> On May 27, 2016, at 10:07 AM, James Henson <jfhens...@gmail.com> wrote:
>
> Greetings Jeff,
> You are correct that the unequal number of levels is not the problem.
> I revised the data frame so that the number of levels was equal and
> the same error message occurred. The code is below, and the
> Eboni2.txt file is attached. This problem baffles me. I appreciate
> any help.
> Best regards,
> James
> Eboni2 <- read.csv("Eboni2.csv", header = TRUE)
>
> library("nlme")
>
> str(Eboni2)
>
> head(Eboni2)
>
> model1 <- lme(preDawn ~ Irrigation, random=~season_order|treeNo, data=Eboni2)
I downloaded the attached file to your first posting that was called a "csv"
file but it was tab-separated (as could be clearly seen with the str output, so
would only load properly with read.delim rather than read.csv. Running then
with the lme call, it produced this message
> model1 <- lme(preDawn ~ Irrigation, random=~season_order|treeNo, data=Eboni2)
Error in na.fail.default(list(season_order = c(5L, 5L, 5L, 5L, 5L, 5L, :
missing values in object
And looking at the str result made it clear that there were many NA's in the
file.
> head(Eboni2)
number Location Season season_order Month treeID treeNo preDawn midday
1 1 UCC November 5 Nov UCCLO 1 60 1.4 1.3
2 2 UCC November 5 Nov UCCLO 2 72 1.2 1.3
3 3 UCC November 5 Nov UCCLO 3 78 1.1 1.2
4 4 UCC November 5 Nov UCCLO 4 79 1.1 2.1
5 5 UCC November 5 Nov UCCLO 5 80 1.4 1.3
6 6 UCC November 5 Nov UCCLO 6 81 0.6 1.8
Irrigation Pnet Gs E WUE d15N d13C Nper Cper include2
1 N 9 0.2907004 3.766207 2.389672 NA NA NA NA no
2 N 11 0.3262582 3.120574 3.524993 NA NA NA NA no
3 N 8 0.2870957 1.693821 4.723050 3.00 -27.44 2.12 52.12 yes
4 N 10 0.2475180 1.839343 5.436724 3.61 -29.50 1.42 51.97 yes
5 N 13 0.3009228 3.082278 4.217660 NA NA NA NA no
6 N 17 0.3487337 2.534550 6.707304 2.79 -30.50 1.49 49.94 yes
And even more importantly, there was one NA in your outcome variable:
> sum( is.na(Eboni2$Irrigation))
[1] 0
> sum( is.na(Eboni2$preDawn))
[1] 1
So after restricting to complete.cases, I then formed the hypothesis that you
reversed the order of the variables in the formula for the random parameter:
> table(Eboni2$season_order)
1 2 3 4 5
83 83 83 83 83
> length( Eboni2$treeNo)
[1] 415
So it seemed unreasonable to have a "grouping" on variable with only one item
per group.
> model1 <- lme(preDawn ~ Irrigation, random=~treeNo|season_order, data=Eboni2[
> complete.cases( Eboni2[ ,
> c('preDawn','Irrigation','season_order','treeNo')]), ] )
> model1
Linear mixed-effects model fit by REML
Data: Eboni2[complete.cases(Eboni2[, c("preDawn", "Irrigation",
"season_order", "treeNo")]), ]
Log-restricted-likelihood: -183.4708
Fixed: preDawn ~ Irrigation
(Intercept) IrrigationY
1.04520145 -0.06037706
Random effects:
Formula: ~treeNo | season_order
Structure: General positive-definite, Log-Cholesky parametrization
StdDev Corr
(Intercept) 0.140239324 (Intr)
treeNo 0.003766019 -0.725
Residual 0.365678898
Number of Observations: 414
Number of Groups: 5
(Warning, I'm not a frequent user of this package or any of the mixed effects
packages.)
Just to correct some misinformation that appeared earlier: You can attach "csv"
or "tsv" files as long as you name them with an .txt extension so the mail
clients and servers consider them to be MIME-text.
--
David.
> On Wed, May 25, 2016 at 6:23 PM, Jeff Newmiller
> <jdnew...@dcn.davis.ca.us> wrote:
>> Please keep the mailing list in the loop by using reply-all.
>>
>> I don't think there is a requirement that the number of levels is equal, but
>> there may be problems if you don't have the minimum number of records
>> corresponding to each combination of levels specified in your model.
>>
>> You can change the csv extension to txt and attach for the mailing list. Or,
>> better yet, you can use the dput function to embed the data directly in your
>> sample code.
>>
>> Also, please learn to post plain text email to avoid corruption of R code by
>> the HTML formatting.
>> --
>> Sent from my phone. Please excuse my brevity.
>>
>> On May 25, 2016 2:26:54 PM PDT, James Henson <jfhens...@gmail.com> wrote:
>>>
>>> Good afternoon Jeff,
>>> The sample sizes for levels of the factor "Irrigation" are not equal. If
>>> 'nlme' requires equal sample sizes this may be the problem. The same data
>>> frame runs in 'lme4' without a problem.
>>>
>>> Best regards,
>>> James
>>>
>>>
>>> On Wed, May 25, 2016 at 3:41 PM, James Henson <jfhens...@gmail.com> wrote:
>>>>
>>>> Good afternoon Jeff,
>>>>
>>>> When working with this data frame, I just open the .csv file in R Studio.
>>>> But, we should not send .csv file to R_help. What should I send?
>>>>
>>>> Best regards,
>>>> James
>>>>
>>>> On Wed, May 25, 2016 at 2:52 PM, Jeff Newmiller
>>>> <jdnew...@dcn.davis.ca.us> wrote:
>>>>>
>>>>> You forgot to show the commands to us that you used to read the data in
>>>>> with (your example is not "reproducible"). This step can make all the
>>>>> difference in the world as to whether your analysis commands will work or
>>>>> not.
>>>>> --
>>>>> Sent from my phone. Please excuse my brevity.
>>>>>
>>>>> On May 25, 2016 11:59:06 AM PDT, James Henson <jfhens...@gmail.com>
>>>>> wrote:
>>>>>>
>>>>>> Greetings R community,
>>>>>>
>>>>>> My aim is to analyze a mixed-effects model with temporal
>>>>>> pseudo-replication
>>>>>> (repeated measures on the same experimental unit) using ‘nlme’.
>>>>>> However,
>>>>>> my code returns the error message “Error in na.fail.default’, even
>>>>>> though
>>>>>> the data frame does not contain missing values. My code is below, and
>>>>>> the
>>>>>> data file is attached as ‘Eboni2.txt.
>>>>>>
>>>>>> library("nlme")
>>>>>>
>>>>>> str(Eboni2)
>>>>>>
>>>>>> head(Eboni2)
>>>>>>
>>>>>> model1 <- lme(preDawn ~ Irrigation, random=~season_order|treeNo,
>>>>>> data=Eboni2)
>>>>>>
>>>>>> I am genuinely confused. Hope someone can help.
>>>>>>
>>>>>> Best regards,
>>>>>>
>>>>>> James F. Henson
>>>>>>
>>>>>> ________________________________
>>>>>>
>>>>>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>>>>> 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@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.
David Winsemius
Alameda, CA, USA
______________________________________________
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