[R-sig-ME] DF in lme

Ben Ward benjamin.ward at bathspa.org
Thu Mar 17 04:03:50 CET 2011

```On 16/03/2011 15:08, Ben Bolker wrote:
> On 11-03-16 03:52 AM, Ben Ward wrote:
>> Hi, I'm using lme and lmer in my dissertation and it's the first time
>> I've used these methods. Taking into account replies from my previous
>> query I decided to go through with a model simplification, and then try
>> to validate the models in various ways and come up with the best one to
>> include in my work, be it a linear mixed effects model or general linear
>> effects model, with log() data or not etc - interestingly it does not
>> seems like doing transofrmations and such makes much difference so far,
>> looking at changes in diagnostic plots and AIC.
>    Be careful about comparing fits of transformed and non-transformed
> data via AIC/log-likelihood: e.g. see
> <http://www.unc.edu/courses/2006spring/ecol/145/001/docs/lectures/lecture18.htm>.
>   (This does *not* refer to the link function, e.g. the log link of the
> Poisson, but to the case where you transform your data prior to analysis.)
>
>> Anywho, I simplified to the model using lme (I've pasted it at the
>> bottom). And looking at the anova output the numDF looks right. However
>> I'm concerned about the 342 df in the denDF in anova() and in the
>> summary() output, as it seems to high to me, because at the observation
>> level is too high and pseudoreplicated; 4 readings per disk, 3 disks,
>> per plate, 3 plates per lineage, 5 lineages per group, 2 groups so:
>> 4*3*3*5*2=360. If I take this to disk level 3*3*5*2=90, and at dish
>> level it's 3*5*2=30 degrees of freedom for error. And either dish or
>> disk (arguments for both) is the level at which one independant point of
>> datum is obtained, most probably Dish. So I'm wondering if either I'de
>> done something wrong, or I'm not understanding how df are presented and
>> used in mixed models. It's not really explained in my texts, and my
>> lecturer told me I'm working at the edge of his personal/professional
>> experience.
>     At what level are Group and Lineage replicated in the model?  Do you
> have different Groups or Lineages represented on the same disk, dish, or
> plate?  If you do have multiple Groups and Lineages present at the
> lowest level of replication, then you have a randomized block design and
> the degrees of freedom may be higher than you think.  If you really want
> denominator degrees of freedom and you want them correct, consult an
> experimental design book and figure out what they should be in the
> classical framework ...
I'm now of the opinion that - (Just trying to get my head around it) -
that I don't have a randomized block design:
I've done a bit like a lenski evolution experiment with my microbes,
which involed two groups, in those two groups i have 5 cultures each,
one group is 5 lineages of bacteria I have been evolving against some
antimicrobial, the other group have not been through this - they are
stock run of the mill organisms. So with those 5 cultures of evolved
bacteria, for each, I'd take some, and spread it on three plates - so
theres no intermingling or randomization/mixing of the cultures: each
gets plated onto a who plate itself three times. Then the three disks,
incubated, and then I took 4 measurements from each zone that formed
around those disks. The disks all have the same antimicrobial on them.
So in that way, if what you say by randomized block design is something
like a split plot experiment, where there are several plots, and
numerous plants, and each one got a different treatment, then I don't
believe my experiment is like that.  In my case that would be like me
having different cultures on the same dish, or using disks with
different antimicrobials on, at least I think this is what you're
asking. In which case Dish is the level at which I get truly indepentent
pieces of data, and 3plates*5lineages*2Groups=30: If I recode my factor
levels then, like so, which I mentioned before as a possibility:
Diameter<-Dataset\$Diameter
Group<-factor(Dataset\$Group)
Lineage<-factor(Dataset\$Lineage)
Dish<-factor(Dataset\$Dish)
Disk<-factor(Dataset\$Disk)
lineage<-Group:Lineage
dish<-Group:Lineage:Dish
disk<-Group:Lineage:Dish:Disk

And then fit the model:

model <- lme(Diameter~Group*Lineage,random=~1|dish/disk, method="REML")

I get the following:

> summary(model)
Linear mixed-effects model fit by REML
Data: NULL
AIC      BIC    logLik
1144.193 1194.346 -559.0966

Random effects:
