Remove old paper directory

Paper/VolumeConvergenceInvestigation/plot_data.py

-import matplotlib.pyplot as plt
-import pandas as pd
-import numpy as np
-import os
-from tqdm import tqdm
-from oct2py import octave
-import glob
-import scipy.stats
-
-filenames = glob.glob("CollectedOutput/*.txt")
-
-plt.style.use('paper')
-
-Tspan = 100 * 86400
-
-df_list = []
-for fn in filenames:
-    if '3356003' in fn:
-        continue
-    else:
-        df = pd.read_csv(
-            fn, sep=' ', names=['V', 'dF0', 'dF1', 'F0_std', 'F1_std', 'DeltaF0',
-                                'DeltaF1', 'MaxtwoF', 'twoF_PM', 'cdF0', 'cdF1', 'runTime'])
-        df['mismatch'] = (df.twoF_PM - df.MaxtwoF)/df.twoF_PM
-        df['F0_fraction'] = df.F0_std / df.DeltaF0
-        df['F1_fraction'] = df.F1_std / df.DeltaF1
-        df['CLUSTER_ID'] = fn.split('_')[1]
-        df['RUN_ID'] = fn.split('_')[2]
-        df_list.append(df)
-
-df = pd.concat(df_list)
-
-df.sort_values('V', inplace=True)
-
-df['cd_ave'] = df[['cdF0', 'cdF1']].mean(axis=1)
-df['fraction_ave'] = df[['F0_fraction', 'F1_fraction']].mean(axis=1)
-df = df[df.V <= 500]
-
-fig, (ax2, ax3) = plt.subplots(nrows=2, figsize=(3.2, 4), sharex=True)
-
-print df.groupby('V')['dF0'].count()
-
-
-Vs = df['V'].unique()
-mismatch_ave = df.groupby('V')['mismatch'].mean()
-ave_cd_ave = df.groupby('V')['cd_ave'].apply(scipy.stats.mstats.gmean)
-cdF0_ave = df.groupby('V')['cdF0'].mean()
-cdF1_ave = df.groupby('V')['cdF1'].mean()
-ave_fraction_ave = df.groupby('V')['fraction_ave'].median()
-F0_fraction_ave = df.groupby('V')['F0_fraction'].mean()
-F1_fraction_ave = df.groupby('V')['F1_fraction'].mean()
-
-ax2.plot(df.V, df.cd_ave, 'o', color='k', alpha=0.5)
-#ax2.plot(Vs, ave_cd_ave, color='r')
-ax2.set_ylim(0, 10)
-ax2.set_ylabel(r'$\langle \textrm{PSRF} \rangle$')
-
-ax3.plot(df.V, df.fraction_ave, 'o', color='k', alpha=0.2)
-#ax3.plot(Vs, ave_fraction_ave, color='r')
-ax3.set_ylabel(r'$\langle \textrm{posterior std. / prior width} \rangle$')
-ax3.set_xlabel(
-    r'$\mathcal{V}_\mathrm{PE}^{(0)}=\mathcal{V}_\mathrm{PE}^{(1)}=\sqrt{\mathcal{V}}$')
-ax3.set_xlim(0, 525)
-
-ax3.set_xticks(Vs)
-
-fig.tight_layout()
-fig.savefig('VolumeConvergenceInvestigation.png')

Paper/VolumeConvergenceInvestigation/submitfile

-Executable=VolumeConvergence_repeater.sh
-Arguments=$(Cluster)_$(Process)
-Universe=vanilla
-Input=/dev/null
-accounting_group=ligo.dev.o2.cw.directedisolatedother.semicoherent 
-Output=CollectedOutput/out.$(Cluster).$(Process)
-Error=CollectedOutput/err.$(Cluster).$(Process)
-Log=CollectedOutput/log.$(Cluster).$(Process)
-request_cpus = 1
-request_memory = 16 GB
-
-Queue 100

Paper/allsky_setup_run_setup.tex

-\begin{tabular}{c|cccccc}
-Stage & $\Nseg$ & $\Tcoh^{\rm days}$ &$\Nsteps$ & $\V$ & $\Vsky$ & $\Vpe$ \\ \hline
-0 & 20 & 5.0 & 50 & $4.2{\times}10^{2}$ & 7.5 & 56.0 \\
-1 & 11 & 9.1 & 50 & $4.4{\times}10^{3}$ & 24.0 & $1.8{\times}10^{2}$ \\
-2 & 6 & 16.7 & 50 & $4.2{\times}10^{4}$ & 69.0 & $6.1{\times}10^{2}$ \\
-3 & 3 & 33.3 & 50 & $2.8{\times}10^{5}$ & $1.2{\times}10^{2}$ & $2.4{\times}10^{3}$ \\
-4 & 1 & 100.0 & 50,50 & $2.0{\times}10^{6}$ & $2.0{\times}10^{2}$ & $1.0{\times}10^{4}$ \\
-\end{tabular}

