[R] Rmarkdown code rendering as LaTeX, not executing?

[Kevin Zembower]

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
 >