MCMCglmm: possible to estimate a covariance with mm() multiple membership structure
Dear List, I am using MCMCglmm for a quantitative genetic analysis of reproductive success data where 1 focal individual competed in an assay against 3 same-sex competitors. We have pedigree information for every individual and so I would like to estimate the direct genetic effects (DGE) variance among focal individuals, indirect genetic effects (IGE) variance among competitors, and the DGE-IGE covariance. My main question is whether it is possible to estimate the DGE-IGE covariance in MCMCglmm? I know this is possible when there is a single term making up the IGE effects, as in a DGE-maternal genetic covariance by including these terms in the `str()` function (for example, as described in another post: https://stat.ethz.ch/pipermail/r-sig-mixed-models/2017q4/026271.html). However, since I have 3 competitors I am using the multiple membership function `mm()` and it seems MCMCglmm does not allow combining `str()` and `mm()`. The code for specifying my random effects terms _without_ a covariance is: ``` # below `id` is the focal individual and `irr_comp_X` is each of the 3 competitors of the focal ?? random = ~ id + mm(irr_comp_1 + irr_comp_2 + irr_comp_3), ?? ginverse = list(id = AinvM, ???? irr_comp_1 = AinvM, irr_comp_2 = AinvM, irr_comp_3 = AinvM), ``` If I try to use `str()` to estimate the DGE-IGE covariance as well: `random = ~str(id + mm(irr_comp_1 + irr_comp_2 + irr_comp_3)) ` I get the error: ``` Error in buildZ(rmodel.terms[r], data = data, nginverse = names(ginverse)) : ? object id and mm(irr_comp_1 and irr_comp_2 and irr_comp_3) not found ``` Is there another way to write the formula or other workaround for using MCMCglmm to estimate the DGE-IGE covariance that anyone knows about or is this currently just not possible? Sincerely, Matthew
**************************************************** Matthew E. Wolak, Ph.D. Associate Professor Department of Biological Sciences Auburn University 306 Funchess Hall Auburn, AL 36849, USA https://qgevoeco.com Email:terps at auburn.edu Tel: 334-844-9242 [[alternative HTML version deleted]]