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docs/build/doctrees/environment.pickle

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docs/build/latex/aim-cu.aux

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docs/build/latex/aim-cu.fdb_latexmk

@@ -1,10 +1,10 @@
 # Fdb version 3
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-  "aim-cu.idx" 1738358436 3264 3c74a69915c90a0e849d9c12c67a7017 "pdflatex"
+["makeindex aim-cu.idx"] 1753464164 "aim-cu.idx" "aim-cu.ind" "aim-cu" 1753464167
+  "aim-cu.idx" 1753465346 3271 dfd54c98c8aa25d693ba667197c2bb69 "pdflatex"
   (generated)
   "aim-cu.ilg"
   "aim-cu.ind"
-["pdflatex"] 1738357407 "aim-cu.tex" "aim-cu.pdf" "aim-cu" 1738357408
+["pdflatex"] 1753464165 "aim-cu.tex" "aim-cu.pdf" "aim-cu" 1753464167
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   "/usr/share/texlive/texmf-dist/fonts/tfm/public/txfonts/t1xttsl.tfm" 1136768653 1624 fb8f48c6308ace0a799f9278aba03e18 ""
+  "/usr/share/texlive/texmf-dist/fonts/tfm/public/txfonts/tcxtt.tfm" 1136768653 1292 b1fa6b76e852700625b1941c32e1e42e ""
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+  "/usr/share/texlive/texmf-dist/fonts/type1/public/txfonts/tcxtt.pfb" 1136849748 19223 eef9d7a2591262b80fbbebb9e94dc374 ""
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   "/var/lib/texmf/web2c/pdftex/pdflatex.fmt" 1738182460 2802951 8e81926bd8c7925ef7f2c2ab47027050 ""
-  "aim-cu.aux" 1738358436 4977 b0b6b27bafd72138494739b6d289d3f0 "pdflatex"
-  "aim-cu.ind" 1738358434 2518 d1db4b42b3661be20e444f491e183348 "makeindex aim-cu.idx"
-  "aim-cu.out" 1738358436 1030 dc97e87c01af9ac4fcbaa2ffec7da0d3 "pdflatex"
-  "aim-cu.tex" 1738358432 29091 bfa568e17d0962b6cf433c7640f5f12a ""
-  "aim-cu.toc" 1738358436 710 855f53881d687323850cac77f4e31bf0 "pdflatex"
+  "aim-cu.aux" 1753465346 6265 4f0df43302e90693bec7061c92300d5d "pdflatex"
+  "aim-cu.ind" 1753465344 2525 1044f3bbab9ab8951f87444c446b5208 "makeindex aim-cu.idx"
+  "aim-cu.out" 1753465346 1554 f7e00bbb0e646da570fee59d717690da "pdflatex"
+  "aim-cu.tex" 1753465342 33851 ddc827a329132a9369adb4719bab66da ""
+  "aim-cu.toc" 1753465346 1066 5ea11c2a312c71852c289d2818ff1dad "pdflatex"
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-  "sphinxhighlight.sty" 1738358432 7553 83fb52292c17957d9f4aadcb28c57a87 ""
+  "sphinxhighlight.sty" 1753465342 7553 83fb52292c17957d9f4aadcb28c57a87 ""
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@@ -175,7 +180,7 @@
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-  "sphinxmessages.sty" 1738358432 745 3f5fcd6cdd7964ed608767954a8ced6f ""
+  "sphinxmessages.sty" 1753465342 745 3f5fcd6cdd7964ed608767954a8ced6f ""
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docs/build/latex/aim-cu.fls

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 INPUT /usr/share/texlive/texmf-dist/tex/latex/base/size10.clo
 INPUT /usr/share/texlive/texmf-dist/tex/latex/base/size10.clo
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+INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/txfonts/t1xbtt.tfm
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+INPUT /usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd
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+INPUT /usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd
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 INPUT /usr/share/texmf/fonts/tfm/public/tex-gyre/ec-qhvr.tfm
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 INPUT ./aim-cu.ind
 INPUT aim-cu.ind
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docs/build/latex/aim-cu.idx

