raab/tracking_raab2018
1
0
Fork 0
Code Issues Pull Requests Releases Wiki Activity

tex file created

Browse Source
This commit is contained in:
tillraab 2018-09-24 13:42:21 +02:00
parent e2ce32ed2b
commit 191598ec4e
20 changed files with 2186 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

BIN
tex/1.pdf Normal file
View File

Binary file not shown.

BIN
tex/10.pdf Normal file
View File

Binary file not shown.

BIN
tex/12.pdf Normal file
View File

Binary file not shown.

BIN
tex/2.pdf Normal file
View File

Binary file not shown.

BIN
tex/3.pdf Normal file
View File

Binary file not shown.

BIN
tex/4.pdf Normal file
View File

Binary file not shown.

BIN
tex/6.pdf Normal file
View File

Binary file not shown.

BIN
tex/7.pdf Normal file
View File

Binary file not shown.

BIN
tex/8.pdf Normal file
View File

Binary file not shown.

BIN
tex/9.pdf Normal file
View File

Binary file not shown.

58
tex/Makefile Normal file
View File

@ -0,0 +1,58 @@
TEXBASE=main
TEXFILE=$(TEXBASE).tex
PDFFILE=$(TEXBASE).pdf
REVISION=64c64649d6eb373dea5b0a7c35a9a5fb8fc173f6
TODAYREV=$(shell git log | grep -A 5 "`date | sed -e 's/ / /g; s/..:..:.. .* /.* /'`" | sed -n -e '/^commit/{s/^commit //; p}' | tail -n 1)
all: bib
bib: $(TEXBASE).bbl
$(TEXBASE).bbl: $(TEXFILE)
pdflatex $(TEXFILE)
bibtex $(TEXBASE)
pdflatex $(TEXFILE)
pdflatex $(TEXFILE)
pdflatex $(TEXFILE)
@echo
@echo "BibTeX log:"
@sed -n -e '1,/You.ve used/p' $(TEXBASE).blg
pdf: $(PDFFILE)
$(PDFFILE) : $(TEXFILE)
pdflatex -interaction=scrollmode $< | tee /dev/stderr | fgrep -q "Rerun to get cross-references right" && pdflatex -interaction=scrollmode $< || true
again :
pdflatex $(TEXFILE)
diffrev :
#latexdiff-git -r $(REVISION) --pdf $(TEXFILE)
latexdiff-git -r $(REVISION) $(TEXFILE)
-pdflatex $(TEXBASE)-diff$(REVISION)
-bibtex $(TEXBASE)-diff$(REVISION)
-pdflatex $(TEXBASE)-diff$(REVISION)
-pdflatex $(TEXBASE)-diff$(REVISION)
-pdflatex $(TEXBASE)-diff$(REVISION)
mv $(TEXBASE)-diff$(REVISION).pdf $(TEXBASE)-diff.pdf
rm $(TEXBASE)-diff$(REVISION).*
difftoday :
latexdiff-git -r $(TODAYREV) --pdf $(TEXFILE)
mv $(TEXBASE)-diff$(TODAYREV).pdf $(TEXBASE)-diff.pdf
rm $(TEXBASE)-diff$(TODAYREV).*
echo $(TODAYREV)
diff :
-latexdiff-git -r --pdf $(TEXFILE)
rm $(TEXBASE)-diff.tex $(TEXBASE)-diff.blg $(TEXBASE)-diff.out
watchpdf :
while true; do ! make -q pdf && make pdf; sleep 0.5; done
clean:
rm -rf auto *~ *.aux *.blg *.bbl *.dvi *.log *.out
cleanall: clean
rm -f $(PDFFILE)

