snail_mesocosm.tex

\documentclass[10,portrait]{article}
\usepackage{lmodern}
\usepackage{amssymb,amsmath}
\usepackage{ifxetex,ifluatex}
\usepackage{fixltx2e} % provides \textsubscript
\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
  \usepackage[T1]{fontenc}
  \usepackage[utf8]{inputenc}
\else % if luatex or xelatex
  \ifxetex
    \usepackage{mathspec}
  \else
    \usepackage{fontspec}
  \fi
  \defaultfontfeatures{Ligatures=TeX,Scale=MatchLowercase}
\fi
% use upquote if available, for straight quotes in verbatim environments
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
% use microtype if available
\IfFileExists{microtype.sty}{%
\usepackage[]{microtype}
\UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
}{}
\PassOptionsToPackage{hyphens}{url} % url is loaded by hyperref
\usepackage[unicode=true]{hyperref}
\PassOptionsToPackage{usenames,dvipsnames}{color} % color is loaded by hyperref
\hypersetup{
            pdftitle={Mesocosm experiment plots},
            colorlinks=true,
            linkcolor=blue,
            citecolor=red,
            urlcolor=blue,
            breaklinks=true}
\urlstyle{same}  % don't use monospace font for urls
\usepackage[margin=1in]{geometry}
\usepackage[]{biblatex}
\usepackage{color}
\usepackage{fancyvrb}
\newcommand{\VerbBar}{|}
\newcommand{\VERB}{\Verb[commandchars=\\\{\}]}
\DefineVerbatimEnvironment{Highlighting}{Verbatim}{commandchars=\\\{\}}
% Add ',fontsize=\small' for more characters per line
\usepackage{framed}
\definecolor{shadecolor}{RGB}{248,248,248}
\newenvironment{Shaded}{\begin{snugshade}}{\end{snugshade}}
\newcommand{\KeywordTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{\textbf{#1}}}
\newcommand{\DataTypeTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{#1}}
\newcommand{\DecValTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
\newcommand{\BaseNTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
\newcommand{\FloatTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
\newcommand{\ConstantTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
\newcommand{\CharTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
\newcommand{\SpecialCharTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
\newcommand{\StringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
\newcommand{\VerbatimStringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
\newcommand{\SpecialStringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
\newcommand{\ImportTok}[1]{#1}
\newcommand{\CommentTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textit{#1}}}
\newcommand{\DocumentationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
\newcommand{\AnnotationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
\newcommand{\CommentVarTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
\newcommand{\OtherTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{#1}}
\newcommand{\FunctionTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
\newcommand{\VariableTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
\newcommand{\ControlFlowTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{\textbf{#1}}}
\newcommand{\OperatorTok}[1]{\textcolor[rgb]{0.81,0.36,0.00}{\textbf{#1}}}
\newcommand{\BuiltInTok}[1]{#1}
\newcommand{\ExtensionTok}[1]{#1}
\newcommand{\PreprocessorTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textit{#1}}}
\newcommand{\AttributeTok}[1]{\textcolor[rgb]{0.77,0.63,0.00}{#1}}
\newcommand{\RegionMarkerTok}[1]{#1}
\newcommand{\InformationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
\newcommand{\WarningTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
\newcommand{\AlertTok}[1]{\textcolor[rgb]{0.94,0.16,0.16}{#1}}
\newcommand{\ErrorTok}[1]{\textcolor[rgb]{0.64,0.00,0.00}{\textbf{#1}}}
\newcommand{\NormalTok}[1]{#1}
\usepackage{graphicx,grffile}
\makeatletter
\def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
\def\maxheight{\ifdim\Gin@nat@height>\textheight\textheight\else\Gin@nat@height\fi}
\makeatother
% Scale images if necessary, so that they will not overflow the page
% margins by default, and it is still possible to overwrite the defaults
% using explicit options in \includegraphics[width, height, ...]{}
\setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio}
\usepackage[normalem]{ulem}
% avoid problems with \sout in headers with hyperref:
\pdfstringdefDisableCommands{\renewcommand{\sout}{}}
\IfFileExists{parskip.sty}{%
\usepackage{parskip}
}{% else
\setlength{\parindent}{0pt}
\setlength{\parskip}{6pt plus 2pt minus 1pt}
}
\setlength{\emergencystretch}{3em}  % prevent overfull lines
\providecommand{\tightlist}{%
  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
\setcounter{secnumdepth}{0}
% Redefines (sub)paragraphs to behave more like sections
\ifx\paragraph\undefined\else
\let\oldparagraph\paragraph
\renewcommand{\paragraph}[1]{\oldparagraph{#1}\mbox{}}
\fi
\ifx\subparagraph\undefined\else
\let\oldsubparagraph\subparagraph
\renewcommand{\subparagraph}[1]{\oldsubparagraph{#1}\mbox{}}
\fi