Paper/bibliography.bib

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-@article{gelman1992,
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-@article{brooks1998,
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-@Article{	  hobbs2010,
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-  doi		= {10.1111/j.1365-2966.2009.15938.x},
-  issn		= {00358711},
-  journal	= {Monthly Notices of the Royal Astronomical Society},
-  keywords	= {1 i n t,6000 years of pulsar,archive of pulsar
-		  observations,contains over,general,pulsars,ro d u
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-		  pulsar timing method},
-  month		= feb,
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-  title		= {{An analysis of the timing irregularities for 366
-		  pulsars}},
-  url		= {http://doi.wiley.com/10.1111/j.1365-2966.2009.15938.x},
-  volume	= {402},
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-@article{ashton2017,
-  title     = {{Statistical characterization of pulsar glitches and their
-                potential impact on searches for continuous gravitational
-                 waves}},
-  author = {Ashton, G. and Prix, R. and Jones, D. I.},
-  note = {In prep},
-  year = {2017}
-}
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-@article{Papa2016,
-  title = {{Hierarchical follow-up of subthreshold candidates of an all-sky Einstein@Home search for continuous gravitational waves on LIGO sixth science run data}},
-  author = {{Papa}, M.~A. and {Eggenstein}, H-B. and {Walsh}, S. and {Di Palma}, I. and {Allen}, B. and {Astone}, P. and {Bock}, O. and {Creighton}, T.~D. and {Keitel}, D. and {Machenschalk}, B. and {Prix}, R. and {Siemens}, X. and {Singh}, A. and {Zhu}, S.~J. and {Schutz}, B.~F.},
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-@book{mackay2003information,
-      title={Information theory, inference and learning algorithms},
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Paper/definitions.tex

-\newcommand{\fdot}{\dot{f}}
-\newcommand{\F}{{\mathcal{F}}}
-\newcommand{\twoFhat}{\widehat{2\F}}
-\newcommand{\twoFtilde}{\widetilde{2\F}}
-\newcommand{\A}{\boldsymbol{\mathcal{A}}}
-\newcommand{\blambda}{\boldsymbol{\mathbf{\lambda}}}
-\newcommand{\blambdaSignal}{\boldsymbol{\mathbf{\lambda}}^{\rm s}}
-\newcommand{\tglitch}{t_{\rm glitch}}
-\newcommand{\tstart}{t_{\rm start}}
-\newcommand{\tend}{t_{\rm end}}
-\newcommand{\Nglitches}{N_{\rm g}}
-\newcommand{\Tspan}{T}
-\newcommand{\Tcoh}{T_{\rm coh}}
-\newcommand{\tref}{t_{\rm ref}}
-\newcommand{\Nseg}{N_{\rm seg}}
-\newcommand{\Nsteps}{N_{\rm steps}}
-\newcommand{\Ntemps}{N_{\rm temps}}
-\newcommand{\Nstages}{N_{\rm stages}}
-\newcommand{\Nspindown}{N_{\rm spindowns}}
-\renewcommand{\H}{\mathcal{H}}
-\newcommand{\Hs}{\H_{\rm s}}
-\newcommand{\Hn}{\H_{\rm n}}
-\newcommand{\ho}{h_0}
-\newcommand{\homax}{\ho^{\rm max}}
-\newcommand{\Bsn}{B_{\rm S/N}}
-\newcommand{\AmplitudePrior}{\Pi_\mathcal{A}}
-\newcommand{\mutilde}{\tilde{\mu}}
-\newcommand{\Sn}{S_{\rm n}}
-\newcommand{\V}{\mathcal{V}}
-\newcommand{\Vsky}{\V_{\rm Sky}}
-\newcommand{\Vpe}{\V_{\rm PE}}
-\newcommand{\smax}{s_{\textrm{max}}}
-\newcommand{\fmax}{f_{\textrm{max}}}
-\newcommand{\rhohatmax}{\hat{\rho}_{\mathrm{max}}}
-\newcommand{\logmintemp}{\log_{10}(T_\textrm{min})}
-

Paper/directed_setup_run_setup.tex

-\begin{tabular}{c|cccc}
-Stage & $\Nseg$ & $\Tcoh^{\rm days}$ &$\Nsteps$ & $\Vpe$ \\ \hline
-0 & 20 & 5.0 & 25 & 56.0 \\
-1 & 7 & 14.3 & 25 & $4.5{\times}10^{2}$ \\
-2 & 2 & 50.0 & 25 & $5.0{\times}10^{3}$ \\
-3 & 1 & 100.0 & 25,25 & $1.0{\times}10^{4}$ \\
-\end{tabular}

