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README.md

@@ -15,49 +15,3 @@ This repository accompanies the manuscript "Viral kinetics of sequential SARS-Co
 - `save_figures.R` saves those figures 
 - `clearbigvars.R` clears storage-heavy variables to avoid crashing R or needlessly slowing down operations. 
 - `indiv_analysis_revised.R` runs the Spearman correlation analysis to detect persistence in viral kinetic parameters within individuals across first and second infections. 
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-## Reviews
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-- [ ] Conduct restricted analysis, considering only individuals with well-documented first and second infections 
-- [ ] Complete editorial policy checklist
-- [ ] Complete reporting summary 
-- [ ] Note in cover letter that sex/gender data were not systematically collected and so not analyzed 
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-- [ ] Find a way to make the comparisons even more concrete... 
-- [ ] Generate schematic to summarize the overall conclusions in the various groups 
-- [ ] Check if there is a relationship between the number of exposures and the clearance rate 
-- [ ] Describe statistical models in full, including: the form of the model, the parameters that are estimated, and the priors. Also: which Ct values were below LOD? How were these treated? Consider incorporating these rather than fully excluding them. 
-- [ ] Clarify that the pairwise clearance analysis really is just Spearman correlation. Maybe reduce some of the explanatory text there. Consider using standard approaches to calculate the p-value rather than bootstrapping. 
-- [ ] Consider including the clearance time consistency in the model itself, or at least including uncertainty in the clearance time estimates in the spearman correlation. 
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-- [ ] Re-phrase the caption in figure 1: "I would suggest to rephrase it and say "no well-documented pre-Omicron infection" or something similar"
-- [ ] Come up with a simplified representation of the comparison groups and present it as Fig 1 panel C (fits in with a previous comment too) - because Supp Table 1 is too confusing. 
-- [ ] Explain unexpected differences in Supp Table 1 counts in the caption. 
-- [ ] 88-90: define mean proliferation time, clearance time, and peak viral load. 
-- [ ] Note that people continued testing daily when possible even after testing positive 
-- [ ] Ask Joseph about standard curve stability over time 
-- [ ] Note brackets in Supp Table 2 are 95% CIs. 
-- [ ] Note in the Discussion/limitations that we didn't measure infectious virus. 
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-- [ ] Clarify "summary of recorded infections" since Supp Table 1 is hard to read. 
-- [ ] Clarify who is being compared in lines 90-96 
-- [ ] Figure 1B: clarify why n = 235 in the caption is greater than 193 in the text. 
-- [ ] Focus main figures on 58 infections with well-documented first and second infections and leave the other analyses to the supplement... (I don't agree) 
-- [ ] Repeat Figure 2 but only including the 58 with two well-documented infections. 
-- [ ] Explain why the confidence intervals in Figure 2A are narrow
-- [ ] 115-117: explain what "greater symmetry" means (rephrase, and maybe a brief mention of why we care) 
-- [ ] 123-126: Clarify differences in numbers here. 
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