R ztable latex output not working

The following MWE should work. I added the table option to the xcolor package to make the code compilable. Since the table is too large to fit onto the page, I used makecell and rotating to rotate the table headers and also reduced the font size to small. In order tom improve the code, I made some more changes, that are commented in the code itself:

documentclass[12pt]{report}
usepackage[letterpaper,top=1in,bottom=1in,right=1in,left=1in]{geometry}


usepackage{graphicx}
usepackage{amsmath}
usepackage{cite}
usepackage{siunitx}
%usepackage[hidelinks]{hyperref} % removed hyperref. this package should be the last package in your preamble (with a few exceptions)
usepackage{enumerate}
usepackage{listings}
usepackage[table]{xcolor} % added table option here, needed for the cellcolor command
usepackage{makecell,rotating} % added makecell and rotating package, needed for rotated column headers.
usepackage{setspace}


usepackage[nottoc]{tocbibind}


usepackage{titlesec}
titleformat{chapter}[display]{normalfontbfseries}{centering CHAPTER thechapter}{0pt}{centering}
titleformat{section}[block]{normalfontbfseries}{thesection}{12pt}{}
titleformat{subsection}[block]{normalfont}{thesubsection}{12pt}{}

usepackage[hidelinks]{hyperref} % moved hyperref. this package should be the last package in your preamble (with a few exceptions)


renewcommand{contentsname}{TABLE OF CONTENTS}
renewcommand{listfigurename}{LIST OF FIGURES}
renewcommand{listtablename}{LIST OF TABLES}
renewcommand{bibname}{LIST OF REFERENCES}


definecolor{tempcolor1}{rgb}{0.98,0.41,0.29}  % added a definition for the color "tempcolor1" since this definition was missing 
definecolor{tempcolor2}{rgb}{0.79,0.09,0.11} 
definecolor{tempcolor3}{rgb}{0.98,0.57,0.45} 
definecolor{tempcolor4}{rgb}{0.93,0.23,0.17} 
definecolor{gray}{rgb}{0.5, 0.5, 0.5} 
definecolor{yellow}{rgb}{1.0, 1.0, 0.0} 
definecolor{tempcolor5}{rgb}{0.98,0.73,0.63} 
definecolor{tempcolor6}{rgb}{0.64,0.06,0.08} 
definecolor{tempcolor7}{rgb}{0.4,0,0.05} 
definecolor{tempcolor8}{rgb}{0.99,0.88,0.82} 
definecolor{tempcolor9}{rgb}{1,0.96,0.94} 
definecolor{black}{rgb}{0.0, 0.0, 0.0} 
definecolor{gray}{rgb}{0.5, 0.5, 0.5}

