186L, 222L, 248L, 125L, 149L, 233L, 145L,
> 154L, 231L,
> 146L, 161L, 150L, 133L, 115L, 145L, 180L, 202L, 158L,
> 210L, 153L,
> 136L, 265L, 255L, 199L, 131L, 110L, 169L, 147L, 133L,
> 108L, 203L,
> 185L, 153L, 154L, 207L, 167L, 233L, 135L, 127L, 197L,
> 245L, 124L,
> 125L, 146L, 139L, 158L, 211L, 183L, 169L, 137L, 114L,
> 176L, 143L,
> 156L, 209L, 163L, 194L, 151L, 238L, 253L, 293L, 208L,
> 147L, 186L,
> 179L, 150L, 203L, 112L, 185L, 156L, 127L, 132L, 243L,
> 177L, 242L,
> 144L, 140L, 194L, 249L, 109L, 91L, 10163L, 10987L,
> 19882L, 19899L,
> 20104L, 20105L, 20167L, 20318L, 20338L, 20392L,
> 20453L, 20454L,
> 20467L, 20500L, 20682L, 20687L, 20692L, 20744L,
> 20750L, 20751L,
> 20806L, 20848L, 20856L, 20959L, 21023L, 21048L,
> 21114L, 21134L,
> 21135L, 21320L, 21329L, 21349L, 21353L, 21521L,
> 21663L, 21784L,
> 22031L, 22081L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 1L,
> 1L, 2L, 2L,
> 2L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 1L,
> 1L, 2L, 1L,
> 2L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L), .Dim = c(38L,
> 5L), .Dimnames = list(
> NULL, c("a", "b", "c",
"ID", "Arm")), na.action > structure(37, class =
"omit"))
> goop
> mySD <- function(x) {sapply(x,sqrt(var(x)))}
> class(mySD)
>
by(goop[,c("a","b","c")],goop[,"Arm"],mySD)
>
>
>
>
>
>
>
> 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)
>
> Confidentiality Statement:
> This email message, including any attachments, is for ...{{dropped:16}}