Initial commit of paper moved from the timing-noise repo

Paper/Makefile

+SHELL = /bin/bash
+
+main = paper_cw_mcmc.pdf
+
+.PHONY : main clean figclean arxiv jones
+
+main : $(main)
+
+git_tag.tex :
+	./git-tag.sh $@
+
+$(main): *.tex git_tag.tex
+	pdflatex ${@:.pdf=} && bibtex ${@:.pdf=} && pdflatex ${@:.pdf=} && pdflatex ${@:.pdf=}
+
+clean :
+	rm -f git_tag.tex $(main:.pdf=){.aux,.bbl,.blg,.log,.out,.pdf,Notes.bib} $(texfigs) $(texonlyfigs)
+
+arxiv :
+	rm -f $(main)
+	rm -f git_tag.tex
+	tar -cvf arxiv_submission.tar *tex *bib bibliography.bib *pdf *.bbl

Paper/bibliography.bib

+@ARTICLE{jks1998,
+   author = {{Jaranowski}, P. and {Kr{\'o}lak}, A. and {Schutz}, B.~F.},
+    title = "{Data analysis of gravitational-wave signals from spinning neutron stars: The signal and its detection}",
+  journal = {\prd},
+   eprint = {gr-qc/9804014},
+ keywords = {Gravitational radiation detectors, mass spectrometers, and other instrumentation and techniques, Gravitational wave detectors and experiments, Mathematical procedures and computer techniques, Pulsars},
+     year = 1998,
+    month = sep,
+   volume = 58,
+   number = 6,
+      eid = {063001},
+    pages = {063001},
+      doi = {10.1103/PhysRevD.58.063001},
+   adsurl = {http://adsabs.harvard.edu/abs/1998PhRvD..58f3001J},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{brady1998,
+   author = {{Brady}, P.~R. and {Creighton}, T. and {Cutler}, C. and {Schutz}, B.~F.
+	},
+    title = "{Searching for periodic sources with LIGO}",
+  journal = {\prd},
+   eprint = {gr-qc/9702050},
+ keywords = {Gravitational radiation detectors, mass spectrometers, and other instrumentation and techniques, Gravitational wave detectors and experiments, Mathematical procedures and computer techniques, Pulsars},
+     year = 1998,
+    month = feb,
+   volume = 57,
+    pages = {2101-2116},
+      doi = {10.1103/PhysRevD.57.2101},
+   adsurl = {http://adsabs.harvard.edu/abs/1998PhRvD..57.2101B},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{brady2000,
+   author = {{Brady}, P.~R. and {Creighton}, T.},
+    title = "{Searching for periodic sources with LIGO. II. Hierarchical searches}",
+  journal = {\prd},
+   eprint = {gr-qc/9812014},
+ keywords = {Gravitational wave detectors and experiments, Gravitational radiation detectors, mass spectrometers, and other instrumentation and techniques, Mathematical procedures and computer techniques, Pulsars},
+     year = 2000,
+    month = apr,
+   volume = 61,
+   number = 8,
+      eid = {082001},
+    pages = {082001},
+      doi = {10.1103/PhysRevD.61.082001},
+   adsurl = {http://adsabs.harvard.edu/abs/2000PhRvD..61h2001B},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{shaltev2013,
+   author = {{Shaltev}, M. and {Prix}, R.},
+    title = "{Fully coherent follow-up of continuous gravitational-wave candidates}",
+  journal = {\prd},
+archivePrefix = "arXiv",
+   eprint = {1303.2471},
+ primaryClass = "gr-qc",
+ keywords = {Gravitational waves: theory},
+     year = 2013,
+    month = apr,
+   volume = 87,
+   number = 8,
+      eid = {084057},
+    pages = {084057},
+      doi = {10.1103/PhysRevD.87.084057},
+   adsurl = {http://adsabs.harvard.edu/abs/2013PhRvD..87h4057S},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+
+@ARTICLE{prix2012,
+   author = {{Prix}, R. and {Shaltev}, M.},
+    title = "{Search for continuous gravitational waves: Optimal StackSlide method at fixed computing cost}",
+  journal = {\prd},
+archivePrefix = "arXiv",
+   eprint = {1201.4321},
+ primaryClass = "gr-qc",
+ keywords = {Gravitational waves: theory, Gravitational-wave astrophysics, Gravitational wave detectors and experiments, Data analysis: algorithms and implementation, data management},
+     year = 2012,
+    month = apr,
+   volume = 85,
+   number = 8,
+      eid = {084010},
+    pages = {084010},
+      doi = {10.1103/PhysRevD.85.084010},
+   adsurl = {http://adsabs.harvard.edu/abs/2012PhRvD..85h4010P},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{krishnan2004,
+   author = {{Krishnan}, B. and {Sintes}, A.~M. and {Papa}, M.~A. and {Schutz}, B.~F. and 
+	{Frasca}, S. and {Palomba}, C.},
+    title = "{Hough transform search for continuous gravitational waves}",
+  journal = {\prd},
+   eprint = {gr-qc/0407001},
+ keywords = {Gravitational wave detectors and experiments, Wave generation and sources, Data analysis: algorithms and implementation, data management, Gravitational radiation detectors, mass spectrometers, and other instrumentation and techniques},
+     year = 2004,
+    month = oct,
+   volume = 70,
+   number = 8,
+      eid = {082001},
+    pages = {082001},
+      doi = {10.1103/PhysRevD.70.082001},
+   adsurl = {http://adsabs.harvard.edu/abs/2004PhRvD..70h2001K},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+
