Kevin Zembower
2023-Jun-13 16:29 UTC
[R] Rmarkdown code rendering as LaTeX, not executing?
Hi, all,
I'm trying to compose an Rmarkdown document and render it as a PDF file.
My first block of R code seems to work okay, but the second on seems to
be interpreted as LaTeX code, and not executed as R code. In the output,
the three back-ticks that mark the R code block are interpreted as an
opening double-quote, followed by an opening single quote.
Here's my test file:
===============================---
title: "An analysis of US 2020 Census Data for the Radnor-Winston
neighborhood"
author: "E. Kevin Zembower"
date: "29 May 2023"
output:
pdf_document:
extra_dependencies: ["array", "booktabs",
"dcolumn"]
---
```{r setup, include = FALSE}
```
\section{Abstract}
In this document, ...
\section{Boundaries of the Radnor-Winston neighborhood}
...
For the purposes of this report, the
boundaries of RW are as shown in figure \ref{RWneigh}. ...
```{r rw_map, fig.width = 6, fig.height = 4, out.width = "80%", dev =
"pdf",
fig.cap = "Map of RW neighborhood\label{RWneigh}"}
## Creating a polygon for RW neighborhood, based on CRS 6487 (NAD83
## (2011) / Maryland ) map in meters:
base_x <- 433000
base_y <- 186000
rw_neigh_pg_m <- data.frame(
matrix(
c(540, 1140,
540, 1070,
480, 1060,
490, 1000,
570, 1000,
570, 940,
550, 930,
550, 890,
580, 890,
590, 820,
640, 820,
650, 590,
520, 580,
470, 580,
350, 660,
350, 710,
180, 725,
190, 900,
220, 900,
220, 1030,
240, 1030,
240, 1110
),
ncol = 2, byrow = TRUE)
) %>% + matrix(c(rep(base_x, nrow(.)), rep(base_y, nrow(.))),
nrow = nrow(.)) %>%
sf::st_as_sf(coords = c(1,2), dim = "XY") %>%
summarize(geometry = st_combine(geometry)) %>%
st_cast("POLYGON") %>%
st_set_crs(6487)
## Map it:
rw_base_blocks <- read_osm(bb(rw_neigh_pg_m, ext = 1.3))
## Line below gives map in meters
(RW_block_map <- tm_shape(rw_base_blocks, projection = 6487) +
## Line below gives map in degrees
## (RW_block_map <- tm_shape(rw_base_blocks, projection = 6487) +
tm_rgb() +
tm_shape(rw_neigh_pg_m) +
tm_fill(col = "green", alpha = 0.2) +
tm_borders(lwd = 2, alpha = 1) +
tm_scale_bar() +
## tm_grid() + tm_xlab("Long") + tm_ylab("Lat") +
tm_grid() +
tm_layout(title = "Radnor-Winston Neighborhood")
)
## tmap_save(RW_block_map, "rw_map.png")
```
===================================================
This code block can also be obtained from
https://gist.github.com/kzembower/f9ad52abf82975102cbf715bcfbc0f51.
I'm using Emacs and ESS to create this document. This seems to produce
its own weirdness, as the text style and font color and sizes change in
the R code block as I edit it and add spaces and lines.
If the block above is saved as "RW_test.Rmd", I use these lines to
create the PDF:
==============================library(rmarkdown)
render("RW_test.Rmd")
===============================
No errors are generated.
Can anyone help me understand what I'm doing wrong? A much shorter test
file I created seems to work okay.
Thanks in advance for any advice.
-Kevin
> sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK:
/usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;
LAPACK version 3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8
LC_ADDRESS=en_US.UTF-8
[10] LC_TELEPHONE=en_US.UTF-8 LC_MEASUREMENT=en_US.UTF-8
LC_IDENTIFICATION=en_US.UTF-8
time zone: America/New_York
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] kableExtra_1.3.4 tidycensus_1.4 lubridate_1.9.2 forcats_1.0.0
stringr_1.5.0 dplyr_1.1.2
[7] purrr_1.0.1 readr_2.1.4 tidyr_1.3.0 tibble_3.2.1
ggplot2_3.4.2 tidyverse_2.0.0
[13] rmarkdown_2.22
loaded via a namespace (and not attached):
[1] gtable_0.3.3 xfun_0.39 raster_3.6-20
tigris_2.0.3 rJava_1.0-6
[6] lattice_0.21-8 tzdb_0.4.0 vctrs_0.6.2
tools_4.3.0 generics_0.1.3
[11] curl_5.0.0 proxy_0.4-27 fansi_1.0.4
pkgconfig_2.0.3 KernSmooth_2.23-21
[16] webshot_0.5.4 uuid_1.1-0 lifecycle_1.0.3
compiler_4.3.0 munsell_0.5.0
[21] tinytex_0.45 terra_1.7-29 codetools_0.2-19
htmltools_0.5.5 class_7.3-22
[26] yaml_2.3.7 crayon_1.5.2 pillar_1.9.0
classInt_0.4-9 tidyselect_1.2.0
[31] rvest_1.0.3 digest_0.6.31 stringi_1.7.12
sf_1.0-13 fastmap_1.1.1
[36] grid_4.3.0 colorspace_2.1-0 cli_3.6.1
magrittr_2.0.3 utf8_1.2.3
[41] e1071_1.7-13 withr_2.5.0 scales_1.2.1
rappdirs_0.3.3 sp_1.6-1
[46] timechange_0.2.0 httr_1.4.6 hms_1.1.3
OpenStreetMap_0.3.4 evaluate_0.21
[51] knitr_1.43 rgdal_1.6-7 viridisLite_0.4.2
rlang_1.1.1 Rcpp_1.0.10
[56] glue_1.6.2 DBI_1.1.3 xml2_1.3.4
svglite_2.1.1 rstudioapi_0.14
[61] jsonlite_1.8.4 R6_2.5.1 systemfonts_1.0.4
units_0.8-2
>
Olivier Crouzet
2023-Jun-13 17:31 UTC
[R] Rmarkdown code rendering as LaTeX, not executing?