55
tex/main.aux Normal file
View File

@ -0,0 +1,55 @@
\relax
\providecommand\hyper@newdestlabel[2]{}
\providecommand\HyperFirstAtBeginDocument{\AtBeginDocument}
\HyperFirstAtBeginDocument{\ifx\hyper@anchor\@undefined
\global\let\oldcontentsline\contentsline
\gdef\contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}}
\global\let\oldnewlabel\newlabel
\gdef\newlabel#1#2{\newlabelxx{#1}#2}
\gdef\newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}}
\AtEndDocument{\ifx\hyper@anchor\@undefined
\let\contentsline\oldcontentsline
\let\newlabel\oldnewlabel
\fi}
\fi}
\global\let\hyper@last\relax
\gdef\HyperFirstAtBeginDocument#1{#1}
\providecommand\HyField@AuxAddToFields[1]{}
\providecommand\HyField@AuxAddToCoFields[2]{}
\babel@aux{english}{}
\@writefile{toc}{\contentsline {section}{Introduction}{1}{section*.1}}
\@writefile{toc}{\contentsline {section}{Materials and Methods}{1}{section*.2}}
\@writefile{toc}{\contentsline {subsection}{Field site}{1}{subsection*.3}}
\@writefile{toc}{\contentsline {subsection}{Field monitiring system}{1}{subsection*.4}}
\@writefile{toc}{\contentsline {subsection}{Extraction on EOD frequencies}{2}{subsection*.5}}
\@writefile{toc}{\contentsline {subsection}{Tracking of individual EODs}{2}{subsection*.6}}
\@writefile{toc}{\contentsline {subsubsection}{$\Delta $-EODf (Electric organ discharge frequency difference)}{2}{subsubsection*.7}}
\@writefile{lof}{\contentsline {figure}{\numberline {1}{\ignorespaces Random caption\relax }}{2}{figure.caption.8}}
\providecommand*\caption@xref[2]{\@setref\relax\@undefined{#1}}
\newlabel{dEODf}{{1}{2}{Random caption\relax }{figure.caption.8}{}}
\@writefile{toc}{\contentsline {subsubsection}{$\Delta $-F (Field difference)}{2}{subsubsection*.9}}
\@writefile{lof}{\contentsline {figure}{\numberline {2}{\ignorespaces Random caption\relax }}{3}{figure.caption.10}}
\newlabel{dField}{{2}{3}{Random caption\relax }{figure.caption.10}{}}
\@writefile{toc}{\contentsline {subsubsection}{Error values composed from $\Delta $-EODf and $\Delta $-Field}{3}{subsubsection*.11}}
\@writefile{toc}{\contentsline {subsubsection}{Frequency error determination}{3}{subsubsection*.13}}
\@writefile{toc}{\contentsline {subsubsection}{Field error determination}{3}{subsubsection*.14}}
\@writefile{lof}{\contentsline {figure}{\numberline {3}{\ignorespaces Random caption\relax }}{4}{figure.caption.12}}
\newlabel{rel_errors}{{3}{4}{Random caption\relax }{figure.caption.12}{}}
\@writefile{toc}{\contentsline {subsubsection}{Total error definition}{4}{subsubsection*.15}}
\@writefile{toc}{\contentsline {subsubsection}{Assign temporal EOD frequency traces}{4}{subsubsection*.16}}
\@writefile{toc}{\contentsline {subsubsection}{Running connection}{5}{subsubsection*.19}}
\@writefile{toc}{\contentsline {section}{Results}{5}{section*.21}}
\@writefile{toc}{\contentsline {subsection}{d-EODf and d-Field of same identity signals vs. non-same identity signals}{5}{subsection*.22}}
\@writefile{toc}{\contentsline {subsection}{Roc analysis}{5}{subsection*.25}}
\@writefile{lof}{\contentsline {figure}{\numberline {4}{\ignorespaces Random caption\relax }}{6}{figure.caption.17}}
\newlabel{tmp_idents}{{4}{6}{Random caption\relax }{figure.caption.17}{}}
\@writefile{lof}{\contentsline {figure}{\numberline {5}{\ignorespaces Random caption\relax }}{7}{figure.caption.18}}
\newlabel{error_matrix}{{5}{7}{Random caption\relax }{figure.caption.18}{}}
\@writefile{lof}{\contentsline {figure}{\numberline {6}{\ignorespaces Random caption\relax }}{8}{figure.caption.20}}
\newlabel{running_connection}{{6}{8}{Random caption\relax }{figure.caption.20}{}}
\@writefile{lof}{\contentsline {figure}{\numberline {7}{\ignorespaces Random caption\relax }}{9}{figure.caption.23}}
\newlabel{Field_error_shift}{{7}{9}{Random caption\relax }{figure.caption.23}{}}
\@writefile{lof}{\contentsline {figure}{\numberline {8}{\ignorespaces Random caption\relax }}{9}{figure.caption.24}}
\newlabel{EODf_error_shift}{{8}{9}{Random caption\relax }{figure.caption.24}{}}
\@writefile{lof}{\contentsline {figure}{\numberline {9}{\ignorespaces Random caption\relax }}{10}{figure.caption.26}}
\newlabel{ROC}{{9}{10}{Random caption\relax }{figure.caption.26}{}}

0
tex/main.bbl Normal file
View File

47
tex/main.blg Normal file
View File

@ -0,0 +1,47 @@
This is BibTeX, Version 0.99d (TeX Live 2017/Debian)
Capacity: max_strings=100000, hash_size=100000, hash_prime=85009
The top-level auxiliary file: main.aux
I found no \citation commands---while reading file main.aux
I found no \bibstyle command---while reading file main.aux
You've used 0 entries,
0 wiz_defined-function locations,
84 strings with 492 characters,
and the built_in function-call counts, 0 in all, are:
= -- 0
> -- 0
< -- 0
+ -- 0
- -- 0
* -- 0
:= -- 0
add.period$ -- 0
call.type$ -- 0
change.case$ -- 0
chr.to.int$ -- 0
cite$ -- 0
duplicate$ -- 0
empty$ -- 0
format.name$ -- 0
if$ -- 0
int.to.chr$ -- 0
int.to.str$ -- 0
missing$ -- 0
newline$ -- 0
num.names$ -- 0
pop$ -- 0
preamble$ -- 0
purify$ -- 0
quote$ -- 0
skip$ -- 0
stack$ -- 0
substring$ -- 0
swap$ -- 0
text.length$ -- 0
text.prefix$ -- 0
top$ -- 0
type$ -- 0
warning$ -- 0
while$ -- 0
width$ -- 0
write$ -- 0
(There were 2 error messages)

1229
tex/main.log Normal file
View File

File diff suppressed because it is too large Load Diff

17
tex/main.out Normal file
View File

@ -0,0 +1,17 @@
\BOOKMARK [1][-]{section*.1}{Introduction}{}% 1
\BOOKMARK [1][-]{section*.2}{Materials and Methods}{}% 2
\BOOKMARK [2][-]{subsection*.3}{Field site}{section*.2}% 3
\BOOKMARK [2][-]{subsection*.4}{Field monitiring system}{section*.2}% 4
\BOOKMARK [2][-]{subsection*.5}{Extraction on EOD frequencies}{section*.2}% 5
\BOOKMARK [2][-]{subsection*.6}{Tracking of individual EODs}{section*.2}% 6
\BOOKMARK [3][-]{subsubsection*.7}{-EODf \(Electric organ discharge frequency difference\)}{subsection*.6}% 7
\BOOKMARK [3][-]{subsubsection*.9}{-F \(Field difference\)}{subsection*.6}% 8
\BOOKMARK [3][-]{subsubsection*.11}{Error values composed from -EODf and -Field}{subsection*.6}% 9
\BOOKMARK [3][-]{subsubsection*.13}{Frequency error determination}{subsection*.6}% 10
\BOOKMARK [3][-]{subsubsection*.14}{Field error determination}{subsection*.6}% 11
\BOOKMARK [3][-]{subsubsection*.15}{Total error definition}{subsection*.6}% 12
\BOOKMARK [3][-]{subsubsection*.16}{Assign temporal EOD frequency traces}{subsection*.6}% 13
\BOOKMARK [3][-]{subsubsection*.19}{Running connection}{subsection*.6}% 14
\BOOKMARK [1][-]{section*.21}{Results}{}% 15
\BOOKMARK [2][-]{subsection*.22}{d-EODf and d-Field of same identity signals vs. non-same identity signals}{section*.21}% 16
\BOOKMARK [2][-]{subsection*.25}{Roc analysis}{section*.21}% 17

BIN
tex/main.pdf Normal file
View File

Binary file not shown.

