[R-meta] Same command works on one machine but not another
Benoît Bediou
Beno|t@Bed|ou @end|ng |rom un|ge@ch
Mon Jun 7 07:56:05 CEST 2021
Hi there
I am facing a strange problem and would welcome some help
My colleague is able to run a command that does not work on my machine and we haven’t been able to figure out why
I am pasting below the command lines and then the sessionInfo from my machine and from my colleague’s
Thank you so much for any help you can provide!
best
Ben
The command is its simple as
## Multilevel model
vcov_mat <- impute_covariance_matrix(es_data$g_var,
cluster = es_data$Paper,
r = 0.8)
mlma_model<- metafor::rma.mv(g ~ 1, # Intercept only MLMA model
V = vcov_mat,
random = ~ 1 | Paper / ES_ID,# NOT WORKING WE COULD ADD COGNITIVE DOMAIN TOO!?
# random = list(~ 1 | Paper, ~ 1 | ES_ID),#
# random = ~ 1 | ES_ID,# WORKING
sparse = TRUE,
data = es_data,
test="t")
## Add RVE using clubSandwich
CHE_model <- clubSandwich::coef_test(mlma_model, vcov = "CR2")
>Error in if (!all(nested)) stop("Random effects are not nested within clustering") :
missing value where TRUE/FALSE needed
>
## SESSION INFO --- NOT WORKING
R version 4.0.4 (2021-02-15)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] matrixStats_0.57.0 doMC_1.3.7 iterators_1.0.13 foreach_1.5.1 partitions_1.10-2 DescTools_0.99.38 ggsci_2.9 RColorBrewer_1.1-2 plotly_4.9.2.1
[10] ggthemes_4.2.0 scales_1.1.1 wesanderson_0.3.6 ggExtra_0.9 ggstatsplot_0.6.5 metafor_2.4-0 Matrix_1.3-2 clubSandwich_0.5.3 robumeta_2.0
[19] zoo_1.8-9 kableExtra_1.3.1 knitr_1.30 summarytools_0.9.6 plyr_1.8.6 forcats_0.5.0 stringr_1.4.0 dplyr_1.0.3 purrr_0.3.4
[28] readr_1.4.0 tidyr_1.1.2 tibble_3.1.0 ggplot2_3.3.3 tidyverse_1.3.0 lavaan_0.6-8 data.table_1.13.6 reshape2_1.4.4 pacman_0.5.1
loaded via a namespace (and not attached):
[1] coda_0.19-4 multcomp_1.4-15 inline_0.3.16 generics_0.1.0 callr_3.5.1 cowplot_1.1.0
[7] TH.data_1.0-10 correlation_0.4.0 webshot_0.5.2 xml2_1.3.2 lubridate_1.7.9.2 httpuv_1.5.4
[13] StanHeaders_2.21.0-6 assertthat_0.2.1 WRS2_1.1-0 xfun_0.20 hms_0.5.3 evaluate_0.14
[19] promises_1.1.1 tidyBF_0.4.0 fansi_0.4.2 dbplyr_2.0.0 readxl_1.3.1 DBI_1.1.0
[25] tmvnsim_1.0-2 htmlwidgets_1.5.2 reshape_0.8.8 kSamples_1.2-9 stats4_4.0.4 Rmpfr_0.8-2
[31] paletteer_1.2.0 ellipsis_0.3.1 crosstalk_1.1.0.1 selectr_0.4-2 rcompanion_2.3.26 ggpubr_0.4.0
