added details to causal story, enabled latex todos, updated laptop layout

Latex/Paper/jmp_layout_laptop.kdl

@@ -33,7 +33,7 @@ layout {
         }
     }
 
-    tab name="sections" cwd="~/research/phd_deliverables/jmp/Latex/Paper" {
+    tab name="sections" cwd="~/research/phd_deliverables/jmp/Latex/Paper/sections" {
         pane size=1 borderless=true {
             plugin location="tab-bar"
         }

Latex/Paper/sections/10_CausalStory.tex

@@ -110,7 +110,9 @@ it continues to completion.
              \tikzfig{../assets/tikzit/CausalGraph2}
     }
     }
+    \todo{check if this is the correct graph}
     \caption{Graphical Causal Model}
+    
     % \small{Crimson boxes are the variables of interest, 
     % white boxes are unobserved, while the gray boxes will be controlled for.}
     \label{Fig:CausalModel}
@@ -119,9 +121,10 @@ it continues to completion.
 
 % Constructing the model more explicitly
 % - quickly describe each node and line.
-% TODO: double check which graphic to use.
+\todo{I think I need to blend the data section in before this, to give some overall information on data.}
+\todo{I may need to add some information on snapshots so that this makes sense.}
 
-A quick summary of the nodes of the DAG and their impact: 
+A quick summary of the nodes of the DAG, the exact representation in the data, and their impact: 
 \begin{itemize}
     \item Main Interests (Crimson Boxes)
         \begin{enumerate}
@@ -129,21 +132,34 @@ A quick summary of the nodes of the DAG and their impact:
                 If the final status of the trial was \textit{terminated} 
                 or \textit{completed}.
             \item \texttt{Enrollment Status}: 
-                Measure of whether enrollment is progressing.
+                    This describes the current enrollment status of the snapshot, e.g. 
+                    \texttt{Recruiting},
+                    \texttt{Enrolling by invitation only},
+                    or
+                    \texttt{Active, not recruting}.
             \item \texttt{Market Measures}: 
                 Various measures of the number of alternate drugs on the market.
+                These are either the number of other drugs with the same active ingredient as the trial
+                (both generic and originators),
+                and those considered alternatives in various formularies published by the United States Pharmacopeia.
         \end{enumerate}
     \item Observed Confounders (Gray Boxes)
         \begin{enumerate}
             \item \texttt{Condition}: 
-                The underlying condition. 
+                The underlying condition, classified by IDC-10 group. 
                 This impacts every other aspect of the model.
             \item \texttt{Population (market size)}: 
-                Multiple measures of the impact the disease has (in DALYs).
+                Multiple measures of the impact the disease.
+                These are measured by the DALY cost of the disease in countries that have a 
+                High, High-Medium, Medium, Medium-Low, and Low development scores.
+                This data comes from the Institute for Health Metrics' Global Burden of Disease study.
             \item \texttt{Elapsed Duration}: 
-                A normalized measure of the trial progression.
+                A normalized measure of the time elapsed in the trial. 
+                Comes from the original estimate of the trial's primary completion date and the registered start date. 
+                I take the difference in days between these, and get the percentage of that time that has elapsed.
             \item \texttt{Decision to Proceed with Phase III}: 
                 If the compound development has progressed to Phase III.
+                This is included in the analysis by only including Phase III trials.
         \end{enumerate}
     \item Unobserved Confounders (White Boxes)
         \begin{enumerate}
@@ -151,9 +167,12 @@ A quick summary of the nodes of the DAG and their impact:
                 The underlying safety of the compound. 
                 Cannot be observed, only estimated through scientific study.
             \item \texttt{Previously observed Efficacy and Safety}: 
-                The information gathered in previous studies.
+                The information gathered in previous studies. 
+                This is not available in my dataset because I don't have links to prior studies.
             \item \texttt{Currently observed Efficiency and Safety}:
                 The information gathered during this study.
+                This is only partially available, and so is treated as unavailable. 
+                After a study is over, the investigators are supposed to publish information about adverse events.
         \end{enumerate}
 \end{itemize}
 

Latex/assets/preambles/GeneralPreamble.tex

@@ -2,6 +2,7 @@
 \usepackage{booktabs} % Allows the use of \toprule, \midrule and \bottomrule in tables
 \usepackage{hyperref} %Includes Hyperlinks
 \usepackage{cleveref} %Simplifies citations and references
+\usepackage{todonotes} % Allows using todo-notes
 
 
 %Setup some language stuff