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I need some help with a mixed effects model in R. I want to know if there is any effect of month on home range size. The following is my set-up and an idea of how it is laid out in an excel sheet: I have 2 parks that I have home range estimates from (labeled parks 1 and 2). There are 6 individuals in each park (individuals 1-6 in park 1 and individuals 7-12 in park 2). There are 2 years worth of data (years 1 and 2), so for each month, each individual should have two home range estimates (one for year 1 and one for year 2).

I know "ID" should be a random effect, and I currently have "park","year", and "month" as fixed effects. My first thought is that "Park", "year" and "month" should all be crossed, but I am lost as to where "ID" is nested.

I have the following in R: 

lme4(Homerangesize~(park/year/month)+(1/ID))

How do i "fix" this bit of code so that it represents my experimental set up?

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I think your issue comes from not using |

for example, it seems like it should be 1|ID in your case. / should only be used after the | in your line of code. I'm using this for reference and extra detail. https://stats.stackexchange.com/questions/228800/crossed-vs-nested-random-effects-how-do-they-differ-and-how-are-they-specified

To further answer actually, I think this might work for you to keep park year and month crossed.

lme4(Homerangesize~(1|park/year/month)+(1|ID))
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Within the "nlme" package there is a function entitled lme(). This function contains a "random" argument which allows you specify the random effect. Seems to me that your code could easily be manipulated to...

lme(Homerangesize~park+year+month, random = ~1|ID)
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  • $\begingroup$ Thanks! In your code though, are park, year, and month considered as crossed effects? $\endgroup$
    – P_Grace
    Commented Jun 20, 2018 at 19:39
  • $\begingroup$ No but the syntax would be the same in the lme() function. lme(Homerangesize~(park/year/month), random = ~1|ID) Hope that solves the issue. $\endgroup$
    – Malcolm Wells
    Commented Jun 20, 2018 at 19:47
  • $\begingroup$ I'm pretty sure nlme::lme doesn't do crossed random effects very well - that was one of the motivations for lme4::lmer. I found this post stackoverflow.com/questions/36643713/… where Ben Bolker describes a method to "trick" lme into crossed random effects, but if you're looking for crossed, I'd stick with lme4. $\endgroup$
    – Melissa Key
    Commented Jun 20, 2018 at 20:12

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