In the below example, the html carriage returns stick around when converting to LaTeX. Is there a way in gt/gtsummary to get return characters that are correct in LaTeX?
library(gtsummary)
tbl <-
lm(time ~ ph.ecog sex, survival::lung) %>%
tbl_regression(label = list(ph.ecog = "ECOG Score", sex = "Sex"))
add_significance_stars_ex3 <-
tbl %>%
add_significance_stars(
hide_se = TRUE,
pattern = "{estimate}{stars}<br>({std.error})"
) %>%
modify_header(estimate ~ "**Beta (SE)**") %>%
modify_footnote(estimate ~ "SE = Standard Error", abbreviation = TRUE) %>%
as_gt() %>%
gt::tab_style(
style = "vertical-align:top",
locations = gt::cells_body(columns = label)
)
add_significance_stars_ex3 %>%
gt::as_latex() %>%
cat()
#> \captionsetup[table]{labelformat=empty,skip=1pt}
#> \setlength{\LTpost}{0mm}
#> \begin{longtable}{lc}
#> \toprule
#> \textbf{Characteristic} & \textbf{Beta (SE)}\textsuperscript{1,2} \\
#> \midrule
#> ECOG Score & -58**<br>(19.1) \\
#> Sex & 52<br>(27.9) \\
#> \bottomrule
#> \end{longtable}
#> \begin{minipage}{\linewidth}
#> \textsuperscript{1}*p\textless{}0.05; **p\textless{}0.01; ***p\textless{}0.001\\
#> \textsuperscript{2}SE = Standard Error\\
#> \end{minipage}
Created on 2022-08-15 by the reprex package (v2.0.1)
Session infosessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.2.1 (2022-06-23)
#> os Ubuntu 22.04.1 LTS
#> system x86_64, linux-gnu
#> ui X11
#> language en_NZ:en
#> collate en_NZ.UTF-8
#> ctype en_NZ.UTF-8
#> tz Pacific/Auckland
#> date 2022-08-15
#> pandoc 2.18 @ /usr/lib/rstudio/bin/quarto/bin/tools/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> assertthat 0.2.1 2019-03-21 [3] RSPM (R 4.2.0)
#> backports 1.4.1 2021-12-13 [3] RSPM (R 4.2.0)
#> broom 1.0.0 2022-07-01 [3] RSPM (R 4.2.0)
#> broom.helpers 1.8.0 2022-07-05 [3] RSPM (R 4.2.0)
#> checkmate 2.1.0 2022-04-21 [3] RSPM (R 4.2.0)
#> cli 3.3.0 2022-04-25 [3] RSPM (R 4.2.0)
#> colorspace 2.0-3 2022-02-21 [3] RSPM (R 4.2.0)
#> commonmark 1.8.0 2022-03-09 [3] RSPM (R 4.2.0)
#> crayon 1.5.1 2022-03-26 [3] RSPM (R 4.2.0)
#> DBI 1.1.3 2022-06-18 [3] RSPM (R 4.2.0)
#> digest 0.6.29 2021-12-01 [3] RSPM (R 4.2.0)
#> dplyr 1.0.9 2022-04-28 [3] RSPM (R 4.2.0)
#> ellipsis 0.3.2 2021-04-29 [3] RSPM (R 4.2.0)
#> evaluate 0.16 2022-08-09 [3] RSPM (R 4.2.0)
#> fansi 1.0.3 2022-03-24 [3] RSPM (R 4.2.0)
#> fastmap 1.1.0 2021-01-25 [3] RSPM (R 4.2.0)
#> forcats 0.5.1 2021-01-27 [3] RSPM (R 4.2.0)
#> fs 1.5.2 2021-12-08 [3] RSPM (R 4.2.0)
#> generics 0.1.3 2022-07-05 [3] RSPM (R 4.2.0)
#> ggplot2 3.3.6 2022-05-03 [3] RSPM (R 4.2.0)
#> glue 1.6.2 2022-02-24 [3] RSPM (R 4.2.0)
#> gt 0.6.0 2022-05-24 [3] RSPM (R 4.2.0)
#> gtable 0.3.0 2019-03-25 [3] RSPM (R 4.2.0)
#> gtsummary * 1.6.1 2022-06-22 [3] RSPM (R 4.2.0)
#> haven 2.5.0 2022-04-15 [3] RSPM (R 4.2.0)
#> highr 0.9 2021-04-16 [3] RSPM (R 4.2.0)
#> hms 1.1.1 2021-09-26 [3] RSPM (R 4.2.0)
#> htmltools 0.5.3 2022-07-18 [3] RSPM (R 4.2.0)
#> knitr 1.39 2022-04-26 [3] RSPM (R 4.2.0)
#> labelled 2.9.1 2022-05-05 [3] RSPM (R 4.2.0)
#> lattice 0.20-45 2021-09-22 [4] CRAN (R 4.2.0)
#> lifecycle 1.0.1 2021-09-24 [3] RSPM (R 4.2.0)
#> magrittr 2.0.3 2022-03-30 [3] RSPM (R 4.2.0)
#> Matrix 1.4-1 2022-03-23 [3] RSPM (R 4.2.0)
#> munsell 0.5.0 2018-06-12 [3] RSPM (R 4.2.0)
#> pillar 1.8.0 2022-07-18 [3] RSPM (R 4.2.0)
#> pkgconfig 2.0.3 2019-09-22 [3] RSPM (R 4.2.0)
#> purrr 0.3.4 2020-04-17 [3] RSPM (R 4.2.0)
#> R.cache 0.16.0 2022-07-21 [3] RSPM (R 4.2.0)
#> R.methodsS3 1.8.2 2022-06-13 [3] RSPM (R 4.2.0)
#> R.oo 1.25.0 2022-06-12 [3] RSPM (R 4.2.0)
#> R.utils 2.12.0 2022-06-28 [3] RSPM (R 4.2.0)
#> R6 2.5.1 2021-08-19 [3] RSPM (R 4.2.0)
#> reprex 2.0.1 2021-08-05 [3] RSPM (R 4.2.0)
#> rlang 1.0.4 2022-07-12 [3] RSPM (R 4.2.0)
#> rmarkdown 2.14 2022-04-25 [3] RSPM (R 4.2.0)
#> rstudioapi 0.13 2020-11-12 [3] RSPM (R 4.2.0)
#> scales 1.2.0 2022-04-13 [3] RSPM (R 4.2.0)
#> sessioninfo 1.2.2 2021-12-06 [3] RSPM (R 4.2.0)
#> stringi 1.7.8 2022-07-11 [3] RSPM (R 4.2.0)
#> stringr 1.4.0 2019-02-10 [3] RSPM (R 4.2.0)
#> styler 1.7.0 2022-03-13 [3] RSPM (R 4.2.0)
#> survival 3.4-0 2022-08-09 [3] RSPM (R 4.2.0)
#> tibble 3.1.8 2022-07-22 [3] RSPM (R 4.2.0)
#> tidyr 1.2.0 2022-02-01 [3] RSPM (R 4.2.0)
#> tidyselect 1.1.2 2022-02-21 [3] RSPM (R 4.2.0)
#> utf8 1.2.2 2021-07-24 [3] RSPM (R 4.2.0)
#> vctrs 0.4.1 2022-04-13 [3] RSPM (R 4.2.0)
#> withr 2.5.0 2022-03-03 [3] RSPM (R 4.2.0)
#> xfun 0.32 2022-08-10 [3] RSPM (R 4.2.0)
#> yaml 2.3.5 2022-02-21 [3] RSPM (R 4.2.0)
#>
#> [1] /home/kendonb/R/x86_64-pc-linux-gnu-library/4.2
#> [2] /usr/local/lib/R/site-library
#> [3] /usr/lib/R/site-library
#> [4] /usr/lib/R/library
#>
#> ──────────────────────────────────────────────────────────────────────────────
CodePudding user response：
You have specified a pattern with an HTML line break hard-coded into the cell: pattern = "{estimate}{stars}<br>({std.error})". Use a latex linebreaker here instead.
However, I recommend to use as_kable_extra() because it's bee written to support \n as a line breaker.
library(gtsummary)
#> #StandWithUkraine
tbl <-
lm(time ~ ph.ecog sex, survival::lung) %>%
tbl_regression(label = list(ph.ecog = "ECOG Score", sex = "Sex"))
add_significance_stars_ex3 <-
tbl %>%
add_significance_stars(
hide_se = TRUE,
pattern = "{estimate}{stars} \n({std.error})"
) %>%
modify_header(estimate ~ "**Beta (SE)**") %>%
modify_footnote(estimate ~ "SE = Standard Error", abbreviation = TRUE)
add_significance_stars_ex3 %>%
as_kable_extra(escape = FALSE, format = 'latex') %>%
cat()
#>
#> \begin{tabular}{l|c}
#> \hline
#> \textbf{Characteristic} & \textbf{Beta (SE)}\\
#> \hline
#> ECOG Score & \makecell[c]{-58**\ \ \\(19.1)}\\
#> \hline
#> Sex & \makecell[c]{52\ \ \\(27.9)}\\
#> \hline
#> \multicolumn{2}{l}{\rule{0pt}{1em}\textsuperscript{1} \textit{p<0.05; \textbf{p<0.01; }}p<0.001}\\
#> \multicolumn{2}{l}{\rule{0pt}{1em}\textsuperscript{2} SE = Standard Error}\\
#> \end{tabular}
Created on 2022-08-15 by the reprex package (v2.0.1)