Table for Honey Bee Colony Collapse

Question

My code is a disaster. I would really appreciate help with getting a table with a title, three columns, five rows, and the following specifications.

Title, horizontally centered and on two lines:

Pathogen Occurrence in Honey Bee Colonies with and

   `without Colony Collapse Disorder`

First row: nothing occupies first column, and text spans second and third columns in two lines.

(blank) | Percent of colonies affected by

(blank) | ..........pathogen............

Second row: Text in each column; the text in second and third columns are typeset on three lines and horizontally centered on each line.

.............. | ..Colonies with.. | Colonies without

Pathogen | colony collapse | colony collapse

.............. | ....disorder.... | ....disorder....

(The dots are only for the post to horizontally center the text.)

In the remaining rows, I would like the % aligned. I would also like a darker vertical line separating the pathogens in the first column from the percentages in the second and third columns. I think using V(3) as an option of the tabular environment.

\documentclass{amsart}

\usepackage{makecell}
\usepackage{boldline}
\setcellgapes{3pt}

\begin{document}

\begin{center}
\begin{tabular}{|| l | c | c||} \hline
%\multicolumn{3}{|| c ||}{\textbf{Pathogen Occurence in Honey Bee Colonies with and}}
%                               without Colony Collapse Disorder}} \\ \hline
%& \multicolumn{2}{ c ||}{%
%                    \begin{tabular}{@{}c@{}}
%                    Percentage of colonies affected by\\
%                    pathogen
%                    \end{tabular}%
%                  } \\ \cline{2-3}
Viruses                             &           &   \\
\hspace*{1em}IAPV                   &   83\%    &   5\% \\
\hspace*{1em}KBV                    &   100\%   &   76\% \\ \hline
Fungi                               &           &   \\ \hline
\hspace*{1em}{\em Nosema apis}      &   90\%    &   48\% \\
\hspace*{1em}{\em Nosema ceranae}   &   100\%   &   81\% \\ \hline
All Four Pathogens                  &   83\%    &   0\% \\ \hline
\end{tabular}
\end{center}

\end{document}

Answer 1

i would design your table like this:

addendum:

as response to edited question and comments below. it is based on guessing, what yo like to have:

for table environment is used threeparttable, for multi line cells are used makecells:

\documentclass{amsart}
\usepackage{booktabs, makecell, threeparttable}
\renewcommand\theadfont{\normalsize}
\renewcommand\theadgape{}
\newcommand\mcm[1]{\multicolumn{1}{c}{\makecell[tl]{#1}}}
\newcommand\mcl[1]{\multicolumn{2}{l}{#1}}
\usepackage{siunitx}

\begin{document}
\begin{threeparttable}
\centering
{Pathogen Occurrence in Honey Bee Colonies with and
 without Colony Collapse Disorder}
\medskip
\begin{tabular}{l l *{2}{S[table-format=2.0,
                           table-space-text-post={\;\%},
                           table-column-width=24mm]<{\,\%}} }
    \toprule
    &   &   \mcl{\thead{Percentage of colonies\\ 
                        affected by pathogen}}      \\
    \midrule
\mcl{Viruses}                   &   \mcl{}          \\
    &   IAPV                    &    83 &    5      \cr
    &   KBV                     &   100 &   76      \cr
    \midrule
\mcl{Pathogen}     &    \mcm{Colonies with  \\
                             colony collapse\\
                             disorder}
                        &   \mcm{Colonies without\\
                                 colony collapse \\
                                 disorder}          \\
    \midrule
\mcl{Fungi}                     &   \mcl{}          \\
    & \textit{Nosema apis}      &    90 &   48      \cr
    &   \textit{Nosema ceranae} &   100 &   81      \cr
    \midrule
\mcl{All Four Pathogens}        &    83 &    0      \cr
    \bottomrule
\end{tabular}
\end{threeparttable}
\end{document}

edit:

after last edit of question, it seems that you like to have the following looks of table (with consideration my taste what is good looking table):

(red lines indicate page layout).

note:

• demand, that can be used only tabular table environments is the very same as required to drill holes with square drill bit ...
• so, i suggest to use packages, which can make your life more relaxing and help you to design professional looks of table.
• differences between above table and previous propositions are minimal.

