bibliography_entries outputting '.na.character'

[kanedan29]

I updated recently to R 4.0.3, reinstalled 'vitae' and 'tinytex' and now bibliography_entries is giving me trouble. I have a few articles in my bib that have no DOI or no volume/issue - white papers basically. bibliography_entries calls those in as NAs, and before a NA element was just left out completely but now it puts those items in and prints ".na.character."

Example of the resulting tex

\leavevmode\hypertarget{ref-kane_carbon_2015}{}%
2. Kane, D. (2015). Carbon sequestration potential on agricultural
lands: A review of current science and available practices.
In\emph{.na.character: Vol.na.character} (Issue.na.character,
p..na.character). \url{https://doi.org/.na.character}

Corresponding entry in bib

@misc{kane_carbon_2015,
	title = {Carbon Sequestration Potential on Agricultural Lands: A Review of Current Science and Available Practices},
	rights = {All rights reserved},
	url = {http://sustainableagriculture.net/wp-content/uploads/2015/12/Soil_C_review_Kane_Dec_4-final-v4.pdf},
	shorttitle = {Carbon Sequestration Potential on Agricultural Lands},
	author = {Kane, Daniel},
	urldate = {2016-09-08},
	date = {2015}
}

[mitchelloharawild]

This is what I get:

\hypertarget{bibliography}{}
\leavevmode\hypertarget{ref-kane_carbon_2015}{}%
\CSLLeftMargin{1. }
\CSLRightInline{Kane, D. (2015). \emph{Carbon sequestration potential on
agricultural lands: A review of current science and available
practices}.
\url{http://sustainableagriculture.net/wp-content/uploads/2015/12/Soil_C_review_Kane_Dec_4-final-v4.pdf}}

Could you let me know what version of pandoc and vitae you are using?

---

MRE:

test.rmd

---
name: vitae
position: "package"
date: "`r format(Sys.time(), '%B %Y')`"
output: 
  vitae::hyndman:
    keep_tex: true
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE, warning = FALSE, message = FALSE)
library(vitae)
```

# Publications