Formula: ~1 | dish
(Intercept)
StdDev:   0.2334716

Formula: ~1 | disk %in% dish
(Intercept) Residual
StdDev:    0.356117 1.079568

Fixed effects: Diameter ~ Group * Lineage
Value Std.Error  DF  t-value
p-value
(Intercept)                         15.049722 0.2542337 270 59.19641  0.0000
Group[T.NEDettol]                    0.980556 0.3595407  20  2.72724  0.0130
Lineage[T.First]                    -0.116389 0.3595407  20 -0.32372  0.7495
Lineage[T.Fourth]                   -0.038056 0.3595407  20 -0.10584  0.9168
Lineage[T.Second]                   -0.177500 0.3595407  20 -0.49369  0.6269
Lineage[T.Third]                     0.221111 0.3595407  20  0.61498  0.5455
Group[T.NEDettol]:Lineage[T.First]   2.275000 0.5084674  20  4.47423  0.0002
Group[T.NEDettol]:Lineage[T.Fourth]  0.955556 0.5084674  20  1.87929  0.0749
Group[T.NEDettol]:Lineage[T.Second]  0.828333 0.5084674  20  1.62908  0.1189
Group[T.NEDettol]:Lineage[T.Third]   0.721667 0.5084674  20  1.41930  0.1712
Correlation:
(Intr) Gr[T.NED] Lng[T.Frs] Lng[T.Frt]
Group[T.NEDettol]                   -0.707
Lineage[T.First]                    -0.707  0.500
Lineage[T.Fourth]                   -0.707  0.500     0.500
Lineage[T.Second]                   -0.707  0.500     0.500      0.500
Lineage[T.Third]                    -0.707  0.500     0.500      0.500
Group[T.NEDettol]:Lineage[T.First]   0.500 -0.707    -0.707     -0.354
Group[T.NEDettol]:Lineage[T.Fourth]  0.500 -0.707    -0.354     -0.707
Group[T.NEDettol]:Lineage[T.Second]  0.500 -0.707    -0.354     -0.354
Group[T.NEDettol]:Lineage[T.Third]   0.500 -0.707    -0.354     -0.354
L[T.S] L[T.T] Grp[T.NEDttl]:Lng[T.Frs]
Group[T.NEDettol]
Lineage[T.First]
Lineage[T.Fourth]
Lineage[T.Second]
Lineage[T.Third]                     0.500
Group[T.NEDettol]:Lineage[T.First]  -0.354 -0.354
Group[T.NEDettol]:Lineage[T.Fourth] -0.354 -0.354  0.500
Group[T.NEDettol]:Lineage[T.Second] -0.707 -0.354  0.500
Group[T.NEDettol]:Lineage[T.Third]  -0.354 -0.707  0.500
Grp[T.NEDttl]:Lng[T.Frt] G[T.NED]:L[T.S
Group[T.NEDettol]
Lineage[T.First]
Lineage[T.Fourth]
Lineage[T.Second]
Lineage[T.Third]
Group[T.NEDettol]:Lineage[T.First]
Group[T.NEDettol]:Lineage[T.Fourth]
Group[T.NEDettol]:Lineage[T.Second]  0.500
Group[T.NEDettol]:Lineage[T.Third]   0.500                    0.500

Standardized Within-Group Residuals:
Min          Q1         Med          Q3         Max
-2.26060119 -0.70948250  0.03630884  0.69899536  3.42475990

Number of Observations: 360
Number of Groups:
dish disk %in% dish
30             90

> anova(model)
numDF denDF  F-value p-value
(Intercept)       1   270 39586.82 <.0001
Group             1    20   145.07 <.0001
Lineage           4    20     4.58  0.0087
Group:Lineage     4    20     5.27  0.0046

This is closer to what I was expecting in terms of DF: 3 plates*5
lineages=15: 15 samples per group, 15-4(the numDF Lineage)=11, 11-1(the
numDF for Group)= 10 x 2 for the two groups/treatments = 20.
Hopefully I've worked that out correctly, and sombody could tell me
whether . Its' awkward because this experiment is unprecedented at my
uni, it was offered up by a teacher as a topic but then got dropped due
to lack of interest. As it's the first time, myself and my supervisor
were in many ways flying blind. If I remove the Lineage main effect
term, and include it as a random effect, leaving only group as a fixed
effect:
> anova(model2)
numDF denDF  F-value p-value
(Intercept)     1   270 8041.429 <.0001
Group           1     8   29.469   6e-04

I get 8DF which by the same reasoning in the above model, is 5-1=4, 4*2
= 8, so I take that as reassurance my working is correct. I'd also like
to ask for opinion, on whether it would be advisable to actually remove
lineage as a fixed effect, and include lineage as a random effect on the
slope, rather than intersect which is what I've put all the others as. I
ask this because, whilst I feel whilst lineage might seem a factor with
informative levels( tha's how I first saw them), I had no way of
predicting which ones would show greatest or smallest differences or how
the five factor levels would interact and shape my data, in that way the
factor levels are not really all that informative at all - they're just
numbered as dish and disk are, and their effects may even be different
within my two groups - they don't really allow any prediction in the
same way a factor for different types of fertiliser would in a plant
study would for example, so I'm thinking maybe it should be a random
effect.