BIN
tex/main.synctex.gz Normal file
View File

Binary file not shown.

226
tex/main.tex Normal file
View File

@ -0,0 +1,226 @@
% ToDos
%
% Discussion: finish; add section on natural sensory scenes or just link to our other manuscript?
% RK: Bennett (1971) könnte was zu Amplituden von verschiedenen Arten haben.
%
% Introduction: on tracking animals in natural habitats
%
% add: references to Figures 11, 12, 13
%
% We might want to spell out that both EOD and movement activity are representative for other days we recorded? We would need to check that, though.
% DATA TODOS
%
% MAYBE
% what is the fraction of fish we captured while swimming up/downwards? did we miss many?
% -> check x and y distribution of fish tracks to see if it is skewed towards the outer curve
%
% are Apteronotus females more stationary than males?
%
% movement speeds: t-test differences between species, up and down speeds
\documentclass[11pt]{article}
\title{Random tracking title}
\author{Till Raab, ..., ..., Jan Benda}
%%%%% page style --------------------------------
\usepackage[left=20mm,right=20mm,top=20mm,bottom=20mm]{geometry}
\pagestyle{myheadings}
\usepackage{lineno}
\linenumbers
\usepackage{setspace}
% section style ---------------------------------
\usepackage[sf,bf,it,big,clearempty]{titlesec}
\setcounter{secnumdepth}{-1}
% units -----------------------------------------
\usepackage[mediumqspace,Gray,squaren]{SIunits} % \ohm, \micro
% -----------------------------------------------
\usepackage[english]{babel}
\usepackage{pslatex} % nice font for pdf file
\usepackage{xcolor}
\usepackage{graphicx}
% \usepackage[font={sf,doublespacing}]{caption}
\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}
\usepackage{textcomp}
\usepackage{array}
\usepackage{amsmath}
% figures --------------------------------------
% captions:
\usepackage[format=plain,singlelinecheck=off,labelfont=bf,font={small,sf,doublespacing}]{caption}
% put caption on separate float:
\newcommand{\breakfloat}{\end{figure}\begin{figure}[t]}
% references to panels of a figure within the caption:
\newcommand{\figitem}[1]{\textsf{\bfseries\uppercase{#1}}}
% references to panels of a figure within the text:
\newcommand{\panel}[1]{\textsf{\uppercase{#1}}}
% references to figures:
\newcommand{\fref}[1]{\textup{\ref{#1}}}
\newcommand{\subfref}[2]{\textup{\ref{#1}}\,\panel{#2}}
% references to figures in normal text:
\newcommand{\fig}{Fig.}
\newcommand{\Fig}{Figure}
\newcommand{\figs}{Figs.}
\newcommand{\Figs}{Figures}
\newcommand{\figref}[1]{\fig~\fref{#1}}
\newcommand{\Figref}[1]{\Fig~\fref{#1}}
\newcommand{\figsref}[1]{\figs~\fref{#1}}
\newcommand{\Figsref}[1]{\Figs~\fref{#1}}
\newcommand{\subfigref}[2]{\fig~\subfref{#1}{#2}}
\newcommand{\Subfigref}[2]{\Fig~\subfref{#1}{#2}}
\newcommand{\subfigsref}[2]{\figs~\subfref{#1}{#2}}
\newcommand{\Subfigsref}[2]{\Figs~\subfref{#1}{#2}}
% references to figures within brackets:
\newcommand{\figb}{Fig.}
\newcommand{\figsb}{Figs.}
\newcommand{\figrefb}[1]{\figb~\fref{#1}}
\newcommand{\figsrefb}[1]{\figsb~\fref{#1}}
\newcommand{\subfigrefb}[2]{\figb~\subfref{#1}{#2}}
\newcommand{\subfigsrefb}[2]{\figsb~\subfref{#1}{#2}}
% bibliography ----------------------------------
%\usepackage[round,colon]{natbib}
%\renewcommand{\bibsection}{\section{References}}
%\setlength{\bibsep}{0pt}
%\setlength{\bibhang}{1.5em}
%\bibliographystyle{jneurosci}
\usepackage[breaklinks=true,colorlinks=true,citecolor=blue!30!black,urlcolor=blue!30!black,linkcolor=blue!30!black]{hyperref}
% notes -----------------------------------------
\usepackage{ifthen}
\newcommand{\note}[2][]{{\itshape[\textbf{\ifthenelse{\equal{#1}{}}{}{#1: }#2]}}}
\newcommand{\notejb}[1]{\note[JB]{#1}}
\newcommand{\notejh}[1]{\note[JH]{#1}}
\newcommand{\red}[1]{\textcolor{green!70!black}{#1}}
% -----------------------------------------------
\hyphenation{mo-da-li-ties court-ship}
% -----------------------------------------------
\begin{document}
\maketitle
\begin{abstract}
work in progress
\end{abstract}
\section{Introduction}
work in progress
\section{Materials and Methods}
\subsection{Field site}
The study site was a small stream called Rio Rubiano in the Colombian part of tropical grassland plain “Los Llanos” near San Martin, Province Meta. The recording site was an easy to access part of the Rio Rubiano near the Finca Altamira (3°76’52.70”N, 73°67’53.41”W) which also served as accommodation. The river bed consists of rocks with a diameter ranging from a few to up to 50 cm and the riverbank consists mainly of soil, rocks and the roots of the surrounding vegetation. The very location the recording equipment was installed was a part of the river where the river width is approximately 9\,m and water depth is around 20\,cm (distance between water surface and stone layer on the riverbed). The temperature of the clear water of Rio Rubiano fluctuated between 23 and 27\,°C on a daily basis and showed a conductivity ranging from 2\,${\mu}$S/cm to 7\,${\mu}$S/cm. Data acquisition started in April 2016, i.e. during the start of the rainy season.
\subsection{Field monitiring system}
The recording system used to obtain our date is similar to the one used by [Henninger et al. (2018)] in the Republic of Panamá. It consists of a custom-build 64-channel electrode and amplifier system (npi electronics GmbH, Tamm, Germany) powered by 12\,V car batteries. Signals detected by the electrodes (low-noise headstages embeded in epoxy resin (1 $\times$ gain, 10 $\times$ 5 $\times$ 5\,mm)) were amplified by the main amplifier (100 $\times$ gain, 1st order high-pass filter 100\,Hz, low-pass 10\,kHz) before being digitalized with 20\,kHz per channel with 16-bit amplitude resolution using a custom build computer with two digital-analog converter cards (PCI-6259, National Instruments, Austin, Texas, USA). Data acquisition and storage for offline analysis were managed by a custom software written in C++ (https://github.com/bendalab/fishgrid). The maximum of 64 electrodes mounted on 8 PVC tubes were arranged in an 8 by 8 electrode grid (50 cm spacing) covering an area of 350$\times$350\,cm. All 64 electrodes were used throughout the whole recording period. Each PVC tube, equipped with 8 electrodes got tied to a rope crossing the river, forming a structure allowing small shifts in electrode distance but being resilient to destruction by rapidly changing environmental factors, i.e. rising water levels after heavy rainfall.
\subsection{Extraction on EOD frequencies}
\subsection{Tracking of individual EODs}
In order to track individual EOD frequency traces for each individual recorded we developed an algorithm based on Python3 using two independent signal variables to reliable assign EOD frequency traces.
\subsubsection{$\Delta$-EODf (Electric organ discharge frequency difference)}
\begin{figure}[h!]
\centerline{\includegraphics[width=1.\linewidth]{3}}
\caption{\label{dEODf} Random caption}
\end{figure}
