The paper is fully published now, so I'm adding final reference info to the repository. I did not modify any scripts for managing or analyzing the data, so I did not re-render the output files. Re-rendering them from this version of the repository should yield same results as shown under 1.0.3 except that the reference entry for the paper will be in final form and the software information sections should now show CHOPStudy v1.0.4 instead of v1.0.3.
README.qmdandREADME.md- Update software version & citation info.
scripts/references.bib- Update software version & citation info.
- Updated to include final citation for the published paper.
The journal requested minor edits to Figures 1 & 2 during proofreading. All changes here aim to satisfy that request and then update associated version information , documentation, and final rendered output.
README.qmdandREADME.md- Update software version & citation info.
- Update example rendering command line to match when I generated final output for the paper.
- Update Repository Structure section to list additional output files.
- Rendered all scripts & committed output to GitHub.
scripts/output/Descriptive_Analysis_2026-01-29.htmlscripts/output/Figure_1.pngscripts/output/Figure_2.pngscripts/output/GLMM_Analys1s_2026-01-29.htmlscripts/output/Import_Data_2026-01-29.htmlscripts/output/Render_Scripts_2026-01-29.html
- Removed outdated output files.
scripts/output/Descriptive_Analysis_2026-01-26.htmlscripts/output/GLMM_Analys1s_2026-01-26.htmlscripts/output/Import_Data_2026-01-26.htmlscripts/output/Render_Scripts_2026-01-26.html
scripts/Descriptive_Analysis.qmd- Fixed symbol for units of measurement in exported Figure 1 file.
scripts/GLMM_Analysis.qmd- Fixed axis tick mark label to use a proper minus sign instead of a hyphen in exported Figure 2 file.
scripts/references.bib- Update software version & citation info.
README.qmdandREADME.md- Update software version & citation info.
- Added final figures rendered with version 1.0.0
scripts/output/Figure_1.pngscripts/output/Figure_2.pngscripts/output/Figure_3.png
scripts/references.bib- Update software version & citation info.
README.qmdandREADME.md- Added DOI badge, updated reference list entry.
scripts/references.bib- Updated entry for the package to include DOI.
The manuscript will be accepted by Animals (https://www.mdpi.com/journal/animals) pending minor revisions due tomorrow. One of the final edits is inserting info about this research compendium. Once version 1.0.0 of this package/repository is published and publicly available, I will get a DOI assigned and then release a version 1.0.1 that adds that information to the repository. Subsequent updates after that may also add final citation information for the paper (after it is published and gets a DOI of its own).
Package changes listed below all relate to final preparations for public release of the package. I'm cleaning things up, removing obsolete files, etc.
DESCRIPTION- Updated Suggests field with final list of packages used in our scripts.
- Updated licensing for the package.
LICENSELICENSE.mdLICENSE.note
README.qmdandREADME.md- Update software version & citation info.
- Updated text to prepare for public release.
- Updated badges and info about repository status.
.gitignore- Stopped ignoring data files to prepare for public release.
data/Imported_CHOP_Data.RData- Added file.
graphics/- Removed folder containing logo files I ended up not using.
R/Placeholder.R- Removed a file that is no longer needed.
man/CHOPStudy-package.Rd- Updated package-level help.
scripts/extdata/Vinc_Cases_2026-01-26.xlsx- Added the raw data file.
- Rendered all scripts & committed output to GitHub.
scripts/output/Descriptive_Analysis_2026-01-26.htmlscripts/output/GLMM_Analys1s_2026-01-26.htmlscripts/output/Import_Data_2026-01-26.htmlscripts/output/Render_Scripts_2026-01-26.html
scripts/Analyze_Data.qmd- Removed an obsolete file associated with earlier iterations of the manuscript that were sent to other journals. It was superceded by scripts that remain in the repository but are better organized and consistent with the final paper.
scripts/Import_Data.qmd- Switched to an updated data file that excludes MRN variable (i.e., to a de-identified data file) and updated code that used that variable.
- Added a callout in Purpose section.
scripts/Render_Scripts.qmd- Updated purpose section, added References section.
- Updated list of R packages loaded.
- Added a callout in in Assumptions section.
- Removed citation style language files that I did not use in this particular
package.
scripts/apa-numeric-superscript.cslscripts/apa-numeric-superscript-brackets.csl
- Removed example scripts that are no longer needed. Final scripts remain in
the repository.
scripts/Example_Render_to_HTML.qmdscripts/Example_Render_to_PDF.qmd
- Removed LaTeX files that were not used (we used HTML output in this project
instead of PDF output).
scripts/compact-title.texscripts/title.tex
scripts/references.bib- Update software version & citation info.
