fiphde

Forecasting Influenza in Support of Public Health Decision Making

https://github.com/signaturescience/fiphde

Science Score: 44.0%

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Low similarity (11.0%) to scientific vocabulary

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Repository

Forecasting Influenza in Support of Public Health Decision Making

Basic Info

Host: GitHub
Owner: signaturescience
License: gpl-3.0
Language: R
Default Branch: main
Homepage: https://signaturescience.github.io/fiphde/
Size: 36.7 MB

Statistics

Stars: 3
Watchers: 2
Forks: 2
Open Issues: 6
Releases: 15

Created over 4 years ago · Last pushed over 1 year ago

Metadata Files

Readme Changelog License Citation

README.Rmd

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# fiphde


[![R-CMD-check](https://github.com/signaturescience/fiphde/workflows/R-CMD-check/badge.svg)](https://github.com/signaturescience/fiphde/actions)
[![CRAN status](https://www.r-pkg.org/badges/version/fiphde)](https://CRAN.R-project.org/package=fiphde)


`fiphde`: **F**orecasting **I**nfluenza in Support of **P**ublic **H**ealth **DE**cision Making

## Motivation

`fiphde` was originally created to operationally forecast influenza hospitalizations during the 2021-22 and 2022-23 seasons of the [FluSight challenge](https://github.com/cdcepi/Flusight-forecast-data). The package includes functions for data retrieval, modeling, near-term forecasting, and forecast summarization. Functionality from `fiphde` has been implemented for other infectious disease forecasting, including the 2022-23 [DoD COVID-like illness forecasting challenge](https://github.com/cdcepi/DoD-CLI-forecast-data).

## Installation

To install `fiphde` from GitHub:

``` r
# install.packages("remotes")
remotes::install_github("signaturescience/fiphde", build_vignettes = TRUE)
```

## Usage

To get started, see the [package vignette](https://signaturescience.github.io/fiphde/articles/basic_usage.html):

```{r, eval=FALSE}
vignette("basic_usage", package="fiphde")
```

Owner

Name: Signature Science
Login: signaturescience
Kind: organization
Location: Austin, TX

Website: http://www.signaturescience.com/
Repositories: 21
Profile: https://github.com/signaturescience

Citation (CITATION.cff)