[37] backports_1.2.1 V8_3.4.0 pbivnorm_0.6.0 insight_0.10.0 ggcorrplot_0.1.3 rapportools_1.0
[43] RcppParallel_5.0.2 libcoin_1.0-6 vctrs_0.3.6 abind_1.4-5 withr_2.4.1 pryr_0.1.4
[49] metaBMA_0.6.5 bdsmatrix_1.3-4 checkmate_2.0.0 prettyunits_1.1.1 fastGHQuad_1.0 mnormt_2.0.2
[55] lazyeval_0.2.2 crayon_1.4.1 labeling_0.4.2 pkgconfig_2.0.3 SuppDists_1.1-9.5 nlme_3.1-152
[61] statsExpressions_0.6.0 rematch_1.0.1 rlang_0.4.10 lifecycle_1.0.0 miniUI_0.1.1.1 LaplacesDemon_16.1.4
[67] MatrixModels_0.4-1 sandwich_3.0-1 mathjaxr_1.0-1 EMT_1.1 modelr_0.1.8 cellranger_1.1.0
[73] tcltk_4.0.4 broomExtra_4.1.0 lmtest_0.9-38 loo_2.3.1 mc2d_0.1-18 carData_3.0-4
[79] boot_1.3-26 reprex_0.3.0 base64enc_0.1-3 processx_3.4.5 viridisLite_0.3.0 PMCMRplus_1.7.0
[85] parameters_0.9.0 rootSolve_1.8.2.1 debugme_1.1.0 pander_0.6.3 multcompView_0.1-8 coin_1.3-1
[91] rstatix_0.6.0 ggsignif_0.6.0 memoise_1.1.0 magrittr_2.0.1 compiler_4.0.4 rstantools_2.1.1
[97] bbmle_1.0.23.1 lme4_1.1-25 cli_2.3.1 pbapply_1.4-3 ps_1.5.0 TMB_1.7.18
[103] Brobdingnag_1.2-6 MASS_7.3-53 mgcv_1.8-33 tidyselect_1.1.0 stringi_1.5.3 highr_0.8
[109] yaml_2.2.1 ggrepel_0.8.2 bridgesampling_1.0-0 grid_4.0.4 polynom_1.4-0 tools_4.0.4
[115] lmom_2.8 rio_0.5.16 rstudioapi_0.13 foreign_0.8-81 gridExtra_2.3 ipmisc_4.1.0
[121] gld_2.6.2 pairwiseComparisons_3.1.0 farver_2.1.0 RcppZiggurat_0.1.6 digest_0.6.27 shiny_1.5.0
[127] nortest_1.0-4 BWStest_0.2.2 Rcpp_1.0.6 car_3.0-10 broom_0.7.3.9000 ez_4.4-0
[133] BayesFactor_0.9.12-4.2 performance_0.5.1 metaplus_0.7-11 later_1.1.0.1 httr_1.4.2 rsconnect_0.8.16
[139] effectsize_0.4.0 colorspace_2.0-0 rvest_0.3.6 fs_1.5.0 splines_4.0.4 statmod_1.4.35
[145] rematch2_2.1.2 expm_0.999-5 Exact_2.1 xtable_1.8-4 gmp_0.6-1 jsonlite_1.7.2
[151] nloptr_1.2.2.2 rstan_2.21.2 Rfast_2.0.1 zeallot_0.1.0 modeltools_0.2-23 R6_2.5.0
[157] broom.mixed_0.2.6 pillar_1.5.1 htmltools_0.5.1 mime_0.9 DT_0.16 glue_1.4.2
[163] fastmap_1.0.1 minqa_1.2.4 class_7.3-18 codetools_0.2-18 pkgbuild_1.2.0 mvtnorm_1.1-1
[169] utf8_1.2.1 lattice_0.20-41 numDeriv_2016.8-1.1 curl_4.3 gtools_3.8.2 magick_2.5.2
[175] logspline_2.1.16 zip_2.1.1 openxlsx_4.2.3 survival_3.2-7 rmarkdown_2.6 munsell_0.5.0
[181] e1071_1.7-4 haven_2.3.1 gtable_0.3.0 bayestestR_0.7.5
## SESSION INFO — WORKING MACHINE
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] DescTools_0.99.37 ggsci_2.9 RColorBrewer_1.1-2 plotly_4.9.3 ggthemes_4.2.0 scales_1.1.1 wesanderson_0.3.6 ggExtra_0.9
