saving current work and plans

Latex/Paper/outline3.txt

@@ -0,0 +1,41 @@
+How do I begin work on stuff
+
+- next step is causal story. key points include
+    - we are trying to separate strategic and operational concerns. (why is this a difficult problem?)
+        - we can't trust what we are told
+        - terminations could be due to safety, strategic, or operational concerns.
+    - explaining confounding between 
+        -population/market and market conditions.
+        - market conditions and enrollment. 
+        - population/market and enrollment.
+    - describe other confounders
+        - safety and effectiveness
+        - duration <--> enrollment/termination
+        - Condition 
+        - Decision to procede with Phase III trial
+    - How do I handle this?
+- Introduce Do-Calculus
+    - DAG model
+    - What do I need to control for, in some form or other?
+- Introduce Data
+    - Clinical Trial Progression
+        - AACT gives us information on
+            - terminated/completed status
+            - compound-indication pairs
+            - MeSH/RxNorm links
+        - Snapshots
+    - Market Conditions
+        - can't directly measure alternate treatments/standards of care.
+        - Can get measures of USP - formulary alternatives
+        - Can get number of generics or brand names with same drug.
+    - Population Sizes
+        - IHME Global Burden of Disease dataset. Best measure of impact of a given disease category.
+            - DALY's
+    - How much data do I have?
+- Econometric model
+    - for a given state, what is the probability it will terminate?
+        - more accurately for my dist-diff analysis: for a given state, what is the distribution of the probabilities it will terminate?
+    - basic bernoulli-logistic model, linear in parameters.
+    - What are the specific things I am looking at?
+        - number of competing treatments.
+        - delaying close of enrollment.

Latex/Paper/sections/03_CausalIdentification.tex

@@ -2,31 +2,33 @@
 \graphicspath{{\subfix{Assets/img/}}}
 
 \begin{document}
-% Introduce clinicaltrials.gov
+% % Introduce clinicaltrials.gov
-% - Describe different statuses 
+% % - Describe different statuses 
-% - status flowchart
+% % - status flowchart
-% Introduce causal model
+% % Introduce causal model
-% - Diagram
+% % - Diagram
-% - List each node and what they influence (and why)
+% % - List each node and what they influence (and why)
-% Begin Discussing Data
+% % Begin Discussing Data
-% - Where did I get data for each node?
+% % - Where did I get data for each node?
-
+%
-When any clinical trial is conducted, it goes through three distinct stages:
+% When any clinical trial is conducted, it goes through three distinct stages:
-pre-trial, active, and decision to conclude.
+% pre-trial, active, and decision to conclude.
-In figure \ref{Fig:Stages}, you can see the component parts of each stage. 
+% In figure \ref{Fig:Stages}, you can see the component parts of each stage. 
+%
+% \begin{figure}[H] %use [H] to fix the figure here.
+%     \includegraphics[width=\textwidth]{../assets/img/ClinicalTrialStagesAndStatuses}
+%     \caption{Model of Statuses}
+%     \label{Fig:Stages}
+% \end{figure}
+%
+% In the pre-trial stage, the sponsoring organization chooses to run the trial,
+% they register the trial on  \url{ClinicalTrials.gov}, and then decide if they
+% will begin enrollment. 
+% Many registered trials are withdrawn at this point, before the trial has opened
+% for enrollment. 
+% Once enrollment has opened 
 
-\begin{figure}[H] %use [H] to fix the figure here.
-    \includegraphics[width=\textwidth]{../assets/img/ClinicalTrialStagesAndStatuses}
-    \caption{Model of Statuses}
-    \label{Fig:Stages}
-\end{figure}
 
-In the pre-trial stage, the sponsoring organization chooses to run the trial,
-they register the trial on  \url{ClinicalTrials.gov}, and then decide if they
-will begin enrollment. 
-Many registered trials are withdrawn at this point, before the trial has opened
-for enrollment. 
-Once enrollment has opened 
 
 Because running randomized experiments on companies running clinical trials 
 is unlikely to to happen anytime soon, 

Latex/Paper/sections/10_CausalStory.tex

@@ -3,6 +3,10 @@
 
 \begin{document}
 
+Begin by talking about goal, what does it mean? This might need some work prior to give more background.
+
+%%%%% \/\/\/\/\/ OLD STUFF \/\/\/\/\/
+
 Because running experiments on companies running clinical trials is not going
 to happen anytime soon, causal identification will depend on creating a 
 structural causal model.

Latex/Paper/sections/12_clinical_trial_background.tex

@@ -14,7 +14,8 @@
 %   - 
 %   - 
 
-To understand how my administrative clinical trial is obtained, 
+To understand how my administrative clinical trial data is obtained
+and what it can be used for, 
 let's take a look at how trial investigators record data on 
 \url{ClinicalTrials.gov} operate.
 Figure \ref{Fig:Stages} illuistrates the process I describe below.
@@ -39,7 +40,7 @@ marked as ``Terminated'' on
 \url{ClinicalTrials.gov}.
 
 
-\begin{figure}[H] %use [H] to fix the figure here.
+\begin{figure}%[H] %use [H] to fix the figure here.
     \includegraphics[width=\textwidth]{../assets/img/ClinicalTrialStagesAndStatuses}
     \par \small 
         Diamonds represent decision points while
@@ -62,55 +63,31 @@ Unfortunately, although termination documentation typically includes a
 description of a reason for the clinical trial termination, this doesn't necessarily
 list all the reasons contributing to the trial termination and may not exist for a given trial.
 
-% SHOULD I EXPLAIN THE CLINICAL TRIALS DATA, i.e. AACT and SCRAPING EFFORT YET?
+As a trial goes through the different stages of recruitment, the investigators
-% For this reason we use administrative data, the records of clinical trial states, to track how trials proceed.
+update the records on ClinicalTrials.gov. 
-% There is also the issue of confounding between different 
+Even though there are only a few times that investigators are required 
+to update this information, it tends to be updated somewhat regularly as it is 
+a way to communicate with potential enrollees. 
+When a trial is first posted, it tends to include information
+such as planned enrollment, 
+planned end dates, 
+the sites at which it is being conducted, 
+the diseases that it is investigating, 
+the drugs or other treatments that will be used,
+the experimental arms that will be used,
+and who is sponsoring the trial.
+As enrollment is opened and closed and sites are added or removed, 
+investigators will update the status and information
+to help doctors and potential participants understand whether they should apply. 
 
 
 
-% \begin{enumerate}
+% - 
-%     \item The compound demonstrates sufficient safety and efficacy, and proceeds in the appoval process. 
+% - 
-%         \label{Item:EndSuccess}
+% - 
-%     \item The compound fails to demonstrate sufficient safety and efficacy, and the approval process halts. 
+% - 
-%         \label{Item:EndFail}
+% - 
-%     \item The trial is terminated before it can acheive one of the first two 
+% - 
-%         outcomes, for reasons unrelated to safety and efficacy concerns. 
-%         \label{Item:Terminate}
-% \end{enumerate}
-% 
-% 
-% \begin{table}
-%     \caption{Potential States of Knowledge from a clinical trial}\label{tab:StatesOfKnowledge}
-%     \begin{center}
-%         \begin{tabular}{p{0.15\textwidth} p{0.2\textwidth}||p{0.25\textwidth}|p{0.25\textwidth}|}
-%         \cline{3-4}
-%             \multicolumn{2}{c|}{Drug-Indication Match}  & safe and efficacious & not safe or not efficatious \\
-%         \hline
-%         \hline
-%             \multirow{2}{0.15\textwidth}{Operations} & Success & Known good & Known bad \\
-%         \cline{2-4}
-%             & Failure & \multicolumn{2}{c|}{Unkown} \\
-%         \cline{2-4}
-%         \end{tabular}
-%     \end{center}
-% \end{table}
-% 
-% 
-% \begin{table}
-%     \caption{Clinical Trial end states}\label{tab:ClinicalTrialEndStates}
-%     \begin{center}
-%         \begin{tabular}{p{0.15\textwidth} p{0.2\textwidth}||p{0.25\textwidth}|p{0.25\textwidth}|}
-%         \cline{3-4}
-%             \multicolumn{2}{c|}{Drug-Indication Match}  & safe and efficacious & not safe or not efficatious \\
-%         \hline
-%         \hline
-%             \multirow{2}{0.15\textwidth}{Operations} & Success & Completion & Completion or Termination \\
-%         \cline{2-4}
-%             & Failure & \multicolumn{2}{c|}{Termination} \\
-%         \cline{2-4}
-%         \end{tabular}
-%     \end{center}
-% \end{table}
 
 
 \end{document}