@@ -1,24 +1,24 @@
-\indexentry{module@\spxentry{module}!package.cusum@\spxentry{package.cusum}|hyperpage}{6}
-\indexentry{package.cusum@\spxentry{package.cusum}!module@\spxentry{module}|hyperpage}{6}
-\indexentry{CUSUM (class in package.cusum)@\spxentry{CUSUM}\spxextra{class in package.cusum}|hyperpage}{6}
-\indexentry{change\_detection() (package.cusum.CUSUM method)@\spxentry{change\_detection()}\spxextra{package.cusum.CUSUM method}|hyperpage}{6}
-\indexentry{compute\_cusum() (package.cusum.CUSUM method)@\spxentry{compute\_cusum()}\spxextra{package.cusum.CUSUM method}|hyperpage}{6}
-\indexentry{initialize() (package.cusum.CUSUM method)@\spxentry{initialize()}\spxextra{package.cusum.CUSUM method}|hyperpage}{6}
-\indexentry{plot\_cusum\_plotly() (package.cusum.CUSUM method)@\spxentry{plot\_cusum\_plotly()}\spxextra{package.cusum.CUSUM method}|hyperpage}{6}
-\indexentry{plot\_input\_metric\_plotly() (package.cusum.CUSUM method)@\spxentry{plot\_input\_metric\_plotly()}\spxextra{package.cusum.CUSUM method}|hyperpage}{6}
-\indexentry{plot\_input\_metric\_plotly\_raw() (package.cusum.CUSUM method)@\spxentry{plot\_input\_metric\_plotly\_raw()}\spxextra{package.cusum.CUSUM method}|hyperpage}{6}
-\indexentry{set\_df\_metric\_csv() (package.cusum.CUSUM method)@\spxentry{set\_df\_metric\_csv()}\spxextra{package.cusum.CUSUM method}|hyperpage}{7}
-\indexentry{set\_df\_metric\_default() (package.cusum.CUSUM method)@\spxentry{set\_df\_metric\_default()}\spxextra{package.cusum.CUSUM method}|hyperpage}{7}
-\indexentry{set\_init\_stats() (package.cusum.CUSUM method)@\spxentry{set\_init\_stats()}\spxextra{package.cusum.CUSUM method}|hyperpage}{7}
-\indexentry{set\_timeline() (package.cusum.CUSUM method)@\spxentry{set\_timeline()}\spxextra{package.cusum.CUSUM method}|hyperpage}{7}
-\indexentry{module@\spxentry{module}!package.ARLTheoretical@\spxentry{package.ARLTheoretical}|hyperpage}{7}
-\indexentry{package.ARLTheoretical@\spxentry{package.ARLTheoretical}!module@\spxentry{module}|hyperpage}{7}
-\indexentry{get\_ARL\_1() (in module package.ARLTheoretical)@\spxentry{get\_ARL\_1()}\spxextra{in module package.ARLTheoretical}|hyperpage}{7}
-\indexentry{get\_ARL\_1\_h\_mu1\_k() (in module package.ARLTheoretical)@\spxentry{get\_ARL\_1\_h\_mu1\_k()}\spxextra{in module package.ARLTheoretical}|hyperpage}{7}
-\indexentry{get\_ref\_value() (in module package.ARLTheoretical)@\spxentry{get\_ref\_value()}\spxextra{in module package.ARLTheoretical}|hyperpage}{8}
-\indexentry{get\_ref\_value\_k() (in module package.ARLTheoretical)@\spxentry{get\_ref\_value\_k()}\spxextra{in module package.ARLTheoretical}|hyperpage}{8}
-\indexentry{module@\spxentry{module}!package.utils@\spxentry{package.utils}|hyperpage}{8}
-\indexentry{package.utils@\spxentry{package.utils}!module@\spxentry{module}|hyperpage}{8}
-\indexentry{get\_greattable\_as\_html() (in module package.utils)@\spxentry{get\_greattable\_as\_html()}\spxextra{in module package.utils}|hyperpage}{8}
-\indexentry{populate\_summary\_table\_ARL0\_k() (in module package.utils)@\spxentry{populate\_summary\_table\_ARL0\_k()}\spxextra{in module package.utils}|hyperpage}{8}
-\indexentry{populate\_summary\_table\_ARL1\_k() (in module package.utils)@\spxentry{populate\_summary\_table\_ARL1\_k()}\spxextra{in module package.utils}|hyperpage}{9}