[9] ggstatsplot_0.7.1 metafor_2.5-57 Matrix_1.2-18 clubSandwich_0.5.0 robumeta_2.0 zoo_1.8-8 kableExtra_1.1.0 knitr_1.29
[17] summarytools_0.9.6 plyr_1.8.6 forcats_0.5.0 stringr_1.4.0 dplyr_1.0.0 purrr_0.3.4 readr_1.3.1 tidyr_1.1.0
[25] tibble_3.0.3 ggplot2_3.3.3 tidyverse_1.3.0 lavaan_0.6-8 data.table_1.13.0 reshape2_1.4.4 pacman_0.5.1
loaded via a namespace (and not attached):
[1] readxl_1.3.1 pairwiseComparisons_3.1.3 backports_1.1.8 selectr_0.4-2 lazyeval_0.2.2 splines_4.0.2
[7] gmp_0.6-2 kSamples_1.2-9 ipmisc_6.0.0 pryr_0.1.4 digest_0.6.25 SuppDists_1.1-9.5
[13] htmltools_0.5.0 magick_2.5.0 fansi_0.4.1 magrittr_1.5 checkmate_2.0.0 memoise_2.0.0
[19] paletteer_1.3.0 modelr_0.1.8 matrixStats_0.57.0 sandwich_2.5-1 colorspace_1.4-1 blob_1.2.1
[25] rvest_0.3.6 ggrepel_0.8.2 haven_2.3.1 xfun_0.16 tcltk_4.0.2 crayon_1.3.4
[31] jsonlite_1.7.0 Exact_2.0 zeallot_0.1.0 glue_1.4.1 gtable_0.3.0 webshot_0.5.2
[37] MatrixModels_0.4-1 statsExpressions_1.0.0 Rmpfr_0.8-3 rapportools_1.0 mvtnorm_1.1-1 DBI_1.1.0
[43] PMCMRplus_1.9.0 miniUI_0.1.1.1 Rcpp_1.0.5 viridisLite_0.3.0 xtable_1.8-4 performance_0.4.8
[49] tmvnsim_1.0-2 stats4_4.0.2 htmlwidgets_1.5.3 httr_1.4.2 ellipsis_0.3.1 farver_2.0.3
[55] pkgconfig_2.0.3 reshape_0.8.8 multcompView_0.1-8 dbplyr_1.4.4 labeling_0.3 tidyselect_1.1.0
[61] rlang_0.4.7 later_1.1.0.1 ggcorrplot_0.1.3 effectsize_0.4.4 munsell_0.5.0 cellranger_1.1.0
[67] tools_4.0.2 cachem_1.0.4 cli_2.0.2 generics_0.0.2 broom_0.7.5 mathjaxr_1.0-1
[73] evaluate_0.14 fastmap_1.0.1 BWStest_0.2.2 yaml_2.2.1 rematch2_2.1.2 fs_1.4.2
[79] pander_0.6.3 WRS2_1.1-1 pbapply_1.4-3 nlme_3.1-148 mime_0.9 xml2_1.3.2
[85] correlation_0.6.0 compiler_4.0.2 rstudioapi_0.11 ggsignif_0.6.1 reprex_0.3.0 pbivnorm_0.6.0
[91] stringi_1.4.6 highr_0.8 parameters_0.12.0 lattice_0.20-41 vctrs_0.3.2 pillar_1.4.6
[97] lifecycle_0.2.0 mc2d_0.1-18 insight_0.13.2 httpuv_1.5.4 patchwork_1.1.1 R6_2.4.1
[103] promises_1.1.1 BayesFactor_0.9.12-4.2 codetools_0.2-16 boot_1.3-25 MASS_7.3-51.6 gtools_3.8.2
[109] assertthat_0.2.1 withr_2.2.0 mnormt_2.0.1 expm_0.999-5 mgcv_1.8-31 bayestestR_0.8.2
[115] parallel_4.0.2 hms_0.5.3 grid_4.0.2 coda_0.19-3 rmarkdown_2.3 shiny_1.5.0
[121] lubridate_1.7.9 base64enc_0.1-3
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