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Sync dev -> main #554

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Oct 21, 2024
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Sync dev -> main #554

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167135a
doc: fix archive demo and make epipredict a link
dshemetov Oct 21, 2024
c901a68
Merge pull request #553 from cmu-delphi/ds/vignettes4
dshemetov Oct 21, 2024
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2 changes: 1 addition & 1 deletion README.Rmd
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Expand Up @@ -16,7 +16,7 @@ knitr::opts_chunk$set(
The `{epiprocess}` package works with epidemiological time series data and
provides tools to manage, analyze, and process the data in preparation for
modeling. It is designed to work in tandem with
`{epipredict}`, which provides
[`{epipredict}`](https://cmu-delphi.github.io/epipredict/), which provides
pre-built epiforecasting models and as well as tools to build custom models.
Both packages are designed to lower the barrier to entry and implementation cost
for epidemiological time series analysis and forecasting.
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9 changes: 5 additions & 4 deletions README.md
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Expand Up @@ -6,10 +6,11 @@
The `{epiprocess}` package works with epidemiological time series data
and provides tools to manage, analyze, and process the data in
preparation for modeling. It is designed to work in tandem with
`{epipredict}`, which provides pre-built epiforecasting models and as
well as tools to build custom models. Both packages are designed to
lower the barrier to entry and implementation cost for epidemiological
time series analysis and forecasting.
[`{epipredict}`](https://cmu-delphi.github.io/epipredict/), which
provides pre-built epiforecasting models and as well as tools to build
custom models. Both packages are designed to lower the barrier to entry
and implementation cost for epidemiological time series analysis and
forecasting.

`{epiprocess}` contains:

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12 changes: 9 additions & 3 deletions vignettes/epiprocess.Rmd
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Expand Up @@ -167,7 +167,10 @@ dv <- pub_covidcast(
geo_values = "ca,fl,ny,tx",
time_values = epirange(20200601, 20211201),
issues = epirange(20200601, 20211201)
)
) %>%
select(geo_value, time_value, issue, percent_cli = value) %>%
as_epi_archive(compactify = TRUE)
dv
```

```{r, echo=FALSE, message=FALSE, warning=FALSE}
Expand All @@ -179,10 +182,13 @@ library(purrr)
library(ggplot2)
dv <- archive_cases_dv_subset$DT %>%
select(-case_rate_7d_av) %>%
rename(issue = version, value = percent_cli) %>%
tibble()
tidyr::drop_na() %>%
as_epi_archive(compactify = TRUE)
dv
```

See `vignette("epi_arcive")` for a more in-depth guide to `epi_archive` objects.

## Data attribution

This document contains a dataset that is a modified part of the [COVID-19 Data
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