sachs notes to sachs

[rainersachs]

To Do

1. Make figures for visual double check of one-ion models: nte, te-only, SLI, Cuc and other strawman models
2. calculate AIC, LOO
3. Use elementary IEA for paper; generalized IEA (both standard conventional and AIVP one-ion models in one dI/dd sum in supplement. 4 Decide on LETs: values in .csv files are masters
4. Formal hypothesis testing
5. Clean up notation and commenting! rename
6. Calculate Polly background (about 4 +- 1 %). Robustness of TE-only vs. NTE-also vis-a-vis changes in Y_0.

[rainersachs]

Edward: I want to move all the files except the six with the prefix "ox_" into the folder "obsolete". Is there a fast way to do that? If the answer is "no" please don't do it, just tell me an I will do it.

More generally, when I display my repositories on my home GitHub page, I get ones that I no longer use, don't own, and don't want to see, all mixed in with others that are, e.g., needed for published papers. Is there a way to get them into some sort of hierarchy/

[rainersachs]

Edward: ox_plots.R still needs work.

There are still references to nte4. I haven't looked at ox_monteCarlo.R to see if it also has anything about nte4

Some of the plots call dataframe rows by row number instead of some method that automatically updates when rows are inserted or deleted in the 1-ion ,csv

I could fix all that but you could do it faster, better, and much more reliably. So please do as much as you can if you still have a bit of extra time. Then turn it over to me.

I still have to update the mixture input file, I'll do that next.

see you Thursday 10:45 unless you are out of time

[eghuang]

Ray:

You may have found the last reference to nte4 in the ox_ files. I looked through ox_dataAndInfo.R, ox_plots.R, and ox_monteCarlo.R, and did not find any remaining references.

I've changed the plotting calls that include ion_data to reference beam type rather than row number. This should better accommodate updates to the data. There are a few calls that use mix_data but they are all commented out aside from one so I will assume they are low priority. The one mix_data call that is not commented out also references beam type so I think that one is okay as is for now. I have not found any other references to the dataframes that involve row numbers/indexing in ox_plots.R. Let me know if you come across any.

[rainersachs]

Good! Thanks. That is rather good news.

On Sun, Feb 10, 2019 at 4:59 PM Edward G. Huang notifications@github.com wrote:

Ray:

You may have found the last reference to nte4 in the ox_ files. I looked through ox_dataAndInfo.R, ox_plots.R, and ox_monteCarlo.R, and did not find any remaining references.

I've changed the plotting calls that include ion_data to reference beam type rather than row number. This should better accommodate updates to the data. There are a few calls that use mix_data but they are all commented out aside from one so I will assume they are low priority. The one mix_data call that is not commented out also references beam type so I think that one is okay as is for now. I have not found any other references to the dataframes that involve row numbers/indexing in ox_plots.R. Let me know if you come across any.

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[rainersachs]

Notes to myself. In PLoS abstract: These endpoints include mammal tumor prevalence as a function of dose and chromosome aberration frequency, sometimes described as a "tumor surrogate", as a function of dose. The endpoint of interest in this paper is radiogenic tumors in murine Harderian glands, 2 small organs, one in each eye that most rodents have. i

[rainersachs]

under construction

[rainersachs]

egh_rks_agenda_2.15.2019.pdf

[rainersachs]

Edward: here are 2 pdfs detailing suggestions for the PloS Biology pre-submission. there is no hurry and the priorities remain: 1. help the CA pod if they request or are seen to need help; 2 (tied) clean up the scripts for the mouse HG pod, which work but are very ugly due to my programming and commenting clumsiness; 2(tied) this presubmission; 3 actual science in the form of the Shuryak paper, which we will hopefully manage to get to a little bit just so we can mix in some fun. As always your classes, your regent's advisory responsibilities, etc should take precedence over URAP.

There will surely be a lot to discuss about those pdfs next Friday! 19sp_cannibalize_minor_mouse_paper_v5.pdf 19sp_minor_mouse_paper_v5_frozen.pdf