Since, the EOD frequency of wave-type weakly electric fish represent on of the most stable oscillating signals known across natural systems and, thus, keeps stable for long periods of time it seems unambiguous to use this signal parameter as main tracking criterion. However, tracking individual EOD frequencies over long periods of time gives rise to further challenges. When wave-type weakly electric fish produce communication signals, such as EOD frequency rises, EOD frequency traces of different individuals frequently cross each other, sometimes multiple times within a short time window. This specially occurs in larger groups of wave-type weakly electric fish. These EOD frequency trace crossings give rise to several algorithmic problems. First, detecting both peaks during the Powerspectrum analysis in the very moment of the EOD frequency traces crossing often fails resulting in missing datapoints for one EOD frequency trace. As a result, correct tracking of EOD frequency traces, only based on EOD frequency comparison, is at chance level during these crossing events.
\subsubsection{$\Delta$-F (Field difference)}
\begin{figure}[h!]
\centerline{\includegraphics[width=1.\linewidth]{9}}
\caption{\label{dField} Random caption}
\end{figure}
To address EOD frequency tracking errors arising from crossing EOD frequency traces, e.g. during the events of EOD frequency rises, we use the individual absolute fields properties as second tracking parameter. Due to our multi electrode recoding setup we are able to estimate the strength of each individual EOD signal at multiple locations within our electrode-grid by extracting the power of the according EOD frequency in the Powerspectrum of each electrode. These two-dimensional representations of the electric fields vary between individuals depending on their very location within the electrode-grid. After normalizing the individual electric fields to eliminate the impact of absolute field strength the obtained field proportions can be used as a second tracking parameter by calculation of the difference between two field proportions using the mean-square-error of different field proportions.
\subsubsection{Error values composed from $\Delta$-EODf and $\Delta$-Field}
The simple comparison of EOD frequency difference and field structure difference is not sufficient to determine the likelihood of two signals originating from the same individual. Therefore, relative EOD frequency errors and relative field errors, both ranging between 0 and 1, are calculated.
\begin{figure}[h!]
\centerline{\includegraphics[width=1.\linewidth]{10}}
\caption{\label{rel_errors} Random caption}
\end{figure}
\subsubsection{Frequency error determination}
With respect to EOD frequency differences we assume EOD frequency differences of above 1 Hz to be equally unlike to originate from the same individual and, thus, result in the maximum relative EOD frequency error. EOD frequencies below 1 Hz result in smaller relative EOD frequency errors and are calculated from a Boltzmann-function resulting in smaller relative EOD frequency difference the lower the real EOD frequency difference is.
\subsubsection{Field error determination}
Considering the difference in field structure the absolute field structure errors are highly dependent on the amount of electrodes used in the recording setup. Therefore, to estimate the relative field structure error we first estimate the distribution of possible field structure errors in a 30 seconds window around the currently datapoints of interest. These possible field structure errors are define as those field structures with a smaller EOD frequency difference than 10 Hz. Deducted from the distribution of possible field structure differences the relative field structure difference of two field structures is the proportion of smaller field structure differences in the distribution of possible field structure differences.
\subsubsection{Total error definition}
The absolute error between two signals is calculated using a cost-function evaluating both, relative EOD frequency error and relative field structure error. Since frequency changes of several Hz within EOD frequency traces are possible due to the uttering of communication signals like EOD frequency rises and rapid spatial changes comparably uncommon (see Results) we use the cost-function displayed in equation 1 to estimate the total error value between different detected EOD signals.
\subsubsection{Assign temporal EOD frequency traces}
To enable the analysis of recordings with limitless duration, the actual tracking algorithm is two-staged. First, we assign so called temporal identities for EOD signals detected in a 30 seconds window. Therefore, we calculated the total error for every possible connection within this 30 seconds window. Besides the limitation of a maximum EOD frequency difference of 10 Hz the possible EOD signal pairs are limited by a maximum compare range of 10 seconds, i.e. two signals that shall be connected show a maximum time difference of 10 seconds. According to the obtained error values temporal identities are assembled starting from the smallest total error representing the best connection to the largest total error representing the least good connection. Connections that would interfere with already existing temporal identities are not made since already made connections are based on smaller total errors and therefore are more likely to be correct. The resulting temporal identities are based on the best possible connections, but only the centered 10 seconds of the 30 seconds window represent valid connections since the connections within the head and tail 10 seconds did not take into account all possible connections within $\pm$ compare range.
\begin{figure}[h!]
\centerline{\includegraphics[width=1.\linewidth]{1}}
\caption{\label{tmp_idents} Random caption}
\end{figure}
\begin{figure}[h!]
\centerline{\includegraphics[width=1.\linewidth]{4}}
\caption{\label{error_matrix} Random caption}
\end{figure}
\subsubsection{Running connection}
The assembly of the center 10 seconds of the temporal identities, containing valid connections, and already tracked real identities, again is based on total errors between respective EOD signals.
Total error values between signals of already assigned read identities and signals within the centered 10 seconds of temporal identities are identified and, again, assembled based on the total error values preferring lower total errors before larger ones. Temporal identities, which could not be assigned to a already existing real identity form a new real identity. The window to identify temporal identities is shifted by the compare range, i.e. 10 seconds, and the identification of temporal identities and their assignment to already tracked real identities continuous until the end of the recording is reached.
\begin{figure}[h!]
\centerline{\includegraphics[width=1.\linewidth]{2}}
\caption{\label{running_connection} Random caption}
\end{figure}
\section{Results}
\subsection{d-EODf and d-Field of same identity signals vs. non-same identity signals}
\begin{figure}[h!]
\centerline{\includegraphics[width=1.\linewidth]{6}}
\caption{\label{Field_error_shift} Random caption}
\end{figure}
\begin{figure}[h!]
\centerline{\includegraphics[width=1.\linewidth]{7}}
\caption{\label{EODf_error_shift} Random caption}
\end{figure}
\subsection{Roc analysis}
\begin{figure}[h!]
\centerline{\includegraphics[width=1.\linewidth]{12}}
\caption{\label{ROC} Random caption}
\end{figure}
\end{document}