+\indexentry{module@\spxentry{module}!package.cusum@\spxentry{package.cusum}|hyperpage}{8}
+\indexentry{package.cusum@\spxentry{package.cusum}!module@\spxentry{module}|hyperpage}{8}
+\indexentry{CUSUM (class in package.cusum)@\spxentry{CUSUM}\spxextra{class in package.cusum}|hyperpage}{8}
+\indexentry{change\_detection() (package.cusum.CUSUM method)@\spxentry{change\_detection()}\spxextra{package.cusum.CUSUM method}|hyperpage}{8}
+\indexentry{compute\_cusum() (package.cusum.CUSUM method)@\spxentry{compute\_cusum()}\spxextra{package.cusum.CUSUM method}|hyperpage}{8}
+\indexentry{initialize() (package.cusum.CUSUM method)@\spxentry{initialize()}\spxextra{package.cusum.CUSUM method}|hyperpage}{8}
+\indexentry{plot\_cusum\_plotly() (package.cusum.CUSUM method)@\spxentry{plot\_cusum\_plotly()}\spxextra{package.cusum.CUSUM method}|hyperpage}{8}
+\indexentry{plot\_input\_metric\_plotly() (package.cusum.CUSUM method)@\spxentry{plot\_input\_metric\_plotly()}\spxextra{package.cusum.CUSUM method}|hyperpage}{8}
+\indexentry{plot\_input\_metric\_plotly\_raw() (package.cusum.CUSUM method)@\spxentry{plot\_input\_metric\_plotly\_raw()}\spxextra{package.cusum.CUSUM method}|hyperpage}{8}
+\indexentry{set\_df\_metric\_csv() (package.cusum.CUSUM method)@\spxentry{set\_df\_metric\_csv()}\spxextra{package.cusum.CUSUM method}|hyperpage}{9}
+\indexentry{set\_df\_metric\_default() (package.cusum.CUSUM method)@\spxentry{set\_df\_metric\_default()}\spxextra{package.cusum.CUSUM method}|hyperpage}{9}
+\indexentry{set\_init\_stats() (package.cusum.CUSUM method)@\spxentry{set\_init\_stats()}\spxextra{package.cusum.CUSUM method}|hyperpage}{9}
+\indexentry{set\_timeline() (package.cusum.CUSUM method)@\spxentry{set\_timeline()}\spxextra{package.cusum.CUSUM method}|hyperpage}{9}
+\indexentry{module@\spxentry{module}!package.ARLTheoretical@\spxentry{package.ARLTheoretical}|hyperpage}{9}
+\indexentry{package.ARLTheoretical@\spxentry{package.ARLTheoretical}!module@\spxentry{module}|hyperpage}{9}
+\indexentry{get\_ARL\_1() (in module package.ARLTheoretical)@\spxentry{get\_ARL\_1()}\spxextra{in module package.ARLTheoretical}|hyperpage}{9}
+\indexentry{get\_ARL\_1\_h\_mu1\_k() (in module package.ARLTheoretical)@\spxentry{get\_ARL\_1\_h\_mu1\_k()}\spxextra{in module package.ARLTheoretical}|hyperpage}{9}
+\indexentry{get\_ref\_value() (in module package.ARLTheoretical)@\spxentry{get\_ref\_value()}\spxextra{in module package.ARLTheoretical}|hyperpage}{10}
+\indexentry{get\_ref\_value\_k() (in module package.ARLTheoretical)@\spxentry{get\_ref\_value\_k()}\spxextra{in module package.ARLTheoretical}|hyperpage}{10}
+\indexentry{module@\spxentry{module}!package.utils@\spxentry{package.utils}|hyperpage}{10}
+\indexentry{package.utils@\spxentry{package.utils}!module@\spxentry{module}|hyperpage}{10}
+\indexentry{get\_greattable\_as\_html() (in module package.utils)@\spxentry{get\_greattable\_as\_html()}\spxextra{in module package.utils}|hyperpage}{10}
+\indexentry{populate\_summary\_table\_ARL0\_k() (in module package.utils)@\spxentry{populate\_summary\_table\_ARL0\_k()}\spxextra{in module package.utils}|hyperpage}{10}
+\indexentry{populate\_summary\_table\_ARL1\_k() (in module package.utils)@\spxentry{populate\_summary\_table\_ARL1\_k()}\spxextra{in module package.utils}|hyperpage}{11}