+@ARTICLE{astone2014,
+   author = {{Astone}, P. and {Colla}, A. and {D'Antonio}, S. and {Frasca}, S. and 
+	{Palomba}, C.},
+    title = "{Method for all-sky searches of continuous gravitational wave signals using the frequency-Hough transform}",
+  journal = {\prd},
+archivePrefix = "arXiv",
+   eprint = {1407.8333},
+ primaryClass = "astro-ph.IM",
+ keywords = {Gravitational waves: theory, Gravitational wave detectors and experiments, Neutron stars},
+     year = 2014,
+    month = aug,
+   volume = 90,
+   number = 4,
+      eid = {042002},
+    pages = {042002},
+      doi = {10.1103/PhysRevD.90.042002},
+   adsurl = {http://adsabs.harvard.edu/abs/2014PhRvD..90d2002A},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{cutler2005,
+   author = {{Cutler}, C. and {Gholami}, I. and {Krishnan}, B.},
+    title = "{Improved stack-slide searches for gravitational-wave pulsars}",
+  journal = {\prd},
+   eprint = {gr-qc/0505082},
+ keywords = {Gravitational wave detectors and experiments, Mathematical procedures and computer techniques, Pulsars},
+     year = 2005,
+    month = aug,
+   volume = 72,
+   number = 4,
+      eid = {042004},
+    pages = {042004},
+      doi = {10.1103/PhysRevD.72.042004},
+   adsurl = {http://adsabs.harvard.edu/abs/2005PhRvD..72d2004C},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{prix2009,
+   author = {{Prix}, R. and {Krishnan}, B.},
+    title = "{Targeted search for continuous gravitational waves: Bayesian versus maximum-likelihood statistics}",
+  journal = {Classical and Quantum Gravity},
+archivePrefix = "arXiv",
+   eprint = {0907.2569},
+ primaryClass = "gr-qc",
+     year = 2009,
+    month = oct,
+   volume = 26,
+   number = 20,
+      eid = {204013},
+    pages = {204013},
+      doi = {10.1088/0264-9381/26/20/204013},
+   adsurl = {http://adsabs.harvard.edu/abs/2009CQGra..26t4013P},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@Article{	  foreman-mackay2013,
+  author	= {{Foreman-Mackey}, D. and {Hogg}, D.~W. and {Lang}, D. and
+		  {Goodman}, J. },
+  title		= "{emcee: The MCMC Hammer}",
+  journal	= {PASP},
+  archiveprefix	= "arXiv",
+  eprint	= {1202.3665},
+  primaryclass	= "astro-ph.IM",
+  keywords	= {Data Analysis and Techniques},
+  year		= 2013,
+  month		= mar,
+  volume	= 125,
+  pages		= {306-312},
+  doi		= {10.1086/670067},
+  adsurl	= {http://adsabs.harvard.edu/abs/2013PASP..125..306F},
+  adsnote	= {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@Article{	  goodman2010,
+  author	= {{Goodman}, J. and {Weare}, J.},
+  title		= {Ensemble samplers with affine invariance},
+  journal	= {Comm. App. Math. Comp. Sci.},
+  year		= 2010,
+  volume	= 5,
+  pages     = {65-80},
+}
+
+@article{     swendsen1986,
+  title = {Replica Monte Carlo Simulation of Spin-Glasses},
+  author = {Swendsen, Robert H. and Wang, Jian-Sheng},
+  journal = {Phys. Rev. Lett.},
+  volume = {57},
+  issue = {21},
+  pages = {2607--2609},
+  numpages = {0},
+  year = {1986},
+  month = {Nov},
+  publisher = {American Physical Society},
+  doi = {10.1103/PhysRevLett.57.2607},
+  url = {http://link.aps.org/doi/10.1103/PhysRevLett.57.2607}
+}
+
+@Article{goggans2004,
+  author = "Goggans, Paul M. and Chi, Ying",
+  title = "Using Thermodynamic Integration to Calculate the Posterior Probability in Bayesian Model Selection Problems",
+  journal = "AIP Conference Proceedings",
+  year = "2004",
+  volume = "707",
+  number = "1", 
+  pages = "59-66",
+  url = "http://scitation.aip.org/content/aip/proceeding/aipcp/10.1063/1.1751356",
+  doi = "http://dx.doi.org/10.1063/1.1751356" 
+}
+
+@ARTICLE{wette2013,
+   author = {{Wette}, K. and {Prix}, R.},
+    title = "{Flat parameter-space metric for all-sky searches for gravitational-wave pulsars}",
+  journal = {\prd},
+archivePrefix = "arXiv",
+   eprint = {1310.5587},
+ primaryClass = "gr-qc",
+ keywords = {Gravitational wave detectors and experiments, Gravitational radiation detectors, mass spectrometers, and other instrumentation and techniques, Mathematical procedures and computer techniques, Neutron stars},
+     year = 2013,
+    month = dec,
+   volume = 88,
+   number = 12,
+      eid = {123005},
+    pages = {123005},
+      doi = {10.1103/PhysRevD.88.123005},
+   adsurl = {http://adsabs.harvard.edu/abs/2013PhRvD..88l3005W},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{wette2015,
+   author = {{Wette}, K.},
+    title = "{Parameter-space metric for all-sky semicoherent searches for gravitational-wave pulsars}",
+  journal = {\prd},
+archivePrefix = "arXiv",
+   eprint = {1508.02372},
+ primaryClass = "gr-qc",
+ keywords = {Gravitational wave detectors and experiments, Gravitational radiation detectors, mass spectrometers, and other instrumentation and techniques, Mathematical procedures and computer techniques, Neutron stars},