554
tex/references.bib Normal file
View File

@ -0,0 +1,554 @@
@ARTICLE{Henninger2018,
AUTHOR = {J\"org Henninger and R\"udiger Krahe and Frank Kirschbaum and Jan Grewe and Jan Benda},
TITLE = {Statistics of natural communication signals observed in the wild identify important yet neglected stimulus regimes in weakly electric fish.},
JOURNAL = {J Neurosci},
YEAR = {2018},
VOLUME = {38},
PAGES = {5456--5465},
DOI = {10.1523/JNEUROSCI.0350-18.2018},
PDF = {Henninger2018.pdf},
URL = {http://www.jneurosci.org/content/early/2018/05/07/JNEUROSCI.0350-18.2018}
}
@ARTICLE{Madhav2018,
AUTHOR = {Manu S. Madhav and Ravikrishnan P. Jayakumar and Alican Demir and Sarah A. Stamper and Eric S. Fortune and Noah J. Cowan},
TITLE = {High-resolution behavioral mapping of electric fishes in Amazonian habitats.},
JOURNAL = {Sci Rep},
YEAR = {2018},
VOLUME = {8},
PAGES = {5830}
}
@ARTICLE{Jun2012,
AUTHOR = {James J. Jun and Andr\'e Longtin and Leonard Maler},
TITLE = {Precision measurement of electric organ discharge timing from freely moving weakly electric fish.},
JOURNAL = {J Neurophysiol},
YEAR = {2012},
VOLUME = {107},
PAGES = {1996--2007}
}
@ARTICLE{Jun2014,
AUTHOR = {James J. Jun and Andr\'e Longtin and Leonard Maler},
TITLE = {Enhanced sensory sampling precedes self-initiated locomotion in an electric fish.},
JOURNAL = {J Exp Biol},
YEAR = {2014},
VOLUME = {217},
PAGES = {3615--3628}
}
@ARTICLE{Westby1988,
AUTHOR = {G. W. Max Westby},
TITLE = {The ecology, discharge diversity and predatory behaviour of gymnotiforme electric fish in the coastal streams of French Guiana.},
JOURNAL = {Behav Ecol Sociobiol},
YEAR = {1988},
VOLUME = {22},
PAGES = {341--354}
}
@ARTICLE{Arnegard2005,
AUTHOR = {Matthew E. Arnegard and Bruce A. Carlson},
TITLE = {Electric organ discharge patterns during group hunting by a mormyrid fish.},
JOURNAL = {Proc R Soc B},
YEAR = {2005},
VOLUME = {272},
PAGES = {1305--1314}
}
@ARTICLE{Friedman1996,
AUTHOR = {M. A. Friedman and C. D. Hopkins},
TITLE = {Tracking individual mormyrid electric fish in the field using electric organ discharge waveforms.},
JOURNAL = {Anim Behav},
YEAR = {1996},
VOLUME = {51},
PAGES = {391--407}
}
@ARTICLE{Lucas2000,
AUTHOR = {Martyn C. Lucas and Etienne Baras},
TITLE = {Methods for studying spatial behaviour of freshwater fishes in the natural environment.},
JOURNAL = {Fish Fisheries},
YEAR = {2000},
VOLUME = {1},
PAGES = {283--316}
}
@ARTICLE{Hawkins1974,
AUTHOR = {A. D. Hawkins and D. N. MacLennan and G. G. Urquhart and C. Robb},
TITLE = {Tracking cod \textit{Gadus morhua} {L.} in a Scottish sea loch.},
JOURNAL = {J Fish Biol},
YEAR = {1974},
VOLUME = {6},
PAGES = {225--236}
}
@ARTICLE{Hughey2018,
AUTHOR = {Lacey F. Hughey and Andrew M. Hein and Ariana Strandburg-Peshkin and Frants H. Jensen},
TITLE = {Challenges and solutions for studying collective animal behaviour in the wild.},
JOURNAL = {Phil Trans R Soc B},
YEAR = {2018},
VOLUME = {373},
PAGES = {20170005}
}
@ARTICLE{Strandburg2015,
AUTHOR = {Ariana Strandburg-Peshkin and Damien R. Farine and Iain D. Couzin and Margaret C. Crofoot},
TITLE = {Shared decision-making drives collective movement in wild baboons.},
JOURNAL = {Science},
YEAR = {2015},
VOLUME = {348},
PAGES = {1358--1361}
}
@ARTICLE{Dell2014,
AUTHOR = {Anthony I. Dell and John A. Bender and Kristin Branson and Iain D. Couzin and Gonzalo G. de Polavieja and Lucas P.J.J. Noldus and Alfonso P\'erez-Escudero and Pietro Perona and Andrew D. Straw and Martin Wikelski and Ulrich Brose},
TITLE = {Automated image-based tracking and its application in ecology.},
JOURNAL = {TIEE},
YEAR = {2014},
VOLUME = {29},
PAGES = {417--428}
}
@ARTICLE{Flack2018,
AUTHOR = {Andrea Flack and M\'at\'e Nagy and Wolfgang Fiedler and Iain D. Couzin and Martin Wikelski},
TITLE = {Automated image-based tracking and its application in ecology.},
JOURNAL = {Science},
YEAR = {2018},
VOLUME = {360},
PAGES = {911--914}
}
@ARTICLE{Juvaste2017,
AUTHOR = {Risto Juvaste and Elena Arriero and Anna Gagliardo and Richard Holland and Markku J. Huttunen and Inge Mueller and Kasper Thorup and Martin Wikelski and Juhani Hannila and Maija-Liisa Penttinen and Ralf Wistbacka},
