Re: [R] glm.nb and Error in x[good, , drop = FALSE] * w : non-conformable arrays
Many thanks Ivan ! This is fairly clear to me, now... When I dumped the data.frame, I found strange to have a "table" declaration for deg, but was not able to judge if it was a problem or not (I would have expected something as "numeric") Your workaround is fine to me (I do not need to carry on with table attributes). Best, Patrick Le 21/04/2023 à 10:08, Ivan Krylov a écrit : > On Fri, 21 Apr 2023 09:02:37 +0200 > Patrick Giraudoux wrote: > >> I meet an error with glm.nb that I cannot explain the origin (and >> find a fix). The model I want to fit is the following: >> >> library(MASS) >> >> glm.nb(deg~offset(log(durobs))+zone,data=db) >> >> and the data.frame is dumped below. > Thank you for providing both the code and a small piece of data that > reproduces the error! > > (It almost worked. Your mailer automatically generated a plain text > version of the e-mail and put Unicode non-breaking spaces in there. R > considers it a syntax error to encounter any of the various Unicode > space-like characters outside string literals.) > >> deg = structure(c(0, 1, 0, 3, 0, 1, 0, 2, 1, 0, 3, 0, 0, 0, 4, 1, 0, >> 0, 0, 0, 4, 0, 0, 0, 4, 3, 2, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, >> 0, 3, 2, 3, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 1, 0, 1, 2, >> 0, 0, 0, 2, 1, 0, 2, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 2, >> 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 2, 1, 0, 0, 1, 3, 2, >> 1, 2, 0, 0, 0, 0, 0, 1, 0, 0, 2, 0, 0, 0, 0, 0, 1, 2, 0, 0, 0, 0, 2, >> 1, 1, 0), dim = 135L, class = "table") > The problem is that `deg` is a table, which ends up making the > effective weights a table too. tables are arrays, and element-wise > product rules are stricter for them than for plain matrices. The code > makes use of the ability to take an element-wise product between a > matrix and a vector of the same length as the number of rows in the > matrix: > > matrix(1:12, 4) * 1:4 # works > matrix(1:12, 4) * as.array(1:4) # results in the same error > > # the right way to take products with an array is to make sure that the > # shapes match exactly > matrix(1:12, 4) * as.array(cbind(1:4, 1:4, 1:4)) > > One possible solution is to to remove all attributes from db$deg: > > db$deg <- as.vector(db$deg) > > This way the values of the expressions involved in glm.fit end up being > of the expected type, and the function completes successfully. > [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] glm.nb and Error in x[good, , drop = FALSE] * w : non-conformable arrays
On Fri, 21 Apr 2023 09:02:37 +0200 Patrick Giraudoux wrote: > I meet an error with glm.nb that I cannot explain the origin (and > find a fix). The model I want to fit is the following: > > library(MASS) > > glm.nb(deg~offset(log(durobs))+zone,data=db) > > and the data.frame is dumped below. Thank you for providing both the code and a small piece of data that reproduces the error! (It almost worked. Your mailer automatically generated a plain text version of the e-mail and put Unicode non-breaking spaces in there. R considers it a syntax error to encounter any of the various Unicode space-like characters outside string literals.) > deg = structure(c(0, 1, 0, 3, 0, 1, 0, 2, 1, 0, 3, 0, 0, 0, 4, 1, 0, > 0, 0, 0, 4, 0, 0, 0, 4, 3, 2, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, > 0, 3, 2, 3, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 1, 0, 1, 2, > 0, 0, 0, 2, 1, 0, 2, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 2, > 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 2, 1, 0, 0, 1, 3, 2, > 1, 2, 0, 0, 0, 0, 0, 1, 0, 0, 2, 0, 0, 0, 0, 0, 1, 2, 0, 0, 0, 0, 2, > 1, 1, 0), dim = 135L, class = "table") The problem is that `deg` is a table, which ends up making the effective weights a table too. tables are arrays, and element-wise product rules are stricter for them than for plain matrices. The code makes use of the ability to take an element-wise product between a matrix and a vector of the same length as the number of rows in the matrix: matrix(1:12, 4) * 1:4 # works matrix(1:12, 4) * as.array(1:4) # results in the same error # the right way to take products with an array is to make sure that the # shapes match exactly matrix(1:12, 4) * as.array(cbind(1:4, 1:4, 1:4)) One possible solution is to to remove all attributes from db$deg: db$deg <- as.vector(db$deg) This way the values of the expressions involved in glm.fit end up being of the expected type, and the function completes successfully. -- Best regards, Ivan __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] glm.nb and Error in x[good, , drop = FALSE] * w : non-conformable arrays
Dear Listers,
I meet an error with glm.nb that I cannot explain the origin (and find a
fix). The model I want to fit is the following:
library(MASS)
glm.nb(deg~offset(log(durobs))+zone,data=db)
and the data.frame is dumped below.
