From 70c2eeb5f5b73de1d38b9d3e510e185a025fc84b Mon Sep 17 00:00:00 2001 From: Will King Date: Tue, 19 Nov 2024 12:30:28 -0800 Subject: [PATCH] added details to causal story, enabled latex todos, updated laptop layout --- Latex/Paper/jmp_layout_laptop.kdl | 2 +- Latex/Paper/sections/10_CausalStory.tex | 33 +++++++++++++++++----- Latex/assets/preambles/GeneralPreamble.tex | 1 + 3 files changed, 28 insertions(+), 8 deletions(-) diff --git a/Latex/Paper/jmp_layout_laptop.kdl b/Latex/Paper/jmp_layout_laptop.kdl index 117747a..b2e6533 100644 --- a/Latex/Paper/jmp_layout_laptop.kdl +++ b/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" } diff --git a/Latex/Paper/sections/10_CausalStory.tex b/Latex/Paper/sections/10_CausalStory.tex index f3aa6aa..9ce9614 100644 --- a/Latex/Paper/sections/10_CausalStory.tex +++ b/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} diff --git a/Latex/assets/preambles/GeneralPreamble.tex b/Latex/assets/preambles/GeneralPreamble.tex index 489970c..1a1535c 100644 --- a/Latex/assets/preambles/GeneralPreamble.tex +++ b/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