[R-sig-ME] Problems running lmer

Hugo.Mildenberger at web.de Hugo.Mildenberger at web.de
Sat May 18 09:59:12 CEST 2013 

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]]
> >>
> >> _______________________________________________
> >> R-sig-mixed-models at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> >>
> >
> >
> >
> >
> 
> 
> -- 
> -----
> 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>

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