I have the following table using kableExtra in R
library(tidyverse)
library(kableExtra)
sr <- c('Positive (+)','Positive (+)','Negative (-)','Positive (+)')
lr <- c('Positive (+)','Neutral','Negative (-)','Positive (+)')
d <- c('GDP Response to Positive','','CPI Response to Positive','')
s <- c('AS Shock','AD Shock','AS Shock','AD Shock')
data.frame(d,s,sr,lr) %>%
kable(col.names = c('','','Short Run Effect','Long Run Effect'),'html') %>%
kable_styling() %>%
row_spec(0, col = 'white', background = '#7c3042') %>%
footnote(general="<b>These signs represent prior expectations for the short and long run dynamics
of variable responses to respective shocks, based on a conventional AS-AD framework<b>", escape = FALSE) %>%
column_spec(1:4,bold = T) %>%
save_kable(file = "table.png", density = 700)
For some odd reason, the table is slightly cropped off at the top when I save it. Any way to overcome this?
EDIT
Here is my session info
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=English_Namibia.1252 LC_CTYPE=English_Namibia.1252 LC_MONETARY=English_Namibia.1252
[4] LC_NUMERIC=C LC_TIME=English_Namibia.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] magick_2.6.0 hrbrthemes_0.8.0 lubridate_1.7.9.2 readxl_1.3.1 tbl2xts_1.0.4 feasts_0.1.6
[7] fabletools_0.3.0 tsbox_0.2.1 tsibble_0.9.3 Rcpp_1.0.6 kableExtra_1.3.1 forcats_0.5.0
[13] stringr_1.4.0 dplyr_1.0.3 purrr_0.3.4 readr_1.4.0 tidyr_1.1.2 tibble_3.0.5
[19] ggplot2_3.3.3 tidyverse_1.3.0
loaded via a namespace (and not attached):
[1] nlme_3.1-151 fs_1.5.0 xts_0.12.1 webshot_0.5.2
[5] httr_1.4.2 tools_4.0.3 backports_1.2.1 R6_2.5.0
[9] DBI_1.1.1 colorspace_2.0-0 withr_2.4.0 tidyselect_1.1.0
[13] processx_3.4.5 extrafontdb_1.0 curl_4.3 compiler_4.0.3
[17] cli_2.2.0 rvest_0.3.6 pacman_0.5.1 xml2_1.3.2
[21] sandwich_3.0-0 tseries_0.10-48 scales_1.1.1 lmtest_0.9-37
[25] quadprog_1.5-8 callr_3.5.1 systemfonts_0.3.2 digest_0.6.27
[29] foreign_0.8-81 rmarkdown_2.6 rio_0.5.16 pkgconfig_2.0.3
[33] htmltools_0.5.0 extrafont_0.17 dbplyr_2.0.0 highr_0.8
[37] rlang_0.4.9 TTR_0.24.2 rstudioapi_0.13 quantmod_0.4.18
[41] farver_2.0.3 generics_0.1.0 zoo_1.8-8 jsonlite_1.7.2
[45] distributional_0.2.1 zip_2.1.1 car_3.0-10 magrittr_2.0.1
[49] munsell_0.5.0 fansi_0.4.2 gdtools_0.2.3 abind_1.4-5
[53] lifecycle_0.2.0 stringi_1.5.3 carData_3.0-4 PerformanceAnalytics_2.0.4
[57] MASS_7.3-53 plyr_1.8.6 grid_4.0.3 parallel_4.0.3
[61] strucchange_1.5-2 crayon_1.3.4 lattice_0.20-41 haven_2.3.1
[65] hms_1.0.0 knitr_1.30 anytime_0.3.9 ps_1.5.0
[69] pillar_1.4.7 ggpubr_0.4.0 ggsignif_0.6.0 reshape2_1.4.4
[73] codetools_0.2-18 reprex_0.3.0 urca_1.3-0 glue_1.4.2
[77] evaluate_0.14 vars_1.5-3 data.table_1.13.6 modelr_0.1.8
[81] vctrs_0.3.6 foreach_1.5.1 Rttf2pt1_1.3.8 cellranger_1.1.0
[85] gtable_0.3.0 PortfolioAnalytics_1.1.0 assertthat_0.2.1 xfun_0.20
[89] openxlsx_4.2.3 broom_0.7.3 rstatix_0.6.0 viridisLite_0.3.0
[93] iterators_1.0.13 ellipsis_0.3.1
Related
I've tried merge and update columns values with this code.
