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Problems running lmer
4 messages · Andrea Goijman, Philippi, Tom, Hugo.Mildenberger at web.de
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Andrea, Tom, I was able to reproduce the problem here. Apart from an unfortunate model specification, the technical reason is a stack overflow which sometimes does not even result in an error message (the program gets killed instead). From the kernel logs I can see that R tried to allocate 13 mega bytes of stack space. Using gdb on the core dump shows that this must have happened in function mer_optimize() at lmer.c:1719. > # varying intercept by route, species fixed effect > m1 <- lmer(cbind(punto6,5) ~ sp + (1|route) ,family=binomial,data = d) > # varying intercept by site within route, species fixed effect > m2 <- lmer(cbind(punto6,5) ~ sp + (site|route) ,family=binomial,data = d) Error: segfault from C stack overflow > sessionInfo() R version 3.0.0 (2013-04-03) Platform: x86_64-pc-linux-gnu (64-bit) [...] other attached packages: [1] lme4_0.999999-2 Matrix_1.0-12 lattice_0.20-15 loaded via a namespace (and not attached): [1] grid_3.0.0 nlme_3.1-109 stats4_3.0.0 Best On Fri, 17 May 2013 16:34:07 -0400
Andrea Goijman <agoijman at cnia.inta.gov.ar> wrote:
Tom, Thanks for your response! R just stops working. No error message. It looks like I'm fitting the wrong model, and I'm not understanding where the 550 levels of site are coming from (I see that is the number with str(d)). Here is what I want to do... As a first step I want to evaluate if there is autocorrelation of the response variable between sites within each route (for each species separately). I just want to know if the sites within routes are more similar to each other than sites from different routes or not. What is the correct model for that? Here is the session Info Thanks! sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] lme4_0.999999-0 Matrix_1.0-6 lattice_0.20-6 loaded via a namespace (and not attached): [1] grid_2.15.1 nlme_3.1-104 stats4_2.15.1 On Fri, May 17, 2013 at 4:07 PM, Philippi, Tom <tom_philippi at nps.gov> wrote:
Andrea-- "Crashes" is not particularly informative. Was there an error message? Also, sessionInfo() would help the real experts know which versions of R and lme4 you are running, and on what hardware. That said, I'm not sure what you expect from or mean by your (1+site|route) random effect. Both site and route are factors, so a "slope" for site is actually N-1 coefficients for unordered levels of sites within each route. Given that you appear to have one observation for each sp by site combination (7sp*42site=294 observations), and sp is a factor included as a main effect, your model appears to fit more parameters than you have observations. And, at least for the data you included, you have 550 levels of site, but only 294 observations. str(d) I hope that this gets you pointed in the right direction for solving your problem. Tom On Fri, May 17, 2013 at 10:35 AM, Andrea Goijman < agoijman at cnia.inta.gov.ar> wrote:
Dear R list,
I'm attaching a sample of my data which consists on the presence/absence
("punto6", binomial n=5 occasions)
of different species ("sp"), on different sites ("site") within routes
('route").
First, I want to be able to find if there is autocorrelation of the
response variable between
the sites within each route. For this I start testing 2 models, but when I
try to run the second model,
to test for the random effects of sites within routes R stops working!
I'm not being able to find out why r is crashing... and whay am I doing
wrong.
Thanks!