# -----------------------------------------------------------
# CITATION file created with {cffr} R package, v0.5.0
# See also: https://docs.ropensci.org/cffr/
# -----------------------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "fiphde" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'fiphde: Forecasting Influenza in Support of Public Health Decision Making'
version: 1.0.0
abstract: Miscellaneous functions for retrieving data, creating and evaluating time
  series forecasting models for influenza-like illness (ILI) and influenza hospitalizations
  in the United States.
authors:
- family-names: Nagraj
  given-names: VP
  email: pnagraj@signaturescience.com
  orcid: https://orcid.org/0000-0003-0060-566X
- family-names: Jessa
  given-names: Shakeel
- family-names: Hulme-Lowe
  given-names: Chris
- family-names: Turner
  given-names: Stephen
  orcid: https://orcid.org/0000-0001-9140-9028
url: https://signaturescience.github.io/fiphde/
contact:
- family-names: Nagraj
  given-names: VP
  email: pnagraj@signaturescience.com
  orcid: https://orcid.org/0000-0003-0060-566X
references:
- type: software
  title: dplyr
  abstract: 'dplyr: A Grammar of Data Manipulation'
  notes: Imports
  url: https://dplyr.tidyverse.org
  repository: https://CRAN.R-project.org/package=dplyr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: François
    given-names: Romain
    orcid: https://orcid.org/0000-0002-2444-4226
  - family-names: Henry
    given-names: Lionel
  - family-names: Müller
    given-names: Kirill
    orcid: https://orcid.org/0000-0002-1416-3412
  - family-names: Vaughan
    given-names: Davis
    email: davis@posit.co
    orcid: https://orcid.org/0000-0003-4777-038X
  year: '2023'
- type: software
  title: fable
  abstract: 'fable: Forecasting Models for Tidy Time Series'
  notes: Imports
  url: https://fable.tidyverts.org
  repository: https://CRAN.R-project.org/package=fable
  authors:
  - family-names: O'Hara-Wild
    given-names: Mitchell
    email: mail@mitchelloharawild.com
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    given-names: Rob
  - family-names: Wang
    given-names: Earo
  year: '2023'
- type: software
  title: fabletools
  abstract: 'fabletools: Core Tools for Packages in the ''fable'' Framework'
  notes: Imports
  url: https://fabletools.tidyverts.org/
  repository: https://CRAN.R-project.org/package=fabletools
  authors:
  - family-names: O'Hara-Wild
    given-names: Mitchell
    email: mail@mitchelloharawild.com
    orcid: https://orcid.org/0000-0001-6729-7695
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    orcid: https://orcid.org/0000-0001-6448-5260
  year: '2023'
  version: '>= 0.3.2'
- type: software
  title: lubridate
  abstract: 'lubridate: Make Dealing with Dates a Little Easier'
  notes: Imports
  url: https://lubridate.tidyverse.org
  repository: https://CRAN.R-project.org/package=lubridate
  authors:
  - family-names: Spinu
    given-names: Vitalie
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    given-names: Garrett
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    given-names: Hadley
  year: '2023'
- type: software
  title: magrittr
  abstract: 'magrittr: A Forward-Pipe Operator for R'
  notes: Imports
  url: https://magrittr.tidyverse.org
  repository: https://CRAN.R-project.org/package=magrittr
  authors:
  - family-names: Bache
    given-names: Stefan Milton
    email: stefan@stefanbache.dk
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  year: '2023'
- type: software
  title: MMWRweek
  abstract: 'MMWRweek: Convert Dates to MMWR Day, Week, and Year'
  notes: Imports
  url: http://wwwn.cdc.gov/nndss/document/MMWR_Week_overview.pdf
  repository: https://CRAN.R-project.org/package=MMWRweek
  authors:
  - family-names: Niemi
    given-names: Jarad
    email: niemi@iastate.edu
  year: '2023'
- type: software
  title: purrr
  abstract: 'purrr: Functional Programming Tools'
  notes: Imports
  url: https://purrr.tidyverse.org/
  repository: https://CRAN.R-project.org/package=purrr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: Henry
    given-names: Lionel
    email: lionel@rstudio.com
  year: '2023'
- type: software
  title: tibble
  abstract: 'tibble: Simple Data Frames'
  notes: Imports
  url: https://tibble.tidyverse.org/
  repository: https://CRAN.R-project.org/package=tibble
  authors:
  - family-names: Müller
    given-names: Kirill
    email: kirill@cynkra.com
    orcid: https://orcid.org/0000-0002-1416-3412
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  year: '2023'
- type: software
  title: tidyr
  abstract: 'tidyr: Tidy Messy Data'
  notes: Imports
  url: https://tidyr.tidyverse.org
  repository: https://CRAN.R-project.org/package=tidyr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Vaughan
    given-names: Davis
    email: davis@posit.co
  - family-names: Girlich
    given-names: Maximilian
  year: '2023'
- type: software
  title: tsibble
