Citations not generating in RMarkdown - r-markdown

Question

new to Stackoverflow, and relatively new to writing documents in RMarkdown. I have most other things down, however, I cannot generate citations and the bibliography in RMarkdown. For the example code below, I have used the \cite{REFNAME} as well as [#REFNAME] syntax. The [#REFNAME] will not even let the document be generated, the \cite{} generates the document but the citation is [?] and the reference is not after the #References section.
I have looked through this site and I cannot get suggested fixes to work. I am hoping that the error I am showing after the code sections will tell someone what the error really is.
---
title: "Title for my document"
date: "`r format(Sys.Date(), '%d %B, %Y')`"
output:
pdf_document:
fig_caption: yes
keep_tex: true
number_sections: true
geometry: margin=0.5in
header-includes: \usepackage{float}
urlcolor: blue
bibliography: bibliography_file.bib
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
knitr::knit_hooks$set(mysize = function(before, options, envir) {
if (before)
return(options$size)
})
```
text written \cite{neil_increasing_2008} more text written
# References
My .bib file entry looks like this
#article{neil_increasing_2008,
title = {Increasing incidence of legionellosis in the {United} {States},
1990-2005: changing epidemiologic trends.},
volume = {47},
journal = {Clinical Infectious Diseases},
author = {Neil, K. and Berkelman, R.},
year = {2008},
pages = {591--599}
}
The error is:
Warning message: LaTeX Warning(s): Citation `neil_increasing_2008'
on page 1 undefined on input lin There were undefined references.
If I use the [#neil_increasing_2008] as opposed to the \cite{} then the following error is generate, and it does not generate the document either
pandoc-citeproc: Cannot decode byte '\x87':
Data.Text.Internal.Encoding.Fusion.streamUtf8: Invalid UTF-8 stream
pandoc.exe: Error running filter pandoc-citeproc Filter returned error
status 1 Error: pandoc document conversion failed with error 83
Execution halted