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repeated measures and random effects question

2 messages · Moore, James Roy, Thierry Onkelinx

Original
Moore, James Roy
# 
Hello list, 

Not sure how to address a list, so let me know if I'm doing something wrong.  

I'm having a difficult time wrapping my mind around how to account for repeated measures and random effects and was directed here.

My experimental design is:
4 sites
2 plots per site (control and treatment, 10m x 10m)
8 subplots per plot (1m x 1m) 
3 years (each subplot sampled once per year every year)

Response variable: proportional plant cover
Potential covariates/predictors: other proportional plant cover, herbivore damage
The treatment is herbivore removal so instead of using the factor treatment in the model I'm using proportional herbivore damage. 

I have to use a package specific for beta distribution with 0's but we can talk about this in the context of a glmm using lme4 since that is the syntax I'm most familiar with.  My limited understanding leads me to:
Plant cover ~ herbivore damage + some covariates +(1|site)+(year|site/plot/subplot)
	Random variation between sites and, to account for repeated measures, subplots nested within plot nested within site sampled at a yearly interval for 	3 years.

As an additional curiosity, is there any problem with excluding the treatment factor and using proportional herbivore damage instead? Also, since site is included in the second random term, is the first term still necessary.  There is definitely variation between sites.  

Thank you for any assistance you're able to provide,
James
3 days later
Thierry Onkelinx
# 
Dear James,

Your models is too complex given the available data. The random part can be
expanded to (1 + year|site) + (1 + year|site:plot) + (1 +
year|site:plot:subplot). The number of data points for each level of the
random effect groups are respectively 48, 24 and 3. I'm not comfortable
fitting a linear trend through only 3 data points... Also consider
http://bbolker.github.io/mixedmodels-misc/glmmFAQ.html#should-i-treat-factor-xxx-as-fixed-or-random,
especially the last paragraph.

I would strongly recommend that you consult a local statistician.

Best regards,



ir. Thierry Onkelinx
Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkelinx at inbo.be
Kliniekstraat 25, B-1070 Brussel
www.inbo.be

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Van 14 tot en met 19 december 2017 verhuizen we uit onze vestiging in
Brussel naar het Herman Teirlinckgebouw op de site Thurn & Taxis.
Vanaf dan ben je welkom op het nieuwe adres: Havenlaan 88 bus 73, 1000
Brussel.

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2017-12-08 0:34 GMT+01:00 Moore, James Roy <jmoore25 at wsu.edu>: