fixest etable highlighting feature

trafficstars

I am having trouble implementing the etable highlighting features from the vignette-- perhaps I am missing a necessary package somewhere. Please let me know how I can fix this issue.

This is my code:

options(echo = T)
pacman::p_load(fixest, tinytex, pdftools)

## Show information about the R session
print(R.Version())
sessionInfo()
packageVersion("fixest")


## Follow the example from the vignette (https://lrberge.github.io/fixest/articles/etable_new_features.html)
dict = c(
    "(Intercept)" = "Constant", 
    Petal.Length = "Petal length", 
    Petal.Width = "Petal width",
    Sepal.Length = "Sepal length", 
    Sepal.Width = "Sepal width",
    note1 = dsb(
        "*Notes*: This is a note that illustrates how to access notes ",
        "from the dictionary."
    ),
    source = "*Sources*: Somewhere from the net."
)

setFixest_dict(dict)

my_style = style.tex("aer", model.format = "(i)")
setFixest_etable(style.tex = my_style, markdown = TRUE, page.width = "a4")

nm = names(iris)
est = feols(.[nm[1]] ~ .[nm[2:4]], iris, fsplit = ~Species)

etable(
    est, 
	arraystretch = 1.5,
	file = "test-table.tex",
	replace = T,
    highlight = .(
        "Sepal@1", 
        "cyan4, square" = "Petal.L@3-4",
        "thick5, sep8, darkgreen!90, se" = "Petal.W"
    )
)

## Generate a Latex document
latex_content <- '\\documentclass{article}
\\usepackage{booktabs}
\\usepackage{tikz}

\\begin{document}

\\input{test-table.tex}

\\end{document}'

file_conn <- file("output.tex")
cat(latex_content, file=file_conn)
close(file_conn)

## Compile the LaTeX file to generate a PDF
system("pdflatex --interaction=nonstopmode output.tex")

This is the stdout:

> options(echo = T)
> pacman::p_load(fixest, tinytex, pdftools)
> 
> ## Show information about the R session
> print(R.Version())
$platform
[1] "x86_64-apple-darwin17.0"

$arch
[1] "x86_64"

$os
[1] "darwin17.0"

$system
[1] "x86_64, darwin17.0"

$status
[1] ""

$major
[1] "4"

$minor
[1] "2.0"

$year
[1] "2022"

$month
[1] "04"

$day
[1] "22"

$`svn rev`
[1] "82229"

$language
[1] "R"

$version.string
[1] "R version 4.2.0 (2022-04-22)"

$nickname
[1] "Vigorous Calisthenics"

> sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur/Monterey 10.16

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/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] pdftools_3.3.3 tinytex_0.45   fixest_0.11.1 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.10         lattice_0.20-45     zoo_1.8-12         
 [4] grid_4.2.0          nlme_3.1-157        pacman_0.5.1       
 [7] dreamerr_1.2.3      qpdf_1.3.2          sandwich_3.0-2     
[10] Formula_1.2-5       tools_4.2.0         numDeriv_2016.8-1.1
[13] xfun_0.39           compiler_4.2.0      askpass_1.1        
> packageVersion("fixest")
[1] ‘0.11.1’
> 
> 
> ## Follow the example from the vignette (https://lrberge.github.io/fixest/articles/etable_new_features.html)
> dict = c(
+     "(Intercept)" = "Constant", 
+     Petal.Length = "Petal length", 
+     Petal.Width = "Petal width",
+     Sepal.Length = "Sepal length", 
+     Sepal.Width = "Sepal width",
+     note1 = dsb(
+         "*Notes*: This is a note that illustrates how to access notes ",
+         "from the dictionary."
+     ),
+     source = "*Sources*: Somewhere from the net."
+ )
> 
> setFixest_dict(dict)
> 
> my_style = style.tex("aer", model.format = "(i)")
> setFixest_etable(style.tex = my_style, markdown = TRUE, page.width = "a4")
> 
> nm = names(iris)
> est = feols(.[nm[1]] ~ .[nm[2:4]], iris, fsplit = ~Species)
> 
> etable(
+     est, 
+ 	arraystretch = 1.5,
+ 	file = "test-table.tex",
+ 	replace = T,
+     highlight = .(
+         "Sepal@1", 
+         "cyan4, square" = "Petal.L@3-4",
+         "thick5, sep8, darkgreen!90, se" = "Petal.W"
+     )
+ )
> 
> ## Generate a Latex document
> latex_content <- '\\documentclass{article}
+ \\usepackage{booktabs}
+ \\usepackage{tikz}
+ 
+ \\begin{document}
+ 
+ \\input{test-table.tex}
+ 
+ \\end{document}'
> 
> file_conn <- file("output.tex")
> cat(latex_content, file=file_conn)
> close(file_conn)
> 
> ## Compile the LaTeX file to generate a PDF
> system("pdflatex --interaction=nonstopmode output.tex")
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./output.tex
LaTeX2e <2021-11-15> patch level 1
L3 programming layer <2022-02-24>
(/usr/local/texlive/2022/texmf-dist/tex/latex/base/article.cls
Document Class: article 2021/10/04 v1.4n Standard LaTeX document class
(/usr/local/texlive/2022/texmf-dist/tex/latex/base/size10.clo))
(/usr/local/texlive/2022/texmf-dist/tex/latex/booktabs/booktabs.sty)
(/usr/local/texlive/2022/texmf-dist/tex/latex/pgf/frontendlayer/tikz.sty
(/usr/local/texlive/2022/texmf-dist/tex/latex/pgf/basiclayer/pgf.sty
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x
(/usr/local/texlive/2022/texmf-dist/tex/generic/pgf/utilities/pgfutil-common-li
sts.tex))
(/usr/local/texlive/2022/texmf-dist/tex/generic/pgf/utilities/pgfutil-latex.def
) (/usr/local/texlive/2022/texmf-dist/tex/generic/pgf/utilities/pgfrcs.code.tex
(/usr/local/texlive/2022/texmf-dist/tex/generic/pgf/pgf.revision.tex)))
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ef
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df.def)))
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)
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m.code.tex)
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code.tex)
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erarithmetics.code.tex)))
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) (/usr/local/texlive/2022/texmf-dist/tex/generic/pgf/math/pgfint.code.tex)
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de.tex)
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ruct.code.tex)
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de.tex)
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ate.code.tex)
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e.tex)
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ode.tex)
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ssing.code.tex)
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de.tex)
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e.tex)
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e.tex
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code.tex))
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de.tex)
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ncy.code.tex)
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code.tex)
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tex)))
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e.tex)
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tex)
(/usr/local/texlive/2022/texmf-dist/tex/latex/pgf/compatibility/pgfcomp-version
-0-65.sty)
(/usr/local/texlive/2022/texmf-dist/tex/latex/pgf/compatibility/pgfcomp-version
-1-18.sty))
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(/usr/local/texlive/2022/texmf-dist/tex/generic/pgf/utilities/pgfkeys.code.tex)
) (/usr/local/texlive/2022/texmf-dist/tex/latex/pgf/math/pgfmath.sty
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dlers.code.tex)
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e.tex)
(/usr/local/texlive/2022/texmf-dist/tex/generic/pgf/frontendlayer/tikz/librarie
s/tikzlibrarytopaths.code.tex)))
(/usr/local/texlive/2022/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def)
(./output.aux)
(/usr/local/texlive/2022/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2022/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty
(/usr/local/texlive/2022/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(./test-table.tex