TITLE = {Satellite tracking of red-listed nominate lesser black-backed gulls (\textit{Larus f. fuscus}): Habitat specialisation in foraging movements raises novel conservation needs.},
JOURNAL = {GEcCo},
YEAR = {2017},
VOLUME = {10},
PAGES = {220--230}
}
@ARTICLE{Baktoft2015,
AUTHOR = {Henrik Baktoft and Petr Zajicek and Thomas Klefoth and Jon C. Svendsen and Lene Jacobsen and Martin W{\ae}ver Pedersen and David March Morla and Christian Skov and Shinnosuke Nakayama and Robert Arlinghaus},
TITLE = {Performance Assessment of Two Whole-Lake Acoustic Positional Telemetry Systems --- Is Reality Mining of Free-Ranging Aquatic Animals Technologically Possible?},
JOURNAL = {PLOS One},
YEAR = {2015},
VOLUME = {10},
PAGES = {e0126534}
}
@ARTICLE{Krause2013,
AUTHOR = {Jens Krause and Stefan Krause and Robert Arlinghaus and Ioannis Psorakis and Stephen Roberts and Christian Rutz},
TITLE = {Reality mining of animal social systems.},
JOURNAL = {TIEE},
YEAR = {2013},
VOLUME = {28},
PAGES = {541--551}
}
@ARTICLE{Krause2011,
AUTHOR = {Jens Krause and Alan F. T. Winfield and Jean-Luis Deneubourg},
TITLE = {Interactive robots in experimental biology.},
JOURNAL = {TIEE},
YEAR = {2011},
VOLUME = {26},
PAGES = {369--375}
}
@ARTICLE{Faria2010,
AUTHOR = {Jolyon J. Faria and John R. G. Dyer and Romain O. Cl\'ement and Iain D. Couzin and Natalie Holt and Ashley J. W. Ward and Dean Waters and Jens Krause},
TITLE = {A novel method for investigating the collective behaviour of fish: introducing `Robofish'.},
JOURNAL = {Behav Ecol Sociobiol},
YEAR = {2010},
VOLUME = {64},
PAGES = {1211--1218}
}
@ARTICLE{Fugere2011,
AUTHOR = {Vincent Fug\`ere and Herman Ortega and R\"udiger Krahe},
TITLE = {Electrical signalling of dominance in a wild population of electric fish.},
JOURNAL = {Biol Lett},
YEAR = {2011},
VOLUME = {7},
PAGES = {197--200}
}
@ARTICLE{Stamper2010,
AUTHOR = {Sarah A. Stamper and Erika Carrera-G and Eric W. Tan and Vincent Fug\`ere d and R\"udiger Krahe and Eric S. Fortune},
TITLE = {Species differences in group size and electrosensory interference in weakly electric fishes: Implications for electrosensory processing.},
JOURNAL = {Behav Brain Res},
YEAR = {2010},
VOLUME = {207},
PAGES = {368--376}
}
@ARTICLE{Dunlap2016,
AUTHOR = {Kent D. Dunlap and Alex Tran and Michael A. Ragazzi1 and R\"udiger Krahe and Vielka L. Salazar},
TITLE = {Predators inhibit brain cell proliferation in natural populations of electric fish, \textit{Brachyhypopomus occidentalis}.},
JOURNAL = {Proc R Soc B},
YEAR = {2016},
VOLUME = {283},
PAGES = {20152113}
}
@ARTICLE{Matias2015,
AUTHOR = {Paulo Matias and Jan Frans Willem Slaets and Reynaldo Daniel Pinto},
TITLE = {Individual discrimination of freely swimming pulse-type electric fish from electrode array recordings.},
JOURNAL = {Neurocomputing},
YEAR = {2015},
VOLUME = {153},
PAGES = {191--198}
}
@ARTICLE{Lissmann1965,
AUTHOR = {Hans W. Lissmann and Hosrt O. Schwassmann},
TITLE = {Activity rhythm of an electric fish, \textit{Gymnorhamphichtys hypostomus}, Ellis.},
JOURNAL = {Z vergl Physiol},
YEAR = {1965},
VOLUME = {51},
PAGES = {153--171}
}
@ARTICLE{Steinbach1970,
AUTHOR = {A. B. Steinbach},
TITLE = {Diurnal movements and discharge characteristics of electric gymnotid fishes in the {Rio Negro}, {Brazil}},
JOURNAL = {Biol Bull},
YEAR = {1970},
VOLUME = {138},
PAGES = {200--210}
}
@ARTICLE{Handegard2012,
AUTHOR = {Nils Olav Handegard and Kevin M. Boswell and Christos C. Ioannou and Simon P. Leblanc and Dag B. Tjøstheim and Iain D. Couzin},
TITLE = {The Dynamics of Coordinated Group Hunting and Collective Information Transfer among Schooling Prey},
JOURNAL = {Current Biol},
YEAR = {2012},
VOLUME = {22},
PAGES = {1213--1217}
}
@ARTICLE{Lin2017,
AUTHOR = {Huai-Ti Lin and Anthony Leonardo},
TITLE = {Heuristic Rules Underlying Dragonfly Prey Selection and Interception},
JOURNAL = {Current Biol},
YEAR = {2017},
VOLUME = {27},
PAGES = {1124--1137}
}
@ARTICLE{Kirschbaum1983,
AUTHOR = {Frank Kirschbaum},
TITLE = {Myogenic electric organ precedes the neurogenic organ in apteronotid fish.},
JOURNAL = {Naturwissenschaften},
YEAR = {1983},
VOLUME = {70},
PAGES = {205--207}
}
@ARTICLE{Cvikel2014,
AUTHOR = {Noam Cvikel and Eran Levin and Edward Hurme and Ivailo Borissov and Arjan Boonman and Eran Amichai and Yossi Yovel},