Paper/follow_up_run_setup.tex

-\begin{tabular}{c|cccccc}
-Stage & $\Nseg$ & $\Tcoh^{\rm days}$ &$\Nsteps$ & $\V$ & $\Vsky$ & $\Vpe$ \\ \hline
-0 & 100 & 1.0 & 200 & 95.0 & 6.8 & 14.0 \\
-1 & 56 & 1.8 & 200 & $9.6{\times}10^{2}$ & 22.0 & 45.0 \\
-2 & 31 & 3.2 & 200 & $1.0{\times}10^{4}$ & 69.0 & $1.5{\times}10^{2}$ \\
-3 & 17 & 5.9 & 200 & $1.1{\times}10^{5}$ & $2.3{\times}10^{2}$ & $4.8{\times}10^{2}$ \\
-4 & 9 & 11.1 & 200 & $1.3{\times}10^{6}$ & $7.5{\times}10^{2}$ & $1.7{\times}10^{3}$ \\
-5 & 5 & 20.0 & 200 & $1.1{\times}10^{7}$ & $2.0{\times}10^{3}$ & $5.5{\times}10^{3}$ \\
-6 & 2 & 50.0 & 200 & $1.0{\times}10^{8}$ & $3.3{\times}10^{3}$ & $3.1{\times}10^{4}$ \\
-7 & 1 & 100.0 & 200,200 & $2.7{\times}10^{8}$ & $4.4{\times}10^{3}$ & $6.2{\times}10^{4}$ \\
-\end{tabular}

Paper/git-tag.sh

-#!/bin/bash
-
-FILE="$1"
-if [ "x$FILE" = x ]; then
-    echo "usage: $0 <file.tex>" >&2
-    exit 1
-fi
-TMPFILE="$FILE.tmp"
-
-gitLOG=`git log -1 --pretty="format:%% generated by $0
-\\newcommand{\\commitDATE}{%ai}
-\\newcommand{\\commitID}{commitID: %H}
-\\newcommand{\\commitIDshort}{commitID: %h}
-"`
-echo "$gitLOG" > $TMPFILE
-
-diffcmd="git diff -- .";
-diff=`$diffcmd`;
-if test -n "$diff"; then
-    echo "\\newcommand{\\commitSTATUS}{UNCLEAN}" >> $TMPFILE
-else
-    echo "\\newcommand{\\commitSTATUS}{CLEAN}" >> $TMPFILE
-fi
-
-if cmp -s $TMPFILE $FILE; then
-    rm -f $TMPFILE
-else
-    mv -f $TMPFILE $FILE
-fi

Paper/macros.tex

-\def\AllSkyMCNoiseN{1.0{\times}10^{4}}
-\def\AllSkyMCNoiseOnlyMaximum{59.8}
-\def\BasicExampleDeltaFone{1.0{\times}10^{-13}}
-\def\BasicExampleDeltaFzero{1.0{\times}10^{-7}}
-\def\BasicExampleDepth{10.0}
-\def\BasicExampleFone{-1.0{\times}10^{-10}}
-\def\BasicExampleFzero{30}
-\def\BasicExampleSqrtSn{1.0{\times}10^{-23}}
-\def\BasicExampleV{120.0}
-\def\BasicExampleVFone{49.0}
-\def\BasicExampleVFzero{2.5}
-\def\BasicExamplehzero{1.0{\times}10^{-24}}
-\def\BasicExamplenburn{50.0}
-\def\BasicExamplenprod{50.0}
-\def\DirectedMCNoiseN{1.0{\times}10^{4}}
-\def\DirectedMCNoiseOnlyMaximum{52.4}
-\def\DirectedMConeGlitchNoiseN{10000}
-\def\DirectedMConeGlitchNoiseOnlyMaximum{82.6}
-\def\DirectedMCtwoGlitchNoiseN{9625}
-\def\DirectedMCtwoGlitchNoiseOnlyMaximum{87.8}
-\def\GridedFrequencySqrtSx{$1.0{\times}10^{-23}$}
-\def\GridedFrequencyT{1}
-\def\GridedFrequencyhzero{$5.0{\times}10^{-24}$}
-\def\SingleGlitchDepth{10.0}
-\def\SingleGlitchFCMismatch{0.7}
-\def\SingleGlitchFCtwoF{718.5}
-\def\SingleGlitchFCtwoFPM{2645.7}
-\def\SingleGlitchFone{-1e-10}
-\def\SingleGlitchFzero{30.0}
-\def\SingleGlitchGlitchtwoF{2622.1}
-\def\SingleGlitchR{0.5}
-\def\SingleGlitchTspan{100.0}
-\def\SingleGlitchdeltaFone{$-2.9{\times}10^{-13}$}
-\def\SingleGlitchdeltaFzero{$3.2{\times}10^{-6}$}