YAML numbersections: true

[lnalborczyk]

Hello,

not really an issue but I'd like to know how to "control" the section-numbering. I've added the following argument "numbersections: true" to the YAML header of a "papaja::apa6_pdf" Markdown file and surprisingly (or maybe not) section numbering starts at Abstract...

Thus, Abstract is numbered "1", then the next page containing the title of the file and a wordcount is numbered "2"... and, my first header in text (i.e., "#Introduction") appears to be numbered 3...

I would like to start section-numbering at "Introduction" (i.e., my first header in text). In other words, I'd like to "unnumber" Abstract and title.

Is there an easy way to do that ?

Thanks for your help and for the great work you did on this package.

Best regards,

Ladislas

[crsh]

Hi, after experimenting a bit with different approaches, the easiest thing I have found is setting numbersections: false and adding \setcounter{secnumdepth}{5} to the beginning of your document. Alternatively, you can install the current development snapshot (devtools::install_github("crsh/papaja", ref = "devel")) in which numbersections: true should just do what you expected.

[lnalborczyk]

It works perfectly, thanks a lot.

Ladislas

[jrennstich]

Unfortunately, when rendering man in the current version [0.1.0.994], the numbering starts with authornote (then abstract), with the first headline in body being numbered 3.

Works like a charm when rendering doc.

[tfjaeger]

This is an issue again (still?) in R 4.2.1, and the most recent CRAN version of papaja. Install the rdevel version (0.1.0.9999) does not seem to fix the issue.

(Amazing library, btw, it's been wonderful to have this)

[mariusbarth]

Hi @tfjaeger, I just tried to reproduce your issue, but at least on my machine (R 4.2.1 on ubuntu 20.04 with all packages up-to-date) everything works as expected (i.e., section numbering starts with the first header in the main body of the document).

Can you paste your output from sessionInfo() here?

[GH-Jaeger]

Thanks for the quick reply. To be clear, it works with the \setcounter{secnumdepth}{5} workaround. But without it, I get the numbering error. First, here's a minimal version of the doc that causes the issue:

---
title             : "title"
shorttitle        : "shorter title"
date              : "`r format(Sys.time(), '%B %d, %Y')`"

author: 
  - name          : "XX"
    affiliation   : "1,2"
    corresponding : yes    # Define only one corresponding author
    address       : "3151 Social Science Plaza B, University of California, Irvine CA 92697–5100"
    email         : "xx@uci.edu"

affiliation:
  - id            : "1"
    institution   : "Language Science, University of California, Irvine"
  - id            : "2"
    institution   : "Brain and Cognitive Sciences, University of Rochester"
  - id            : "3"
    institution   : "Computer Science, University of Rochester"

authornote: |
  We are grateful to ### ommitted for review ###

abstract: |
  Bliblablub

keywords          : "speech perception; computational model; accent adaptation; perceptual recalibration"
wordcount         : "X"

bibliography      : ["latex-stuff/library.bib", "latex-stuff/r-references.bib"]
link-citations    : yes
csl               : latex-stuff/apa-6th-edition.csl

floatsintext      : yes
figurelist        : no
tablelist         : no
footnotelist      : no
linenumbers       : yes
numbersections    : true
mask              : no
draft             : no

header-includes: 
 - \usepackage{animate}
 - \usepackage{amsmath}
 - \usepackage{tikz}
 - \usetikzlibrary{bayesnet}
 - \usepackage{booktabs}
 - \usepackage{siunitx}
 - \usepackage{soul}
 - \usepackage{tabto}
 - \usepackage{xcolor}
 - \usepackage{placeins}
 - \setstcolor{red}
 - \usepackage{sectsty}
 - \sectionfont{\color{black}}
 - \subsectionfont{\color{black}}
 - \subsubsectionfont{\color{black}}
 - \usepackage{setspace}\doublespacing
 - \usepackage{subfig}

documentclass     : "apa6"
classoption       : "man"
fontsize          : 11pt
output: 
  papaja::apa6_pdf:
    latex_engine: xelatex
    extra_dependencies: "subfig" 
    includes:
      in_header: latex-stuff/header.tex
always_allow_html: true
---

# START OF CHUNK HERE {r libraries, include=FALSE, message=FALSE}
library(curl)               # Check availability of internet for install of remote libraries
if (has_internet()) devtools::install_github("crsh/papaja")
library(papaja)             # APA formatted ms
# END OF CHUNK HERE (omitted for formatting reasons)

# First heading

And here's the session info:

R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.5.1

Matrix products: default
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] papaja_0.1.1     tinylabels_0.2.3 curl_4.3.2      

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.9        compiler_4.2.1    later_1.3.0       urlchecker_1.0.1  prettyunits_1.1.1
 [6] profvis_0.3.7     remotes_2.4.2     tools_4.2.1       digest_0.6.29     pkgbuild_1.3.1   
[11] pkgload_1.3.0     memoise_2.0.1     lifecycle_1.0.1   rlang_1.0.4       shiny_1.7.2      
[16] cli_3.3.0         rstudioapi_0.13   xfun_0.32         fastmap_1.1.0     stringr_1.4.1    
[21] knitr_1.40        vctrs_0.4.1       fs_1.5.2          htmlwidgets_1.5.4 devtools_2.4.4   
[26] glue_1.6.2        R6_2.5.1          processx_3.7.0    sessioninfo_1.2.2 purrr_0.3.4      
[31] callr_3.7.1       magrittr_2.0.3    ps_1.7.1          promises_1.2.0.1  ellipsis_0.3.2   
[36] htmltools_0.5.3   usethis_2.1.6     mime_0.12         xtable_1.8-4      httpuv_1.6.5     
[41] stringi_1.7.8     miniUI_0.1.1.1    cachem_1.0.6      crayon_1.5.1