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Andrea Goijman

2013-May-17 17:02 UTC

[R] Problems using lmer {lme4}

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]]

Bert Gunter

2013-May-17 17:21 UTC

head link

[R] Problems using lmer {lme4}

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]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> 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.


-- 

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm

Patrick Coulombe

2013-May-17 18:15 UTC

head link

[R] Problems using lmer {lme4}

Hi Andrea,

I'm not exactly sure what you're trying to do, but you've included a
random effect for a "site" coefficient that's not even in your
list of
fixed effects... you're basically allowing the coefficient for site to
vary across routes, but you're never including the coefficient in the
first place. Given the appropriate nested structure (I haven't looked
at your data), a model that should run would be:

m2 <- lmer(cbind(punto6,5) ~ sp + site + (site|route) ,family=binomial,data =
d)

The problem here is I'm not sure this is what you mean to do... If you
could way simplify your example (for example, by including a small
number of mock observations with only the relevant variables, in a
table instead of in R syntax), that would be helpful.

Patrick

2013/5/17 Andrea Goijman <agoijman at
cnia.inta.gov.ar>:> 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]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> 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 help - May 2013 - Problems using lmer {lme4}

[R] Problems using lmer {lme4}

[R] Problems using lmer {lme4}

[R] Problems using lmer {lme4}