begin{document}

 
begin{table}[!hbtp]
small % removed normalsize environment, used small font size instad, otehrwise table would be too large
centering % replaced the center environment with the centering command since the former adds additional vertical white space which might be undesired
settowidthrotheadsize{theadfont spectral} % set width maximum width of rotated text. Longer text is split up into multiple lines.
begin{tabular}{rlrrrrrrrrrr}
hline
& species & rothead{topo (2)} & rothead{topo (3)}&rothead{spectral (2)}&rothead{spectral (3)}&rothead{topo spectral (2)}&rothead{topo spectral (3)}&rothead{soil (2)}&rothead{soil (3)}&rothead{all (2)}&rothead{all (3)} 
hline
1&ABIBAL&cellcolor{tempcolor1}color{white}0.64&cellcolor{tempcolor4}color{white}0.71&cellcolor{tempcolor1}color{white}0.65&cellcolor{tempcolor3}0.56&cellcolor{tempcolor4}color{white}0.68&cellcolor{tempcolor2}color{white}0.73&cellcolor{tempcolor4}color{white}0.72&cellcolor{tempcolor2}color{white}0.76&cellcolor{tempcolor1}color{white}0.66&cellcolor{tempcolor6}color{white}0.81 
2&ACEPEN&cellcolor{tempcolor2}color{white}0.74&cellcolor{tempcolor2}color{white}0.73&cellcolor{tempcolor5}0.53&cellcolor{tempcolor5}0.52&cellcolor{tempcolor2}color{white}0.74&cellcolor{tempcolor2}color{white}0.73&cellcolor{tempcolor2}color{white}0.76&cellcolor{tempcolor2}color{white}0.77&cellcolor{tempcolor6}color{white}0.81&cellcolor{tempcolor7}color{white}0.84 
3&ACERUB&cellcolor{tempcolor3}0.56&cellcolor{tempcolor3}0.60&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{tempcolor3}0.56&cellcolor{tempcolor3}0.59&cellcolor{tempcolor5}0.54&cellcolor{tempcolor3}0.60&cellcolor{tempcolor5}0.55&cellcolor{tempcolor4}color{white}0.68 
4&ACESAC&cellcolor{tempcolor4}color{white}0.71&cellcolor{tempcolor4}color{white}0.71&cellcolor{tempcolor5}0.51&cellcolor{tempcolor5}0.54&cellcolor{tempcolor4}color{white}0.69&cellcolor{tempcolor2}color{white}0.76&cellcolor{tempcolor1}color{white}0.62&cellcolor{tempcolor1}color{white}0.65&cellcolor{tempcolor4}color{white}0.68&cellcolor{tempcolor2}color{white}0.76 
5&ACESPI&cellcolor{tempcolor4}color{white}0.69&cellcolor{tempcolor2}color{white}0.74&cellcolor{tempcolor8}0.48&cellcolor{gray}color{gray}0.42&cellcolor{tempcolor4}color{white}0.69&cellcolor{tempcolor4}color{white}0.67&cellcolor{tempcolor1}color{white}0.65&cellcolor{tempcolor1}color{white}0.65&cellcolor{tempcolor3}0.61&cellcolor{tempcolor6}color{white}0.78 
6&ARANUD&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{tempcolor2}color{white}0.73&cellcolor{tempcolor2}color{white}0.76&cellcolor{tempcolor7}color{white}0.86&cellcolor{tempcolor2}color{white}0.73&cellcolor{tempcolor6}color{white}0.83 
7&ARITRI&cellcolor{yellow}0.65&cellcolor{tempcolor2}color{white}0.75&cellcolor{yellow}0.75&cellcolor{yellow}0.47&cellcolor{tempcolor1}color{white}0.63&cellcolor{tempcolor2}color{white}0.74&cellcolor{tempcolor1}color{white}0.66&cellcolor{yellow}0.76&cellcolor{yellow}0.59&cellcolor{yellow}0.80 
8&ATHANG&cellcolor{tempcolor1}color{white}0.62&cellcolor{tempcolor1}color{white}0.66&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{tempcolor1}color{white}0.62&cellcolor{tempcolor2}color{white}0.76&cellcolor{tempcolor4}color{white}0.71&cellcolor{tempcolor4}color{white}0.71&cellcolor{tempcolor1}color{white}0.65&cellcolor{tempcolor2}color{white}0.77 
9&BETALL&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{tempcolor3}0.58&cellcolor{tempcolor5}0.54&cellcolor{tempcolor3}0.61&cellcolor{tempcolor1}color{white}0.63&cellcolor{tempcolor5}0.50&cellcolor{tempcolor4}color{white}0.69&cellcolor{tempcolor3}0.60&cellcolor{tempcolor4}color{white}0.70 
