Packaged: 2020-07-23 15:05:34 UTC; hkatsumata

Title: Naive Bayes Transmission Analysis
Authors@R: person("Sarah V", "Leavitt", email = "sv1205@bu.edu", role = c("aut", "cre", "cph"))
Maintainer: Sarah V Leavitt <sv1205@bu.edu>
Description: Estimates the relative transmission probabilities between cases in an infectious disease outbreak or cluster using naive Bayes. Included are various functions to use these probabilities to estimate transmission parameters such as the generation/serial interval and reproductive number as well as finding the contribution of covariates to the probabilities and visualizing results. The ideal use is for an infectious disease dataset with metadata on the majority of cases but more informative data such as contact tracing or pathogen whole genome sequencing on only a subset of cases. For a detailed description of the methods see Leavitt et al. (2020) <doi:10.1093/ije/dyaa031>.
Imports: dplyr, rlang, caret, lubridate, poisbinom, stats, tidyr, utils
Suggests: ggplot2, Hmisc, igraph, knitr, pheatmap, RColorBrewer,

Description: Palettes generated from NBA jersey colorways.

Title: Bayes Classifier for Verbal Autopsy Data
Description: An implementation of the Naive Bayes Classifier (NBC) algorithm used for Verbal Autopsy (VA) built on code from Miasnikof et al (2015) <DOI:10.1186/s12916-015-0521-2>.

person(given = "Richard", family = "Wen", email = "rrwen.dev@gmail.com", role = c("aut", "cre")),
person(given = "Pierre", family = "Miasnikof", role = "ctb"),
person(given = "Vasily", family = "Giannakeas", role = "ctb"),
person(given = "Mireille", family = "Gomes", role = "ctb"))
Description: An implementation of the Naive Bayes Classifier (NBC) algorithm
used for Verbal Autopsy (VA) built on code from Miasnikof et al (2015)
Suggests: bookdown, knitr, rmarkdown, shiny, testthat

Imports: graphics, methods, utils, shiny

Title: Vignette Engine Wrapping IPython Notebooks
Calls the 'Jupyter'/'IPython' script 'nbconvert' to create vignettes from notebooks.
Those notebooks ('.ipynb' files) are files containing rich text, code, and its output.
Code cells can be edited and evaluated interactively.
See <http://ipython.org/notebook.html> for more information.
SystemRequirements: pandoc, ipython (>= 3.0) or jupyter,
ipython/jupyter notebook optional dependencies, pywin32 (on