! Package pgfkeys Error: I do not know the key '/tikz/fit', to which you passed
 '(marker-f1-a.north west) (marker-f1-b.south east)', and I am going to ignore 
it. Perhaps you misspelled it.

See the pgfkeys package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.52 ...jrnhd{f1} 0.6508$^{***}$ \markSEqjrnhd{f1}
                                                     & 0.6548$^{***}$ & 0.38...


! Package pgfkeys Error: I do not know the key '/tikz/fit', to which you passed
 '(marker-f2-a.north west) (marker-f2-b.south east)', and I am going to ignore 
it. Perhaps you misspelled it.

See the pgfkeys package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.54 ...{***}$  & 0.9455$^{***}$ \markSEtlcvqz{f2}
                                                  \\

! Package pgfkeys Error: I do not know the key '/tikz/fit', to which you passed
 '(marker-f3-a.north west) (marker-f3-b.south east)', and I am going to ignore 
it. Perhaps you misspelled it.

See the pgfkeys package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.57 ...              & (0.1981) \markSEvhrkmh{f3}
                                                  \\
) [1{/usr/local/texlive/2022/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
(./output.aux) )
(see the transcript file for additional information)</usr/local/texlive/2022/te
xmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pfb></usr/local/texlive/2022/texm
f-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/local/texlive/2022/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmsy7.pfb>
Output written on output.pdf (1 page, 36441 bytes).
Transcript written on output.log.
>

output.pdf looks like this:

Thank you for all of your help and for an excellent package!

Sep 20 '23 17:09 tlcaputi

I can reproduce this. To fix it, you also need to load a special tikz library: \usetikzlibrary{fit}. This should probably be mentioned in the docs.

Here's an example with an R Markdown document but you can simply use the command above in a tex file.

---
output: pdf_document
header-includes:
  - \usepackage{booktabs}
  - \usepackage{tikz}
  - \usetikzlibrary{fit}
---

```{r, eval=TRUE, results="asis"}
library(fixest)

nm = names(iris)
est = feols(.[nm[1]] ~ .[nm[2:4]], iris, fsplit = ~Species)

etable(
    est,
	arraystretch = 1.5,
	tex = TRUE,
	replace = T,
    highlight = .(
        "Sepal@1",
        "cyan4, square" = "Petal.L@3-4",
        "thick5, sep8, darkgreen!90, se" = "Petal.W"
    )
)
```

Sep 22 '23 08:09 etiennebacher

Two quick thoughts:

We should probably just take a stance on recommending TinyTex as the most convenient way to ensure that you have all of the necessary libraries that integrate well with your R installation. Looking at the docs, I believe the "TinyTex" bundle covers all of the necessary libraries. So users could just do something like:

# install.package("tinytex")
tinytex::install_tinytex(bundle = "TinyTeX")

The two etable vignettes should really be combined at this point. I'll try to take a crack at this when I get a sec (ha!) and put in a PR for Laurent to look at.

Oct 06 '23 17:10 grantmcdermott

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etable highlighting feature

fixest
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