[R-sig-ME] Error using MCMCglmm
Walid Crampton-Mawass
w@||dm@w@@@10 @end|ng |rom gm@||@com
Mon Dec 27 20:13:09 CET 2021
Hey Kamal,
one possible solution is to run the same code in a new session where you
only call the MCMCglmm package and input your data and phylogenetic
pedigree as dataframes. That way you can figure out if there were any
conflicts in the attached packages in your session.
Cheers
--
Walid Crampton-Mawass
On Mon, Dec 27, 2021 at 12:06 PM Kamal Atmeh <kamal.atmeh using hotmail.com>
wrote:
> Hi Jarrod,
>
> Thank you for your answer.
>
> Yes I transformed the dataset to a classic dataframe but the error
> remained.
>
> If it can help, please find below my sessionInfo(). I eventually loaded
> the tidyverse.
>
> Cheers,
>
> Kamal
>
>
> R version 4.0.3 (2020-10-10)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 10 x64 (build 19043)
>
> Matrix products: default
>
> locale:
> [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252
> [3] LC_MONETARY=French_France.1252 LC_NUMERIC=C
> [5] LC_TIME=French_France.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] MCMCglmm_2.29 ape_5.4-1 coda_0.19-4 performance_0.7.0
> [5] MuMIn_1.43.17 visreg_2.7.0 merTools_0.5.2 arm_1.11-2
> [9] MASS_7.3-53 glmmTMB_1.1.2.3 lmerTest_3.1-3 lme4_1.1-27.1
> [13] Matrix_1.4-0 scales_1.1.1 forcats_0.5.1 stringr_1.4.0
> [17] dplyr_1.0.7 purrr_0.3.4 readr_1.4.0 tidyr_1.1.3
> [21] tibble_3.0.4 ggplot2_3.3.5 tidyverse_1.3.1 plyr_1.8.6
>
> loaded via a namespace (and not attached):
> [1] cubature_2.0.4.2 TH.data_1.0-10 minqa_1.2.4 colorspace_1.4-1
> [5] ellipsis_0.3.2 estimability_1.3 htmlTable_2.2.1
> corpcor_1.6.9
> [9] base64enc_0.1-3 fs_1.5.0 rstudioapi_0.13 fansi_0.4.1
> [13] mvtnorm_1.1-1 lubridate_1.7.10 xml2_1.3.2 codetools_0.2-16
> [17] splines_4.0.3 knitr_1.33 Formula_1.2-4 jsonlite_1.7.2
> [21] nloptr_1.2.2.2 packrat_0.6.0 broom_0.7.8 cluster_2.1.0
> [25] dbplyr_2.1.1 png_0.1-7 broom.mixed_0.2.6
> shiny_1.5.0
> [29] compiler_4.0.3 httr_1.4.2 emmeans_1.6.1
> backports_1.2.1
> [33] fastmap_1.1.0 assertthat_0.2.1 cli_2.5.0 later_1.2.0
> [37] htmltools_0.5.1.1 tools_4.0.3 gtable_0.3.0 glue_1.4.2
> [41] reshape2_1.4.4 Rcpp_1.0.7 cellranger_1.1.0 vctrs_0.3.8
> [45] nlme_3.1-149 iterators_1.0.13 insight_0.14.2
> tensorA_0.36.1
> [49] xfun_0.24 rvest_1.0.0 mime_0.9 lifecycle_1.0.0
> [53] zoo_1.8-8 promises_1.1.1 hms_1.1.0 parallel_4.0.3
> [57] sandwich_3.0-0 TMB_1.7.22 RColorBrewer_1.1-2
> gridExtra_2.3
> [61] rpart_4.1-15 latticeExtra_0.6-29 stringi_1.5.3
> bayestestR_0.10.0
> [65] foreach_1.5.1 blme_1.0-5 checkmate_2.0.0 boot_1.3-25
> [69] rlang_0.4.11 pkgconfig_2.0.3 lattice_0.20-41
> htmlwidgets_1.5.3
> [73] tidyselect_1.1.0 magrittr_2.0.1 R6_2.4.1 generics_0.1.0
> [77] Hmisc_4.5-0 multcomp_1.4-14 DBI_1.1.1 pillar_1.6.4
> [81] haven_2.4.1 foreign_0.8-80 withr_2.3.0 survival_3.2-7
> [85] abind_1.4-5 nnet_7.3-14 modelr_0.1.8 crayon_1.4.1
> [89] utf8_1.1.4 jpeg_0.1-8.1 grid_4.0.3 readxl_1.3.1
> [93] data.table_1.14.0 reprex_2.0.0 digest_0.6.27 xtable_1.8-4
> [97] httpuv_1.6.1 numDeriv_2016.8-1.1 stats4_4.0.3 munsell_0.5.0
>
>
>
> Le 27/12/2021 à 19:49, Jarrod Hadfield a écrit :
> > Hi,
> >
> > Is your data frame a tibble? If so, make it a standard data frame and
> > retry.
> >
> > Cheers,
> >
> > Jarrod
> >
> > On 27/12/2021 18:46, Kamal Atmeh wrote:
> >> This email was sent to you by someone outside the University.
> >> You should only click on links or attachments if you are certain that
> >> the email is genuine and the content is safe.
> >>
> >> Dear list,
> >>
> >> I am trying to run bayesian phylogenetic mixed models using MCMCglmm but
> >> I keep getting the following error:
> >>
> >> " Error in MCMCglmm(ltau ~ x * x2 + lbmM + age + lmean_ndvi + :
> >> no slot of name "i" for this object of class "ddiMatrix" "
> >>
> >> This is not the first time I use MCMCglmm and it usually works
> >> flawlessly. I thought that there may be a conflict with the "tidyverse"
> >> package since some functions of "Matrix" are masked, but I tried to run
> >> the model without loading the "tidyverse" package and still received the
> >> same error. I was not able to find answers online and am thus turning to
> >> this list for answers if you can help please.
> >>
> >> I am running the following model:
> >>
> >> >>> prior1 <-list (G = list(G1 = list(V = 1, nu = 0.02)
> >> ,G2 = list(V = 1, nu = 0.02)
> >> ,G3 = list(V = 1, nu = 0.02)
> >> ,G4 = list(V = 1, nu = 0.02)),
> >> R = list(V = 1, nu = 0.02)
> >> )
> >>
> >> >>> mod_tau_mc <- MCMCglmm(ltau ~ x * x2+ # x and x2 are categorical
> >> variables
> >> lbmM + # continuous variable
> >> age + # categorical
> >> lmean_ndvi + # continuous
> >> lrange_ndvi + # continuous
> >> lnb.loc + # continuous
> >> lduration # continuous
> >> , random =
> >> ~sp_phylo+species2+phylo_pop+phylo_pop_id
> >> , ginverse = list(sp_phylo = inv.phylo$Ainv)
> >> # include a custom matrix for argument sp_phylo
> >> , family = "gaussian"
> >> , prior = prior1
> >> , data = dt
> >> , nitt = 22e+03 # number of iteration
> >> after burnin
> >> , burnin = 2000 # number of iteration
> >> before beginning sample
> >> , thin = 100 # nb of iteration between
> >> sample
> >> , pr = TRUE) #save random posterior
> >> distribution
> >>
> >> I would greatly appreciate your help and happy to provide further
> >> information if needed!
> >>
> >> Thank you in advance!
> >>
> >> Kamal
> >>
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