[R] Problems using lmer {lme4}

Fri May 17 19:21:24 CEST 2013

It would be better to post this on the r-sig-mixed-models list, I think.

-- Bert

On Fri, May 17, 2013 at 10:02 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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> and provide commented, minimal, self-contained, reproducible code.

-- 

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: 467-7374
Website:
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