Thank you very much to everyone that's replied to me and assisted me
with this, it's a tough learning curve, but I do think I'm beginning to
grasp how to use lme and lmer for my basic ends. Once I'm confident on
the above, I'm next considering, whether to try an introduce some
weighting options to see what happens to a small amount of
heterscedacity I have between the two groups.

Ben W.
>> I've used lmer and the function in languageR to extract p-values without
>> it even mentioning df. Now if the lmer method with pvals.fnc() makes it
>> so as I don't have to worry about these df then in a way it makes my
>> issue a bit redundant. But it is playing on my mind a bit so felt I
>>
>> My second question is about when I do the equivalent model using lmer:
>> "lmer(Diameter~Group*Lineage+(1|Dish)+(1|Disk), data=Dataset)" - which
>> I'm sure does the same because all my plots of residuals against fitted
>> and such are the same, if I define it with the poisson family, which
>> uses log, then I get a much lower AIC of about 45, compared to over 1000
>> without family defined, which I think defaults to gaussian/normal.
>    I don't think you should try to pick the family on the basis of AIC --
> you should pick it on the basis of the qualitative nature of the data.
> If you have count data, you should probably use Poisson (but you may
> want to add an observation-level random effect to allow for
> overdispersion.)  If your response variable is Diameter, it is **not** a
> count variable, and you shouldn't use Poisson -- you should use an
> appropriately transformed response variable.
I've tried transforming my response variable in a few ways, like natural
log, sqrt, and (x/1) but they don't really seem to alter the
distribution or shape of my data at all.
Interestingly, if I look at the spread of the data by splitting the
response variable between the two groups, I see much more symmetry -
although still not a nice neat normal distribution, but in Biology I've
been taught never to expect one.
>
>   And
>> my diagnostic plots still give me all the same patters, but just looking
>> a bit different because of the family distribution specified. I then did
>> a model logging the response variable by using log(Diameter), again, I
>> get the same diagnostic plot patterns, but on a different scale, and I
>> get an AIC of - 795.6. Now normally I'd go for the model with the lowest
>> AIC, however, I've never observed this beahviour before, and can't help
>> but think thhat the shift from a posotive 1000+ AIC to a negative one is
>> due to the fact the data has been logged, rather than that the model
>> fitted to log data in this way is genuinley better.
>>
>> Finally, I saw in a text, an example of using lmer but "Recoding Factor
>> Levels" like:
>> lineage<-Group:Lineage
>> dish<-Group:Lineage:Dish
>> disk<-Group:Lineage:Dish:Disk
>> model<-lmer(Diameter~Group+(1|lineage)+(1|dish)+(1|disk)
>>
>> However I don't see why this should need to be done, considering, the
>> study was hieracheal, just like all other examples in that chapter, and
>> it does not give a reason why, but says it does the same job as a nested
>> anova, which I though mixed models did anyway.
>    (1|lineage)+(1|dish)+(1|disk)
>
>    is the same as
>
>    (1|Lineage/Dish/Disk)
>
>    (1|Dish) + (1|Disk) is **not** the same as (1|Dish/Disk), if Disk is
> not labeled uniquely (i.e. if Dishes are A, B, C, .. and Disks are 1, 2,
> 3, ... then you need Dish/Disk.  If you have labeled Disks A1, A2, ...
> B1, B2, ... then the specifications are equivalent.
>
>    For a linear mixed model (i.e. not Poisson counts) you should be able
> to run the same model in lmer and lme and get extremely similar results.
>
>> Hopefully sombody can shed light on my concerns. In terms of my work and
>> university, I could include what I've done here and be as transparrant
>> as possible and discuss these issues, because log() of the data or
>> defining a distribution in the model is leading to the same plots and
>> conclusions. But I'd like to make sure I come to term with what's
>> actually happening here.
>>
>> A million thanks,
>> Ben W.
