From 167135a86ac1d58342c8dd28eab23035dd4e51cf Mon Sep 17 00:00:00 2001
From: Dmitry Shemetov <dshemetov@ucdavis.edu>
Date: Mon, 21 Oct 2024 13:46:34 -0700
Subject: [PATCH] doc: fix archive demo and make epipredict a link

---
 README.Rmd               |  2 +-
 README.md                |  9 +++++----
 vignettes/epiprocess.Rmd | 12 +++++++++---
 3 files changed, 15 insertions(+), 8 deletions(-)

diff --git a/README.Rmd b/README.Rmd
index d99c4fae..02c56a12 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -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.
diff --git a/README.md b/README.md
index 2cf3b8c7..ec9527ff 100644
--- a/README.md
+++ b/README.md
@@ -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:
 
diff --git a/vignettes/epiprocess.Rmd b/vignettes/epiprocess.Rmd
index a455472b..6faa9efb 100644
--- a/vignettes/epiprocess.Rmd
+++ b/vignettes/epiprocess.Rmd
@@ -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}
@@ -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