```{r}
library(dplyr)
bibliography_entries("test.bib")
```

test.bib

@misc{kane_carbon_2015,
	title = {Carbon Sequestration Potential on Agricultural Lands: A Review of Current Science and Available Practices},
	rights = {All rights reserved},
	url = {http://sustainableagriculture.net/wp-content/uploads/2015/12/Soil_C_review_Kane_Dec_4-final-v4.pdf},
	shorttitle = {Carbon Sequestration Potential on Agricultural Lands},
	author = {Kane, Daniel},
	urldate = {2016-09-08},
	date = {2015}
}

[kanedan29]

Pandoc v2.7.3 and Vitae v0.3.0

Realized something else. It occurs when there are two different bibtypes in the .bib file.

test.bib

@Article{williams_soil_2016,
  author = {Alwyn Williams and Mitchell C. Hunter and Melanie Kammerer and Daniel A. Kane and Nicholas R. Jordan and David A. Mortensen and Richard G. Smith and Sieglinde Snapp and Adam S. Davis},
  year = {2016},
  title = {Soil {Water} {Holding} {Capacity} {Mitigates} {Downside} {Risk} and {Volatility} in {US} {Rainfed} {Maize}: {Time} to {Invest} in {Soil} {Organic} {Matter}?},
  journaltitle = {PLOS ONE},
  volume = {11},
  number = {8},
  pages = {e0160974},
  doi = {10.1371/journal.pone.0160974},
  url = {http://doi.org/10.1371/journal.pone.0160974},
  key = {9},
}

@Misc{kane_carbon_2015,
  author = {Daniel Kane},
  year = {2015},
  title = {Carbon {Sequestration} {Potential} on {Agricultural} {Lands}: {A} {Review} of {Current} {Science} and {Available} {Practices}},
  url = {http://sustainableagriculture.net/wp-content/uploads/2015/12/Soil_C_review_Kane_Dec_4-final-v4.pdf},
  key = {11},
}

@Article{kane_ridge_2015,
  author = {Daniel A. Kane and Sieglinde S. Snapp and Adam S. Davis},
  year = {2015},
  title = {Ridge {Tillage} {Concentrates} {Potentially} {Mineralizable} {Soil} {Nitrogen}, {Facilitating} {Maize} {Nitrogen} {Uptake}},
  journaltitle = {Soil Science Society of America Journal},
  volume = {79},
  number = {1},
  pages = {81},
  doi = {10.2136/sssaj2014.07.0273},
  url = {http://doi.org/10.2136/sssaj2014.07.0273},
  key = {12},
}

So bibliography_entries creates a column for volume, number, etc., but there's no corresponding data for the @Misc entry in the bib file.

[kanedan29]

Reverting to vitae v0.2.0 fixed the problem. So perhaps has something to do with changing to pandoc_citeproc to handle bibliographies.

[mitchelloharawild]

Odd, I imagine this is a result of pandoc v2.7.3. Using pandoc v2.11.2, it seems to work fine:

\hypertarget{bibliography}{}
\leavevmode\hypertarget{ref-williams_soil_2016}{}%
\CSLLeftMargin{1. }
\CSLRightInline{Williams, A., Hunter, M. C., Kammerer, M., Kane, D. A.,
Jordan, N. R., Mortensen, D. A., Smith, R. G., Snapp, S., \& Davis, A.
S. (2016). Soil Water Holding Capacity Mitigates Downside Risk and
Volatility in US Rainfed Maize: Time to Invest in Soil Organic Matter?
\emph{PLOS ONE}, \emph{11}(8), e0160974.
\url{https://doi.org/10.1371/journal.pone.0160974}}

\leavevmode\hypertarget{ref-kane_carbon_2015}{}%
\CSLLeftMargin{2. }
\CSLRightInline{Kane, D. (2015). \emph{Carbon Sequestration Potential on
Agricultural Lands: A Review of Current Science and Available
Practices}.
\url{http://sustainableagriculture.net/wp-content/uploads/2015/12/Soil_C_review_Kane_Dec_4-final-v4.pdf}}

\leavevmode\hypertarget{ref-kane_ridge_2015}{}%
\CSLLeftMargin{3. }
\CSLRightInline{Kane, D. A., Snapp, S. S., \& Davis, A. S. (2015). Ridge
Tillage Concentrates Potentially Mineralizable Soil Nitrogen,
Facilitating Maize Nitrogen Uptake. \emph{Soil Science Society of
America Journal}, \emph{79}(1), 81.
\url{https://doi.org/10.2136/sssaj2014.07.0273}}

[psadil]

Hi, just reporting that I'm also seeing ".na.character" in the citations (using this test.bib and this test.Rmd), although I'm working with pandoc v2.11.0.4

> rmarkdown::pandoc_version()
[1] ‘2.11.0.4’

> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.1 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

loaded via a namespace (and not attached):
 [1] here_1.0.1       crayon_1.3.4     digest_0.6.27    dplyr_1.0.2      rprojroot_2.0.2  R6_2.5.0         lifecycle_0.2.0  magrittr_2.0.1  
 [9] evaluate_0.14    pillar_1.4.7     rlang_0.4.10     renv_0.12.5      ellipsis_0.3.1   generics_0.1.0   vctrs_0.3.6      rmarkdown_2.6   
[17] tools_4.0.3      glue_1.4.2       purrr_0.3.4      xfun_0.20        yaml_2.2.1       compiler_4.0.3   pkgconfig_2.0.3  htmltools_0.5.0 
[25] vitae_0.3.0      tidyselect_1.1.0 knitr_1.30       tibble_3.0.4   

[mitchelloharawild]

This should be fixed now, thanks for the bug report!