\documentclass{amsart}

\usepackage{caption}
\usepackage{booktabs, makecell, threeparttable}
\renewcommand\theadfont{\small}
\renewcommand\theadgape{}
\newcommand\mcm[1]{\multicolumn{1}{c}{\thead[tl]{#1}}}
\newcommand\mcl[1]{\multicolumn{2}{l}{\textbf{#1}}}
\usepackage{siunitx}

%-------------------------------- show page layout, only for test
\usepackage{showframe}
\renewcommand\ShowFrameLinethickness{0.15pt}
\renewcommand*\ShowFrameColor{\color{red}}
%---------------------------------------------------------------%

\begin{document}
\begin{center}
\begin{threeparttable}
\captionsetup{skip=1ex, margin=11mm, justification=centering}
\caption*{Pathogen Occurrence in Honey Bee Colonies with and
without Colony Collapse Disorder}
\begin{tabular}{l l *{2}{S[table-format=2.0,
                           table-space-text-post={\;\%},
                           table-column-width=24mm]<{\,\%}} }
    \toprule
\mcl{Pathogen}     &    \mcm{Percentage affected in \\
                             colonies with colony   \\
                             collapse disorder}
                        &   \mcm{Percentage affected in \\
                                 colonies without colony\\
                                 collapse disorder}          \\
    \midrule
\mcl{Viruses}                   &   \mcl{}                          \\
    &   IAPV                    &    83 &    5                      \cr
    &   KBV                     &   100 &   76                      \cr
    \midrule
\mcl{Fungi}                     &   \mcl{}                          \\
    & \textit{Nosema apis}      &    90 &   48                      \cr
    &   \textit{Nosema ceranae} &   100 &   81                      \cr
    \midrule
\mcl{All Four Pathogens}        &    83 &    0                      \cr
    \bottomrule
\end{tabular}
\end{threeparttable}
\end{center}
\end{document}

• if you like to have table with vertical lines -- what i strongly dissuade -- than just add | in column specification, where you like to have them, remove package booktabs from preamble and replace \toprule, \midrule and \bottomrule with \hline and after some tweaks obtain:

\documentclass{amsart}

\usepackage{caption}
\usepackage{threeparttable}
\newcommand\mcl[1]{\multicolumn{2}{l|}{\textbf{#1}}}
\usepackage{siunitx}

%-------------------------------- show page layout, only for test
\usepackage{showframe}
\renewcommand\ShowFrameLinethickness{0.15pt}
\renewcommand*\ShowFrameColor{\color{red}}
%---------------------------------------------------------------%

\begin{document}
\begin{center}
\begin{threeparttable}
\captionsetup{skip=1ex, margin=11mm, justification=centering}
\sisetup{table-format=2.0,
         table-space-text-post={\;\%},
         table-column-width=24mm
         }
\renewcommand\arraystretch{1.2}
\caption*{Pathogen Occurrence in Honey Bee Colonies with and
without Colony Collapse Disorder}
\begin{tabular}{l l | S<{\,\%} | S<{\,\%} }
    \hline
\mcl{Pathogen}     &    \multicolumn{1}{p{33mm}|}{\centering
                            Percentage affected in  
                            colonies with colony    
                            collapse disorder}
                        &   \multicolumn{1}{p{33mm}}{\centering
                                Percentage affected in  
                                colonies without colony 
                                collapse disorder}                  \\
    \hline
\mcl{Viruses}                   &   \multicolumn{1}{c|}{}       
                                    &   \multicolumn{1}{c}{}        \\
    &   IAPV                    &    83 &    5                      \cr
    &   KBV                     &   100 &   76                      \cr
    \hline
\mcl{Fungi}                     &   \multicolumn{1}{c|}{}
                                    &   \multicolumn{1}{c}{}        \\
    & \textit{Nosema apis}      &    90 &   48                      \cr
    & \textit{Nosema ceranae}   &   100 &   81                      \cr
    \hline
\mcl{All Four Pathogens}        &    83 &    0                      \cr
\end{tabular}
\end{threeparttable}
\end{center}
\end{document}

Answer 2

Those are my suggestions (and if you don't like them... well, I have others, as Groucho would have said):

It is not clear if you are against the ordinary numbered \caption{} in a table float but usually there are little reasons to do not in this way.

Use the caption package to change the default caption format.

You can use \centering instead of center environment to avoid vertical empty spaces.

As you are not in two column mode, there are no reason to use only three columns forcing two more rows.

I strongly advise against vertical rules in tables. Elegant journals never use Excel-like tables.

Also against irrelevant headers. With a caption about of the "Pathogen Occurrence in Honey Bee Colonies" and one column of pathogens and two columns of percentages with the % symbol in each cell, Two header to explain where are the "Pathogens" and where the "Percentages of colonies" is rather superfluous. Always consider simply your table as far as possible. Easier to construct, easier to read and easier to understand.

To align percentages without r columns you can use the siunitx package.

Off-topic: Microsporidia have been considered inside Fungi for more than two decades, but now are (again) within Protozoa (see Ruggiero et al., 2015).