  abstract: 'tsibble: Tidy Temporal Data Frames and Tools'
  notes: Imports
  url: https://tsibble.tidyverts.org
  repository: https://CRAN.R-project.org/package=tsibble
  authors:
  - family-names: Wang
    given-names: Earo
    email: earo.wang@gmail.com
    orcid: https://orcid.org/0000-0001-6448-5260
  - family-names: Cook
    given-names: Di
    orcid: https://orcid.org/0000-0002-3813-7155
  - family-names: Hyndman
    given-names: Rob
    orcid: https://orcid.org/0000-0002-2140-5352
  - family-names: O'Hara-Wild
    given-names: Mitchell
    orcid: https://orcid.org/0000-0001-6729-7695
  year: '2023'
- type: software
  title: trending
  abstract: 'trending: Model Temporal Trends'
  notes: Imports
  url: https://github.com/reconverse/trending
  repository: https://CRAN.R-project.org/package=trending
  authors:
  - family-names: Taylor
    given-names: Tim
    email: tim.taylor@hiddenelephants.co.uk
    orcid: https://orcid.org/0000-0002-8587-7113
  year: '2023'
- type: software
  title: trendeval
  abstract: 'trendeval: Evaluate Trending Models'
  notes: Imports
  url: https://github.com/reconverse/trendeval
  repository: https://CRAN.R-project.org/package=trendeval
  authors:
  - family-names: Schumacher
    given-names: Dirk
    email: mail@dirk-schumacher.net
  - family-names: Jombart
    given-names: Thibaut
    email: thibautjombart@gmail.com
  year: '2023'
- type: software
  title: ggplot2
  abstract: 'ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics'
  notes: Imports
  url: https://ggplot2.tidyverse.org
  repository: https://CRAN.R-project.org/package=ggplot2
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: Chang
    given-names: Winston
    orcid: https://orcid.org/0000-0002-1576-2126
  - family-names: Henry
    given-names: Lionel
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomas.pedersen@posit.co
    orcid: https://orcid.org/0000-0002-5147-4711
  - family-names: Takahashi
    given-names: Kohske
  - family-names: Wilke
    given-names: Claus
    orcid: https://orcid.org/0000-0002-7470-9261
  - family-names: Woo
    given-names: Kara
    orcid: https://orcid.org/0000-0002-5125-4188
  - family-names: Yutani
    given-names: Hiroaki
    orcid: https://orcid.org/0000-0002-3385-7233
  - family-names: Dunnington
    given-names: Dewey
    orcid: https://orcid.org/0000-0002-9415-4582
  year: '2023'
- type: software
  title: yardstick
  abstract: 'yardstick: Tidy Characterizations of Model Performance'
  notes: Imports
  url: https://yardstick.tidymodels.org
  repository: https://CRAN.R-project.org/package=yardstick
  authors:
  - family-names: Kuhn
    given-names: Max
    email: max@posit.co
  - family-names: Vaughan
    given-names: Davis
    email: davis@posit.co
  - family-names: Hvitfeldt
    given-names: Emil
    email: emil.hvitfeldt@posit.co
    orcid: https://orcid.org/0000-0002-0679-1945
  year: '2023'
- type: software
  title: stringr
  abstract: 'stringr: Simple, Consistent Wrappers for Common String Operations'
  notes: Imports
  url: https://stringr.tidyverse.org
  repository: https://CRAN.R-project.org/package=stringr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  year: '2023'
- type: software
  title: jsonlite
  abstract: 'jsonlite: A Simple and Robust JSON Parser and Generator for R'
  notes: Imports
  url: https://arxiv.org/abs/1403.2805
  repository: https://CRAN.R-project.org/package=jsonlite
  authors:
  - family-names: Ooms
    given-names: Jeroen
    email: jeroen@berkeley.edu
    orcid: https://orcid.org/0000-0002-4035-0289
  year: '2023'
- type: software
  title: stats
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  location:
    name: Vienna, Austria
  year: '2023'
  institution:
    name: R Foundation for Statistical Computing
- type: software
  title: scales
  abstract: 'scales: Scale Functions for Visualization'
  notes: Imports
  url: https://scales.r-lib.org
  repository: https://CRAN.R-project.org/package=scales
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  - family-names: Seidel
    given-names: Dana
  year: '2023'
- type: software
  title: readr
  abstract: 'readr: Read Rectangular Text Data'
  notes: Imports
  url: https://readr.tidyverse.org
  repository: https://CRAN.R-project.org/package=readr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Hester
    given-names: Jim
  - family-names: Bryan
    given-names: Jennifer
    email: jenny@posit.co
    orcid: https://orcid.org/0000-0002-6983-2759
  year: '2023'
- type: software
  title: shiny
  abstract: 'shiny: Web Application Framework for R'
  notes: Imports
  url: https://shiny.rstudio.com/
  repository: https://CRAN.R-project.org/package=shiny
  authors:
  - family-names: Chang
    given-names: Winston
    email: winston@rstudio.com
    orcid: https://orcid.org/0000-0002-1576-2126
  - family-names: Cheng
    given-names: Joe
    email: joe@rstudio.com
  - family-names: Allaire
    given-names: JJ
