Notes and plans for writing

Paper/plan_to_update.md

@@ -0,0 +1,27 @@
+Plan
+
+get list of things that Tom says I'm Missing
+
+- Needs more citations
+- Standard econometric concerns: Endogenetiy, Simultineatiy, etc.
+- Needs to justify why I am doing what I am doing. What do I add? 
+    Marketwide attempt to measure the impact of enrollment, an operational concern.
+- 
+
+Integrate additional literature I've worked with.
+    - How big of a concern is operational results (about 22% of failures)
+    - Topics of how to address issues and what issues arise are common (give a couple of examples)
+    - Efforts to reduce failures include better pharmokinetics, attempts at improving enrollment, better enrollment prediction (huge lit).
+
+Then look at my outline:
+- How can I adjust it to address those missing bits?
+- How can I simplify the structure?
+
+Maybe a discussion of concerns about simultineity/endogeneity/other confounds/etc is where I 
+bring up the confounding parameters and then build a list of how things interact.
+I then use this to flesh out the DAG, and introduce the backdoor criterion.
+
+
+I think I'll put this together as a bullet point draft, using the * and - 
+notation for paragraphs and sentences respectively. Try to get the main points 
+of each sentence/paragraph out.

logs.org

@@ -5,3 +5,64 @@
     Need to decide whether or not to include this set of sentences.
 **** [2025-01-18 Sat 11:58] [[[[file:/home/will/research/phd_deliverables/JobMarketPaper/Paper/sections/11_intro_and_lit.tex::45]]]] 
     decide whether to include these details here
+** 2025-W17
+*** 2025-04-21 Monday
+**** [2025-04-21 Mon 11:17] Plan based on last weeks thinking things through
+   
+   get list of things that Tom says I'm Missing
+   
+   - Needs more citations
+   - Standard econometric concerns: Endogenetiy, Simultineatiy, etc.
+   - Needs to justify why I am doing what I am doing. What do I add? 
+       Marketwide attempt to measure the impact of enrollment, an operational concern.
+   - 
+   
+   Integrate additional literature I've worked with.
+       - How big of a concern is operational results (about 22% of failures)
+       - Topics of how to address issues and what issues arise are common (give a couple of examples)
+       - Efforts to reduce failures include better pharmokinetics, attempts at improving enrollment, better enrollment prediction (huge lit).
+   
+   Then look at my outline:
+   - How can I adjust it to address those missing bits?
+   - How can I simplify the structure?
+   
+   Maybe a discussion of concerns about simultineity/endogeneity/other confounds/etc is where I 
+   bring up the confounding parameters and then build a list of how things interact.
+   I then use this to flesh out the DAG, and introduce the backdoor criterion.
+   
+   
+   I think I'll put this together as a bullet point draft, using the * and - 
+   notation for paragraphs and sentences respectively. Try to get the main points 
+   of each sentence/paragraph out.
+   
+***** List of issues identified by Tom:
+
+      Reference style (Author year)
+      Reference better and more often.
+      Introduction needs to motivate the problem & what I am trying to do. (could use the sources I have on reasons for failures)
+      Various issues with tense etc. Use Claude.ai as editor for those.
+      Reorder sections or outline better
+
+      Causal inference vs DAG approach
+      - standard concens in causal inference
+      - DAG isn't causal inference in Toms view. He is right, DAG isn't but backdoor criterion is.
+      - Will need to discuss standard concerns and how they may be related and then incorporate that into the DAG
+      - Then will need to discuss backdoor criterion, the backdoor paths that exist, and choosing adjustment sets
+      - Replace bullet points with paragraphs (page 12) maybe use claude to convert that?
+      - Page 18 comment: Refer to Robins What IF book to get citation
+
+
+      Thoughts: 
+      Chapter 10: Lists 3 sources of bias in preceeding chapters (7,8,9)
+      - Selection
+      - Measurement
+      - Confounders
+      As I understand it, setting up the graph allows you to note where you 
+      might have issues with all 3. Do-calc gives you the adjustment set to 
+      handle confounding and selection, while measurement is handled either 
+      through modelling uncertanty or improving you measurement approach.
+
+***** Reading to complete before rewriting:
+
+      I think I should start by rereading (and taking notes on) What If and 
+      the Causal Mixtape.

todo.org

@@ -31,10 +31,10 @@
      Realized that this was readded by mistake. I integrated lit review into intro in 11
 ** 2025-W04
 *** 2025-01-20 Monday
-**** TODO get a citation for the AACT project  
+**** DONE get a citation for the AACT project  
     [[[[file:/home/will/research/phd_deliverables/JobMarketPaper/Paper/sections/10_CausalStory.tex::114]]]] 
 *** 2025-01-23 Thursday
-**** TODO Pickup citation fixes here  
+**** DONE Pickup citation fixes here  
     [[[[file:/home/will/research/phd_deliverables/JobMarketPaper/Paper/sections/06_Results.tex::174]]]] 
 ** 2025-W05
 *** 2025-01-30 Thursday
@@ -42,3 +42,26 @@
    
      So I need to create a cbo branch, remove references to betas, and finish 
      edits for submission tomorrow.
+*** 2025-02-01 Saturday
+**** TODO Plan for finishing jmp draft
+***** analysis updates 
+****** DONE apply fixes to main analysis
+****** DONE Remove rebased etc work
+       CLOSED: [2025-02-01 Sat 11:24]
+****** DONE reenable fit summary
+****** DONE increase sampleing size
+****** DONE reparameterize sigma
+       CLOSED: [2025-02-01 Sat 13:27]
+       Chagned to lognormal
+****** RECINDED remove last few groups that are not actual diseases
+       CLOSED: [2025-02-01 Sat 13:42]
+       decided to leave as is for now.
+***** graphics updates
+****** TODO remove quantity beta comparisons 
+****** TODO save status_diff analysis
+****** TODO change distdiff by group to include more groups
+***** writing updates
+****** TODO Remove discussions related to previous betas work
+****** TODO add in status_diff analysis
+****** TODO change mode info to match new lognormal(location,scale) priors
+