From d3827a341b0bfde0265ea1dfb377caf5e76449e7 Mon Sep 17 00:00:00 2001 From: "Logan C. Brooks" Date: Wed, 29 May 2024 10:38:59 -0700 Subject: [PATCH 1/3] Address Guidehouse feedback on landing page --- DESCRIPTION | 2 +- NEWS.md | 1 + vignettes/epiprocess.Rmd | 50 ++++++++++++++++++++++++++++++++++++---- 3 files changed, 48 insertions(+), 5 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index cc7cba12..3c409c31 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package Package: epiprocess Title: Tools for basic signal processing in epidemiology -Version: 0.7.9 +Version: 0.7.10 Authors@R: c( person("Jacob", "Bien", role = "ctb"), person("Logan", "Brooks", email = "lcbrooks@andrew.cmu.edu", role = c("aut", "cre")), diff --git a/NEWS.md b/NEWS.md index a1591d8d..1bfdd9c5 100644 --- a/NEWS.md +++ b/NEWS.md @@ -31,6 +31,7 @@ Pre-1.0.0 numbering scheme: 0.x will indicate releases, while 0.x.y will indicat (#441). - Clarified "Get started" example of getting Ebola line list data into `epi_df` format. +- Improved documentation web site landing page's introduction. # epiprocess 0.7.0 diff --git a/vignettes/epiprocess.Rmd b/vignettes/epiprocess.Rmd index 91daa455..2d67e28a 100644 --- a/vignettes/epiprocess.Rmd +++ b/vignettes/epiprocess.Rmd @@ -9,14 +9,56 @@ editor_options: chunk_output_type: console --- -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") From 5c8322dcced748e5372f74dbc0f59b2498ef4d06 Mon Sep 17 00:00:00 2001 From: "Logan C. Brooks" Date: Tue, 4 Jun 2024 11:47:54 -0700 Subject: [PATCH 2/3] docs (epiprocess.Rmd): attempt short intro intro + ref dplyr "verbs" --- vignettes/epiprocess.Rmd | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/vignettes/epiprocess.Rmd b/vignettes/epiprocess.Rmd index 2d67e28a..f278f827 100644 --- a/vignettes/epiprocess.Rmd +++ b/vignettes/epiprocess.Rmd @@ -9,16 +9,21 @@ editor_options: chunk_output_type: console --- -The [`{epiprocess}`](https://cmu-delphi.github.io/epiprocess/) package provides +The [`{epiprocess}`](https://cmu-delphi.github.io/epiprocess/) package works +with epidemiological time series and version data to provide situational +awareness, processing and transformations in preparation for modeling, and +version-faithful model backtesting. It contains: - `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); +- [`{dplyr}`](https://dplyr.tidyverse.org/)-esque "verbs" 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. +- [`{dplyr}`](https://dplyr.tidyverse.org/)-esque "verbs" for version-faithful + "pseudoprospective" backtesting of models, and other version history analysis + and transformations. It is part of a broader suite of packages including [`{epidatr}`](https://cmu-delphi.github.io/epidatr/), From e64f3c313da6d3c32ae348794e6c94d8df533caf Mon Sep 17 00:00:00 2001 From: brookslogan Date: Tue, 4 Jun 2024 13:19:16 -0700 Subject: [PATCH 3/3] docs(epiprocess.Rmd): order package links by importance/relevance Co-authored-by: nmdefries <42820733+nmdefries@users.noreply.github.com> --- vignettes/epiprocess.Rmd | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/vignettes/epiprocess.Rmd b/vignettes/epiprocess.Rmd index f278f827..c0cb0011 100644 --- a/vignettes/epiprocess.Rmd +++ b/vignettes/epiprocess.Rmd @@ -25,11 +25,11 @@ version-faithful model backtesting. It contains: "pseudoprospective" backtesting of models, and other version history analysis and transformations. -It is part of a broader suite of packages including +It is part of a broader suite of packages that includes +[`{epipredict}`](https://cmu-delphi.github.io/epipredict/), [`{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, +[`{epidatasets}`](https://cmu-delphi.github.io/epidatasets/), 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/).