added some images for errors report

plot.sh

@@ -4,7 +4,7 @@
 # document-rady plots.
 
 # Only analyses with this error type will be represented in the atlas
-errtype="CM"
+errtype="LF"
 ref_band="1367Å"
 
 case $1 in

press/errors/errors.tex

@@ -0,0 +1,37 @@
+\documentclass[11pt,letterpaper]{article}
+
+\usepackage{natbib}
+%\usepackage{cite}
+\usepackage{graphicx}
+\usepackage[margin=1.in,centering]{geometry}
+\usepackage{hyperref}
+\usepackage{caption}
+\usepackage[export]{adjustbox}
+\usepackage{float}
+
+\begin{document}
+
+\title{Computational Anomalies in Error Estimation}
+
+\date{August 25, 2016}
+
+\maketitle
+
+I'll print grids of results for each error type. Errors extracted from the covariance matrix (error code 0)
+
+Psdlag includes three methods for computing errors. These are designated by their error codes:
+    * 0 - Extracting from the covariance matrix
+    * 1 - Scanning the likelihood function
+    * 2 - Monte Carlo
+
+The covariance matrix method, i.e. the "quick" method, is the method we had our early successes with. Here are the grids of PSD and timelags. We do see some possible issues with errors here, with those that are too small 
+
+\includegraphics{../img/timelag_atlas_err0.pdf}
+\includegraphics{../img/timelag_atlas_err1.pdf}
+\includegraphics{../img/timelag_atlas_err2.pdf}
+
+\includegraphics{../img/psd_atlas_err0.pdf}
+\includegraphics{../img/psd_atlas_err1.pdf}
+\includegraphics{../img/psd_atlas_err2.pdf}
+
+\end{document}

scripts/plot_MC_against_CM.sh

@@ -1,3 +1,5 @@
+mkdir -p analyses/plots
+
 for table in analyses/tables/timelag*MC}.tab
 do
     #ref_band=$(basename $table|sed 's|\([^≺]*\)_≺_[^≺_]*_[^_]*_[^_]*\.tab|\1|')
@@ -11,7 +13,7 @@ do
 
     echo Plotting timelag error fit comparison for $echo_band.
 
-    plotfile=analyses/plots/timelag_${echo_band}_error_compare.png
+    plotfile=analyses/plots/timelag_${echo_band}_error_compare.pdf
 
     echo_band_noUTF=$(echo $echo_band|
         sed 's|𝛌|λ|g'|
@@ -28,14 +30,14 @@ do
         sed 's|Å|A|g')
 
     cat scripts/templates/timelag_compare.gp|
-        sed "s|%TITLE|Error Fit Comparison for Time Lag of $echo_band|"|
-        sed "s|%SUBTITLE|referred to ${ref_band}, as reported by Fausnaugh et. al, STORM III, 2016|"|
-        sed "s|%FILE1|$table|"|
-        sed "s|%LABEL1|${echo_band} Delay with Monte Carlo Fit|"|
-        sed "s|%FILE2|$CMtable|"|
-        sed "s|%LABEL2|${echo_band} Delay with Covariance Matrix Fit|"|
-        sed "s|%YMIN|$ymin|"|sed "s|%YMAX|$ymax|"|
-        sed "s|%OUTPUTFILE|$plotfile|" > tmp.gp
+        sed "s|%TITLE%|Error Fit Comparison for Time Lag of $echo_band|"|
+        sed "s|%SUBTITLE%|referred to ${ref_band}, as reported by Fausnaugh et. al, STORM III, 2016|"|
+        sed "s|%FILE1%|$table|"|
+        sed "s|%LABEL1%|${echo_band} Delay with Monte Carlo Fit|"|
+        sed "s|%FILE2%|$CMtable|"|
+        sed "s|%LABEL2%|${echo_band} Delay with Covariance Matrix Fit|"|
+        sed "s|%YMIN%|$ymin|"|sed "s|%YMAX|$ymax|"|
+        sed "s|%OUTPUTFILE%|$plotfile|" > tmp.gp
     gnuplot tmp.gp
 
 done
@@ -53,7 +55,7 @@ do
 
     echo Plotting PSD error fit comparison for $echo_band.
 
-    plotfile=analyses/plots/PSD_${echo_band}_error_compare.png
+    plotfile=analyses/plots/PSD_${echo_band}_error_compare.pdf
 
     echo_band_noUTF=$(echo $echo_band|
         sed 's|𝛌|λ|g'|
@@ -70,14 +72,14 @@ do
         sed 's|Å|A|g')
 
     cat scripts/templates/psd.gp|
-        sed "s|%TITLE|Error Fit Comparison for PSD of $echo_band|"|
-        sed "s|%SUBTITLE|as reported by Fausnaugh et. al, STORM III, 2016|"|
-        sed "s|%FILE1|$table|"|
-        sed "s|%LABEL1|${echo_band} PSD with Monte Carlo Fit|"|
-        sed "s|%FILE2|$CMtable|"|
-        sed "s|%LABEL2|${echo_band} PSD with Covariance Matrix Fit|"|
-        sed "s|%YMIN|$ymin|"|sed "s|%YMAX|$ymax|"|
-        sed "s|%OUTPUTFILE|$plotfile|" > tmp.gp
+        sed "s|%TITLE%|Error Fit Comparison for PSD of $echo_band|"|
+        sed "s|%SUBTITLE%|as reported by Fausnaugh et. al, STORM III, 2016|"|
+        sed "s|%FILE1%|$table|"|
+        sed "s|%LABEL1%|${echo_band}|"|
+        sed "s|%FILE2%|$CMtable|"|
+        sed "s|%LABEL2%|${echo_band} PSD with Covariance Matrix Fit|"|
+        sed "s|%YMIN%|$ymin|"|sed "s|%YMAX|$ymax|"|
+        sed "s|%OUTPUTFILE%|$plotfile|" > tmp.gp
     gnuplot tmp.gp
 
 done

scripts/templates/timelag_compare.gp

@@ -1,9 +1,9 @@
-set terminal pngcairo
+set terminal pdf
 set termoption dash
 set termopt enhanced
-set output "%OUTPUTFILE"
+set output "%OUTPUTFILE%"
 
-set title "%TITLE\n{/*0.7 %SUBTITLE}"
+set title "%TITLE%\n{/*0.7 %SUBTITLE%}"
 set xlabel "Temporal Frequency [days^{-1}]"
 set xrange [0.005:0.620]
 set logscale x
@@ -17,5 +17,5 @@ set key center bottom
 # Draw line at origin
 set arrow from 0.005,0 to 0.620,0 nohead lt 3 lc rgb 'black'
 set pointsize 0
-plot '%FILE1' using 1:2:3:4 with xyerrorbars title "%LABEL1", \
-"%FILE2" using 1:2:3:4 with xyerrorbars title "%LABEL2"
+plot '%FILE1%' using 1:2:3:4 with xyerrorbars title "%LABEL1%", \
+"%FILE2%" using 1:2:3:4 with xyerrorbars title "%LABEL2%"