Dear Kevin,
actually you're mixing markdown and LaTeX syntax, which is the reason
why you see LaTeX code in the PDF. You have to choose...
1) Either you wish to produce an RMarkdown document and your sections,
subsections... should read:
# Abstract
In this document, ...
## Boundaries of the Radnor-Winston neighborhood
```{r rw_map, fig.width = 6, fig.height = 4, out.width = "80%", dev
= "pdf",
fig.cap = "Map of RW neighborhood\label{RWneigh}"}
## Creating a polygon for RW neighborhood, based on CRS 6487 (NAD83
## (2011) / Maryland ) map in meters:
base_x <- 433000
base_y <- 186000
[etc]...
```
But you may not use all the power of LaTeX (easily at least).
2) Or you wish to produce a .Rnw (knitr / Sweave file using LaTeX) and
you should use another R code delimitation convention (and change the
heading part of the document to LaTeX usage, that is
\documentclass{}... \usepackage{}...):
<<r rw_map, fig.width = 6, fig.height = 4, out.width = "80%",
dev "pdf", fig.cap = "Map of RW
neighborhood\label{RWneigh}">
## Creating a polygon for RW neighborhood, based on CRS 6487 (NAD83
## (2011) / Maryland ) map in meters:
base_x <- 433000
base_y <- 186000
[etc]
@
Depending on your choice, compiling the document goes through a
different process but both are possible and relatively simple (either
from within RStudio or using any other editor).
Hope this helps for a first approach.
Olivier.
On Tue, 13 Jun 2023 16:29:57 +0000 Kevin
Zembower via R-help <r-help at r-project.org> wrote:
> Hi, all,
>
> I'm trying to compose an Rmarkdown document and render it as a PDF
> file. My first block of R code seems to work okay, but the second on
> seems to be interpreted as LaTeX code, and not executed as R code. In
> the output, the three back-ticks that mark the R code block are
> interpreted as an opening double-quote, followed by an opening single
> quote.
>
> Here's my test file:
> ===============================> ---
> title: "An analysis of US 2020 Census Data for the Radnor-Winston
> neighborhood"
> author: "E. Kevin Zembower"
> date: "29 May 2023"
> output:
> pdf_document:
> extra_dependencies: ["array", "booktabs",
"dcolumn"]
>
> ---
>
> ```{r setup, include = FALSE}
>
> ```
>
> \section{Abstract}
> In this document, ...
>
> \section{Boundaries of the Radnor-Winston neighborhood}
>
> ...
>
> For the purposes of this report, the
> boundaries of RW are as shown in figure \ref{RWneigh}. ...