TITLE = {On-board recordings reveal no jamming avoidance in wild bats.},
JOURNAL = {Proc R Soc B},
YEAR = {2014},
VOLUME = {282},
PAGES = {20142274}
}
@ARTICLE{Egnor2016,
AUTHOR = {S.E. Roian Egnor and Kristin Branson},
TITLE = {Computationalof analysis of behavior.},
JOURNAL = {Annu Rev Neurosci},
YEAR = {2016},
VOLUME = {39},
PAGES = {217--236}
}
@ARTICLE{Gomez2014,
AUTHOR = {Alex Gomez-Marin and Joseph J. Paton and Adam R. Kampff and Rui M. Costa and Zachary F. Mainen},
TITLE = {Big behavioral data: psychology, ethology and the foundations of neuroscience.},
JOURNAL = {Nat Neurosci},
YEAR = {2014},
VOLUME = {17},
PAGES = {1455--1462}
}
@Article{Anderson2014,
Title = {Toward a science of computational ethology},
Author = {Anderson, D J and Perona, P},
Journal = {Neuron},
Year = {2014},
Number = {1},
Pages = {18--31},
Volume = {84}
}
@Article{Meyer1987,
Title = {Hormone-induced and maturational changes in electric organ discharges and electroreceptor tuning in the weakly electric fish \textit{Apteronotus}.},
Author = {Meyer, J H and Leong, M and Keller, C H},
Journal = {J Comp Physiol A},
Year = {1987},
Pages = {385--394},
Volume = {160},
Abstract = {Plasticity in the frequency of the electric organ discharge (EOD) and electroreceptor tuning of weakly electric fish was studied in the genus Apteronotus. Both hormone-induced and maturational changes in EOD frequency and electroreceptor tuning were examined. Apteronotus is different from all other steroid-responsive weakly electric fish in that estradiol-17 beta, rather than androgens, induces discharge frequency decreases. This result can account for the 'reversed' discharge frequency dimorphism found in Apteronotus in which, counter to all other known sexually dimorphic electric fish, females have lower discharge frequencies than males. Studies of electroreceptor tuning in Apteronotus indicate that electroreceptors are closely tuned to the frequency of the EOD. This finding was noted not only in adult animals, but also in juvenile animals shortly after the onset of their EODs. Tuning plasticity in Apteronotus, as in other species studied, is associated with altered EOD frequencies and was noted in both maturational EOD changes and in estrogen-induced changes. Thus, tuning plasticity appears to be a general phenomenon which occurs concurrent with a variety of EOD changes.},
ISBN = {0340-7594 (Print)},
Pmid = {3572854}
}
@article{Rodriguez2010,
author = {Rodriguez-Munoz, R and Bretman, A and Slate, J and
Walling, CA and Tregenza, T},
journal = {Science},
pages = {1269-1272},
title = {Natural and sexual selection in a wild insect
population.},
volume = {328},
year = {2010},
}
@article{Nelson1999,
author = {Nelson, Mark E and MacIver, Malcolm A},
journal = {J Exp Biol},
number = {10},
pages = {1195--1203},
title = {{Prey capture in the weakly electric fish
\textit{Apteronotus albifrons}: sensory acquisition
strategies and electrosensory consequences.}},
volume = {202},
year = {1999},
}
@article{Fotowat2013a,
author = {Fotowat, H and Harrison, RR and Krahe, R},
institution = {Department of Biology, McGill University, Montréal,
Québec, Canada. haleh.fotowat@mcgill.ca},
journal = {J Neurosci},
month = {Aug},
number = {34},
pages = {13758--13772},
title = {Statistics of the electrosensory input in the freely
swimming weakly electric fish \textit{Apteronotus
leptorhynchus}.},
volume = {33},
year = {2013},
language = {eng},
}
@article{Smith2013,
author = {Smith, GT},
journal = {J Exp Biol},
pages = {2421--33},
title = {{Evolution and hormonal regulation of sex differences
in the electrocommunication behavior of ghost
knifefishes (Apteronotidae).}},
volume = {216},
year = {2013},
issn = {1477-9145},
}
@article{Bullock1970,
author = {Bullock, TH},
journal = {J Gen Physiol},
month = {May},
number = {5},
pages = {565--584},
title = {The reliability of neurons.},
volume = {55},
year = {1970},
language = {eng},
}
@article{Moortgat1998,
author = {Moortgat, KT and Keller, CH and Bullock, TH and
Sejnowski, TJ},
journal = {Proc Natl Acad Sci USA},
number = {8},
pages = {4684--4689},
title = {{Submicrosecond pacemaker precision is behaviorally
modulated: the gymnotiform electromotor pathway.}},
volume = {95},
year = {1998},
isbn = {0027-8424 (Print)},
issn = {0027-8424},
