Walid Crampton-Mawass
On Mon, Dec 27, 2021 at 12:06 PM Kamal Atmeh <kamal.atmeh at 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 ? 19:49, Jarrod Hadfield a ?crit :
> > 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
> >>
> >> _______________________________________________
> >> R-sig-mixed-models at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> > The University of Edinburgh is a charitable body, registered in
> > Scotland, with registration number SC005336. Is e buidheann
> > carthannais a th? ann an Oilthigh Dh?n ?ideann, cl?raichte an Alba,
> > ?ireamh cl?raidh SC005336.
> >
> > _______________________________________________
> > R-sig-mixed-models at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>
> _______________________________________________
> R-sig-mixed-models at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>
[[alternative HTML version deleted]]