docs/build/latex/aim-cu.ind

@@ -5,53 +5,53 @@
 \let\spxextra \sphinxstyleindexextra
 
   \bigletter C
-  \item \spxentry{change\_detection()}\spxextra{package.cusum.CUSUM method}, \hyperpage{6}
-  \item \spxentry{compute\_cusum()}\spxextra{package.cusum.CUSUM method}, \hyperpage{6}
-  \item \spxentry{CUSUM}\spxextra{class in package.cusum}, \hyperpage{6}
+  \item \spxentry{change\_detection()}\spxextra{package.cusum.CUSUM method}, \hyperpage{8}
+  \item \spxentry{compute\_cusum()}\spxextra{package.cusum.CUSUM method}, \hyperpage{8}
+  \item \spxentry{CUSUM}\spxextra{class in package.cusum}, \hyperpage{8}
 
   \indexspace
   \bigletter G
-  \item \spxentry{get\_ARL\_1()}\spxextra{in module package.ARLTheoretical}, \hyperpage{7}
+  \item \spxentry{get\_ARL\_1()}\spxextra{in module package.ARLTheoretical}, \hyperpage{9}
   \item \spxentry{get\_ARL\_1\_h\_mu1\_k()}\spxextra{in module package.ARLTheoretical}, 
-		\hyperpage{7}
-  \item \spxentry{get\_greattable\_as\_html()}\spxextra{in module package.utils}, \hyperpage{8}
-  \item \spxentry{get\_ref\_value()}\spxextra{in module package.ARLTheoretical}, \hyperpage{8}
-  \item \spxentry{get\_ref\_value\_k()}\spxextra{in module package.ARLTheoretical}, \hyperpage{8}
+		\hyperpage{9}
+  \item \spxentry{get\_greattable\_as\_html()}\spxextra{in module package.utils}, \hyperpage{10}
+  \item \spxentry{get\_ref\_value()}\spxextra{in module package.ARLTheoretical}, \hyperpage{10}
+  \item \spxentry{get\_ref\_value\_k()}\spxextra{in module package.ARLTheoretical}, \hyperpage{10}
 
   \indexspace
   \bigletter I
-  \item \spxentry{initialize()}\spxextra{package.cusum.CUSUM method}, \hyperpage{6}
+  \item \spxentry{initialize()}\spxextra{package.cusum.CUSUM method}, \hyperpage{8}
 
   \indexspace
   \bigletter M
   \item \spxentry{module}
-    \subitem \spxentry{package.ARLTheoretical}, \hyperpage{7}
-    \subitem \spxentry{package.cusum}, \hyperpage{6}
-    \subitem \spxentry{package.utils}, \hyperpage{8}
+    \subitem \spxentry{package.ARLTheoretical}, \hyperpage{9}
+    \subitem \spxentry{package.cusum}, \hyperpage{8}
+    \subitem \spxentry{package.utils}, \hyperpage{10}
 
   \indexspace
   \bigletter P
   \item \spxentry{package.ARLTheoretical}
-    \subitem \spxentry{module}, \hyperpage{7}
+    \subitem \spxentry{module}, \hyperpage{9}
   \item \spxentry{package.cusum}
-    \subitem \spxentry{module}, \hyperpage{6}
-  \item \spxentry{package.utils}
     \subitem \spxentry{module}, \hyperpage{8}
-  \item \spxentry{plot\_cusum\_plotly()}\spxextra{package.cusum.CUSUM method}, \hyperpage{6}
+  \item \spxentry{package.utils}
+    \subitem \spxentry{module}, \hyperpage{10}
+  \item \spxentry{plot\_cusum\_plotly()}\spxextra{package.cusum.CUSUM method}, \hyperpage{8}
   \item \spxentry{plot\_input\_metric\_plotly()}\spxextra{package.cusum.CUSUM method}, 
-		\hyperpage{6}
+		\hyperpage{8}
   \item \spxentry{plot\_input\_metric\_plotly\_raw()}\spxextra{package.cusum.CUSUM method}, 
-		\hyperpage{6}
-  \item \spxentry{populate\_summary\_table\_ARL0\_k()}\spxextra{in module package.utils}, 
 		\hyperpage{8}
+  \item \spxentry{populate\_summary\_table\_ARL0\_k()}\spxextra{in module package.utils}, 
+		\hyperpage{10}
   \item \spxentry{populate\_summary\_table\_ARL1\_k()}\spxextra{in module package.utils}, 
-		\hyperpage{9}
+		\hyperpage{11}
 