+     year = 2015,
+    month = oct,
+   volume = 92,
+   number = 8,
+      eid = {082003},
+    pages = {082003},
+      doi = {10.1103/PhysRevD.92.082003},
+   adsurl = {http://adsabs.harvard.edu/abs/2015PhRvD..92h2003W},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{prix2007,
+   author = {{Prix}, R.},
+    title = "{Template-based searches for gravitational waves: efficient lattice covering of flat parameter spaces}",
+  journal = {Classical and Quantum Gravity},
+archivePrefix = "arXiv",
+   eprint = {0707.0428},
+ primaryClass = "gr-qc",
+     year = 2007,
+    month = oct,
+   volume = 24,
+    pages = {S481-S490},
+      doi = {10.1088/0264-9381/24/19/S11},
+   adsurl = {http://adsabs.harvard.edu/abs/2007CQGra..24S.481P},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@article{prix2007metric,
+    archivePrefix = {arXiv},
+    arxivId = {gr-qc/0606088},
+    author = {Prix, Reinhard},
+    doi = {10.1103/PhysRevD.75.023004},
+    eprint = {0606088},
+    file = {:home/greg/Dropbox/Papers/Prix{\_}2007.pdf:pdf},
+    issn = {15507998},
+    journal = {Physical Review D - Particles, Fields, Gravitation and Cosmology},
+    number = {2},
+    pages = {1--20},
+    primaryClass = {gr-qc},
+    title = {{Search for continuous gravitational waves: Metric of the multidetector F-statistic}},
+    volume = {75},
+    year = {2007}
+}
+
+
+@ARTICLE{cutlershutz2005,
+   author = {{Cutler}, C. and {Schutz}, B.~F.},
+    title = "{Generalized F-statistic: Multiple detectors and multiple gravitational wave pulsars}",
+  journal = {\prd},
+   eprint = {gr-qc/0504011},
+ keywords = {Gravitational radiation detectors, mass spectrometers, and other instrumentation and techniques, Gravitational wave detectors and experiments, Mathematical procedures and computer techniques, Pulsars},
+     year = 2005,
+    month = sep,
+   volume = 72,
+   number = 6,
+      eid = {063006},
+    pages = {063006},
+      doi = {10.1103/PhysRevD.72.063006},
+   adsurl = {http://adsabs.harvard.edu/abs/2005PhRvD..72f3006C},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@Article{	  prix2005,
+  author	= {{Prix}, R. and {Itoh}, Y.},
+  title		= "{Global parameter-space correlations of coherent searches
+		  for continuous gravitational waves}",
+  journal	= {Classical and Quantum Gravity},
+  eprint	= {gr-qc/0504006},
+  year		= 2005,
+  month		= sep,
+  volume	= 22,
+  pages		= {1003},
+  doi		= {10.1088/0264-9381/22/18/S14},
+  adsurl	= {http://adsabs.harvard.edu/abs/2005CQGra..22S1003P},
+  adsnote	= {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@misc{lalsuite,
+  title = {{LALSuite: FreeSoftware (GPL) Tools for Data-Analysis}},
+  author = {{LIGO Scientific Collaboration}},
+  year   = 2014,
+  note    = {\url{https://www.lsc-group.phys.uwm.edu/daswg/projects/lalsuite.html}}
+}
+
+@ARTICLE{allyskyS42008,
+   author = {{Abbott}, B. and {Abbott}, R. and {Adhikari}, R. and {Agresti}, J. and 
+	{Ajith}, P. and {Allen}, B. and {Amin}, R. and {Anderson}, S.~B. and 
+	{Anderson}, W.~G. and {Arain}, M. and et al.},
+    title = "{All-sky search for periodic gravitational waves in LIGO S4 data}",
+  journal = {\prd},
+archivePrefix = "arXiv",
+   eprint = {0708.3818},
+ primaryClass = "gr-qc",
+ keywords = {Gravitational wave detectors and experiments, Data analysis: algorithms and implementation, data management, Gravitational radiation detectors, mass spectrometers, and other instrumentation and techniques, Pulsars},
+     year = 2008,
+    month = jan,
+   volume = 77,
+   number = 2,
+      eid = {022001},
+    pages = {022001},
+      doi = {10.1103/PhysRevD.77.022001},
+   adsurl = {http://adsabs.harvard.edu/abs/2008PhRvD..77b2001A},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@article{pletsch2010,
+    archivePrefix = {arXiv},
+    arxivId = {1005.0395},
+    author = {Pletsch, Holger J.},
+    doi = {10.1103/PhysRevD.82.042002},
+    eprint = {1005.0395},
+    file = {:home/greg/Dropbox/Papers/Pletsch{\_}2014.pdf:pdf},
+    issn = {15507998},
+    journal = {Physical Review D},
+    number = {4},
+    title = {{Parameter-space metric of semicoherent searches for continuous gravitational waves}},
+    volume = {82},
+    year = {2010}
+}
+
+@article{leaci2015,
+    archivePrefix = {arXiv},
+    arxivId = {1502.00914},
+    author = {Leaci, Paola and Prix, Reinhard},
+    doi = {10.1103/PhysRevD.91.102003},
+    eprint = {1502.00914},
+    file = {:home/greg/Dropbox/Papers/Leaci{\_}Prix{\_}2015.pdf:pdf},
+    issn = {15502368},
+    journal = {Physical Review D},
+    number = {10},
+    pages = {1--25},
+    title = {{Directed searches for continuous gravitational waves from binary systems: Parameter-space metrics and optimal scorpius X-1 sensitivity}},
+    volume = {91},
+    year = {2015}
+}
+