- Update citation for our manuscript.
README.qmdandREADME.md- Update software version & citation info.
- Updated example Terminal command for rendering
Render_Scripts.qmdto date-stamped output.
scripts/Import_Data.qmd- Update to use new data file because we added an extra variable.
scripts/Descriptive_Analysis.qmd- Added Sickness section and other output relevant to sickness variables.
- Added Bandemia by Visit Number section.
- Added output in Drug Sequences section.
scripts/references.bib- Update software version & citation info.
README.qmdandREADME.md- Update software version & citation info.
- Updated example Terminal command for rendering
Render_Scripts.qmdto date-stamped output.
scripts/Descriptive_Analysis.qmd- Updated dosage variable name to use correct units.
scripts/GLMM_Analysis.qmd- Improved narrative text.
scripts/Import_Data.qmd- Update to use new data file because we detected and corrected a data entry error for Patient = 26 in which drug was used at visit 1.
- Update to use new data file because we detected and corrected a data entry error for Patient = 30, Visit_Number = 5 where dosage was incorrect (detected because it was too small for the drug used). Also updated dose variable name to use correct units.
- Removed an old callout that's not useful anymore.
scripts/references.bib- Update software version & citation info.
DESCRIPTION- Replace the term "incidence" with "prevalence" (more accurate term) in text and then fix line breaks for readability.
README.qmdandREADME.md- Update software version & citation info.
- Replace the term "incidence" with "prevalence" (more accurate term) in text and then fix line breaks for readability.
scripts/Descriptive_Analysis.qmd- Added a table about numbers of patients with specific combinations across visit 1 and 2.
scripts/GLMM_Analysis.qmd- Replace the term "incidence" with "prevalence" (more accurate term) in text and then fix line breaks for readability.
scripts/references.bib- Update software version & citation info.
README.qmdandREADME.md- Update software version & citation info.
scripts/GLMM_Analysis.qmd- Reverted Model 2 predictors to previous state and added Model 3 to better test the new age and sex effects.
scripts/references.bib- Update software version & citation info.
DESCRIPTION- Updated Suggests field to include more packages used by Quarto scripts.
README.qmdandREADME.md- Update software version & citation info.
scripts/Descriptive_Analysis.qmd- Added analyses for new variables.
scripts/GLMM_Analysis.qmd- Added predictors to Model 2.
scripts/Import_Data.qmd- Update to use a new data file containing exctra variables: Age_Yrs, Sex, Breed, Diagnosis, Stage, Substage, Phenotype, In_Final_Patients, In_Final_Visits, and Dose_mgpkg. Fixed 2 cases with missing values on patient characteristics and removed 4 rows that were repeat CBCs after the same chemo event (we kept the earliest record for each event), fixed a couple dose values .
- Improve narrative text.
- Fix method for creating initial All_Patients dataset with unique patient records.
- Recoded Sex & created Neutered variable.
- Recoded some missing data.
- Add variables to All_Patients.
scripts/references.bib- Update software version & citation info.
- Update manuscript title.
scripts/Render_Scripts.qmd- Load another package so version info will be more complete.
README.qmdandREADME.md- Update software version & citation info.
scripts/Descriptive_Analysis.qmd- Update resolution for exported figures to meet journal requirements.
scripts/GLMM_Analysis.qmd- Update resolution for exported figures to meet journal requirements.
scripts/references.bib- Update software version & citation info.
.gitignore- Omit Windows thumbnail image files from tracking.
- Omit png files from tracking.
README.qmdandREADME.md- Update software version & citation info.
- Added instructions for getting date-stamped output for production runs.
scripts/Descriptive_Analysis.qmd- Export figure to graphics file suitable for journal submission.
- Add callout about figure used in manuscript.
scripts/GLMM_Analysis.qmd- Export figures to graphics file suitable for journal submission.
- Update callouts about which figures are used in manuscript.
scripts/Import_Data.qmd- Updated external data file being imported (filled in 1 missing value for total neutrophils based on reviewing medical chart).
scripts/references.bib- Update software version & citation info.
DESCRIPTION- Updated RoxygenNote and Suggests fields.
README.qmdandREADME.md- Update software version & citation info.
scripts/Descriptive_Analysis.qmd- Removed a callout about a figure we are no longer including in the manuscript.
scripts/GLMM_Analysis.qmd- Updated callouts about which figures we are including in the paper.
- Add citations for glmmTMB.
scripts/references.bib- Update software version & citation info.
