Moving code to master branch #88 #89
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Fix beach correlation heatmap (Issue #65)
Added references to the sources of FIB in Lake Michigan. Limited the research to Lake Michigan-specific research. Need to add formal citations instead of plain-text citations. Updated the bibliography file to prepare for this step.
Zotero made a chance where one of the bibliography entries was exported with the name "office_of_research_&_development_predictive_nodate". The "&" character is illegal as a naming character, which broke the Pandoc build process. I've replaced it with a better reference to the same paper, which fully specifies the author names.
Added references for #50
Calculate AUC values for various model ROCs
Resolves #75
Merge branch 'dev' into issue54 Conflicts: predicting-e-coli-concentrations.Rmd
* Replaces with Matthews Correlation Coefficient * Closes #62
* Pilot does not predict South Shore by design * South Shore was correctly excluded
Replace Chi-Squared Test with Matthews Correlation Coefficient
# Abstract * Rearranged some lines of text for readability # Introduction * Several grammar fixes # Material and Methods * Grammar fixes * Moved the map to within the section * Clarified that numbers applied to all beaches and timeframe for data # Results and Dsicussion * Updated phrasing and rearranged some sentences for clarity. * Removed a paragraph on qPCR and culture-based testing availability because it was mentioned in Section 1 # Supplementary Materials * Updated citation style. * Some wording updates for clarity.
Updated after full read-through; please review
Moved the narrative on the multivariate model from the appendix to a new section (now called Section 2.5). Moved the table A.4 from the appendix to accompany the narrative in section 2.5. The discussion on the model results was moved to section 3. Cleaned-up the language to fit within the existing text.
* Change test/train data for comparison with Pilot * Update table/figure numbers * Add modified multivariate model to table 2
Made a tweak from Table 2 to Table 3 for the fit data -- table order is changing. Changed reference from Figure 2 to Table 2 Added discussion on multivariate model in Section 3.2
I've combined new language mentioned in the comments with the existing language.
Revised discussion section to close #53
The underlying issue was LaTeX thought the best location for the table was at the end of the document. This would then place it in the appenix, also giving it the appendix table numbering. `kable()` invoked `longtable` in the resulting LaTeX, which keeps the table in the same location of the code. However, the use of kableExtra seemed to invoke the simple `table` in LaTeX, which floats the table. Interestingly, `kable_styling(latex_options = "hold_position")` did not work (which placed the [!h] option in LaTeX). However, invoking `longtable` in the `kable()` command did work. I've also swapped `setwd()` with `opts_knit$set(root.dir = ...)` per the documentation. This was not the cause of the issue, but did it to eliminate the possibility.
This table is spread over two-pages. This adjustment adds a "continued" header. It's likely the editors are picky about this.
Changed the reduction of false positive rate from 61.7% to 59.2% based on latest results. Added consistency to using "sensitivity" instead of "accuracy" throughout paper. Grammar corrections.
nicklucius
approved these changes
Sep 6, 2018
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I've pushed some grammar edits and one number correction to
devand opened a pull request.This is my last change. Please make any other changes to
devas needed.Please review as needed and add other comments as needed.