Various improvements to the paper

Paper/Examples/grided_frequency_search.py

@@ -28,10 +28,10 @@ data = pyfstat.Writer(
     Delta=Delta, h0=h0, sqrtSX=sqrtSX)
 data.make_data()
 
-m = 0.001
+m = 1
 dF0 = np.sqrt(12*m)/(np.pi*duration)
-DeltaF0 = 800*dF0
-F0s = [F0-DeltaF0/2., F0+DeltaF0/2., dF0]
+DeltaF0 = 30*dF0
+F0s = [F0-DeltaF0/2., F0+DeltaF0/2., 1e-2*dF0]
 F1s = [F1]
 F2s = [F2]
 Alphas = [Alpha]
@@ -47,18 +47,19 @@ frequencies = np.unique(search.data[:, xidx])
 twoF = search.data[:, -1]
 
 #mismatch = np.sign(x-F0)*(duration * np.pi * (x - F0))**2 / 12.0
-ax.plot(frequencies, twoF, 'k', lw=1)
+ax.plot(frequencies, twoF, 'k', lw=0.8)
 DeltaF = frequencies - F0
 sinc = np.sin(np.pi*DeltaF*duration)/(np.pi*DeltaF*duration)
 A = np.abs((np.max(twoF)-4)*sinc**2 + 4)
-ax.plot(frequencies, A, '-r', lw=1)
+ax.plot(frequencies, A, 'r', lw=1.2, dashes=(0.2, 0.2))
 ax.set_ylabel('$\widetilde{2\mathcal{F}}$')
 ax.set_xlabel('Frequency')
 ax.set_xlim(F0s[0], F0s[1])
 dF0 = np.sqrt(12*1)/(np.pi*duration)
 xticks = [F0-10*dF0, F0, F0+10*dF0]
 ax.set_xticks(xticks)
-xticklabels = ['$f_0 {-} 10\Delta f$', '$f_0$', '$f_0 {+} 10\Delta f$']
+xticklabels = [r'$f_0 {-} 10\Delta f(\tilde{\mu}=1)$', '$f_0$',
+               r'$f_0 {+} 10\Delta f(\tilde{\mu}=1)$']
 ax.set_xticklabels(xticklabels)
 plt.tight_layout()
 fig.savefig('{}/{}_1D.png'.format(search.outdir, search.label), dpi=300)

Paper/Examples/transient_search_using_MCMC.py

@@ -16,7 +16,7 @@ data_tstart = tstart - duration
 data_tend = data_tstart + 3*duration
 tref = .5*(data_tstart+data_tend)
 
-h0 = 5e-24
+h0 = 3e-24
 sqrtSX = 1e-22
 
 transient = pyfstat.Writer(

Paper/bibliography.bib

@@ -494,3 +494,62 @@ year = {2015}
   year={1998},
   publisher={Taylor \& Francis}
 }
+
+@Article{	  hobbs2010,
+  author	= {Hobbs, G. and Lyne, A.~G. and Kramer, M.},
+  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
+		  c,rotational history,t i o n,the jodrell bank data,the
+		  pulsar timing method},
+  month		= feb,
+  number	= {2},
+  pages		= {1027-1048},
+  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},
+  year		= {2010}
+}
+
+@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}
+}
+
+@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.},
+  journal = {Phys. Rev. D},
+  volume = {94},
+  issue = {12},
+  pages = {122006},
+  numpages = {14},
+  year = {2016},
+  month = {Dec},
+  publisher = {American Physical Society},
+  doi = {10.1103/PhysRevD.94.122006},
+  url = {http://link.aps.org/doi/10.1103/PhysRevD.94.122006}
+}
+
+@article{dupuis2005,
+  title = {Bayesian estimation of pulsar parameters from gravitational wave data},
+  author = {Dupuis, R\'ejean J. and Woan, Graham},
+  journal = {Phys. Rev. D},
+  volume = {72},
+  issue = {10},
+  pages = {102002},
+  numpages = {9},
+  year = {2005},
+  month = {Nov},
+  publisher = {American Physical Society},
+  doi = {10.1103/PhysRevD.72.102002},
+  url = {http://link.aps.org/doi/10.1103/PhysRevD.72.102002}
+}
+

Paper/definitions.tex

@@ -9,7 +9,7 @@
 \newcommand{\tstart}{t_{\rm start}}
 \newcommand{\tend}{t_{\rm end}}
 \newcommand{\Nglitches}{N_{\rm g}}
-\newcommand{\Tspan}{T_{\rm span}}
+\newcommand{\Tspan}{T}
 \newcommand{\Tcoh}{T_{\rm coh}}
 \newcommand{\tref}{t_{\rm ref}}
 \newcommand{\Nseg}{N_{\rm seg}}
@@ -23,7 +23,7 @@
 \newcommand{\ho}{h_0}
 \newcommand{\homax}{\ho^{\rm max}}
 \newcommand{\Bsn}{B_{\rm S/N}}
-\newcommand{\Pic}{\Pi_{\rm c}}
+\newcommand{\AmplitudePrior}{\Pi_\mathcal{A}}
 \newcommand{\mutilde}{\tilde{\mu}}
 \newcommand{\Sn}{S_{\rm n}}
 \newcommand{\V}{\mathcal{V}}

Paper/macros.tex

@@ -12,7 +12,6 @@
 \def\BasicExamplehzero{1.0{\times}10^{-24}}
 \def\BasicExamplenburn{50.0}
 \def\BasicExamplenprod{50.0}
-\def\DirectedMC{}GlitchNoiseN{970.0}
 \def\DirectedMCNoiseN{1.0{\times}10^{4}}
 \def\DirectedMCNoiseOnlyMaximum{52.4}
 \def\DirectedMConeGlitchNoiseN{10000}