Paper/definitions.tex

+\newcommand{\F}{{\mathcal{F}}}
+\newcommand{\A}{\boldsymbol{\mathcal{A}}}
+\newcommand{\blambda}{\boldsymbol{\mathbf{\lambda}}}
+\newcommand{\blambdaSignal}{\boldsymbol{\mathbf{\lambda}}^{\rm s}}
+\newcommand{\Tspan}{T_{\rm span}}
+\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{\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{\Pic}{\Pi_{\rm c}}
+\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}}}
+

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/weak_signal_follow_up_run_setup.tex

+\begin{tabular}{c|cccccc}
+Stage & $\Nseg$ & $\Tcoh^{\rm days}$ &$\Nsteps$ & $\V$ & $\Vsky$ & $\Vpe$ \\ \hline
+0 & 80 & 1.25 & 100 & 20.0 & 2.0 & 10.0 \\
+1 & 40 & 2.5 & 100 & $2{\times}10^{2}$ & 7.0 & 20.0 \\
+2 & 20 & 5.0 & 100 & $1{\times}10^{3}$ & 30.0 & 50.0 \\
+3 & 10 & 10.0 & 100 & $1{\times}10^{4}$ & $1{\times}10^{2}$ & 90.0 \\
+4 & 5 & 20.0 & 100 & $7{\times}10^{4}$ & $4{\times}10^{2}$ & $2{\times}10^{2}$ \\
+5 & 1 & 100.0 & 100,100 & $1{\times}10^{6}$ & $1{\times}10^{3}$ & $9{\times}10^{2}$ \\
+\end{tabular}