% set default figure placement to htbp
\makeatletter
\def\fps@figure{htbp}
\makeatother


\title{Mesocosm experiment plots}
\author{Matthew Malishev\textsuperscript{1}* \& David Civitello
\textsuperscript{1}\\[2\baselineskip]\emph{\textsuperscript{1}
Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta,
GA, USA, 30322}}
\date{}

\begin{document}
\maketitle

{
\hypersetup{linkcolor=black}
\setcounter{tocdepth}{3}
\tableofcontents
}
~

Date: 2018-08-17\\
R version: 3.5.0\\
Corresponding author:
\href{mailto:matthew.malishev@gmail.com}{\nolinkurl{matthew.malishev@gmail.com}}\\
This document can be found at
\url{https://github.com/darwinanddavis/SchistoMesocosm}

\newpage  

\textbf{Follow instructions in code chunks labelled `fileoutput' to
toggle pdf of plots saved to directory on/off
(`Size\_per\_tank\_over\_time.pdf')}

~

\paragraph{TO DO}\label{to-do}

\begin{itemize}
\tightlist
\item
  How much of the population does the sampling effort capture?
\item
  \sout{Scale diameter densities per tank over time to upper limit of
  each tank (set ylim to highest value for each tank)}\\
\item
  Scale diameter densities per tank over time to upper limit of all
  tanks (set ylim to highest value for all tanks)\\
\item
  Split plots by line color code showing point where snails are
  reproductive viable (8 mm and above).
\item
  Which tanks and conditions reach reproductive size?\\
\item
  \sout{Replot by size class and resource combo e.g.~low resources and
  small size class v low resources and large size class}
\end{itemize}

\subsection{Overview}\label{overview}

This document uses the schisto mesocosm 2016 data to explore cercariae
production from snail hosts of different body sizes (diameter in mm and
mass in mg) over a 14 week period under high and low N/P nutrient
conditions. Host reproduction (egg masses) is also calculated.

\subsubsection{Install dependencies}\label{install-dependencies}

\subsubsection{Get data}\label{get-data}

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{wd <-}\StringTok{ }\NormalTok{params}\OperatorTok{$}\NormalTok{dir }\CommentTok{# working dir is set in yaml header}
\KeywordTok{setwd}\NormalTok{(}\KeywordTok{paste0}\NormalTok{(wd,}\StringTok{"/"}\NormalTok{))}
\NormalTok{f <-}\StringTok{ "meso1_.csv"}
\NormalTok{f2 <-}\StringTok{ "meso2_.csv"} 
\end{Highlighting}
\end{Shaded}

\subsubsection{Load data}\label{load-data}

\begin{verbatim}
'data.frame':   720 obs. of  13 variables:
 $ Tank                : int  1 2 3 4 5 6 7 8 9 10 ...
 $ NP                  : chr  "High" "Low" "Low" "High" ...
 $ Size                : chr  "Small" "Intermediate" "Intermediate" "Small" ...
 $ Schisto             : chr  "No" "Yes" "Yes" "Yes" ...
 $ Week                : int  0 0 0 0 0 0 0 0 0 0 ...
 $ Snail               : int  60 60 60 60 60 60 60 60 60 60 ...
 $ Total_Biomass       : num  96 620.6 670.5 86.7 121.4 ...
 $ Cercarial_production: int  0 0 0 0 0 0 0 0 0 0 ...
 $ Infected_abundance  : int  0 0 0 0 0 0 0 0 0 0 ...
 $ Sampling_Effort     : int  NA NA NA NA NA NA NA NA NA NA ...
 $ Eggs                : int  NA NA NA NA NA NA NA NA NA NA ...
 $ Phyto_F             : num  NA NA NA NA NA NA NA NA NA NA ...
 $ Peri_F              : num  NA NA NA NA NA NA NA NA NA NA ...
\end{verbatim}