Has anyone an idea about what the trouble comes from ? (except computing
leads to a non-conformable array somewhere... the question is why;
fitting goes through without any problem eg with a Poisson link)
Best,
Patrick
db <-
structure(list(deg = structure(c(0, 1, 0, 3, 0, 1, 0, 2, 1, 0,
3, 0, 0, 0, 4, 1, 0, 0, 0, 0, 4, 0, 0, 0, 4, 3, 2, 0, 0, 0, 0,
0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 3, 2, 3, 0, 1, 1, 0, 0, 0, 0, 1,
0, 0, 0, 0, 0, 1, 0, 1, 0, 1, 2, 0, 0, 0, 2, 1, 0, 2, 0, 1, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 2, 1, 0, 1, 0, 0, 0, 0, 0,
0, 0, 0, 0, 1, 0, 0, 0, 2, 1, 0, 0, 1, 3, 2, 1, 2, 0, 0, 0, 0,
0, 1, 0, 0, 2, 0, 0, 0, 0, 0, 1, 2, 0, 0, 0, 0, 2, 1, 1, 0), dim = 135L,
class = "table"),
durobs = c(371, 371, 371, 371, 371, 371, 239, 266, 234, 71,
436, 407, 407, 414, 415, 418, 415, 329, 414, 414, 415, 330,
435, 436, 210, 436, 214, 436, 436, 210, 434, 438, 438, 402,
402, 289, 264, 264, 434, 435, 434, 434, 434, 434, 434, 427,
427, 427, 328, 422, 291, 412, 221, 417, 416, 416, 79, 322,
213, 440, 434, 462, 397, 457, 419, 406, 316, 392, 392, 392,
392, 392, 452, 386, 399, 305, 240, 404, 226, 226, 381, 385,
392, 388, 388, 391, 396, 392, 385, 385, 385, 237, 378, 378,
378, 381, 126, 315, 379, 314, 185, 313, 312, 301, 312, 312,
310, 310, 307, 306, 304, 455, 472, 472, 466, 467, 334, 565,
429, 429, 425, 422, 421, 419, 417, 417, 410, 405, 195, 422,
419, 419, 426, 426, 442), zone = c("MO1", "MO1", "MO1", "MO1",
"MO1", "MO1", "MO1", "MO1", "MO1", "MO1", "MO1", "MO1", "MO1",
"MO1", "MO1", "MO1", "MO1", "MO1", "MO1", "MO1", "MO1", "MO1",
"MO1", "MO1", "MO1", "MO1", "MO1", "MO1", "MO1", "MO1", "MO1",
"MO1", "MO1", "MO1", "MO1", "MO1", "MO1", "MO1", "MO1", "MO1",
"MO1", "MO1", "MO1", "MO1", "MO1", "MO1", "MO1", "MO1", "MO1",
"MO1", "MO1", "MO1", "MO1", "MO1", "MO1", "MO1", "MO1", "MO1",
"MO1", "MO1", "MO1", "MO1", "MO1", "MO1", "MO1", "MO1", "MO1",
"MO2", "MO2", "MO2", "MO2", "MO2", "MO2", "MO2", "MO2", "MO2",
"MO2", "MO2", "MO2", "MO2", "MO2", "MO2", "MO2", "MO2", "MO2",
"MO2", "MO2", "MO2", "MO2", "MO2", "MO2", "MO2", "MO2", "MO2",
"MO2", "MO2", "MO2", "MO2", "MO2", "MO2", "MO2", "MO2", "MO2",
"MO2", "MO2", "MO2", "MO2", "MO2", "MO2", "MO2", "MO2", "MO2",
"MO2", "MO2", "MO2", "MO2", "MO2", "MO2", "MO2", "MO2", "MO2",
"MO2", "MO2", "MO2", "MO2", "MO2", "MO2", "MO2", "MO2", "MO2",
"MO2", "MO2", "MO2", "MO2", "MO2")), row.names = c(NA, 135L
), class = "data.frame")
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