>>
>>
>> lme14<- lme(Diameter~Group*Lineage,random=~1|Dish/Disk, data=Dataset,
>> method="REML")
>>
>>> anova(lme14):
>>   numDF denDF   F-value p-value
>> (Intercept)       1   342 16538.253<.0001
>> Group             1   342   260.793<.0001
>> Lineage           4   342     8.226<.0001
>> Group:Lineage     4   342     9.473<.0001
>>
>>> summary(lme14)
>> Linear mixed-effects model fit by REML
>>   Data: Dataset
>>         AIC      BIC    logLik
>>    1148.317 1198.470 -561.1587
>>
>> Random effects:
>>   Formula: ~1 | Dish
>>          (Intercept)
>> StdDev:   0.1887527
>>
>>   Formula: ~1 | Disk %in% Dish
>>           (Intercept) Residual
>> StdDev: 6.303059e-05 1.137701
>>
>> Fixed effects: Diameter ~ Group * Lineage
>>                                          Value Std.Error  DF  t-value
>> p-value
>> (Intercept)                         15.049722 0.2187016 342 68.81396
>> 0.0000
>> Group[T.NEDettol]                    0.980556 0.2681586 342  3.65662
>> 0.0003
>> Lineage[T.First]                    -0.116389 0.2681586 342 -0.43403
>> 0.6645
>> Lineage[T.Fourth]                   -0.038056 0.2681586 342 -0.14191
>> 0.8872
>> Lineage[T.Second]                   -0.177500 0.2681586 342 -0.66192
>> 0.5085
>> Lineage[T.Third]                     0.221111 0.2681586 342  0.82455
>> 0.4102
>> Group[T.NEDettol]:Lineage[T.First]   2.275000 0.3792336 342  5.99894
>> 0.0000
>> Group[T.NEDettol]:Lineage[T.Fourth]  0.955556 0.3792336 342  2.51970
>> 0.0122
>> Group[T.NEDettol]:Lineage[T.Second]  0.828333 0.3792336 342  2.18423
>> 0.0296
>> Group[T.NEDettol]:Lineage[T.Third]   0.721667 0.3792336 342  1.90296
>> 0.0579
>>   Correlation:
>>                                      (Intr) Gr[T.NED] Lng[T.Frs] Lng[T.Frt]
>> Group[T.NEDettol]                   -0.613
>> Lineage[T.First]                    -0.613  0.500
>> Lineage[T.Fourth]                   -0.613  0.500     0.500
>> Lineage[T.Second]                   -0.613  0.500     0.500      0.500
>> Lineage[T.Third]                    -0.613  0.500     0.500      0.500
>> Group[T.NEDettol]:Lineage[T.First]   0.434 -0.707    -0.707     -0.354
>> Group[T.NEDettol]:Lineage[T.Fourth]  0.434 -0.707    -0.354     -0.707
>> Group[T.NEDettol]:Lineage[T.Second]  0.434 -0.707    -0.354     -0.354
>> Group[T.NEDettol]:Lineage[T.Third]   0.434 -0.707    -0.354     -0.354
>>                                      L[T.S] L[T.T] Grp[T.NEDttl]:Lng[T.Frs]
>> Group[T.NEDettol]
>> Lineage[T.First]
>> Lineage[T.Fourth]
>> Lineage[T.Second]
>> Lineage[T.Third]                     0.500
>> Group[T.NEDettol]:Lineage[T.First]  -0.354 -0.354
>> Group[T.NEDettol]:Lineage[T.Fourth] -0.354 -0.354  0.500
>> Group[T.NEDettol]:Lineage[T.Second] -0.707 -0.354  0.500
>> Group[T.NEDettol]:Lineage[T.Third]  -0.354 -0.707  0.500
>>                                      Grp[T.NEDttl]:Lng[T.Frt] G[T.NED]:L[T.S
>> Group[T.NEDettol]
>> Lineage[T.First]
>> Lineage[T.Fourth]
>> Lineage[T.Second]
>> Lineage[T.Third]
>> Group[T.NEDettol]:Lineage[T.First]
>> Group[T.NEDettol]:Lineage[T.Fourth]
>> Group[T.NEDettol]:Lineage[T.Second]  0.500
>> Group[T.NEDettol]:Lineage[T.Third]   0.500                    0.500
>>
>> Standardized Within-Group Residuals:
>>          Min          Q1         Med          Q3         Max
>> -2.47467771 -0.75133489  0.06697157  0.67851126  3.27449064
>>
>> Number of Observations: 360
>> Number of Groups:
>>            Dish Disk %in% Dish
>>               3              9
>>
>> _______________________________________________
>> R-sig-mixed-models at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>
>

```