    email: jj@rstudio.com
  - family-names: Sievert
    given-names: Carson
    email: carson@rstudio.com
    orcid: https://orcid.org/0000-0002-4958-2844
  - family-names: Schloerke
    given-names: Barret
    email: barret@rstudio.com
    orcid: https://orcid.org/0000-0001-9986-114X
  - family-names: Xie
    given-names: Yihui
    email: yihui@rstudio.com
  - family-names: Allen
    given-names: Jeff
    email: jeff@rstudio.com
  - family-names: McPherson
    given-names: Jonathan
    email: jonathan@rstudio.com
  - family-names: Dipert
    given-names: Alan
  - family-names: Borges
    given-names: Barbara
  year: '2023'
- type: software
  title: httr
  abstract: 'httr: Tools for Working with URLs and HTTP'
  notes: Imports
  url: https://httr.r-lib.org/
  repository: https://CRAN.R-project.org/package=httr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2023'
- type: software
  title: 'R: A Language and Environment for Statistical Computing'
  notes: Depends
  url: https://www.R-project.org/
  authors:
  - name: R Core Team
  location:
    name: Vienna, Austria
  year: '2023'
  institution:
    name: R Foundation for Statistical Computing
  version: '>= 2.10'
- type: software
  title: testthat
  abstract: 'testthat: Unit Testing for R'
  notes: Suggests
  url: https://testthat.r-lib.org
  repository: https://CRAN.R-project.org/package=testthat
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2023'
  version: '>= 3.0.0'
- type: software
  title: plotly
  abstract: 'plotly: Create Interactive Web Graphics via ''plotly.js'''
  notes: Suggests
  url: https://plotly-r.com
  repository: https://CRAN.R-project.org/package=plotly
  authors:
  - family-names: Sievert
    given-names: Carson
    email: cpsievert1@gmail.com
    orcid: https://orcid.org/0000-0002-4958-2844
  - family-names: Parmer
    given-names: Chris
    email: chris@plot.ly
  - family-names: Hocking
    given-names: Toby
    email: tdhock5@gmail.com
  - family-names: Chamberlain
    given-names: Scott
    email: myrmecocystus@gmail.com
  - family-names: Ram
    given-names: Karthik
    email: karthik.ram@gmail.com
  - family-names: Corvellec
    given-names: Marianne
    email: marianne.corvellec@igdore.org
    orcid: https://orcid.org/0000-0002-1994-3581
  - family-names: Despouy
    given-names: Pedro
    email: pedro@plot.ly
  year: '2023'
- type: software
  title: shinyWidgets
  abstract: 'shinyWidgets: Custom Inputs Widgets for Shiny'
  notes: Suggests
  url: https://dreamrs.github.io/shinyWidgets/
  repository: https://CRAN.R-project.org/package=shinyWidgets
  authors:
  - family-names: Perrier
    given-names: Victor
    email: victor.perrier@dreamrs.fr
  - family-names: Meyer
    given-names: Fanny
  - family-names: Granjon
    given-names: David
  year: '2023'
- type: software
  title: DT
  abstract: 'DT: A Wrapper of the JavaScript Library ''DataTables'''
  notes: Suggests
  url: https://github.com/rstudio/DT
  repository: https://CRAN.R-project.org/package=DT
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
  - family-names: Cheng
    given-names: Joe
  - family-names: Tan
    given-names: Xianying
  year: '2023'
- type: software
  title: knitr
  abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
  notes: Suggests
  url: https://yihui.org/knitr/
  repository: https://CRAN.R-project.org/package=knitr
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2023'
- type: software
  title: urca
  abstract: 'urca: Unit Root and Cointegration Tests for Time Series Data'
  notes: Suggests
  repository: https://CRAN.R-project.org/package=urca
  authors:
  - family-names: Pfaff
    given-names: Bernhard
    email: bernhard@pfaffikus.de
  year: '2023'

GitHub Events

Total

Create event: 9
Release event: 1
Issues event: 21
Delete event: 5
Issue comment event: 9
Push event: 34
Pull request event: 14
Fork event: 1

Last Year

Create event: 9
Release event: 1
Issues event: 21
Delete event: 5
Issue comment event: 9
Push event: 34
Pull request event: 14
Fork event: 1

Dependencies

.github/workflows/R-CMD-check.yaml actions

actions/checkout v2 composite
r-lib/actions/check-r-package v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/pkgdown.yaml actions

actions/checkout v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

DESCRIPTION cran

R >= 2.10 depends
MMWRweek * imports
dplyr * imports
fable * imports
fabletools >= 0.3.2 imports
ggplot2 * imports
httr * imports
jsonlite * imports
lubridate * imports
magrittr * imports
purrr * imports
readr * imports
scales * imports
shiny * imports
stats * imports
stringr * imports
tibble * imports
tidyr * imports
trendeval * imports
trending * imports
tsibble * imports
yardstick * imports
DT * suggests
feasts * suggests
here * suggests
knitr * suggests
plotly * suggests
rmarkdown * suggests
shinyWidgets * suggests
testthat >= 3.0.0 suggests
urca * suggests

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science