For now the joined fields are correct. (#1)
Now I want update the fields of column.x with values in column.y.
I'm using the second part (#2) but without success.
#1 - code to merge table 'parcelas_sql' with 'tbd_con_sig' by 'codigo'
join_sig_csv <- merge(parcelas_sql, tbd_cons_sig, by.x = "codigo", by.y = "codigo", duplicateGeoms=TRUE)
#2 - update field 'n.cont.x' with 'n.cont.y' values
join_sig_csv[join_sig_csv$n.cont.x == n.cont.x] <- n.cont.y
error_message:
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'i' in selecting a method for function '[<-': object 'n.cont.x' not found
-------------------------------------- sessionInfo() -----------------
version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
Matrix products: default
locale:
[1] LC_COLLATE=Portuguese_Portugal.1252 LC_CTYPE=Portuguese_Portugal.1252 LC_MONETARY=Portuguese_Portugal.1252 LC_NUMERIC=C
[5] LC_TIME=Portuguese_Portugal.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] RODBC_1.3-19 maptools_1.1-4 sf_1.0-7 terra_1.5-21 spData_2.0.1 rgdal_1.5-32 rgeos_0.5-9 sp_1.4-6 rvest_1.0.2 showtext_0.9-5
[11] showtextdb_3.0 sysfonts_0.8.8 classInt_0.4-3 tmap_3.3-3 lubridate_1.8.0 fs_1.5.2 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7 purrr_0.3.4
[21] readr_2.1.1 tidyr_1.1.4 tibble_3.1.6 ggplot2_3.3.5 tidyverse_1.3.1
loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-2 httr_1.4.2 tools_4.1.2 backports_1.4.1 utf8_1.2.2 R6_2.5.1
[7] KernSmooth_2.23-20 DBI_1.1.2 colorspace_2.0-2 raster_3.5-15 withr_2.4.3 tidyselect_1.1.1
[13] leaflet_2.1.1 compiler_4.1.2 leafem_0.2.0 cli_3.1.0 xml2_1.3.3 scales_1.1.1
[19] proxy_0.4-26 digest_0.6.29 foreign_0.8-81 base64enc_0.1-3 dichromat_2.0-0.1 pkgconfig_2.0.3
[25] htmltools_0.5.2 dbplyr_2.1.1 fastmap_1.1.0 htmlwidgets_1.5.4 rlang_0.4.12 readxl_1.3.1
[31] rstudioapi_0.13 generics_0.1.1 jsonlite_1.7.2 crosstalk_1.2.0 magrittr_2.0.1 Rcpp_1.0.7
[37] munsell_0.5.0 fansi_0.5.0 abind_1.4-5 lifecycle_1.0.1 stringi_1.7.6 leafsync_0.1.0
[43] tmaptools_3.1-1 grid_4.1.2 parallel_4.1.2 crayon_1.4.2 lattice_0.20-45 stars_0.5-5
[49] haven_2.4.3 hms_1.1.1 pillar_1.6.4 codetools_0.2-18 reprex_2.0.1 XML_3.99-0.8
[55] glue_1.6.0 leaflet.providers_1.9.0 modelr_0.1.8 png_0.1-7 vctrs_0.3.8 tzdb_0.2.0
[61] cellranger_1.1.0 gtable_0.3.0 assertthat_0.2.1 lwgeom_0.2-8 broom_0.7.11 e1071_1.7-9
[67] class_7.3-19 viridisLite_0.4.0 units_0.8-0 ellipsis_0.3.2
I would like to know how I can solve the problem of accents and special characters, I don't know why special characters (´,ñ, etc) appear wrong, with the code I don't have any problem but when running the shiny app all the labels where this type of characters are appear as an attachment in the image below. I have read about saving with utf-8 encoding but the problem is still not fixed, below I share information about my session.
wrong labels: Número, Gráfico, Comunicación
R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)
Matrix products: default
locale:
[1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252
[3] LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C
[5] LC_TIME=Spanish_Spain.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
other attached packages:
[1] stringi_1.6.1 plotly_4.10.0 ggplot2_3.3.5
[4] dplyr_1.0.7 shinyFiles_0.9.1 visNetwork_2.1.0
[7] openxlsx_4.2.4 shinyalert_2.0.0 lubridate_1.7.10
[10] data.table_1.14.2 DT_0.20 shinyjs_2.0.0
[13] shiny_1.7.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 lattice_0.20-38 tidyr_1.1.4
[4] assertthat_0.2.1 digest_0.6.27 utf8_1.2.1
[7] mime_0.10 R6_2.5.1 evaluate_0.14
[10] httr_1.4.2 pillar_1.6.4 rlang_0.4.11
[13] uuid_0.1-4 lazyeval_0.2.2 fontawesome_0.2.2
[16] rstudioapi_0.13 jquerylib_0.1.4 rmarkdown_2.11
[19] foreign_0.8-75 htmlwidgets_1.5.4 munsell_0.5.0
[22] compiler_3.6.3 httpuv_1.6.1 xfun_0.30
[25] pkgconfig_2.0.3 htmltools_0.5.2 tidyselect_1.1.1
[28] tibble_3.1.1 fansi_0.4.2 viridisLite_0.4.0
[31] crayon_1.4.2 withr_2.4.2 later_1.2.0
[34] grid_3.6.3 jsonlite_1.7.2 xtable_1.8-4
[37] gtable_0.3.0 lifecycle_1.0.1 DBI_1.1.2
[40] magrittr_2.0.1 scales_1.1.1 zip_2.2.0
[43] cli_3.1.0 cachem_1.0.4 fs_1.5.0
[46] promises_1.2.0.1 sp_1.4-6 bslib_0.3.1
[49] ellipsis_0.3.2 generics_0.1.1 vctrs_0.3.8
[52] tools_3.6.3 glue_1.4.2 purrr_0.3.4
[55] crosstalk_1.1.1 rsconnect_0.8.25 fastmap_1.1.0
[58] yaml_2.2.1 colorspace_2.0-1 maptools_1.1-2
[61] knitr_1.36 sass_0.4.0
I am trying to get Beta files using the minfi packacge. I succeeded with almost all my datasets. Therefor I ran the following code:
# find idat files
test_data <- list.files(path = "./Idat Files",
pattern = "_Grn.idat",
full.names = TRUE)
# load data
test_data <- minfi::read.metharray(basenames = test_data) %>%
preprocessNoob %>%
getBeta
Problem #1: Unfortunately I got the following error:
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'object' in selecting a method for function 'getBeta': cannot load annotation package IlluminaHumanMethylationEPICanno.ilm10b4.hg19
Problem #2: Calling Beta values from another data set, using the same code as above, gave me another error:
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'object' in selecting a method for function 'getBeta': [read.metharray] Trying to parse IDAT files with different array size but seemingly all of the same type.
You can force this by 'force=TRUE', see the man page ?read.metharray
Question: Does someone know what is going wrong?
sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)
Matrix products: default
locale:
[1] LC_COLLATE=Dutch_Netherlands.1252 LC_CTYPE=Dutch_Netherlands.1252 LC_MONETARY=Dutch_Netherlands.1252
[4] LC_NUMERIC=C LC_TIME=Dutch_Netherlands.1252
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] IlluminaHumanMethylationEPICmanifest_0.3.0 forcats_0.5.1
[3] stringr_1.4.0 dplyr_1.0.8
[5] purrr_0.3.4 readr_2.1.2
[7] tidyr_1.2.0 tibble_3.1.6
[9] ggplot2_3.3.5 tidyverse_1.3.1
[11] minfiData_0.40.0 IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0
[13] IlluminaHumanMethylation450kmanifest_0.4.0 RFpurify_0.1.2
[15] minfi_1.40.0 bumphunter_1.36.0
[17] locfit_1.5-9.5 iterators_1.0.14
[19] foreach_1.5.2 Biostrings_2.62.0
[21] XVector_0.34.0 SummarizedExperiment_1.24.0
[23] Biobase_2.54.0 MatrixGenerics_1.6.0
[25] matrixStats_0.61.0 GenomicRanges_1.46.1
[27] GenomeInfoDb_1.30.1 IRanges_2.28.0
[29] S4Vectors_0.32.4 BiocGenerics_0.40.0
loaded via a namespace (and not attached):
[1] readxl_1.4.0 backports_1.4.1 BiocFileCache_2.2.1 plyr_1.8.7
[5] splines_4.1.3 BiocParallel_1.28.3 digest_0.6.29 htmltools_0.5.2
[9] fansi_1.0.3 magrittr_2.0.3 memoise_2.0.1 tzdb_0.3.0
[13] limma_3.50.3 annotate_1.72.0 modelr_0.1.8 askpass_1.1
[17] siggenes_1.68.0 prettyunits_1.1.1 colorspace_2.0-3 rvest_1.0.2
[21] blob_1.2.3 rappdirs_0.3.3 haven_2.4.3 xfun_0.30
[25] jsonlite_1.8.0 crayon_1.5.1 RCurl_1.98-1.6 genefilter_1.76.0
[29] GEOquery_2.62.2 survival_3.2-13 glue_1.6.2 gtable_0.3.0
[33] zlibbioc_1.40.0 DelayedArray_0.20.0 Rhdf5lib_1.16.0 HDF5Array_1.22.1
[37] scales_1.2.0 DBI_1.1.2 rngtools_1.5.2 Rcpp_1.0.8.3
[41] xtable_1.8-4 progress_1.2.2 bit_4.0.4 mclust_5.4.9
[45] preprocessCore_1.56.0 httr_1.4.2 RColorBrewer_1.1-3 ellipsis_0.3.2
[49] farver_2.1.0 pkgconfig_2.0.3 reshape_0.8.9 XML_3.99-0.9
[53] dbplyr_2.1.1 utf8_1.2.2 labeling_0.4.2 tidyselect_1.1.2
[57] rlang_1.0.2 AnnotationDbi_1.56.2 cellranger_1.1.0 munsell_0.5.0
[61] tools_4.1.3 cachem_1.0.6 cli_3.2.0 generics_0.1.2
[65] RSQLite_2.2.12 broom_0.8.0 evaluate_0.15 fastmap_1.1.0
[69] yaml_2.3.5 fs_1.5.2 knitr_1.38 bit64_4.0.5
[73] beanplot_1.3.1 scrime_1.3.5 randomForest_4.7-1 KEGGREST_1.34.0
[77] nlme_3.1-155 doRNG_1.8.2 sparseMatrixStats_1.6.0 nor1mix_1.3-0
[81] xml2_1.3.3 biomaRt_2.50.3 compiler_4.1.3 rstudioapi_0.13
[85] filelock_1.0.2 curl_4.3.2 png_0.1-7 reprex_2.0.1
[89] stringi_1.7.6 GenomicFeatures_1.46.5 lattice_0.20-45 Matrix_1.4-0
[93] multtest_2.50.0 vctrs_0.4.0 pillar_1.7.0 lifecycle_1.0.1
[97] rhdf5filters_1.6.0 data.table_1.14.2 bitops_1.0-7 rtracklayer_1.54.0
[101] R6_2.5.1 BiocIO_1.4.0 codetools_0.2-18 MASS_7.3-55
[105] assertthat_0.2.1 rhdf5_2.38.1 openssl_2.0.0 rjson_0.2.21
[109] withr_2.5.0 GenomicAlignments_1.30.0 Rsamtools_2.10.0 GenomeInfoDbData_1.2.7
[113] hms_1.1.1 quadprog_1.5-8 grid_4.1.3 base64_2.0
[117] rmarkdown_2.13 DelayedMatrixStats_1.16.0 illuminaio_0.36.0 lubridate_1.8.0
I'm trying to export table made with kableExtra in R. It looks ok in the R Studio environment but if I try to export it it gives me this error:
> kable(csv) %>%
+ kable_styling("striped", full_width = F, htmltable_class = 'Liberation Sans') %>%
+ kable_minimal() %>%
+ save_kable(file = paste0(outdir, name, '.png'), bs_theme = "flatly",
+ zoom = 1.5)
QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-cesarkero'
error: XDG_RUNTIME_DIR not set in the environment.
TypeError: Attempting to change the setter of an unconfigurable property.
TypeError: Attempting to change the setter of an unconfigurable property.
Error in magick_image_trim(image, fuzz) :
rsession: geometry does not contain image `/home/cesarkero/HDD/D4/GoogleDrive/Proyectos/Master_UNED/01_Materias/06_EE/07_Trabajo/03_Resultados/04_CONSOLIDADOS/07a.png' # warning/attribute.c/GetImageBoundingBox/247
The file is exported but totally empty.
Here is the file used as csv object: https://drive.google.com/file/d/1fmplGNKB7MSKvXpNI_YrThE1F2EKszTf/view?usp=sharing
Update 19/04/2022
If I try this I get a similar error:
> webshot::install_phantomjs()
Error: invalid version specification ‘QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-cesarkero'’
I had already installed phantomjs in linux terminal with:
sudo apt-get install -y phantomjs
Here is my sessionInfo():
> sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3
locale:
[1] LC_CTYPE=es_ES.UTF-8 LC_NUMERIC=C
[3] LC_TIME=es_ES.UTF-8 LC_COLLATE=es_ES.UTF-8
[5] LC_MONETARY=es_ES.UTF-8 LC_MESSAGES=es_ES.UTF-8
[7] LC_PAPER=es_ES.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] landtools_0.1.0 lubridate_1.8.0 plyr_1.8.6
[4] data.table_1.14.2 raster_3.5-15 rgeos_0.5-9
[7] rgdal_1.5-28 sp_1.4-6 exifr_0.3.2
[10] nngeo_0.4.5 spatstat_2.3-3 spatstat.linnet_2.3-2
[13] spatstat.core_2.4-0 rpart_4.1.16 nlme_3.1-157
[16] spatstat.random_2.1-0 spatstat.geom_2.3-2 spatstat.data_2.1-2
[19] purrr_0.3.4 readODS_1.7.0 stringr_1.4.0
[22] mapview_2.10.0 dplyr_1.0.8 readr_2.1.2
[25] sf_1.0-7 magrittr_2.0.3 magick_2.7.3
[28] kableExtra_1.3.4
loaded via a namespace (and not attached):
[1] spatstat.sparse_2.1-0 satellite_1.0.4 webshot_0.5.2
[4] httr_1.4.2 tools_4.1.3 utf8_1.2.2
[7] R6_2.5.1 KernSmooth_2.23-20 DBI_1.1.2
[10] mgcv_1.8-40 colorspace_2.0-3 processx_3.5.2
[13] tidyselect_1.1.2 leaflet_2.1.0 compiler_4.1.3
[16] leafem_0.1.6 cli_3.2.0 rvest_1.0.2
[19] xml2_1.3.3 scales_1.1.1 classInt_0.4-3
[22] callr_3.7.0 proxy_0.4-26 rappdirs_0.3.3
[25] goftest_1.2-3 systemfonts_1.0.4 digest_0.6.29
[28] foreign_0.8-82 spatstat.utils_2.3-0 rmarkdown_2.13
[31] svglite_2.1.0 base64enc_0.1-3 pkgconfig_2.0.3
[34] htmltools_0.5.2 fastmap_1.1.0 htmlwidgets_1.5.4
[37] rlang_1.0.2 rstudioapi_0.13 generics_0.1.2
[40] crosstalk_1.2.0 Matrix_1.4-1 Rcpp_1.0.8.2
[43] munsell_0.5.0 fansi_1.0.3 abind_1.4-5
[46] lifecycle_1.0.1 terra_1.5-21 stringi_1.7.6
[49] maptools_1.1-3 grid_4.1.3 crayon_1.5.1
[52] deldir_1.0-6 lattice_0.20-45 splines_4.1.3
[55] tensor_1.5 hms_1.1.1 ps_1.6.0
[58] knitr_1.37 pillar_1.7.0 codetools_0.2-18
[61] stats4_4.1.3 glue_1.6.2 evaluate_0.15
[64] png_0.1-7 vctrs_0.4.0 tzdb_0.2.0
[67] polyclip_1.10-0 assertthat_0.2.1 xfun_0.30
[70] e1071_1.7-9 class_7.3-20 viridisLite_0.4.0
[73] tibble_3.1.6 units_0.8-0 ellipsis_0.3.2
First you need to install the phantomjs from the webshot package using the following code:
webshot::install_phantomjs()
After that, you can run the following code which will output your table as table.png:
library(knitr)
library(kableExtra)
library(magrittr)
kable(csv) %>%
kable_styling("striped", full_width = F, htmltable_class = 'Liberation Sans') %>%
kable_minimal() %>%
save_kable(file = "table.png", bs_theme = "flatly", zoom = 1.5)
The output looks like this:
Please note that your table is really big.
Here is my sessionInfo:
> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS 12.3.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] nl_NL.UTF-8/nl_NL.UTF-8/nl_NL.UTF-8/C/nl_NL.UTF-8/nl_NL.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] readxl_1.3.1 ggforce_0.3.3 dummies_1.5.6 plyr_1.8.6 magrittr_2.0.3 knitr_1.37
[7] kableExtra_1.3.4 terra_1.5-21 reshape_0.8.8 epitools_0.5-10.1 forcats_0.5.1 stringr_1.4.0
[13] readr_2.1.2 tidyverse_1.3.1 DALEXtra_2.1.1 DALEX_2.4.0 mlbench_2.1-3 yardstick_0.0.9
[19] workflowsets_0.1.0 workflows_0.2.4 tune_0.1.6 tidyr_1.2.0 tibble_3.1.6 rsample_0.1.1
[25] recipes_0.2.0 purrr_0.3.4 parsnip_0.2.0 modeldata_0.1.1 infer_1.0.0 ggplot2_3.3.5
[31] dplyr_1.0.8 dials_0.1.0 scales_1.1.1 broom_0.7.12 tidymodels_0.1.4 mapview_2.10.0
loaded via a namespace (and not attached):
[1] utf8_1.2.2 reticulate_1.24 tidyselect_1.1.2 htmlwidgets_1.5.4 grid_4.1.0 pROC_1.18.0
[7] munsell_0.5.0 codetools_0.2-18 units_0.8-0 future_1.24.0 withr_2.5.0 colorspace_2.0-3
[13] highr_0.9 uuid_1.0-4 rstudioapi_0.13 stats4_4.1.0 Rttf2pt1_1.3.8 listenv_0.8.0
[19] labeling_0.4.2 polyclip_1.10-0 plotROC_2.2.1 bit64_4.0.5 DiceDesign_1.9 farver_2.1.0
[25] rprojroot_2.0.2 parallelly_1.30.0 vctrs_0.4.0 generics_0.1.2 ipred_0.9-12 xfun_0.30
[31] R6_2.5.1 doParallel_1.0.17 ggiraph_0.8.2 flexmix_2.3-17 lhs_1.1.4 assertthat_0.2.1
[37] vroom_1.5.7 nnet_7.3-17 gtable_0.3.0 globals_0.14.0 processx_3.5.2 timeDate_3043.102
[43] rlang_1.0.2 systemfonts_1.0.4 modMax_1.1 splines_4.1.0 rgdal_1.5-28 extrafontdb_1.0
[49] lazyeval_0.2.2 ModelMetrics_1.2.2.2 yaml_2.3.5 reshape2_1.4.4 modelr_0.1.8 crosstalk_1.2.0
[55] backports_1.4.1 caret_6.0-90 extrafont_0.17 tools_4.1.0 lava_1.6.10 ellipsis_0.3.2
[61] raster_3.5-15 jquerylib_0.1.4 proxy_0.4-26 Rcpp_1.0.8.3 base64enc_0.1-3 progress_1.2.2
[67] classInt_0.4-3 ps_1.6.0 prettyunits_1.1.1 rpart_4.1.16 haven_2.4.3 fs_1.5.2
[73] here_1.0.1 leafem_0.1.6 furrr_0.2.3 magick_2.7.3 data.table_1.14.2 SparseM_1.81
[79] reprex_2.0.1 GPfit_1.0-8 hms_1.1.1 evaluate_0.15 leaflet_2.0.3.9000 compiler_4.1.0
[85] ingredients_2.2.0 KernSmooth_2.23-20 crayon_1.5.1 htmltools_0.5.2 tzdb_0.2.0 lubridate_1.8.0
[91] DBI_1.1.2 tweenr_1.0.2 dbplyr_2.1.1 MASS_7.3-55 sf_1.0-7 Matrix_1.4-0
[97] cli_3.2.0 parallel_4.1.0 gower_1.0.0 igraph_1.2.11 pkgconfig_2.0.3 sp_1.4-6
[103] plotly_4.10.0 xml2_1.3.3 foreach_1.5.2 svglite_2.1.0 bslib_0.3.1 hardhat_0.2.0
[109] webshot_0.5.2 prodlim_2019.11.13 rvest_1.0.2 callr_3.7.0 digest_0.6.29 rmarkdown_2.13
[115] cellranger_1.1.0 kernlab_0.9-29 gtools_3.9.2 satellite_1.0.4 modeltools_0.2-23 lifecycle_1.0.1
[121] nlme_3.1-155 jsonlite_1.8.0 viridisLite_0.4.0 fansi_1.0.3 pillar_1.7.0 lattice_0.20-45
[127] fastmap_1.1.0 httr_1.4.2 survival_3.3-1 glue_1.6.2 png_0.1-7 iterators_1.0.14
[133] bit_4.0.4 class_7.3-20 stringi_1.7.6 sass_0.4.1 e1071_1.7-9 future.apply_1.8.1
In playing around with the tidybayes package (I replicated the data from the code simulated in the vignette: http://mjskay.github.io/tidybayes/articles/tidybayes.html), I continue to stumble onto the error: Error: All list elements must be lists themselves when using the spread_draws function (or any other functions in the tidybayes, for that matter). Here is the simulated data from the vignette:
library(tidyverse)
library(tidybayes)
library(brms)
set.seed(5)
n = 10
n_condition = 5
ABC =
tibble(
condition = rep(c("A","B","C","D","E"), n),
response = rnorm(n * 5, c(0,1,2,1,-1), 0.5)
)
Here is the code for fitting the model:
m = brm(
response ~ (1|condition),
data = ABC,
prior = c(
prior(normal(0, 1), class = Intercept),
prior(student_t(3, 0, 1), class = sd),
prior(student_t(3, 0, 1), class = sigma)
),
control = list(adapt_delta = .99)
)
But, even in trying to use the get_variables function, I get the same error as mentioned above. Has anyone else had a similar problem or been able to solve this one?
Here is the session info.
> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
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] stats graphics grDevices utils datasets methods base
other attached packages:
[1] tidybayes_3.0.1 see_0.6.7 bayestestR_0.11.0 semTools_0.5-5
[5] lavaan_0.6-9 HDInterval_0.2.2 brms_2.15.0 Rcpp_1.0.6
[9] ggsignif_0.6.2 reshape2_1.4.4 ggsci_2.9 psych_2.0.12
[13] jtools_2.1.3 magrittr_2.0.1 extrafont_0.17 ggthemes_4.2.4
[17] forcats_0.5.1 stringr_1.4.0 dplyr_1.0.4 purrr_0.3.4
[21] tidyr_1.1.2 tibble_3.0.6 tidyverse_1.3.0 gridExtra_2.3
[25] ggpubr_0.4.0 ggplot2_3.3.5 readr_1.4.0
loaded via a namespace (and not attached):
[1] utf8_1.1.4 tidyselect_1.1.0 lme4_1.1-26
[4] htmlwidgets_1.5.3 grid_4.0.3 munsell_0.5.0
[7] codetools_0.2-18 statmod_1.4.35 DT_0.18
[10] miniUI_0.1.1.1 withr_2.4.1 Brobdingnag_1.2-6
[13] colorspace_2.0-0 knitr_1.31 rstudioapi_0.13
[16] stats4_4.0.3 Rttf2pt1_1.3.9 bayesplot_1.8.1