Andrea
#######################################################
#dput(d)
d<-structure(list(site = structure(c(55L, 56L, 57L, 58L, 59L, 60L,
55L, 56L, 57L, 58L, 59L, 60L, 55L, 56L, 57L, 58L, 59L, 60L, 55L,
56L, 57L, 58L, 59L, 60L, 55L, 56L, 57L, 58L, 59L, 60L, 55L, 56L,
57L, 58L, 59L, 60L, 55L, 56L, 57L, 58L, 59L, 60L, 229L, 230L,
231L, 232L, 233L, 234L, 229L, 230L, 231L, 232L, 233L, 234L, 229L,
230L, 231L, 232L, 233L, 234L, 229L, 230L, 231L, 232L, 233L, 234L,
229L, 230L, 231L, 232L, 233L, 234L, 229L, 230L, 231L, 232L, 233L,
234L, 229L, 230L, 231L, 232L, 233L, 234L, 331L, 332L, 333L, 334L,
335L, 336L, 331L, 332L, 333L, 334L, 335L, 336L, 331L, 332L, 333L,
334L, 335L, 336L, 331L, 332L, 333L, 334L, 335L, 336L, 331L, 332L,
333L, 334L, 335L, 336L, 331L, 332L, 333L, 334L, 335L, 336L, 331L,
332L, 333L, 334L, 335L, 336L, 389L, 390L, 391L, 392L, 393L, 394L,
389L, 390L, 391L, 392L, 393L, 394L, 389L, 390L, 391L, 392L, 393L,
394L, 389L, 390L, 391L, 392L, 393L, 394L, 389L, 390L, 391L, 392L,
393L, 394L, 389L, 390L, 391L, 392L, 393L, 394L, 389L, 390L, 391L,
392L, 393L, 394L, 205L, 206L, 207L, 208L, 209L, 210L, 205L, 206L,
207L, 208L, 209L, 210L, 205L, 206L, 207L, 208L, 209L, 210L, 205L,
206L, 207L, 208L, 209L, 210L, 205L, 206L, 207L, 208L, 209L, 210L,
205L, 206L, 207L, 208L, 209L, 210L, 205L, 206L, 207L, 208L, 209L,
210L, 163L, 164L, 165L, 166L, 167L, 168L, 163L, 164L, 165L, 166L,
167L, 168L, 163L, 164L, 165L, 166L, 167L, 168L, 163L, 164L, 165L,
166L, 167L, 168L, 163L, 164L, 165L, 166L, 167L, 168L, 163L, 164L,
165L, 166L, 167L, 168L, 163L, 164L, 165L, 166L, 167L, 168L, 247L,
248L, 249L, 250L, 251L, 252L, 247L, 248L, 249L, 250L, 251L, 252L,
247L, 248L, 249L, 250L, 251L, 252L, 247L, 248L, 249L, 250L, 251L,
252L, 247L, 248L, 249L, 250L, 251L, 252L, 247L, 248L, 249L, 250L,
251L, 252L, 247L, 248L, 249L, 250L, 251L, 252L), .Label = c("102-1",
"102-2", "102-3", "102-4", "102-5", "102-6", "1023-1", "1023-2",
"1023-3", "1023-4", "1023-5", "1023-6", "1027-1", "1027-2", "1027-3",
"1027-4", "1027-5", "1027-6", "1028-1", "1028-2", "1028-3", "1028-4",
"1028-5", "1028-6", "1032-1", "1032-2", "1032-3", "1032-4", "1032-5",
"1032-6", "1034-1", "1034-2", "1034-3", "1034-4", "1034-5", "1034-6",
"1036-1", "1036-2", "1036-3", "1036-4", "1036-5", "1036-6", "1041-1",
"1041-2", "1041-3", "1041-4", "1041-5", "1041-6", "1046-1", "1046-2",
"1046-3", "1046-4", "1046-5", "1046-6", "105-1", "105-2", "105-3",
"105-4", "105-5", "105-6", "107-1", "107-2", "107-3", "107-4",
"107-5", "107-6", "108-1", "108-2", "108-3", "108-4", "108-5",
"108-6", "1101-1", "1101-2", "1101-3", "1101-4", "1101-5", "1101-6",
"1104-1", "1104-2", "1104-3", "1104-4", "1104-5", "1104-6", "1108-1",
"1108-2", "1108-3", "1108-4", "1108-5", "1108-6", "111-1", "111-2",
"111-3", "111-4", "111-5", "111-6", "1113-1", "1113-2", "1113-3",
"1113-4", "1113-5", "1113-6", "1116-1", "1116-2", "1116-3", "1116-4",
"1116-5", "1116-6", "1121-1", "1121-2", "1121-3", "1121-4", "1121-5",
"1121-6", "1204-1", "1204-2", "1204-3", "1204-4", "1204-5", "1204-6",