10&CARARC&cellcolor{yellow}0.55&cellcolor{yellow}0.75&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{yellow}0.59&cellcolor{yellow}0.78&cellcolor{yellow}0.64&cellcolor{yellow}0.66&cellcolor{yellow}0.65&cellcolor{yellow}0.78 
11&CARINT&cellcolor{gray}color{gray}0.42&cellcolor{tempcolor1}color{white}0.62&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{tempcolor3}0.59&cellcolor{tempcolor4}color{white}0.68&cellcolor{tempcolor2}color{white}0.76&cellcolor{tempcolor1}color{white}0.61&cellcolor{tempcolor2}color{white}0.77 
12&CINLAT&cellcolor{tempcolor3}0.57&cellcolor{tempcolor3}0.58&cellcolor{tempcolor8}0.49&cellcolor{tempcolor5}0.53&cellcolor{tempcolor1}color{white}0.61&cellcolor{tempcolor1}color{white}0.65&cellcolor{tempcolor1}color{white}0.61&cellcolor{tempcolor4}color{white}0.67&cellcolor{tempcolor3}0.60&cellcolor{tempcolor6}color{white}0.80 
13&CLIBOR&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{tempcolor1}color{white}0.63&cellcolor{tempcolor3}0.59&cellcolor{tempcolor4}color{white}0.68&cellcolor{tempcolor2}color{white}0.75&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{tempcolor1}color{white}0.63&cellcolor{tempcolor2}color{white}0.73 
14&DENPUN&cellcolor{tempcolor5}0.54&cellcolor{tempcolor1}color{white}0.63&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{tempcolor5}0.53&cellcolor{tempcolor1}color{white}0.65&cellcolor{tempcolor3}0.58&cellcolor{tempcolor1}color{white}0.65&cellcolor{tempcolor4}color{white}0.67&cellcolor{tempcolor4}color{white}0.69 
15&DRYCAM&cellcolor{yellow}0.56&cellcolor{yellow}0.61&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{yellow}0.52&cellcolor{yellow}0.63&cellcolor{yellow}0.58&cellcolor{yellow}0.68&cellcolor{yellow}0.66&cellcolor{yellow}0.66 
16&DRYINT&cellcolor{tempcolor2}color{white}0.73&cellcolor{tempcolor2}color{white}0.74&cellcolor{tempcolor1}color{white}0.67&cellcolor{tempcolor3}0.61&cellcolor{tempcolor2}color{white}0.73&cellcolor{tempcolor7}color{white}0.83&cellcolor{tempcolor1}color{white}0.64&cellcolor{yellow}0.75&cellcolor{tempcolor2}color{white}0.75&cellcolor{tempcolor6}color{white}0.82 
17&FAGGRA&cellcolor{tempcolor6}color{white}0.79&cellcolor{tempcolor7}color{white}0.84&cellcolor{tempcolor1}color{white}0.62&cellcolor{tempcolor3}0.59&cellcolor{tempcolor6}color{white}0.80&cellcolor{tempcolor6}color{white}0.82&cellcolor{tempcolor3}0.57&cellcolor{tempcolor4}color{white}0.69&cellcolor{tempcolor2}color{white}0.75&cellcolor{tempcolor6}color{white}0.82 
18&FRAAME&cellcolor{tempcolor4}color{white}0.69&cellcolor{tempcolor4}color{white}0.69&cellcolor{gray}color{gray}0.42&cellcolor{tempcolor1}color{white}0.64&cellcolor{tempcolor4}color{white}0.67&cellcolor{tempcolor4}color{white}0.72&cellcolor{tempcolor5}0.55&cellcolor{tempcolor1}color{white}0.62&cellcolor{tempcolor1}color{white}0.66&cellcolor{tempcolor2}color{white}0.77 
19&HUPLUC&cellcolor{tempcolor3}0.57&cellcolor{tempcolor1}color{white}0.67&cellcolor{tempcolor3}0.58&cellcolor{tempcolor1}color{white}0.65&cellcolor{tempcolor3}0.58&cellcolor{tempcolor4}color{white}0.67&cellcolor{tempcolor1}color{white}0.66&cellcolor{tempcolor4}color{white}0.70&cellcolor{tempcolor1}color{white}0.64&cellcolor{tempcolor2}color{white}0.74 
20&LONCAN&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{tempcolor3}0.59&cellcolor{yellow}0.59&cellcolor{yellow}0.58&cellcolor{yellow}0.67&cellcolor{yellow}0.72 
