added some prewriting notes

press/intro/motivation

@@ -0,0 +1,5 @@
+There are a number of reasons we care about AGN. For one, they are the engines of active galaxies, which are especially prevalent during the early universe, and we think that the more we know about them, the more we will learn about the evolution of galaxies and the universe. They are also the most luminous objects in the sky, and in a way somewhat analogous to supernovae, if we can work out the dependencies of their observed spectral energy distributions, we can use them as "posts" to obtain more accurate maps of the universe. I swear I had a third reason, but it's late, and I'll probably think of it as I go to sleep.
+
+The systems that contain AGN are apparently complex, involving at least the broad line regions, accretion disks, and possibly matter jets. We are, in almost all cases, unable to resolve the configurations of these systems directly, so we need to infer their configurations. Reverberation mapping refers to the technique of inferring the configuring of the systems by analysing the time lags observed for frequency bands, and comparing these with the predictions of photo-matter interactions for systems with assumed configurations.
+
+Reverberation mapping in the optical bands has thus-far involved primarily time domain analysis. The shortcoming of this technique is that is requires evenly distributed (in time) data. You (Dr. Cackett) along with Zoghbi and Reynolds have developed a frequency domain analysis technique, the "maximum likelihood" technique, that allows for analysis of unevenly distributed (in time) data. This technique has been demonstrated useful in the X-ray bands. We want to take the next step in the analysis of these astrophysical objects of interest by extending the utility of the maximum likelihood technique to the optical bands. That's where I come in.

press/report/report.tex

@@ -12,6 +12,7 @@
 \newcommand{\mnras}{MNRAS}
 \newcommand{\apj}{ApJ}
 \newcommand{\aapr}{A\&ARv}
+\newcommand{\nat}{Nature}
 
 \begin{document}
 
@@ -38,15 +39,18 @@ Power spectral densities and time lags of 19 wavelength bands are recovered as p
 
 \section{Introduction}
 
-Active galactic nuclei are powerful objects, both in luminosity and in the imaginations of modern astronomers. They are some of the brightest objects in the sky, with highly variable spectra 
+Active galactic nuclei are powerful objects, both in luminosity and in the imaginations of modern astronomers. They are some of the brightest objects in the sky, with strongly variable spectra 
 Seyfert galaxies are thought to have active galactic nuclei (AGN) at their center: very luminous and variable sources of electromagnetic radiation. The variability in these objects do not follow any pattern astronomers have been able to recognize. The Type-I Seyfert galaxy NGC 5548 is one of the most studied Seyfert galaxies, and yet remains an object of intense interest and study to modern astronomy. 
 
- Direct observation of active galactic nuclei (AGN) such as that thought to exist at the center of NGC 5548 is rarely possible. The astronomer may infer the properties of AGN from the dynamics of their variable spectra. \cite{2016ApJ...821...56F} published the most complete set of time-dependent light curves yet collected from an active galactic nucleus as part III of STORM, an extensive optical/UV observational campaign carried out on NGC 5548. We now attempt to use frequency-domain analyses to map the reverberation in the observed light curves.
+Direct observation of active galactic nuclei (AGN) such as that thought to exist at the center of NGC 5548 is rarely possible. The Space Telescope and Optical Reverberation Mapping Project encompasses the most in-depth study of NGC 5548 yet performed \citep{2015ApJ...806..128D} \citep{2015ApJ...806..129E} \citep{2016ApJ...821...56F}.
+
+
+ The astronomer may infer the properties of AGN from the dynamics of their variable spectra. \cite{2016ApJ...821...56F} published the most complete set of time-dependent light curves yet collected from an active galactic nucleus as part III of STORM, an extensive optical/UV observational campaign carried out on NGC 5548. We now attempt to use frequency-domain analyses to map the reverberation in the observed light curves.
 
 \section{Reverberation Mapping}
 	One model for AGN suggests that a hot accretion disk is incident upon a central super-massive black hole (SMBH). Electromagnetic emission emergent from the gas surrounding the SMBH is reprocessed by the disk, resulting in observed time lags between emission peaks. If the temperature of the disk decreases radially from the SMBH, the time lags can be expected to increase with decreasing wavelength. Furthermore, as the emission is reprocessed in the disk, it becomes blurred, so the variability can be expected to decrease with wavelength. A transfer function encodes the geometry of the system by describing the time-dependent response of each light curve against the others. Recovering the function from the observed light curves is a primary goal of reverberation mapping.
 
-	This technique has become a standard for calculating the black hole mass of AGN. It is well-described by \cite{2007MNRAS.380..669C} and \cite{2014A&ARv..22...72U} and many others. It continues to be refined, and may also become a tool to measure the black hole spin of these systems (\cite{2016arXiv160606736K}).
+	This technique has become a standard for calculating the black hole mass of AGN. It is well-described by \cite{2007MNRAS.380..669C} and \cite{2014A&ARv..22...72U} and many others. It continues to be refined, and may also become a tool to measure the black hole spin of these systems \citep{2016Natur.535..388K}.
 
 	\begin{figure}
 		\centering
@@ -114,7 +118,7 @@ Seyfert galaxies are thought to have active galactic nuclei (AGN) at their cente
 
     Traditional frequency-domain analyses require data that is evenly sampled. Due primarily to weather, optical reverberation mapping datasets generally contain unevenly sampling. Because of this, until now, optical reverberation mapping has been limited mainly to time-domain analyses, e.g., cross-correlation. While it can handle datasets with significant sampling-variability, cross-correlation is only able to determine the average time lag for a given light curve; however, more information is contained within the light curves than just their average time lag.
 
-    Some X-ray datasets contain gaps due to orbital mechanics, which motivated the work by \cite{2013ApJ...777...24Z}, where a maximum likelihood method is used to perform Fourier analysis on light curves with gaps. Since its development, this technique has found success among studies of observations captured by low-orbit X-ray telescopes that exceed the telescopes' orbital periods, such as the analysis performed by \cite{2016arXiv160606736K}. This technique is now being applied to the optical datasets published in STORM III. If successful, it may provide new insight into the reverberations present in the accretion disk and other structures of the nucleus in NGC 5548.
+    Some X-ray datasets contain gaps due to orbital mechanics, which motivated the work by \cite{2013ApJ...777...24Z}, where a maximum likelihood method is used to perform Fourier analysis on light curves with gaps. Since its development, this technique has found success among studies of observations captured by low-orbit X-ray telescopes that exceed the telescopes' orbital periods, such as the analysis performed by \cite{2016Natur.535..388K}. This technique is now being applied to the optical datasets published in STORM III. If successful, it may provide new insight into the reverberations present in the accretion disk and other structures of the nucleus in NGC 5548.
 
 \section{Analysis}
 
@@ -197,7 +201,7 @@ The time lags show an increase in overall magnitude as wavelength increases. Thi
 \begin{figure}
     \centering
     \begin{minipage}{.475\textwidth}
-        \centeringQ
+        \centering
         \includegraphics[width=1\linewidth]{../img/tophat_freqdomain.pdf}
         \captionof{figure}{Time lags modeled from tophat impulse responses.}
         \label{fig:top_freq_comp}
@@ -214,8 +218,8 @@ The time lags show an increase in overall magnitude as wavelength increases. Thi
 The analytical method developed by \cite{2013ApJ...777...24Z} applies well to the quality of data available for optical reverberation mapping. The analyses performed on these data have elucidated clear trends in the PSD and time lags. With reverberation mapping, the goal is to recover the transfer function, which encodes the geometry of the system. Recovering the time lags is a significant step toward that goal. The transfer function is within the reach of this analysis, and should be recovered in the next few steps. The error computation issues must be remedied so that any conclusions made from this analysis may be judged valid. It is our hope that this mode of analysis will be judged valid so it can be applied to datasets across the landscape of optical reverberation mapping, where consider information awaits discovery.
 
 %\bsp
-\bibliographystyle{plainnat}
+\bibliographystyle{mnras}
-\bibliography{wsu_reu}
+\bibliography{wsu_reu}{}
 
 
 

press/report/rewrites

@@ -0,0 +1,20 @@
+Hi Otho,
+
+This is getting there, but, still a few things to do.  I’ll give you just some general comments, and leave most of the nit-picky phrasing of words for after these are done.
+
+* You need to think about the audience - most of the people who will read this will either be Wayne State Physics professors (who know little about astronomy) or potential REU students who are looking at the website, and probably know little about astronomy.  So, your introduction needs to be broader, bigger picture stuff (why do we even care about AGN in the first place?!).  I think you need at least one paragraph at the beginning that explains what an AGN is, and the evidence for accretion onto a supermassive black hole (use one of your Intro astronomy textbooks as a guide there), and why we should care about this.  This will setup the rest of the report for the non-AGN astronomer.
+
+* Accretion disk reverberation needs describing in more detail.  How are the lags expected change with wavelength? [see equations in Collier et al. 1999: http://adsabs.harvard.edu/abs/1999MNRAS.302L..24C, Cackett et al. 2007, or Fausnaugh et al 2016]. Giving the equations will help.  More clearly explain why the UV part of the ley, disk has a shorter lag than the cooler, optical part of the disk - you have Figure 1 there, refer to it!  You can then refer back to these equations and expectations when discussing the results - are the wavelength dependent lags we see consistent with this picture?
+
+* Every figure needs to be cited in the text. Figure 10 and 11 are repeats of Figures earlier in the report - just reference the earlier figure number.
+
+* FIgure 2 and 3 deserved to be described in more detail in section 2.2.  Why do the lags look like they do? How does the size of the top-hat function correspond to the lags and the frequency at which the lags start to oscillate?  Why do the lags oscillate?  I think writing these things down will really help your understanding of this.  (Hint: all the answers are in Uttley et al. 2014).
+
+✓ We always write 'emission' rather than 'emissions'
+
+✓  convoluted -> convolved
+
+Once you’ve done these, send me along the revised version for hopefully the last set of comments…..
+
+Ed
+

press/report/wsu_reu.bib

@@ -41,24 +41,25 @@ archivePrefix = "arXiv",
   adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
 
-@ARTICLE{2016AN....337..473K,
+@ARTICLE{2016Natur.535..388K,
-   author = {{Kara}, E. and {Alston}, W. and {Fabian}, A.},
+   author = {{Kara}, E. and {Miller}, J.~M. and {Reynolds}, C. and {Dai}, L.
-    title = "{A global look at X-ray time lags in Seyfert galaxies}",
+  },
-  journal = {Astronomische Nachrichten},
+    title = "{Relativistic reverberation in the accretion flow of a tidal disruption event}",
+  journal = {\nat},
 archivePrefix = "arXiv",
-   eprint = {1605.02631},
+   eprint = {1606.06736},
  primaryClass = "astro-ph.HE",
- keywords = {accretion, accretion disks, black hole physics, galaxies: nuclei, galaxies: Seyfert, X-rays: galaxies},
      year = 2016,
-    month = may,
+    month = jul,
-   volume = 337,
+   volume = 535,
-    pages = {473},
+    pages = {388-390},
-      doi = {10.1002/asna.201612332},
+      doi = {10.1038/nature18007},
-   adsurl = {http://adsabs.harvard.edu/abs/2016AN....337..473K},
+   adsurl = {http://adsabs.harvard.edu/abs/2016Natur.535..388K},
   adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
 
 
+
 @ARTICLE{2007MNRAS.380..669C,
    author = {{Cackett}, E.~M. and {Horne}, K. and {Winkler}, H.},
     title = "{Testing thermal reprocessing in active galactic nuclei accretion discs}",
@@ -112,22 +113,6 @@ archivePrefix = "arXiv",
   adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
 
-@ARTICLE{2016arXiv160606736K,
-   author = {{Kara}, E. and {Miller}, J.~M. and {Reynolds}, C. and {Dai}, L.
-    },
-    title = "{Relativistic reverberation in the accretion flow of a tidal disruption event}",
-  journal = {ArXiv e-prints},
-archivePrefix = "arXiv",
-   eprint = {1606.06736},
- primaryClass = "astro-ph.HE",
- keywords = {Astrophysics - High Energy Astrophysical Phenomena, Astrophysics - Astrophysics of Galaxies},
-     year = 2016,
-    month = jun,
-   adsurl = {http://adsabs.harvard.edu/abs/2016arXiv160606736K},
-  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
-}
-
-
 @ARTICLE{2015ApJ...806..129E,
    author = {{Edelson}, R. and {Gelbord}, J.~M. and {Horne}, K. and {McHardy}, I.~M. and 
   {Peterson}, B.~M. and {Ar{\'e}valo}, P. and {Breeveld}, A.~A. and 
@@ -157,3 +142,34 @@ archivePrefix = "arXiv",
    adsurl = {http://adsabs.harvard.edu/abs/2015ApJ...806..129E},
   adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
+
+@ARTICLE{2015ApJ...806..128D,
+   author = {{De Rosa}, G. and {Peterson}, B.~M. and {Ely}, J. and {Kriss}, G.~A. and 
+  {Crenshaw}, D.~M. and {Horne}, K. and {Korista}, K.~T. and {Netzer}, H. and 
+  {Pogge}, R.~W. and {Ar{\'e}valo}, P. and {Barth}, A.~J. and 
+  {Bentz}, M.~C. and {Brandt}, W.~N. and {Breeveld}, A.~A. and 
+  {Brewer}, B.~J. and {Dalla Bont{\`a}}, E. and {De Lorenzo-C{\'a}ceres}, A. and 
+  {Denney}, K.~D. and {Dietrich}, M. and {Edelson}, R. and {Evans}, P.~A. and 
+  {Fausnaugh}, M.~M. and {Gehrels}, N. and {Gelbord}, J.~M. and 
+  {Goad}, M.~R. and {Grier}, C.~J. and {Grupe}, D. and {Hall}, P.~B. and 
+  {Kaastra}, J. and {Kelly}, B.~C. and {Kennea}, J.~A. and {Kochanek}, C.~S. and 
+  {Lira}, P. and {Mathur}, S. and {McHardy}, I.~M. and {Nousek}, J.~A. and 
+  {Pancoast}, A. and {Papadakis}, I. and {Pei}, L. and {Schimoia}, J.~S. and 
+  {Siegel}, M. and {Starkey}, D. and {Treu}, T. and {Uttley}, P. and 
+  {Vaughan}, S. and {Vestergaard}, M. and {Villforth}, C. and 
+  {Yan}, H. and {Young}, S. and {Zu}, Y.},
+    title = "{Space Telescope and Optical Reverberation Mapping Project.I. Ultraviolet Observations of the Seyfert 1 Galaxy NGC 5548 with the Cosmic Origins Spectrograph on Hubble Space Telescope}",
+  journal = {\apj},
+archivePrefix = "arXiv",
+   eprint = {1501.05954},
+ keywords = {galaxies: active, galaxies: individual: NGC 5548, galaxies: nuclei, galaxies: Seyfert},
+     year = 2015,
+    month = jun,
+   volume = 806,
+      eid = {128},
+    pages = {128},
+      doi = {10.1088/0004-637X/806/1/128},
+   adsurl = {http://adsabs.harvard.edu/abs/2015ApJ...806..128D},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+