>
> ```{r rw_map, fig.width = 6, fig.height = 4, out.width = "80%",
dev
> = "pdf",
> fig.cap = "Map of RW neighborhood\label{RWneigh}"}
>
> ## Creating a polygon for RW neighborhood, based on CRS 6487 (NAD83
> ## (2011) / Maryland ) map in meters:
> base_x <- 433000
> base_y <- 186000
> rw_neigh_pg_m <- data.frame(
> matrix(
> c(540, 1140,
> 540, 1070,
> 480, 1060,
> 490, 1000,
> 570, 1000,
> 570, 940,
> 550, 930,
> 550, 890,
> 580, 890,
> 590, 820,
> 640, 820,
> 650, 590,
> 520, 580,
> 470, 580,
> 350, 660,
> 350, 710,
> 180, 725,
> 190, 900,
> 220, 900,
> 220, 1030,
> 240, 1030,
> 240, 1110
> ),
> ncol = 2, byrow = TRUE)
> ) %>% + matrix(c(rep(base_x, nrow(.)), rep(base_y, nrow(.))),
> nrow = nrow(.)) %>%
> sf::st_as_sf(coords = c(1,2), dim = "XY") %>%
> summarize(geometry = st_combine(geometry)) %>%
> st_cast("POLYGON") %>%
> st_set_crs(6487)
>
> ## Map it:
> rw_base_blocks <- read_osm(bb(rw_neigh_pg_m, ext = 1.3))
>
> ## Line below gives map in meters
> (RW_block_map <- tm_shape(rw_base_blocks, projection = 6487) +
> ## Line below gives map in degrees
> ## (RW_block_map <- tm_shape(rw_base_blocks, projection = 6487) +
> tm_rgb() +
> tm_shape(rw_neigh_pg_m) +
> tm_fill(col = "green", alpha = 0.2) +
> tm_borders(lwd = 2, alpha = 1) +
> tm_scale_bar() +
> ## tm_grid() + tm_xlab("Long") + tm_ylab("Lat") +
> tm_grid() +
> tm_layout(title = "Radnor-Winston Neighborhood")
> )
>
> ## tmap_save(RW_block_map, "rw_map.png")
>
> ```
> ===================================================>
> This code block can also be obtained from
> https://gist.github.com/kzembower/f9ad52abf82975102cbf715bcfbc0f51.
>
> I'm using Emacs and ESS to create this document. This seems to
> produce its own weirdness, as the text style and font color and sizes
> change in the R code block as I edit it and add spaces and lines.
>
> If the block above is saved as "RW_test.Rmd", I use these lines
to
> create the PDF:
> ==============================> library(rmarkdown)
> render("RW_test.Rmd")
> ===============================>
> No errors are generated.
>
> Can anyone help me understand what I'm doing wrong? A much shorter
> test file I created seems to work okay.
>
> Thanks in advance for any advice.
>
> -Kevin
>
> > sessionInfo()
> R version 4.3.0 (2023-04-21)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 22.04.2 LTS
>
> Matrix products: default
> BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
> LAPACK:
> /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;
> LAPACK version 3.10.0
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> LC_TIME=en_US.UTF-8
> [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
> LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8
> LC_ADDRESS=en_US.UTF-8
> [10] LC_TELEPHONE=en_US.UTF-8 LC_MEASUREMENT=en_US.UTF-8
> LC_IDENTIFICATION=en_US.UTF-8
>
> time zone: America/New_York
> tzcode source: system (glibc)
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] kableExtra_1.3.4 tidycensus_1.4 lubridate_1.9.2
> forcats_1.0.0 stringr_1.5.0 dplyr_1.1.2
> [7] purrr_1.0.1 readr_2.1.4 tidyr_1.3.0 tibble_3.2.1
> ggplot2_3.4.2 tidyverse_2.0.0
> [13] rmarkdown_2.22
>
> loaded via a namespace (and not attached):
> [1] gtable_0.3.3 xfun_0.39 raster_3.6-20
> tigris_2.0.3 rJava_1.0-6
> [6] lattice_0.21-8 tzdb_0.4.0 vctrs_0.6.2
> tools_4.3.0 generics_0.1.3
> [11] curl_5.0.0 proxy_0.4-27 fansi_1.0.4
> pkgconfig_2.0.3 KernSmooth_2.23-21
> [16] webshot_0.5.4 uuid_1.1-0 lifecycle_1.0.3
> compiler_4.3.0 munsell_0.5.0
> [21] tinytex_0.45 terra_1.7-29 codetools_0.2-19
> htmltools_0.5.5 class_7.3-22
> [26] yaml_2.3.7 crayon_1.5.2 pillar_1.9.0
> classInt_0.4-9 tidyselect_1.2.0
> [31] rvest_1.0.3 digest_0.6.31 stringi_1.7.12
> sf_1.0-13 fastmap_1.1.1
> [36] grid_4.3.0 colorspace_2.1-0 cli_3.6.1
> magrittr_2.0.3 utf8_1.2.3
> [41] e1071_1.7-13 withr_2.5.0 scales_1.2.1
> rappdirs_0.3.3 sp_1.6-1
> [46] timechange_0.2.0 httr_1.4.6 hms_1.1.3
> OpenStreetMap_0.3.4 evaluate_0.21
> [51] knitr_1.43 rgdal_1.6-7 viridisLite_0.4.2
> rlang_1.1.1 Rcpp_1.0.10
> [56] glue_1.6.2 DBI_1.1.3 xml2_1.3.4
> svglite_2.1.1 rstudioapi_0.14
> [61] jsonlite_1.8.4 R6_2.5.1 systemfonts_1.0.4
> units_0.8-2
> >
>
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html and provide commented,
> minimal, self-contained, reproducible code.
--
Olivier Crouzet, PhD
http://olivier.ghostinthemachine.space
/Ma?tre de Conf?rences/
@LLING - Laboratoire de Linguistique de Nantes
UMR6310 CNRS / Universit? de Nantes