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Address Guidehouse feedback on landing page
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brookslogan committed May 29, 2024
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Type: Package
Package: epiprocess
Title: Tools for basic signal processing in epidemiology
Version: 0.7.8
Version: 0.7.10
Authors@R: c(
person("Jacob", "Bien", role = "ctb"),
person("Logan", "Brooks", email = "[email protected]", role = c("aut", "cre")),
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1 change: 1 addition & 0 deletions NEWS.md
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argument checking (#413).
- Fix logic to auto-assign `epi_df` `time_type` to `week` (#416) and `year`
(#441).
- Improved documentation landing page introduction.

## Breaking changes

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50 changes: 46 additions & 4 deletions vignettes/epiprocess.Rmd
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---

This package introduces a common data structure for epidemiological data sets
measured over space and time, and offers associated utilities to perform basic
signal processing tasks.
The [`{epiprocess}`](https://cmu-delphi.github.io/epiprocess/) package provides

- `epi_df`, a class for working with epidemiological time series data;
- `epi_archive`, a class for working with the version history of such time series data;
- sample data in these formats;
- functions for common data transformations (e.g., 7-day averages);
- functions for exploratory data analysis and situational awareness (e.g.,
outlier detection and growth rate estimation); and
- functions for version-faithful "pseudoprospective" backtesting of models, and
other version history analysis.

It is part of a broader suite of packages including
[`{epidatr}`](https://cmu-delphi.github.io/epidatr/),
[`{epidatasets}`](https://cmu-delphi.github.io/epidatasets/),
[`{rtestim}`](https://dajmcdon.github.io/rtestim/), and
[`{epipredict}`](https://cmu-delphi.github.io/epipredict/), for accessing,
analyzing, and forecasting epidemiological time series data. We have expanded
documentation and demonstrations for some of these packages available in an
online "book" format [here](https://cmu-delphi.github.io/delphi-tooling-book/).

## Motivation

[`{epiprocess}`](https://cmu-delphi.github.io/epiprocess/) and
[`{epipredict}`](https://cmu-delphi.github.io/epipredict/) are designed to lower
the barrier to entry and implementation cost for epidemiological time series
analysis and forecasting. Epidemiologists and forecasting groups repeatedly and
separately have had to rush to implement this type of functionality in a much
more ad hoc manner; we are trying to save such effort in the future by providing
well-documented, tested, and general packages that can be called for many common
tasks instead.

[`{epiprocess}`](https://github.com/cmu-delphi/epiprocess/) also provides tools
to help avoid a particularly common pitfall in analysis and forecasting:
ignoring reporting latency and revisions to a data set. This can, for example,
lead to one retrospectively analyzing a surveillance signal or forecasting model
and concluding that it is much more accurate than it actually was in real time,
or producing always-decreasing forecasts on data sets where initial surveillance
estimates are systematically revised upward. Storing and working with version
history can help avoid these issues.

## Intended audience

We expect users to be proficient in R, and familiar with the
[`{dplyr}`](https://dplyr.tidyverse.org/) and
[`{tidyr}`](https://tidyr.tidyverse.org/) packages.

## Installing

This package is not on CRAN yet, so it can be installed using the
[`devtools`](https://devtools.r-lib.org) package:
[`{devtools}`](https://devtools.r-lib.org) package:

```{r, eval = FALSE}
devtools::install_github("cmu-delphi/epiprocess", ref = "main")
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