\documentclass{amsart}
\usepackage{booktabs,tabulary,siunitx,caption}
\captionsetup{justification=centering}
\begin{document}
\begin{table}
\centering
\caption{Pathogen Occurrence in Honey Bee Colonies with 
         and without Colony Collapse Disorder (CCD).} 

\begin{tabular}{
llS[table-format = 2.0]<{{\si{ \percent} }}
  S[table-format = 2.0]<{{\si{ \percent} }}} 
\toprule
 &   &  \multicolumn{1}{c}{With CCD} & \multicolumn{1}{c}{Without CCD} \\
\midrule                                      
Viruses  & IAPV                   &   83    &  5 \cr
         & KBV                    &   100   & 76 \cr
\addlinespace[1ex]
Protozoa & {\em Nosema apis}      &    90   & 48 \cr
         & {\em Nosema ceranae}   &   100   & 81 \cr 
\midrule    
\multicolumn{2}{l}{All Four Pathogens}  &   83 &  0 \cr
\bottomrule 
\end{tabular}
\end{table}
\end{document}

Answer 3

Based on your description it seems you want a table like the first one below. However, as Zarko mentioned I think reformatting it to perhaps something like the second one below would be a good idea.

The code for the centered fixed length columns comes from lockstep's answer to How to create fixed width table columns with text raggedright/centered/raggedleft?

Code:

\documentclass{amsart}

\usepackage{array}
\newcolumntype{C}[1]{>{\centering\let\newline\\\arraybackslash\hspace{0pt}}m{#1}}

\begin{document}

\begin{center}
\begin{tabular}{l||c|c}
\multicolumn{3}{c}{Pathogen Occurrence in Honey Bee Colonies with and}\\
\multicolumn{3}{c}{without Colony Collapse Disorder}\\
&\multicolumn{2}{c}{Percent of colonies affected by}\\
&\multicolumn{2}{c}{pathogen}\\
&Colonies with&Colonies without\\
Pathogen&colony collapse&colony collapse\\
&disorder&disorder\\
Viruses                             &           &   \\
\hspace*{1em}IAPV                   &   83\%    &   5\% \\
\hspace*{1em}KBV                    &   100\%   &   76\% \\ \hline
Fungi                               &           &   \\ \hline
\hspace*{1em}{\em Nosema apis}      &   90\%    &   48\% \\
\hspace*{1em}{\em Nosema ceranae}   &   100\%   &   81\% \\ \hline
All Four Pathogens                  &   83\%    &   0\% \\ \hline
\end{tabular}
%%%%%%%%%%%
\vskip .5 in
%%%%%%%%%%%
\begin{tabular}{l||rr}
\multicolumn{3}{c}{\textbf{Pathogen Occurrence in Honey Bee Colonies with and}}\\
\multicolumn{3}{c}{\textbf{without Colony Collapse Disorder}}\\
\multicolumn{3}{c}{}\\
\textbf{Pathogen}&\multicolumn{1}{C{1.5in}}{\textbf{\% affected in colonies with colony collapse disorder}}&\multicolumn{1}{C{1.75in}}{\textbf{\% affected in colonies without colony collapse disorder}}\\\hline\hline

\textbf{Viruses}                                    &                       &               \\
\hspace*{1em}IAPV                       &   83\%            &   5\%         \\
\hspace*{1em}KBV                        &   100\%           &   76\%        \\ 
\textbf{Fungi}                                      &                       &               \\
\hspace*{1em}{\em Nosema apis}          &   90\%            &   48\%        \\
\hspace*{1em}{\em Nosema ceranae}       &   100\%           &   81\%        \\ \hline
\textbf{All Four Pathogens}                     &   \textbf{83\%}   &   \textbf{0\%}    \\ 
\end{tabular}
\end{center}
\end{document}

Which yields:

EDIT:

Code:

\documentclass{amsart}

\usepackage{array}
\newcolumntype{C}[1]{>{\centering\let\newline\\\arraybackslash\hspace{0pt}}m{#1}}

\begin{document}

\begin{center}
\begin{tabular}{l||r|r}
\hline
\multicolumn{3}{c}{\textbf{Pathogen Occurrence in Honey Bee Colonies with and}}\\
\multicolumn{3}{c}{\textbf{without Colony Collapse Disorder}}\\\hline\hline
\textbf{Pathogen}&\multicolumn{1}{C{1.5in}|}{\textbf{\% affected in colonies with colony collapse disorder}}&\multicolumn{1}{C{1.75in}}{\textbf{\% affected in colonies without colony collapse disorder}}\\\hline

\textbf{Viruses}                                    &                       &               \\
\hspace*{1em}IAPV                       &   83\%            &   5\%         \\
\hspace*{1em}KBV                        &   100\%           &   76\%        \\ \hline
\textbf{Fungi}                                      &                       &               \\
\hspace*{1em}{\em Nosema apis}          &   90\%            &   48\%        \\
\hspace*{1em}{\em Nosema ceranae}       &   100\%           &   81\%        \\ \hline
\textbf{All Four Pathogens}                     &   \textbf{83\%}   &   \textbf{0\%}    \\ 
\hline
\end{tabular}
\end{center}
\end{document}

Yields: