spiroview is an R package that provides the tools to visualize and explore spirometry data in demographic studies. This package is targeted for the healthcare focused researcher who may not have an extensive coding background but wishes to use R for their research study. The spiroview package was developed using R version 4.2.1 (2022-06-23), Platform: x86_64-apple-darwin17.0 (64-bit), and Running under: macOS Big Sur 11.7.4.

To install the latest version of this package:

require("devtools")
devtools::install_github("annie951977/spiroview", build_vignettes = TRUE)

To run the Shiny app

spiroview::runspiroview()

spiroview at a glance:

ls("package:spiroview")
data(package = "spiroview")
browseVignettes("spiroview")

spiroview contains 10 functions:

formatData is a helper function that reads a csv or tsv datafile and reformats the dataframe so that the dataframe can be easily read into other functions in this dataset.

segregateBy splits a dataframe by a demographic value to allow for the extraction of data relating to a subset of interest.

calculateLLNPret calculates the lower limit of normal for a spirometric measurement based off of inputted demographic variables such as height, age, and gender and the spirometry reference of interest.

calculatePctPret calculates the percent predicted of a spirometry value in your dataset.

calculateMeanPret calculates the mean predicted value for a spirometric measurement based off of inputted demographic variables such as height, age, and gender.

summarizeAllByCategory extracts datainputs matching a certain demographic threshold and outputs summary statistics on a spirometric measurement in the dataset.

viewCategorical produces plots correlating a categorical variable to a spirometric measurement.

viewCategoricalCounts produces plots that showcase the number of datapoints that exist in the dataset for a categorical variable of interest

viewNumerical produces plots correlating a numerical variable to a spirometric measurement.

compareNumerical produces plots correlating a numerical variable to a spirometric measurement annotated by other categorical or numerical demographic variables of interest.

A work flow of the package can be seen below:

For more information on each function, refer to the respective help documentation. For a brief tutorial on how to use the package, view the provided vignette with the function browseVignettes("spiroview").

• formatData uses packages utils and readr to handle file reading

• segregateBy uses package stringr for string matching

• calculateLLNPret, calculatePctPret, calculateMeanPret use package rspiro for spirometric equations and calculations

• summarizeAllByCategory uses package stringr for string matching and package dplyr for filtering

• viewCategorical,viewCategoricalCounts, and viewNumerical use package ggplot2 for generating plots

• compareNumerical uses package ggplot2 for generating plots. This function also uses stringr for string matching and dplyr for dataset filtering

• Chang W, Cheng J, Allaire J, Sievert C, Schloerke B, Xie Y, Allen J, McPherson J, Dipert A, Borges B (2023). shiny: Web Application Framework for R. R package version 1.7.4.9002, https://shiny.rstudio.com/.

• Cooper, B. G., Stocks, J., Hall, G. L., Culver, B., Steenbruggen, I., Carter, K. W., Thompson, B. R., Graham, B. L., Miller, M. R., Ruppel, G., Henderson, J., Vaz Fragoso, C. A., & Stanojevic, S. (2017).The Global Lung Function Initiative (GLI) Network: bringing the world’s respiratory reference values together. Breathe (Sheffield, England), 13(3), e56–e64. https://doi.org/10.1183/20734735.012717

• Grolemund, G. (2015). Learn Shiny - Video Tutorials. URL:https://shiny.rstudio.com/tutorial/

• Hankinson, J. L., Odencrantz, J. R., & Fedan, K. B. (1999). Spirometric reference values from a sample of the general U.S. population. American journal of respiratory and critical care medicine, 159(1), 179–187.https://doi.org/10.1164/ajrccm.159.1.9712108

• Lytras T (2020). rspiro: Implementation of Spirometry Equations. R package version 0.2, https://CRAN.R-project.org/package=rspiro.

• R Core Team (2021). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.

• Silva, A. (2022) TestingPackage: An Example R Package For BCB410H. Unpublished. URL https://github.com/anjalisilva/TestingPackage.”

• Wickham, H. and Bryan, J. (2019). R Packages (2nd edition). Newton, Massachusetts: O’Reilly Media. https://r-pkgs.org/

• Wickham H, François R, Henry L, Müller K, Vaughan D (2023). dplyr: A Grammar of Data Manipulation. https://dplyr.tidyverse.org, https://github.com/tidyverse/dplyr.

• Wickham H, Hester J, Bryan J (2023). readr: Read Rectangular Text Data. https://readr.tidyverse.org, https://github.com/tidyverse/readr.

• Wickham H (2016). ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. ISBN 978-3-319-24277-4, https://ggplot2.tidyverse.org.

• Wickham H (2022). stringr: Simple, Consistent Wrappers for Common String Operations. R package version 1.5.0, https://CRAN.R-project.org/package=stringr.

This package was developed as part of an assessment for 2022 BCB410H: Applied Bioinformatics course at the University of Toronto, Toronto, CANADA. spiroview welcomes issues, enhancement requests, and other contributions. To submit an issue, use the GitHub issues.

The package tree structure is provided below.

- spiroview
  ├── DESCRIPTION
  ├── LICENSE
  ├── LICENSE.md
  ├── NAMESPACE
  ├── R
  │   ├── calculatedPredicted.R
  │   ├── data.R
  │   ├── formatData.R
  │   ├── runspiroview.R    
  │   ├── segregateBy.R
  │   ├── summarize.R
  │   ├── viewCategorical.R
  │   └── viewNumerical.R
  ├── README.Rmd
  ├── README.md
  ├── data
  │   ├── GLIData.rda
  │   └── NHANES3Data.rda
  ├── inst
  │   ├── CITATION
  │   ├── extdata
  │   │   ├── GLI_simulated_DB.csv
  │   │   ├── NHANES3_simulated_DB.csv
  │   │   ├── example_dataset_1.csv
  │   │   ├── example_dataset_2.csv
  │   │   ├── example_dataset_3.csv
  │   │   ├── example_dataset_4.csv
  │   │   └── spiroview_overview.png
  │   └── shiny-scripts
  │       └── app.R
  ├── man
  │   ├── GLIData.Rd
  │   ├── NHANES3Data.Rd
  │   ├── calculateLLNPret.Rd
  │   ├── calculateMeanPret.Rd
  │   ├── calculatePctPret.Rd
  │   ├── compareNumerical.Rd
  │   ├── figures
  │   ├── formatData.Rd
  │   ├── segregateBy.Rd
  │   ├── summarizeAllByCategory.Rd
  │   ├── viewCategorical.Rd
  │   ├── viewCategoricalCounts.Rd
  │   └── viewNumerical.Rd
  ├── spiroview.Rproj
  ├── tests
  │   ├── testthat
  │   │   ├── test-calculatedPredicted.R
  │   │   ├── test-formatData.R
  │   │   ├── test-segregateBy.R
  │   │   ├── test-summarize.R
  │   │   ├── test-viewCategorical.R
  │   │   └── test-viewNumerical.R
  │   └── testthat.R
  └── vignettes
      └── Introduction_spiroview.Rmd