\subsubsection{Set plotting graphics}\label{set-plotting-graphics}

Set plotting parameters

Get only infected snails

\begin{center}\rule{0.5\linewidth}{\linethickness}\end{center}

~

\textbf{Mesocosm 1 data sheet}

\subsubsection{Snail size per tank}\label{snail-size-per-tank}

Shell diameter (mm) per tank\\
\includegraphics{snail_mesocosm_files/figure-latex/unnamed-chunk-10-1.pdf}

\begin{verbatim}

    Welch Two Sample t-test

data:  Diameter and Tank
t = -292.67, df = 54609, p-value < 2.2e-16
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 -19.45879 -19.19989
sample estimates:
mean of x mean of y 
 5.821956 25.151292 
\end{verbatim}

\subsubsection{Snail diameter (mm)
distribution}\label{snail-diameter-mm-distribution}

\includegraphics{snail_mesocosm_files/figure-latex/unnamed-chunk-11-1.pdf}
\includegraphics{snail_mesocosm_files/figure-latex/unnamed-chunk-11-2.pdf}

\begin{verbatim}
  xchar= 0.9529 ; (yextra,ychar)= -0.004785 0.004785 
  points2( 29.8 29.8 , 0.1 0.09522 , pch= 20 20 , ...) 
\end{verbatim}

\subsubsection{Snail size over time
(weeks)}\label{snail-size-over-time-weeks}

Shell diameter (mm) over time (weeks)\\
\textasciitilde{}1000 eggs inoculated at 0,2,4,6 weeks
\includegraphics{snail_mesocosm_files/figure-latex/unnamed-chunk-12-1.pdf}

\subsubsection{Snail size over time (weeks) per
tank}\label{snail-size-over-time-weeks-per-tank}

\textbf{For all tanks (n = 48), see `Size\_per\_tank\_over\_time.pdf' ~
in /Users/malishev/Documents/Emory/research/mesocosm}

~ \textasciitilde{}1000 eggs inoculated at 0,2,4,6 weeks

Select tank. Max 48

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{tank <-}\StringTok{ }\DecValTok{12} \CommentTok{# Select tank #. Max 48   }
\KeywordTok{paste0}\NormalTok{(}\StringTok{"Tank "}\NormalTok{,tank) }
\end{Highlighting}
\end{Shaded}

\begin{verbatim}
[1] "Tank 12"
\end{verbatim}

\includegraphics{snail_mesocosm_files/figure-latex/unnamed-chunk-15-1.pdf}

\subsubsection{Snail size over time (weeks) per tank (High
resources)}\label{snail-size-over-time-weeks-per-tank-high-resources}

~ \textbf{See ``Size\_per\_tank\_over\_time\_HIGH.pdf'' ~ in
/Users/malishev/Documents/Emory/research/mesocosm}

\subsubsection{Snail size over time (weeks) per tank (Low
resources)}\label{snail-size-over-time-weeks-per-tank-low-resources}

~ \textbf{See ``Size\_per\_tank\_over\_time\_LOW.pdf'' ~ in
/Users/malishev/Documents/Emory/research/mesocosm}

\subsubsection{Large snails over time (weeks) per tank (High
resources)}\label{large-snails-over-time-weeks-per-tank-high-resources}

~ \textbf{See ``Size\_per\_tank\_over\_time\_HIGH\_LARGE.pdf'' ~ in
/Users/malishev/Documents/Emory/research/mesocosm}

\subsubsection{Large snails over time (weeks) per tank (low
resources)}\label{large-snails-over-time-weeks-per-tank-low-resources}

~ \textbf{See ``Size\_per\_tank\_over\_time\_LOW\_LARGE.pdf'' ~ in
/Users/malishev/Documents/Emory/research/mesocosm}

\subsubsection{Small snails over time (weeks) per tank (High
resources)}\label{small-snails-over-time-weeks-per-tank-high-resources}

~ \textbf{See ``Size\_per\_tank\_over\_time\_HIGH\_SMALL.pdf'' ~ in
/Users/malishev/Documents/Emory/research/mesocosm}

\subsubsection{Small snails over time (weeks) per tank (low
resources)}\label{small-snails-over-time-weeks-per-tank-low-resources}

~ \textbf{See ``Size\_per\_tank\_over\_time\_LOW\_SMALL.pdf'' ~ in
/Users/malishev/Documents/Emory/research/mesocosm}

\subsubsection{Body mass (mg) over time
(weeks)}\label{body-mass-mg-over-time-weeks}