[19] labeling_0.4.2 emmeans_1.5.4 rstan_2.21.2
[22] mnormt_2.0.2 farver_2.0.3 datawizard_0.2.0.1
[25] bridgesampling_1.1-2 coda_0.19-4 vctrs_0.3.6
[28] generics_0.1.0 TH.data_1.0-10 xfun_0.25
[31] R6_2.5.0 markdown_1.1 gamm4_0.2-6
[34] projpred_2.0.2 assertthat_0.2.1 promises_1.2.0.1
[37] scales_1.1.1 multcomp_1.4-16 debugme_1.1.0
[40] gtable_0.3.0 processx_3.5.2 sandwich_3.0-0
[43] rlang_0.4.10 splines_4.0.3 rstatix_0.7.0
[46] extrafontdb_1.0 checkmate_2.0.0 broom_0.7.7
[49] inline_0.3.17 yaml_2.2.1 abind_1.4-5
[52] modelr_0.1.8 threejs_0.3.3 crosstalk_1.1.1
[55] backports_1.2.1 httpuv_1.5.5 rsconnect_0.8.18
[58] tensorA_0.36.2 tools_4.0.3 ellipsis_0.3.1
[61] posterior_1.0.1 ggridges_0.5.3 plyr_1.8.6
[64] base64enc_0.1-3 ps_1.5.0 prettyunits_1.1.1
[67] zoo_1.8-8 haven_2.3.1 fs_1.5.0
[70] data.table_1.14.0 ggdist_3.0.0 openxlsx_4.2.3
[73] colourpicker_1.1.0 reprex_1.0.0 tmvnsim_1.0-2
[76] mvtnorm_1.1-1 matrixStats_0.58.0 hms_1.0.0
[79] shinyjs_2.0.0 mime_0.10 evaluate_0.14
[82] arrayhelpers_1.1-0 xtable_1.8-4 shinystan_2.5.0
[85] rio_0.5.16 readxl_1.3.1 rstantools_2.1.1
[88] compiler_4.0.3 V8_3.4.2 crayon_1.4.1
[91] minqa_1.2.4 StanHeaders_2.21.0-7 htmltools_0.5.1.1
[94] mgcv_1.8-34 later_1.1.0.1 RcppParallel_5.1.4
[97] lubridate_1.7.10 DBI_1.1.1 dbplyr_2.1.0
[100] MASS_7.3-54 boot_1.3-27 Matrix_1.3-2
[103] car_3.0-10 cli_2.5.0 parallel_4.0.3
[106] insight_0.14.4 igraph_1.2.6 pkgconfig_2.0.3
[109] foreign_0.8-81 xml2_1.3.2 svUnit_1.0.6
[112] dygraphs_1.1.1.6 pbivnorm_0.6.0 estimability_1.3
[115] rvest_1.0.0 distributional_0.2.2 callr_3.7.0
[118] digest_0.6.27 rmarkdown_2.10 cellranger_1.1.0
[121] curl_4.3 shiny_1.6.0 gtools_3.8.2
[124] nloptr_1.2.2.2 lifecycle_1.0.0 nlme_3.1-152
[127] jsonlite_1.7.2 carData_3.0-4 fansi_0.4.2
[130] pillar_1.5.0 lattice_0.20-41 loo_2.4.1
[133] fastmap_1.1.0 httr_1.4.2 pkgbuild_1.2.0
[136] survival_3.2-11 glue_1.4.2 xts_0.12.1
[139] zip_2.1.1 shinythemes_1.2.0 pander_0.6.3
[142] stringi_1.5.3
If you need any other information or if I oversaw providing something, please let me know!
Many thanks for your help and all the best.
I just encountered the same problem. It seems to be a bug in the recent version 3.0.1. If you fall back on the previous version, your code should work.
devtools::install_version("tidybayes", version = "3.0.0", repos = "http://cran.us.r-project.org")
I've posted the issue on GitHub: https://github.com/mjskay/tidybayes/issues/289