   \indexspace
   \bigletter S
-  \item \spxentry{set\_df\_metric\_csv()}\spxextra{package.cusum.CUSUM method}, \hyperpage{7}
-  \item \spxentry{set\_df\_metric\_default()}\spxextra{package.cusum.CUSUM method}, \hyperpage{7}
-  \item \spxentry{set\_init\_stats()}\spxextra{package.cusum.CUSUM method}, \hyperpage{7}
-  \item \spxentry{set\_timeline()}\spxextra{package.cusum.CUSUM method}, \hyperpage{7}
+  \item \spxentry{set\_df\_metric\_csv()}\spxextra{package.cusum.CUSUM method}, \hyperpage{9}
+  \item \spxentry{set\_df\_metric\_default()}\spxextra{package.cusum.CUSUM method}, \hyperpage{9}
+  \item \spxentry{set\_init\_stats()}\spxextra{package.cusum.CUSUM method}, \hyperpage{9}
+  \item \spxentry{set\_timeline()}\spxextra{package.cusum.CUSUM method}, \hyperpage{9}
 
 \end{sphinxtheindex}

docs/build/latex/aim-cu.log

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-{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2
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+{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./aim-cu.toc)
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 Chapter 1.
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 Chapter 2.
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+]
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+[4
+
+]
+Chapter 4.
+[5
+
+]
+Chapter 5.
+[6
+
+]
+Chapter 6.
+
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+Chapter 7.
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docs/build/latex/aim-cu.out

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docs/build/latex/aim-cu.pdf

@@ -1,3 +1,3 @@
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-oid sha256:43d5c4317b6206ef1cbbecf90ef47516a795e6fccecd683b267962e9cb3c6c64
-size 242546
+oid sha256:5f97a44b0e6d1adc725a2534549e41d563846bb224592baf4259cd92931c569f
+size 239122

docs/build/latex/aim-cu.tex

@@ -1,6 +1,6 @@
 %% Generated by Sphinx.
 \def\sphinxdocclass{report}
-\documentclass[letterpaper,10pt,english]{sphinxmanual}
+\documentclass[letterpaper,10pt,oneside,english]{sphinxmanual}
 \ifdefined\pdfpxdimen
    \let\sphinxpxdimen\pdfpxdimen\else\newdimen\sphinxpxdimen
 \fi \sphinxpxdimen=.75bp\relax
@@ -67,7 +67,7 @@
     
 
 \title{AIM\sphinxhyphen{}CU}
-\date{Jan 31, 2025}
+\date{Jul 25, 2025}
 \release{1.0.0}
 \author{Smriti Prathapan, Berkman Sahiner, Dhaval Kadia, Ravi K.\@{} Samala}
 \newcommand{\sphinxlogo}{\vbox{}}
@@ -92,7 +92,13 @@
 A CUSUM\sphinxhyphen{}based tool for AI Monitoring
 
 \sphinxAtStartPar
-AIM\sphinxhyphen{}CU is a statistical tool for AI monitoring using cumulative sum (AIM\sphinxhyphen{}CU). AIM\sphinxhyphen{}CU computes:
+Monitoring a clinically deployed AI device to detect performance drift is an essential step to ensure the safety and effectiveness of AI.
+
+\sphinxAtStartPar
+AIM\sphinxhyphen{}CU is a statistical tool for AI monitoring using cumulative sum (AIM\sphinxhyphen{}CU).
+
+\sphinxAtStartPar
+AIM\sphinxhyphen{}CU computes:
 \begin{itemize}
 \item {} 
 \sphinxAtStartPar
@@ -105,6 +111,27 @@ Detection delay estimates for a given displacement of the performance metric fro
 \end{itemize}
 