(Soft tissue dry mass in mg = 0.0096 * Diameter{[}in mm{]}\^{}3)\\
\textasciitilde{}1000 eggs inoculated at 0,2,4,6 weeks

\includegraphics{snail_mesocosm_files/figure-latex/unnamed-chunk-16-1.pdf}

\begin{verbatim}
# A tibble: 1 x 2
  Biomass Cercariae
*   <dbl>     <int>
1    245.         0
\end{verbatim}

\textbf{Without max value of \texttt{as.numeric(outer){[}1{]}}}

\includegraphics{snail_mesocosm_files/figure-latex/unnamed-chunk-18-1.pdf}

\subsubsection{Snail size and number of cercariae
produced}\label{snail-size-and-number-of-cercariae-produced}

Point size by cercariae number\\
\includegraphics{snail_mesocosm_files/figure-latex/unnamed-chunk-19-1.pdf}
Linear log

\subsubsection{Snail mass and cercariae produced
(mg)}\label{snail-mass-and-cercariae-produced-mg}

\includegraphics{snail_mesocosm_files/figure-latex/unnamed-chunk-21-1.pdf}

\subsubsection{Snail size per tank}\label{snail-size-per-tank-1}

Shell diameter (mm)\\
Select tank. Max 48

\begin{verbatim}
[1] "Tank 24"
\end{verbatim}

\includegraphics{snail_mesocosm_files/figure-latex/unnamed-chunk-23-1.pdf}

\subsubsection{Cercariae production over
time}\label{cercariae-production-over-time}

Cercariae shed over 90 mins per week\\
\textasciitilde{}1000 eggs inoculated at 0,2,4,6 weeks\\
Snail abundance over time (weeks)\\
\includegraphics{snail_mesocosm_files/figure-latex/unnamed-chunk-24-1.pdf}

\subsubsection{Tank cercariae production over time per
tank}\label{tank-cercariae-production-over-time-per-tank}

Select tank. Max 48

\begin{verbatim}
[1] "Tank 24"
\end{verbatim}

\begin{verbatim}
[1] 2300
\end{verbatim}

\includegraphics{snail_mesocosm_files/figure-latex/unnamed-chunk-26-1.pdf}

\newpage    

\textbf{Mesocosm 2 data sheet}

\subsubsection{Egg mass distribution}\label{egg-mass-distribution}

\includegraphics{snail_mesocosm_files/figure-latex/unnamed-chunk-27-1.pdf}

\subsubsection{N/P concentration v egg
mass}\label{np-concentration-v-egg-mass}

\includegraphics{snail_mesocosm_files/figure-latex/unnamed-chunk-28-1.pdf}

\subsubsection{Phyto and Peri
Distribution}\label{phyto-and-peri-distribution}

phyto = flourescence units\\
peri = flourescence per 2 weeks / 3.5 inch\^{}2 tile (gross productivity
biomass rate)\\
\includegraphics{snail_mesocosm_files/figure-latex/unnamed-chunk-29-1.pdf}

\subsubsection{Egg Mass over time v presence of
schisto}\label{egg-mass-over-time-v-presence-of-schisto}

\textasciitilde{}1000 eggs inoculated at 0,2,4,6 weeks

\includegraphics{snail_mesocosm_files/figure-latex/unnamed-chunk-30-1.pdf}

\subsubsection{Size class vs Egg mass (with
schisto)}\label{size-class-vs-egg-mass-with-schisto}

\includegraphics{snail_mesocosm_files/figure-latex/unnamed-chunk-31-1.pdf}

\begin{verbatim}
  xchar= 4.765 ; (yextra,ychar)= -0.001435 0.001435 
  points2( 141.7 141.7 141.7 , 0.03072 0.02928 0.02785 , pch= 20 20 20 , ...) 
\end{verbatim}

\subsubsection{Egg Mass over time
(weeks)}\label{egg-mass-over-time-weeks}

\textasciitilde{}1000 eggs inoculated at 0,2,4,6 weeks

\includegraphics{snail_mesocosm_files/figure-latex/unnamed-chunk-32-1.pdf}
\includegraphics{snail_mesocosm_files/figure-latex/unnamed-chunk-32-2.pdf}
\includegraphics{snail_mesocosm_files/figure-latex/unnamed-chunk-32-3.pdf}

\printbibliography

\end{document}