"1205-1", "1205-2", "1205-3", "1205-4", "1205-5", "1205-6", "1207-1",
"1207-2", "1207-3", "1207-4", "1207-5", "1207-6", "1212-1", "1212-2",
"1212-3", "1212-4", "1212-5", "1212-6", "202-1", "202-2", "202-3",
"202-4", "202-5", "202-6", "205-1", "205-2", "205-3", "205-4",
"205-5", "205-6", "207-1", "207-2", "207-3", "207-4", "207-5",
"207-6", "208-1", "208-2", "208-3", "208-4", "208-5", "208-6",
"211-1", "211-2", "211-3", "211-4", "211-5", "211-6", "213-1",
"213-2", "213-3", "213-4", "213-5", "213-6", "214-1", "214-2",
"214-3", "214-4", "214-5", "214-6", "217-1", "217-2", "217-3",
"217-4", "217-5", "217-6", "218-1", "218-2", "218-3", "218-4",
"218-5", "218-6", "219-1", "219-2", "219-3", "219-4", "219-5",
"219-6", "223-1", "223-2", "223-3", "223-4", "223-5", "223-6",
"302-1", "302-2", "302-3", "302-4", "302-5", "302-6", "305-1",
"305-2", "305-3", "305-4", "305-5", "305-6", "308-1", "308-2",
"308-3", "308-4", "308-5", "308-6", "311-1", "311-2", "311-3",
"311-4", "311-5", "311-6", "401-1", "401-2", "401-3", "401-4",
"401-5", "401-6", "402-1", "402-2", "402-3", "402-4", "402-5",
"402-6", "405-1", "405-2", "405-3", "405-4", "405-5", "405-6",
"407-1", "407-2", "407-3", "407-4", "407-5", "407-6", "408-1",
"408-2", "408-3", "408-4", "408-5", "408-6", "410-1", "410-2",
"410-3", "410-4", "410-5", "410-6", "411-1", "411-2", "411-3",
"411-4", "411-5", "411-6", "414-1", "414-2", "414-3", "414-4",
"414-5", "414-6", "416-1", "416-2", "416-3", "416-4", "416-5",
"416-6", "417-1", "417-2", "417-3", "417-4", "417-5", "417-6",
"420-1", "420-2", "420-3", "420-4", "420-5", "420-6", "423-1",
"423-2", "423-3", "423-4", "423-5", "423-6", "501-1", "501-2",
"501-3", "501-4", "501-5", "501-6", "502-1", "502-2", "502-3",
"502-4", "502-5", "502-6", "504-1", "504-2", "504-3", "504-4",
"504-5", "504-6", "505-1", "505-2", "505-3", "505-4", "505-5",
"505-6", "507-1", "507-2", "507-3", "507-4", "507-5", "507-6",
"508-1", "508-2", "508-3", "508-4", "508-5", "508-6", "511-1",
"511-2", "511-3", "511-4", "511-5", "511-6", "602-1", "602-2",
"602-3", "602-4", "602-5", "602-6", "604-1", "604-2", "604-3",
"604-4", "604-5", "604-6", "605-1", "605-2", "605-3", "605-4",
"605-5", "605-6", "608-1", "608-2", "608-3", "608-4", "608-5",
"608-6", "611-1", "611-2", "611-3", "611-4", "611-5", "611-6",
"613-1", "613-2", "613-3", "613-4", "613-5", "613-6", "614-1",
"614-2", "614-3", "614-4", "617-1", "617-2", "617-3", "617-4",
"617-5", "617-6", "620-1", "620-2", "620-3", "620-4", "620-5",
"620-6", "623-1", "623-2", "623-3", "623-4", "623-5", "623-6",
"702-1", "702-2", "702-3", "702-4", "702-5", "702-6", "705-1",
"705-2", "705-3", "705-4", "705-5", "705-6", "708-1", "708-2",
"708-3", "708-4", "708-5", "708-6", "712-1", "712-2", "712-3",
"712-4", "712-5", "712-6", "713-1", "713-2", "713-3", "713-4",
"713-5", "713-6", "715-1", "715-2", "715-3", "715-4", "715-5",
"715-6", "717-1", "717-2", "717-3", "717-4", "717-5", "717-6",
"718-1", "718-2", "718-3", "718-4", "718-5", "718-6", "803-1",
"803-2", "803-3", "803-4", "803-5", "803-6", "807-1", "807-2",