 
+\chapter{System setup}
+\label{\detokenize{index:system-setup}}
+\sphinxAtStartPar
+Make sure R is installed in the system. Instructions for linux (the below setup is only performed in linux):
+
+\begin{sphinxVerbatim}[commandchars=\\\{\}]
+wget\PYG{+w}{ }\PYGZhy{}qO\PYGZhy{}\PYG{+w}{ }https://cloud.r\PYGZhy{}project.org/bin/linux/ubuntu/marutter\PYGZus{}pubkey.asc\PYG{+w}{ }\PYG{p}{|}\PYG{+w}{  }tee\PYG{+w}{ }\PYGZhy{}a\PYG{+w}{ }/etc/apt/trusted.gpg.d/cran\PYGZus{}ubuntu\PYGZus{}key.asc
+add\PYGZhy{}apt\PYGZhy{}repository\PYG{+w}{ }\PYG{l+s+s2}{\PYGZdq{}}\PYG{l+s+s2}{deb https://cloud.r\PYGZhy{}project.org/bin/linux/ubuntu }\PYG{k}{\PYGZdl{}(}lsb\PYGZus{}release\PYG{+w}{ }\PYGZhy{}cs\PYG{k}{)}\PYG{l+s+s2}{\PYGZhy{}cran40/}\PYG{l+s+s2}{\PYGZdq{}}
+apt\PYGZhy{}get\PYG{+w}{ }install\PYG{+w}{ }\PYGZhy{}y\PYG{+w}{ }\PYGZhy{}\PYGZhy{}no\PYGZhy{}install\PYGZhy{}recommends\PYG{+w}{ }r\PYGZhy{}base\PYG{+w}{ }r\PYGZhy{}base\PYGZhy{}dev
+
+\PYG{c+c1}{\PYGZsh{} setup R configs}
+\PYG{n+nb}{echo}\PYG{+w}{ }\PYG{l+s+s2}{\PYGZdq{}r \PYGZlt{}\PYGZhy{} getOption(\PYGZsq{}repos\PYGZsq{}); r[\PYGZsq{}CRAN\PYGZsq{}] \PYGZlt{}\PYGZhy{} \PYGZsq{}http://cran.us.r\PYGZhy{}project.org\PYGZsq{}; options(repos = r);\PYGZdq{}}\PYG{+w}{ }\PYGZgt{}\PYG{+w}{ }\PYGZti{}/.Rprofile
+Rscript\PYG{+w}{ }\PYGZhy{}e\PYG{+w}{ }\PYG{l+s+s2}{\PYGZdq{}install.packages(\PYGZsq{}ggplot2\PYGZsq{})\PYGZdq{}}
+Rscript\PYG{+w}{ }\PYGZhy{}e\PYG{+w}{ }\PYG{l+s+s2}{\PYGZdq{}install.packages(\PYGZsq{}hexbin\PYGZsq{})\PYGZdq{}}
+Rscript\PYG{+w}{ }\PYGZhy{}e\PYG{+w}{ }\PYG{l+s+s2}{\PYGZdq{}install.packages(\PYGZsq{}lazyeval\PYGZsq{})\PYGZdq{}}
+Rscript\PYG{+w}{ }\PYGZhy{}e\PYG{+w}{ }\PYG{l+s+s2}{\PYGZdq{}install.packages(\PYGZsq{}cusumcharter\PYGZsq{})\PYGZdq{}}
+Rscript\PYG{+w}{ }\PYGZhy{}e\PYG{+w}{ }\PYG{l+s+s2}{\PYGZdq{}install.packages(\PYGZsq{}RcppCNPy\PYGZsq{})\PYGZdq{}}
+Rscript\PYG{+w}{ }\PYGZhy{}e\PYG{+w}{ }\PYG{l+s+s2}{\PYGZdq{}install.packages(\PYGZsq{}spc\PYGZsq{})\PYGZdq{}}
+\end{sphinxVerbatim}
+
+
 \chapter{Code execution}
 \label{\detokenize{index:code-execution}}
 \sphinxAtStartPar
@@ -128,6 +155,7 @@ pip\PYG{+w}{ }install\PYG{+w}{ }\PYGZhy{}r\PYG{+w}{ }requirements.txt
 Run AIM\sphinxhyphen{}CU.
 
 \begin{sphinxVerbatim}[commandchars=\\\{\}]
+\PYG{n+nb}{cd}\PYG{+w}{ }src/package
 python3\PYG{+w}{ }app.py
 \end{sphinxVerbatim}
 
@@ -135,11 +163,45 @@ python3\PYG{+w}{ }app.py
 Open the URL \sphinxurl{http://0.0.0.0:7860} that is running the AIM\sphinxhyphen{}CU locally.
 
 
+\chapter{Example code execution}
+\label{\detokenize{index:example-code-execution}}
+\sphinxAtStartPar
+Example code can be run in a Jupyter Notebook after opening it with \sphinxcode{\sphinxupquote{jupyter notebook}} command from \sphinxcode{\sphinxupquote{/src/package/}} directory. The tool is designed to used through UI, not from console.
+
+
 \chapter{Demo}
 \label{\detokenize{index:demo}}
 \sphinxAtStartPar
 AIM\sphinxhyphen{}CU can also be run through the demo available at \sphinxurl{https://huggingface.co/spaces/didsr/AIM-CU}. If Space is paused, click on Restart button.
 