}
@article{Hagedorn1985,
author = {Hagedorn, M and Heiligenberg, W},
journal = {Anim Behav},
pages = {254--265},
title = {{Court and spark: electric signals in the courtship
and mating of gymnotid fish}},
volume = {33},
year = {1985},
}
@article{knudsen1974behavioral,
author = {Knudsen, EI},
journal = {J Comp Physiol A},
number = {4},
pages = {333--353},
publisher = {Springer},
title = {{Behavioral thresholds to electric signals in high
frequency electric fish}},
volume = {91},
year = {1974},
}
@article{Fotowat2013,
author = {Fotowat, H and Harrison, RR. and Krahe, R},
journal = {J Neurosci},
number = {34},
pages = {13758--13772},
title = {{Statistics of the electrosensory input in the freely
swimming weakly electric fish \textit{Apteronotus
leptorhynchus}.}},
volume = {33},
year = {2013},
isbn = {0270-6474},
issn = {1529-2401},
}
@article{dunlap2002hormonal,
author = {Dunlap, KD},
journal = {Horm Behav},
number = {2},
pages = {187--194},
publisher = {Elsevier},
title = {Hormonal and body size correlates of
electrocommunication behavior during dyadic
interactions in a weakly electric fish, Apteronotus
leptorhynchus},
volume = {41},
year = {2002},
}
@article{triefenbach2003effects,
author = {Triefenbach, F and Zakon, H},
journal = {Anim Behav},
number = {1},
pages = {19--28},
publisher = {Elsevier},
title = {Effects of sex, sensitivity and status on cue
recognition in the weakly electric fish Apteronotus
leptorhynchus},
volume = {65},
year = {2003},
}
@article{Bullock1972b,
author = {Bullock, TH and H, RH and Scheich, H},
journal = {J Comp Physiol},
number = {1},
pages = {23--48},
publisher = {Springer Berlin / Heidelberg},
title = {{The jamming avoidance response of high frequency
electric fish. II. Quantitative aspects.}},
volume = {77},
year = {1972},
annote = {10.1007/BF00696518},
issn = {0340-7594},
}
@incollection{caputi2005electric,
author = {Caputi, AA and Carlson, BA and Macadar, O},
booktitle = {Electroreception},
pages = {410--451},
publisher = {Springer},
title = {Electric organs and their control},
year = {2005},
}
@article{Jun2013,
author = {Jun, JJ and Longtin, A and Maler, L},
journal = {PLoS ONE},
number = {6},
title = {{Real-time localization of moving dipole sources for
tracking multiple free-swimming weakly electric
fish}},
volume = {8},
year = {2013},
issn = {19326203},
}
@article{Kirschbaum2002,
author = {Kirschbaum, F and Schugardt, C},
journal = {J Physiol Paris},
pages = {557--566},
title = {{Reproductive strategies and developmental aspects in
mormyrid and gymnotiform fishes}},
volume = {96},
year = {2002},
issn = {09284257},
}
@article{Dunlap1998,
author = {Dunlap, KD and Thomas, P and Zakon, HH},
institution = {Department of Zoology, University of Texas, Austin
78712, USA. dunlapk@uts.cc.utexas.edu},
journal = {J Comp Physiol A},
month = jul,
number = {1},
pages = {77--86},
title = {{Diversity of sexual dimorphism in
electrocommunication signals and its androgen
regulation in a genus of electric fish,
\textit{Apteronotus}.}},
volume = {183},
year = {1998},
}
@article{Zakon2002,
author = {Zakon, HH and Oestreich, J and Tallarovic, S and
Triefenbach, F},
journal = {J Physiol Paris},
number = {5--6},
pages = {451--458},
title = {{EOD modulations of brown ghost electric fish: JARs,
chirps, rises, and dips}},
volume = {96},
year = {2002},
issn = {09284257},
}
@article{Todd1999,
author = {Todd, BS and Andrews, DC},
journal = {Comput Biomed Res},
pages = {322--335},
title = {{The identification of peaks in physiological
signals.}},
volume = {32},
year = {1999},
isbn = {0010-4809},
issn = {0010-4809},
}
@article{Hopkins1973,
author = {Hopkins, CD},
journal = {Nature},
number = {5395},
pages = {268--270},
title = {{Lightning as background noise for communication
among electric fish}},
volume = {242},
year = {1973},
}
@article{knudsen1975spatial,
author = {Knudsen, EI},
journal = {J Comp Physiol A},
number = {2},
pages = {103--118},
publisher = {Springer},
title = {{Spatial aspects of the electric fields generated by
weakly electric fish}},
volume = {99},
year = {1975},
}
@book{wright1999numerical,
author = {Wright, SJ and Nocedal, J},
publisher = {Springer New York},
title = {{Numerical optimization}},
volume = {2},
year = {1999},
}