Incorrect number of dimensions in margins::cplot if using data.table
AJFOWLER opened this issue · 1 comments
AJFOWLER commented
Please specify whether your issue is about:
- a possible bug
- a question about package functionality
- a suggested code or documentation change, improvement to the code, or feature request
If you are reporting (1) a bug or (2) a question about code, please supply:
- a fully reproducible example using a publicly available dataset (or provide your data)
- if an error is occurring, include the output of
traceback()run immediately after the error occurs - the output of
sessionInfo()
I've found an odd bug when using data.table:
Put your code here:
## load package
library("margins")
library("data.table")
set.seed(100)
dfer = data.frame('age' = sample(0:100, 500, replace=T),
'disease' = rbinom(500,1, 0.3),
'dead' = rbinom(500,1,0.14), stringsAsFactors = F)
setDT(dfer)
# if data.table is removed as a class, then the function runs and returns as expected.
# create model
moder = glm(dead~disease*age, family = binomial, data = dfer)
# cplot
margins::cplot(moder, dx="age")
traceback()
3: lapply(dat[, names(dat) != xvar, drop = FALSE], mean_or_mode)
2: cplot.glm(moder, dx = "age")
1: margins::cplot(moder, dx = "age")
## session info for your system
sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.1252
[2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices
[4] utils datasets methods
[7] base
other attached packages:
[1] data.table_1.13.0
[2] margins_0.3.23
[3] comorbidgroupr_0.0.1
[4] testthat_2.3.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5
[2] prettyunits_1.1.1
[3] ps_1.3.3
[4] assertthat_0.2.1
[5] rprojroot_1.3-2
[6] digest_0.6.25
[7] R6_2.4.1
[8] backports_1.1.7
[9] ggplot2_3.3.2
[10] pillar_1.4.6
[11] rlang_0.4.7
[12] rstudioapi_0.11
[13] callr_3.4.3
[14] desc_1.2.0
[15] devtools_2.3.1
[16] stringr_1.4.0
[17] munsell_0.5.0
[18] compiler_4.0.2
[19] xfun_0.16
[20] pkgconfig_2.0.3
[21] pkgbuild_1.1.0
[22] tidyselect_1.1.0
[23] tibble_3.0.3
[24] roxygen2_7.1.1
[25] fansi_0.4.1
[26] crayon_1.3.4
[27] dplyr_1.0.1
[28] withr_2.2.0
[29] MASS_7.3-51.6
[30] grid_4.0.2
[31] gtable_0.3.0
[32] lifecycle_0.2.0
[33] magrittr_1.5
[34] scales_1.1.1
[35] cli_2.0.2
[36] stringi_1.4.6
[37] fs_1.4.2
[38] remotes_2.2.0
[39] xml2_1.3.2
[40] ellipsis_0.3.1
[41] generics_0.0.2
[42] vctrs_0.3.2
[43] prediction_0.3.14
[44] tools_4.0.2
[45] rcmdcheck_1.3.3
[46] glue_1.4.1
[47] purrr_0.3.4
[48] processx_3.4.3
[49] pkgload_1.1.0
[50] colorspace_1.4-1
[51] xopen_1.0.0
[52] sessioninfo_1.1.1
[53] memoise_1.1.0
[54] knitr_1.29
[55] usethis_1.6.1
I think this should be fixable either by modifying this lapply or perhaps by calling class(data) <- 'data.frame' near the top which seems to resolve this issue? Happy to open PR to help.
dshkol commented
I had this same issue with my own dataset that I can't replicate here, but was fixed by wrapping the data.table object with as.data.frame(...) in the glm() call.
> class(df)
[1] "data.table" "data.frame"
# fails with cplot(x, "x1")
x <- glm(y ~ x1 + x2 + x2 + x3, data = df, family = binomial)
# works
x <- glm(y ~ x1 + x2 + x2 + x3, data = as.data.frame(df), family = binomial)
R version 4.0.2 (2020-06-22)
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] margins_0.3.26 ggplot2_3.3.3 dplyr_1.0.5
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 pillar_1.6.0 compiler_4.0.2 tools_4.0.2 digest_0.6.27
[6] bit_4.0.4 gtable_0.3.0 evaluate_0.14 lifecycle_1.0.0 tibble_3.1.1
[11] pkgconfig_2.0.3 rlang_0.4.10 cli_2.5.0 DBI_1.1.0 rstudioapi_0.13
[16] curl_4.3 yaml_2.2.1 xfun_0.22 withr_2.4.2 httr_1.4.2
[21] knitr_1.33 generics_0.0.2 vctrs_0.3.8 geohashTools_0.3.1 hms_0.5.3
[26] grid_4.0.2 bit64_4.0.5 tidyselect_1.1.0 fasttime_1.0-2 glue_1.4.2
[31] data.table_1.13.0 R6_2.5.0 fansi_0.4.2 prediction_0.3.14 rmarkdown_2.7
[36] farver_2.1.0 readr_1.3.1 purrr_0.3.4 magrittr_2.0.1 MASS_7.3-51.6
[41] scales_1.1.1 ellipsis_0.3.2 htmltools_0.5.1.1 assertthat_0.2.1 colorspace_2.0-0
[46] labeling_0.4.2 utf8_1.2.1 tinytex_0.31 munsell_0.5.0 RcppSimdJson_0.1.1
[51] crayon_1.4.1