+
+\chapter{Usability}
+\label{\detokenize{index:usability}}\begin{itemize}
+\item {} 
+\sphinxAtStartPar
+Example AI output CSV file is available as \sphinxurl{config/spec-60-60.csv} to be uploaded in monitoring phase.
+
+\item {} 
+\sphinxAtStartPar
+Workflow instruction to run the tool is available at bottom\sphinxhyphen{}left of UI.
+
+\item {} 
+\sphinxAtStartPar
+Sample UI output is available at \sphinxurl{assets/ui.png}.
+
+\item {} 
+\sphinxAtStartPar
+Setting \sphinxcode{\sphinxupquote{control:save\_figure}} to \sphinxcode{\sphinxupquote{true}} from \sphinxhref{config/config.toml}{config.toml} will save tables and plots in \sphinxurl{figure/}.
+
+\item {} 
+\sphinxAtStartPar
+Running AIM\sphinxhyphen{}CU does not take time longer than a few seconds, and it does not require GPU.
+
+\end{itemize}
+
+
+\chapter{AIM\sphinxhyphen{}CU}
+\label{\detokenize{index:aim-cu}}
 \sphinxstepscope
 
 
@@ -479,11 +541,11 @@ Read the provided performance metric data to be used for CUSUM for an example.
 {{ $\rightarrow$ None}}
 \pysigstopsignatures
 \sphinxAtStartPar
-Use initial days to calculate in\sphinxhyphen{}control mean and standard deviation.
+Use number of baseline observations to calculate in\sphinxhyphen{}control mean and standard deviation.
 \begin{quote}\begin{description}
 \sphinxlineitem{Parameters}
 \sphinxAtStartPar
-\sphinxstyleliteralstrong{\sphinxupquote{init\_days}} (\sphinxstyleliteralemphasis{\sphinxupquote{int}}\sphinxstyleliteralemphasis{\sphinxupquote{, }}\sphinxstyleliteralemphasis{\sphinxupquote{optional}}) \textendash{} Initial days when observations are considered stable. Defaults to 30.
+\sphinxstyleliteralstrong{\sphinxupquote{init\_days}} (\sphinxstyleliteralemphasis{\sphinxupquote{int}}\sphinxstyleliteralemphasis{\sphinxupquote{, }}\sphinxstyleliteralemphasis{\sphinxupquote{optional}}) \textendash{} Number of baseline observations when observations are considered stable. Defaults to 30.
 
 \end{description}\end{quote}
 
@@ -791,6 +853,12 @@ gt.GT
 
 
 
+\chapter{Disclaimer}
+\label{\detokenize{index:disclaimer}}
+\sphinxAtStartPar
+This software and documentation was developed at the Food and Drug Administration (FDA) by employees of the Federal Government in the course of their official duties. Pursuant to Title 17, Section 105 of the United States Code, this work is not subject to copyright protection and is in the public domain. Permission is hereby granted, free of charge, to any person obtaining a copy of the Software, to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, or sell copies of the Software or derivatives, and to permit persons to whom the Software is furnished to do so. FDA assumes no responsibility whatsoever for use by other parties of the Software, its source code, documentation or compiled executables, and makes no guarantees, expressed or implied, about its quality, reliability, or any other characteristic. Further, use of this code in no way implies endorsement by the FDA or confers any advantage in regulatory decisions. Although this software can be redistributed and/or modified freely, we ask that any derivative works bear some notice that they are derived from it, and any modified versions bear some notice that they have been modified.
+
+
 \renewcommand{\indexname}{Python Module Index}
 \begin{sphinxtheindex}
 \let\bigletter\sphinxstyleindexlettergroup

