[R-sig-ME] nlme issue since 3.40
Jinsong Zhao
jszhao at yeah.net
Thu May 11 05:29:08 CEST 2017
Working with Win10 64 bit. Same point estimates as Tom.
R version 3.4.0 (2017-04-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 14393)
Matrix products: default
Best,
Jinsong
On 2017/5/11 4:54, Philippi, Tom wrote:
> Jochen--
>
> Using R 3.4 and nlme 3.1-131 on MS win7 and the data you included in the
> other message thread, I cannot duplicate your error. It also runs fine
> under MRAN 3.3.2 on MS win7 which uses the Intel MKL. I haven't yet
> updated R to 3.4 on my linux ubuntu box to test there, but my best guess
> now is that something failed in your update to 3.4.
>
>
>> library(nlme)
>> library(broom)
>>
>> data2 <- structure(list(Place = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
> + 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L,
> + 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L,
> + 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), .Label =
> + c("Cambridge Bay",
> + "Iqaluit", "Rankin Inlet"), class = "factor"), year_c = c(-2,
> + -1, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, -2,
> + -1, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, -2,
> + -1, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15), SR_Total_ctd
> + = c(NA,
> + NA, 5.48961420000001, 7.24637679999999, 3.76569040000001, 6.9014085,
> + 9.3088858, 5.1771117, 7.51366120000002, 7.18157180000001, 3.7275064,
> + 5.7397959, 6.87500000000001, 6.25, 5.84577109999999, 6.2421973,
> + 4.70446319999999, NA, NA, NA, 11.9192688, 9.6291013, 8.54640980000001,
> + 8.7893297, 7.42343539999999, 5, 5.3674121, 6.1322261, 6.4182843,
> + 5.75692960000001, 6.3861534, 6.6706021, 7.76642339999999,
> 6.91983119999999,
> + 5.3634631, NA, NA, NA, 0.0870321999999959, -1.19047620000001,
> + -1.8723404, -0.4244482, 1.18443319999999, 2.19594590000001,
> + 1.57545610000001,
> + 3.080766, 1.8744906, 5.51053480000002, 6.31412790000002, 7.4451411,
> + 8.1226054, 9.52743899999999, 9.4339623, NA)), .Names = c("Place",
> + "year_c", "SR_Total_ctd"), row.names = c(NA, -54L), class = "data.frame")
>>
>>
>> uncmod <- lme(fixed = year_c~1, random = ~1|Place, data = data2,
> method="ML")
>> tidy(uncmod)
> group level term estimate
> 1 Place Cambridge Bay (Intercept) 6.5
> 2 Place Iqaluit (Intercept) 6.5
> 3 Place Rankin Inlet (Intercept) 6.5
>> summary(uncmod)
> Linear mixed-effects model fit by maximum likelihood
> Data: data2
> AIC BIC logLik
> 337.0536 343.0206 -165.5268
>
> Random effects:
> Formula: ~1 | Place
> (Intercept) Residual
> StdDev: 0.0001350644 5.188127
>
> Fixed effects: year_c ~ 1
> Value Std.Error DF t-value p-value
> (Intercept) 6.5 0.7126441 51 9.120962 0
>
> Standardized Within-Group Residuals:
> Min Q1 Med Q3 Max
> -1.638356e+00 -8.673650e-01 -1.193490e-15 8.673650e-01 1.638356e+00
>
> Number of Observations: 54
> Number of Groups: 3
>> VarCorr(uncmod)
> Place = pdLogChol(1)
> Variance StdDev
> (Intercept) 1.824240e-08 0.0001350644
> Residual 2.691667e+01 5.1881274721
>>
>> sessionInfo()
> R version 3.4.0 (2017-04-21)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 7 x64 (build 7601) Service Pack 1
>
> Matrix products: default
>
> 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] broom_0.4.2 nlme_3.1-131
>
> loaded via a namespace (and not attached):
> [1] Rcpp_0.12.10 lattice_0.20-35 tidyr_0.6.1 psych_1.7.3.21
> [5] dplyr_0.5.0 assertthat_0.2.0 grid_3.4.0 R6_2.2.0
> [9] plyr_1.8.4 DBI_0.6-1 magrittr_1.5 stringi_1.1.5
> [13] lazyeval_0.2.0 reshape2_1.4.2 tools_3.4.0 stringr_1.2.0
> [17] foreign_0.8-67 parallel_3.4.0 compiler_3.4.0 mnormt_1.5-5
> [21] tibble_1.3.0
>
>
> Tom 2
>
>
> On Wed, May 10, 2017 at 1:05 PM, Jochen Wirsing <jw1085 at wildcats.unh.edu>
> wrote:
>
>> Dear All,
>>
>>
>> thanks again for your nice feedback. The Session Info etc was mentioned
>> in the previous email, but one of the folks here on the list asked me to
>> use dput() so I could paste my data in textform here.
>>
>> So here you go:
>>
>> structure(list(Place = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
>> 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L,
>> 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L,
>> 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), .Label =
>> c("Cambridge Bay",
>> "Iqaluit", "Rankin Inlet"), class = "factor"), year_c = c(-2,
>> -1, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, -2,
>> -1, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, -2,
>> -1, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15), SR_Total_ctd
>> = c(NA,
>> NA, 5.48961420000001, 7.24637679999999, 3.76569040000001, 6.9014085,
>> 9.3088858, 5.1771117, 7.51366120000002, 7.18157180000001, 3.7275064,
>> 5.7397959, 6.87500000000001, 6.25, 5.84577109999999, 6.2421973,
>> 4.70446319999999, NA, NA, NA, 11.9192688, 9.6291013, 8.54640980000001,
>> 8.7893297, 7.42343539999999, 5, 5.3674121, 6.1322261, 6.4182843,
>> 5.75692960000001, 6.3861534, 6.6706021, 7.76642339999999, 6.91983119999999,
>> 5.3634631, NA, NA, NA, 0.0870321999999959, -1.19047620000001,
>> -1.8723404, -0.4244482, 1.18443319999999, 2.19594590000001,
>> 1.57545610000001,
>> 3.080766, 1.8744906, 5.51053480000002, 6.31412790000002, 7.4451411,
>> 8.1226054, 9.52743899999999, 9.4339623, NA)), .Names = c("Place",
>> "year_c", "SR_Total_ctd"), row.names = c(NA, -54L), class = "data.frame")
>>>
>>
>>
>> I was also asked, whether using lme4 would be an option, but I don't
>> think that this will help fix the issue that I believe occurred through
>> updating to R 3.40. Also, nlme provides some information in a nicer way
>> (covariances etc, if I remember correctly - all this is still very new
>> to me....), so I'd really rather see nlme fixed.
>>
>>
>> Thanks again!
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