- Updated citation for manuscript in preparation.
- Add citations for glmmTMB.
.Rbuildignore- Omit the
graphicsfolder to resolve a devtools::check() note.
- Omit the
DESCRIPTION- Moved piercer from Depends to Suggests field to resolve devtools::check() note.
README.qmdandREADME.md- Update software version & citation info.
- Add citation for manuscript in preparation.
scripts/Descriptive_Analysis.qmd- Remove blank lines.
- Add citation for manuscript in preparation.
- Remove obsolete callouts.
scripts/GLMM_Analysis.qmd- Add callouts about which figures will be used in manuscript.
- Fix spelling.
- Improve narrative text.
- Update interpretation to reflect results after updated case selection.
- Omit a warning message.
scripts/Import_Data.qmd- Update case selection to use only dogs whose visit 1 was within 10 days of CHOP start.
- Improve narrative text.
- Remove blank lines.
- Add citation for manuscript in preparation.
scripts/references.bib- Update software version & citation info.
- Add citation for manuscript in preparation.
README.qmdandREADME.md- Update software version & citation info.
scripts/Descriptive_Analysis.qmd- Capitalize names of drugs.
- Add table of drug sequences that start with cyclophosphamide.
- Update labeling of band cagegories in a figure.
scripts/GLMM_Analysis.qmd- Capitalize names of drugs.
scripts/Import_Data.qmd- Capitalize names of drugs.
- Update definition & labeling of Bandemia and Band_Category. This should not affect summaries because Total_Bands is only stored to 1 decimal precision.
scripts/references.bib- Update software version & citation info.
README.qmdandREADME.md- Update software version & citation info.
scripts/Descriptive_Analysis.qmd- Add a frequency table for Band_Category.
- Compute additional weight summaries.
scripts/GLMM_Analysis.qmd- Improve narrative text.
- Update figure & table captions.
- Switch from relative risk to risk differences.
scripts/references.bib- Update software version & citation info.
README.qmdandREADME.md- Update software version & citation info.
scripts/_quarto.yml- Update render key to include another script.
scripts/GLMM_Analysis.qmd- Change figure size.
scripts/references.bib- Update software version & citation info.
README.qmdandREADME.md- Update software version & citation info.
scripts/Descriptive_Analysis.qmd- Stop loading a package we no longer use.
scripts/GLMM_Analysis.qmd- Improve narrative text.
- Improve table formatting.
- Change figure sizes.
- Improve figure formatting.
- Stop loading packages we no longer use.
scripts/Render_scripts.qmd- Load more packages.
- Update chunks for running other scripts.
scripts/references.bib- Update software version & citation info.
README.qmdandREADME.md- Update software version & citation info.
scripts/GLMM_Analysis.qmd- Add comments about packages loaded.
- Update methods text.
- Update modeling output and narrative text.
scripts/Import_Data.qmd- Updated Final_Visits and Final_Patients with additional variables.
scripts/references.bib- Update software version & citation info.
README.qmdandREADME.md- Update software version & citation info.
scripts/GLMM_Analysis.qmd- Load more packages.
- Improve narrative text.
- Improve model output and diagnostic checks.
scripts/references.bib- Update software version & citation info.
- Add references.
README.qmdandREADME.md- Update software version & citation info.
scripts/Descriptive_Analysis.qmd- Load another R package.
- Add missing data summaries.
- Add a plot of total bands vs total neutrophils.
- Switch to black & white theme for figures.
- Remove output for Total_Bands_rescaled.
- Improve figure caption and labeling.
- Improve table caption.
- Reorganize and improve total bands section.
- Reorganize and improve total bands by drug section.
- Reorganize and improve total bands by visit section.
- Extensively renamed chunks
- Switched to ggplot for several figures to make code clearer.
scripts/GLMM_Analysis.qmd- Added file.
scripts/Import_Data.qmd- Added centered variables needed for GLMM analyses.
scripts/references.bib- Update software version & citation info.
- Added references.
scripts/_quarto.yml- Updated Render key to include modeling script.
README.qmdandREADME.md- Update software version & citation info.
scripts/Descriptive_Analysis.qmd- Added meta-data details about data file loaded.
- Improve narrative text.
- Improve table formatting.
- Add table of drug sequences.
- Updated table of band category distribution by drug and added a figure of those results.
scripts/Import_Data.qmd- Added meta-data details about files read in and saved out.
- Improve narrative text.
- Added Band_Category and Name variables.
scripts/references.bib- Update software version & citation info.
README.qmdandREADME.md- Update software version & citation info.