docs/build/latex/aim-cu.toc

@@ -1,11 +1,16 @@
 \babel@toc {english}{}\relax 
-\contentsline {chapter}{\numberline {1}Code execution}{3}{chapter.1}%
-\contentsline {chapter}{\numberline {2}Demo}{5}{chapter.2}%
-\contentsline {section}{\numberline {2.1}Methods}{5}{section.2.1}%
-\contentsline {subsection}{\numberline {2.1.1}CUSUM parameters}{5}{subsection.2.1.1}%
-\contentsline {subsection}{\numberline {2.1.2}CUSUM chart}{5}{subsection.2.1.2}%
-\contentsline {section}{\numberline {2.2}CUSUM}{6}{section.2.2}%
-\contentsline {section}{\numberline {2.3}ARLTheoretical}{7}{section.2.3}%
-\contentsline {section}{\numberline {2.4}Utils}{8}{section.2.4}%
-\contentsline {chapter}{Python Module Index}{11}{section*.21}%
-\contentsline {chapter}{Index}{13}{section*.22}%
+\contentsline {chapter}{\numberline {1}System setup}{2}{chapter.1}%
+\contentsline {chapter}{\numberline {2}Code execution}{3}{chapter.2}%
+\contentsline {chapter}{\numberline {3}Example code execution}{4}{chapter.3}%
+\contentsline {chapter}{\numberline {4}Demo}{5}{chapter.4}%
+\contentsline {chapter}{\numberline {5}Usability}{6}{chapter.5}%
+\contentsline {chapter}{\numberline {6}AIM\sphinxhyphen {}CU}{7}{chapter.6}%
+\contentsline {section}{\numberline {6.1}Methods}{7}{section.6.1}%
+\contentsline {subsection}{\numberline {6.1.1}CUSUM parameters}{7}{subsection.6.1.1}%
+\contentsline {subsection}{\numberline {6.1.2}CUSUM chart}{7}{subsection.6.1.2}%
+\contentsline {section}{\numberline {6.2}CUSUM}{8}{section.6.2}%
+\contentsline {section}{\numberline {6.3}ARLTheoretical}{9}{section.6.3}%
+\contentsline {section}{\numberline {6.4}Utils}{10}{section.6.4}%
+\contentsline {chapter}{\numberline {7}Disclaimer}{12}{chapter.7}%
+\contentsline {chapter}{Python Module Index}{13}{section*.21}%
+\contentsline {chapter}{Index}{14}{section*.22}%

docs/source/conf.py

@@ -58,4 +58,5 @@ latex_elements = {
     \DeclareUnicodeCharacter{03BC}{\textmu}
     \DeclareUnicodeCharacter{03C3}{\ensuremath{\sigma}}
     ''',
+    'classoptions': ',oneside',
 }

src/package/cusum.py

@@ -442,65 +442,6 @@ class CUSUM:
             legend=dict(orientation="h", yanchor="bottom", y=1.02, xanchor="right", x=1)
         )
 
-        # # add histogram (like marginal histogram)
-        # nbinsx = 15  # 6
-
-        # # add subplots
-        # fig.add_trace(
-        #     go.Histogram(
-        #         y=self.data[: self.pre_change_days],
-        #         nbinsy=nbinsx,
-        #         # name=f"""Pre-change S<sub>p</sub>""",
-        #         showlegend=False,
-        #         marker=dict(color="mediumturquoise"),
-        #         opacity=0.4,
-        #         orientation="h",
-        #     ),
-        #     row=1,
-        #     col=2,
-        # )
-
-        # fig.add_trace(
-        #     go.Histogram(
-        #         y=self.data[self.pre_change_days : self.total_days],
-        #         nbinsy=nbinsx,
-        #         # name=f"""Post-change S<sub>p</sub>""",
-        #         showlegend=False,
-        #         marker=dict(color="coral"),
-        #         opacity=0.4,
-        #         orientation="h",
-        #     ),
-        #     row=1,
-        #     col=2,
-        # )
-
-        # fig.add_trace(
-        #     go.Scatter(
-        #         x=[0, 20],  # [! y_max can should be used]
-        #         y=[
-        #             np.mean(self.data[: self.pre_change_days]),
-        #             np.mean(self.data[: self.pre_change_days]),
-        #         ],
-        #         mode="lines",
-        #         # name="Reference mean",
-        #         showlegend=False,
-        #         line=dict(color="mediumturquoise", dash="dash"),
-        #     ),
-        #     row=1,
-        #     col=2,
-        # )
-
-        # fig.update_xaxes(
-        #     title_text="Count",
-        #     title_font_size=font_size_legend,
-        #     title_font_weight="bold",
-        #     row=1,
-        #     col=2,
-        # )
-
-        # # update layout
-        # fig.update_layout(barmode="overlay")
-
         if self.config["control"]["save_figure"] == "true":
             fig.write_image(
                 os.path.join(