"807-3", "807-4", "807-5", "807-6", "809-1", "809-2", "809-3",
"809-4", "809-5", "809-6", "812-1", "812-2", "812-3", "812-4",
"812-5", "812-6", "814-1", "814-2", "814-3", "814-4", "814-5",
"814-6", "818-1", "818-2", "818-3", "818-4", "818-5", "818-6",
"820-1", "820-2", "820-3", "820-4", "820-5", "820-6", "823-1",
"823-2", "823-3", "823-4", "823-5", "823-6", "825-1", "825-2",
"825-3", "825-4", "825-5", "825-6", "903-1", "903-2", "903-3",
"903-4", "903-5", "903-6", "907-1", "907-2", "907-3", "907-4",
"907-5", "907-6", "909-1", "909-2", "909-3", "909-4", "909-5",
"909-6", "913-1", "913-2", "913-3", "913-4", "913-5", "913-6",
"915-1", "915-2", "915-3", "915-4", "915-5", "915-6", "920-1",
"920-2", "920-3", "920-4", "920-5", "920-6", "925-1", "925-2",
"925-3", "925-4", "925-5", "925-6", "926-1", "926-2", "926-3",
"926-4", "926-5", "926-6"), class = "factor"), sp = structure(c(4L,
4L, 4L, 4L, 4L, 4L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L,
2L, 3L, 3L, 3L, 3L, 3L, 3L, 6L, 6L, 6L, 6L, 6L, 6L, 7L, 7L, 7L,
7L, 7L, 7L, 5L, 5L, 5L, 5L, 5L, 5L, 4L, 4L, 4L, 4L, 4L, 4L, 1L,
1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L,
3L, 6L, 6L, 6L, 6L, 6L, 6L, 7L, 7L, 7L, 7L, 7L, 7L, 5L, 5L, 5L,
5L, 5L, 5L, 4L, 4L, 4L, 4L, 4L, 4L, 1L, 1L, 1L, 1L, 1L, 1L, 2L,
2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 6L, 6L, 6L, 6L, 6L,
6L, 7L, 7L, 7L, 7L, 7L, 7L, 5L, 5L, 5L, 5L, 5L, 5L, 4L, 4L, 4L,
4L, 4L, 4L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 3L,
3L, 3L, 3L, 3L, 3L, 6L, 6L, 6L, 6L, 6L, 6L, 7L, 7L, 7L, 7L, 7L,
7L, 5L, 5L, 5L, 5L, 5L, 5L, 4L, 4L, 4L, 4L, 4L, 4L, 1L, 1L, 1L,
1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 6L,
6L, 6L, 6L, 6L, 6L, 7L, 7L, 7L, 7L, 7L, 7L, 5L, 5L, 5L, 5L, 5L,
5L, 4L, 4L, 4L, 4L, 4L, 4L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L,
2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 6L, 6L, 6L, 6L, 6L, 6L, 7L,
7L, 7L, 7L, 7L, 7L, 5L, 5L, 5L, 5L, 5L, 5L, 4L, 4L, 4L, 4L, 4L,
4L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L,
3L, 3L, 3L, 6L, 6L, 6L, 6L, 6L, 6L, 7L, 7L, 7L, 7L, 7L, 7L, 5L,
5L, 5L, 5L, 5L, 5L), .Label = c("LEAN", "MICH", "SPCU", "STSU",
"TRAE", "TYSA", "ZOCA"), class = "factor"), route = c("105",
"105", "105", "105", "105", "105", "105", "105", "105", "105",
"105", "105", "105", "105", "105", "105", "105", "105", "105",
"105", "105", "105", "105", "105", "105", "105", "105", "105",
"105", "105", "105", "105", "105", "105", "105", "105", "105",
"105", "105", "105", "105", "105", "401", "401", "401", "401",
"401", "401", "401", "401", "401", "401", "401", "401", "401",
"401", "401", "401", "401", "401", "401", "401", "401", "401",
"401", "401", "401", "401", "401", "401", "401", "401", "401",
"401", "401", "401", "401", "401", "401", "401", "401", "401",
"401", "401", "508", "508", "508", "508", "508", "508", "508",
"508", "508", "508", "508", "508", "508", "508", "508", "508",
"508", "508", "508", "508", "508", "508", "508", "508", "508",
"508", "508", "508", "508", "508", "508", "508", "508", "508",