21&MAICAN&cellcolor{tempcolor6}color{white}0.80&cellcolor{tempcolor4}color{white}0.71&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{tempcolor6}color{white}0.81&cellcolor{tempcolor2}color{white}0.76&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{tempcolor2}color{white}0.77&cellcolor{tempcolor6}color{white}0.79 
22&MAIRAC&cellcolor{tempcolor3}0.60&cellcolor{tempcolor2}color{white}0.76&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{tempcolor1}color{white}0.62&cellcolor{tempcolor2}color{white}0.75&cellcolor{tempcolor3}0.58&cellcolor{tempcolor4}color{white}0.68&cellcolor{tempcolor1}color{white}0.65&cellcolor{tempcolor6}color{white}0.78 
23&MEDVIR&cellcolor{tempcolor3}0.58&cellcolor{tempcolor1}color{white}0.64&cellcolor{tempcolor3}0.56&cellcolor{gray}color{gray}0.42&cellcolor{tempcolor1}color{white}0.65&cellcolor{tempcolor4}color{white}0.70&cellcolor{tempcolor4}color{white}0.69&cellcolor{tempcolor1}color{white}0.65&cellcolor{tempcolor1}color{white}0.65&cellcolor{tempcolor2}color{white}0.76 
24&NABSPP&cellcolor{tempcolor5}0.55&cellcolor{tempcolor1}color{white}0.63&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{tempcolor5}0.55&cellcolor{tempcolor1}color{white}0.65&cellcolor{tempcolor4}color{white}0.72&cellcolor{tempcolor4}color{white}0.71&cellcolor{tempcolor4}color{white}0.70&cellcolor{tempcolor2}color{white}0.74 
25&OCLACU&cellcolor{tempcolor5}0.53&cellcolor{tempcolor5}0.54&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{tempcolor5}0.52&cellcolor{tempcolor5}0.52&cellcolor{tempcolor5}0.56&cellcolor{tempcolor1}color{white}0.62&cellcolor{tempcolor5}0.55&cellcolor{tempcolor1}color{white}0.62 
26&OXAMON&cellcolor{tempcolor5}0.55&cellcolor{tempcolor1}color{white}0.61&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{tempcolor3}0.56&cellcolor{tempcolor5}0.53&cellcolor{tempcolor4}color{white}0.71&cellcolor{tempcolor1}color{white}0.66&cellcolor{tempcolor4}color{white}0.70&cellcolor{tempcolor2}color{white}0.75 
27&PARNOV&cellcolor{yellow}0.63&cellcolor{yellow}0.70&cellcolor{yellow}0.62&cellcolor{yellow}0.65&cellcolor{yellow}0.65&cellcolor{yellow}0.70&cellcolor{yellow}0.59&cellcolor{tempcolor4}color{white}0.67&cellcolor{yellow}0.59&cellcolor{yellow}0.71 
28&PHECON&cellcolor{tempcolor1}color{white}0.62&cellcolor{tempcolor4}color{white}0.71&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{tempcolor1}color{white}0.62&cellcolor{tempcolor4}color{white}0.71&cellcolor{tempcolor4}color{white}0.67&cellcolor{tempcolor2}color{white}0.75&cellcolor{tempcolor1}color{white}0.62&cellcolor{tempcolor2}color{white}0.74 
29&PICRUB&cellcolor{tempcolor1}color{white}0.64&cellcolor{tempcolor1}color{white}0.66&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{tempcolor1}color{white}0.64&cellcolor{tempcolor4}color{white}0.70&cellcolor{tempcolor3}0.60&cellcolor{tempcolor1}color{white}0.65&cellcolor{tempcolor3}0.57&cellcolor{tempcolor1}color{white}0.66 
30&RUBIDA&cellcolor{tempcolor3}0.60&cellcolor{tempcolor1}color{white}0.61&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{tempcolor3}0.58&cellcolor{tempcolor4}color{white}0.68&cellcolor{tempcolor3}0.58&cellcolor{tempcolor1}color{white}0.66&cellcolor{tempcolor1}color{white}0.62&cellcolor{tempcolor4}color{white}0.69 
31&SAMRAC&cellcolor{tempcolor1}color{white}0.65&cellcolor{tempcolor4}color{white}0.71&cellcolor{tempcolor8}0.49&cellcolor{tempcolor5}0.51&cellcolor{tempcolor1}color{white}0.65&cellcolor{tempcolor2}color{white}0.74&cellcolor{tempcolor2}color{white}0.76&cellcolor{tempcolor6}color{white}0.78&cellcolor{tempcolor4}color{white}0.72&cellcolor{tempcolor2}color{white}0.77 
32&STRAMP&cellcolor{gray}color{gray}0.42&cellcolor{yellow}0.56&cellcolor{yellow}0.53&cellcolor{yellow}0.53&cellcolor{yellow}0.57&cellcolor{yellow}0.67&cellcolor{yellow}0.60&cellcolor{tempcolor1}color{white}0.62&cellcolor{tempcolor5}0.54&cellcolor{yellow}0.66 
33&TIACOR&cellcolor{tempcolor3}0.59&cellcolor{tempcolor4}color{white}0.68&cellcolor{tempcolor5}0.52&cellcolor{tempcolor9}0.44&cellcolor{tempcolor1}color{white}0.62&cellcolor{tempcolor4}color{white}0.68&cellcolor{tempcolor2}color{white}0.75&cellcolor{tempcolor6}color{white}0.79&cellcolor{tempcolor2}color{white}0.73&cellcolor{tempcolor2}color{white}0.77 
34&TRIBOR&cellcolor{tempcolor1}color{white}0.66&cellcolor{tempcolor2}color{white}0.75&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{tempcolor1}color{white}0.66&cellcolor{tempcolor4}color{white}0.70&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{tempcolor1}color{white}0.65&cellcolor{tempcolor2}color{white}0.73 
35&TRIERE&cellcolor{tempcolor1}color{white}0.64&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{tempcolor4}color{white}0.70&cellcolor{tempcolor2}color{white}0.73&cellcolor{tempcolor2}color{white}0.73&cellcolor{tempcolor1}color{white}0.65&cellcolor{tempcolor7}color{white}0.83 
36&TRIUND&cellcolor{tempcolor4}color{white}0.68&cellcolor{tempcolor1}color{white}0.65&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{tempcolor4}color{white}0.68&cellcolor{tempcolor4}color{white}0.68&cellcolor{tempcolor1}color{white}0.62&cellcolor{tempcolor4}color{white}0.68&cellcolor{tempcolor4}color{white}0.68&cellcolor{tempcolor4}color{white}0.71 
37&TSUCAN&cellcolor{yellow}0.67&cellcolor{yellow}0.77&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{yellow}0.69&cellcolor{yellow}0.72&cellcolor{yellow}0.60&cellcolor{yellow}0.68&cellcolor{yellow}0.70&cellcolor{yellow}0.79 
38&UVUSES&cellcolor{tempcolor1}color{white}0.64&cellcolor{tempcolor2}color{white}0.75&cellcolor{tempcolor5}0.53&cellcolor{tempcolor3}0.57&cellcolor{tempcolor4}color{white}0.67&cellcolor{tempcolor2}color{white}0.75&cellcolor{tempcolor3}0.58&cellcolor{tempcolor1}color{white}0.65&cellcolor{tempcolor1}color{white}0.66&cellcolor{tempcolor2}color{white}0.75 
39&VIBLAN&cellcolor{tempcolor4}color{white}0.70&cellcolor{tempcolor4}color{white}0.71&cellcolor{tempcolor1}color{white}0.64&cellcolor{tempcolor4}color{white}0.68&cellcolor{tempcolor2}color{white}0.72&cellcolor{tempcolor2}color{white}0.72&cellcolor{tempcolor4}color{white}0.67&cellcolor{tempcolor4}color{white}0.70&cellcolor{tempcolor2}color{white}0.73&cellcolor{tempcolor6}color{white}0.83 
40&VIOBLA&cellcolor{tempcolor3}0.59&cellcolor{tempcolor4}color{white}0.69&cellcolor{gray}color{gray}0.42&cellcolor{gray}color{gray}0.42&cellcolor{tempcolor1}color{white}0.64&cellcolor{tempcolor4}color{white}0.68&cellcolor{tempcolor3}0.59&cellcolor{tempcolor1}color{white}0.65&cellcolor{tempcolor4}color{white}0.68&cellcolor{tempcolor2}color{white}0.74 
41&VIOROT&cellcolor{tempcolor4}color{white}0.69&cellcolor{tempcolor2}color{white}0.73&cellcolor{tempcolor5}0.55&cellcolor{tempcolor5}0.55&cellcolor{tempcolor6}color{white}0.80&cellcolor{tempcolor6}color{white}0.79&cellcolor{tempcolor4}color{white}0.72&cellcolor{tempcolor2}color{white}0.74&cellcolor{tempcolor2}color{white}0.76&cellcolor{tempcolor6}color{white}0.80 
hline
end{tabular}

end{table}


end{document}