- Update repository contents section.
scripts/Descriptive_Analysis.qmd- Add references section.
- Improved marrative text and chunk labels.
- Fixed a table that was broken by solving missing data.
- Fixed a warning about using outdated code for histograms.
- Fix Bandemia Grade table.
- Add table for leukemic status.
scripts/Import_Data.qmd- Read an updated data file that fixed some missing data issues, clarified that Leukemia and steroid variabkles are time-invariant within a CHOP cycle, standardarized steroid names, and confirmed some date corrections.
- Add references section.
- Add Leukemic to Final_Patients data.
scripts/references.bib- Update software version & citation info.
README.qmdandREADME.md- Updated software version info & references.
scripts/Descriptive_Analysis.qmd- Added default output file name.
- Enabled global chunk option for warnings.
- Removed FloatBarrier commands (only need those for PDF output).
scripts/Import_Data.qmd- Added default output file name.
- Enabled global chunk option for warnings.
- Removed FloatBarrier commands (only need those for PDF output).
- Improved narrative text.
- Update load-packages chunk.
scripts/Render_scripts.qmd- Add a subtitle.
- Convert from PDF to html output.
scripts/references.bib- Updated software version info & references.
README.qmdandREADME.md- Improved narrative text.
- Updated software version info & references.
scripts/references.bib- Updated software version info & references.
DESCRIPTION- Updated Depends field to require newer version of R.
README.qmdandREADME.md- Improved narrative text.
- Updated software version info & references.
scripts/Example_Script.Rmd- Deleted file because this project uses Quarto instead of R Markdown.
scripts/Import_Data.qmd- Read a newer data file.
scripts/references.bib- Updated software version info & references.
scripts/Descriptive_Analysis.qmd- Rename some chunks.
- Update patient descriptive table to show number of visits.
- Remove obsolete tables.
- Fix table captions.
- Improve narrative text.
- Improve table structure and labeling.
- Add frequency table of categorical biomarker variables.
- Update heading structure.
- Move and improve table for drug frequency distribution.
- Add frequency table for visit number.
- Simplify table code.
- Add table of continuous biomarkers broken down by bandemia.
- Change table order and add another table.
scripts/Import_Data.qmd- Improved narrative text and code comments.
- Add some binary variables.
- Improved heading structure.
- Updated data file being read in. This one has additional variables, plus it corrected a couple inaccurate CBC_Date values. Removed code no longer required because of that.
- Recoded toxic change variable.
- Remove obsolete output.
scripts/Descriptive_Analysis.qmd- Load additional packages.
- Add patient and visit-level descriptive tables.
- Improve histograms of total bands.
- Update data frame names.
scripts/Import_Data.qmd- Renamed data frames and chunks.
- Added assumption checks.
- Added patient-level dataset.
- Add variables to an intermediate data frame.
- Add tables to show which records were dropped.
- Updated list of data frames saved out.
- Move code for renaming data frame.
- Subset the patient-level data.
- Update heading structure.
- Fix patient's data frame.
scripts/.gitignore- Added file.
scripts/_quarto.yml- Add output-dir key and list scripts to render.
scripts/Descriptive_Analysis.qmd- Add file based on copying parts from
scripts/Analyze_data.qmd
- Add file based on copying parts from
scripts/Import_Data.qmd- Improve narrative text.
- Improve figure caption.
- Improve section on subsetting the data.
- Update saving out data.
- Add a subtitle.
- Remove cfsize knitr chunk option (not relevant in HTML output).
- Define new variables.
scripts/references.bib- Updated references.
scripts/Import_Data.qmd- Change author order because I'm re-working things a lot.
- Improve narrative text and callouts.
- Update load-packages chunk.
- Change i_am() call to reflect new filename.
- Change chunk labels and object names to clarify the code.
- Simplify and reorganize data cleaning.
- Add a section for further subsetting data.
- Add a section for saving data file.
- Sorted the data.
- Improved data cleaning sections and code.
- Updated descriptive statistics on visit timing after data cleaning.
- Added section for identifying cases where visit 1 happened within 2 weeks of starting CHOP.
- Started summarizing amount of data at each step of case selection.
- Temporarily disable saving out data.
scripts/Analyze_Data.qmd- Update section for loading data.
scripts/Render_Scripts.qmd- Added file.
scripts/_brand.yml- Switch to Arial for base font.
scripts/Import_Data.qmd- Added file.
scripts/Analyze_Data.qmd- Added file.
scripts/Render_Scripts.qmd- Added file.
- Created package and did initial setup.