"508", "508", "508", "508", "508", "508", "508", "508", "620",
"620", "620", "620", "620", "620", "620", "620", "620", "620",
"620", "620", "620", "620", "620", "620", "620", "620", "620",
"620", "620", "620", "620", "620", "620", "620", "620", "620",
"620", "620", "620", "620", "620", "620", "620", "620", "620",
"620", "620", "620", "620", "620", "302", "302", "302", "302",
"302", "302", "302", "302", "302", "302", "302", "302", "302",
"302", "302", "302", "302", "302", "302", "302", "302", "302",
"302", "302", "302", "302", "302", "302", "302", "302", "302",
"302", "302", "302", "302", "302", "302", "302", "302", "302",
"302", "302", "211", "211", "211", "211", "211", "211", "211",
"211", "211", "211", "211", "211", "211", "211", "211", "211",
"211", "211", "211", "211", "211", "211", "211", "211", "211",
"211", "211", "211", "211", "211", "211", "211", "211", "211",
"211", "211", "211", "211", "211", "211", "211", "211", "407",
"407", "407", "407", "407", "407", "407", "407", "407", "407",
"407", "407", "407", "407", "407", "407", "407", "407", "407",
"407", "407", "407", "407", "407", "407", "407", "407", "407",
"407", "407", "407", "407", "407", "407", "407", "407", "407",
"407", "407", "407", "407", "407"), punto6 = c(3, 5, 3, 2, 2,
2, 0, 0, 0, 0, 0, 0, 3, 3, 5, 4, 5, 2, 1, 0, 0, 1, 1, 2, 1, 1,
0, 2, 1, 0, 0, 0, 0, 0, 0, 3, 0, 0, 2, 3, 3, 1, 3, 2, 2, 3, 3,
2, 0, 0, 0, 0, 0, 0, 0, 0, 3, 3, 0, 1, 1, 1, 1, 1, 0, 2, 1, 2,
1, 2, 2, 0, 4, 2, 2, 2, 0, 3, 2, 0, 2, 0, 2, 2, 0, 0, 1, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0,
2, 2, 0, 0, 0, 1, 1, 1, 1, 2, 0, 2, 0, 0, 0, 0, 0, 0, 2, 1, 0,
0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 2,
2, 1, 0, 2, 1, 1, 5, 1, 3, 1, 0, 0, 1, 1, 0, 2, 2, 4, 5, 4, 4,
2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 2, 0, 0, 0,
1, 4, 2, 1, 0, 2, 0, 1, 1, 0, 1, 0, 2, 3, 1, 1, 1, 1, 1, 2, 2,
1, 0, 0, 0, 0, 0, 0, 1, 2, 2, 0, 3, 0, 0, 1, 0, 1, 0, 0, 1, 3,
1, 3, 4, 2, 4, 5, 5, 3, 3, 3, 0, 0, 0, 0, 0, 1, 1, 3, 0, 0, 1,
2, 0, 0, 0, 0, 0, 0, 2, 1, 1, 4, 2, 0, 1, 2, 1, 2, 2, 2, 2, 1,
3, 0, 1, 0, 2, 3, 3, 2, 1, 4, 1, 0, 1, 1, 1, 1)), .Names = c("site",
"sp", "route", "punto6"), class = "data.frame", row.names = c(NA,
-294L))
d
library(lme4)
# varying intercept by route, species fixed effect
m1 <- lmer(cbind(punto6,5) ~ sp + (1|route) ,family=binomial,data = d)
# varying intercept by site within route, species fixed effect
m2 <- lmer(cbind(punto6,5) ~ sp + (site|route) ,family=binomial,data = d)
### CRASHES!
[[alternative HTML version deleted]]
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-- ----- Lic. Andrea Paula Goijman, PhD Candidate Grupo Ecolog_a y Gesti_n Ambiental de la Biodiversidad IRB - INTA Castelar, Argentina agoijman at cnia.inta.gov.ar <http://inta.gob.ar/personas/goijman.andrea/> http://inta.gob.ar/personas/goijman.andrea/ D.B. Warnell School of Forestry and Natural Resources University of Georgia Athens, GA 30602 USA Tel. +706.206.4805 andreapg at uga.edu [[alternative HTML version deleted]]
Hugo Mildenberger <hm at zotac.lan>