Message-ID: <DBBP189MB1340AC1087BE1FCC3836A69DFE429@DBBP189MB1340.EURP189.PROD.OUTLOOK.COM>
Date: 2021-12-27T19:05:51Z
From: Kamal Atmeh
Subject: Error using MCMCglmm
In-Reply-To: <532604ae-da23-5aa5-5321-841768a7da95@ed.ac.uk>
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
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