remove epidatr calls in vignettes; dontrun failing example code

cmu-delphi · Oct 1, 2024 · 5518c67 · 5518c67
1 parent 779ec2a
commit 5518c67
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Showing 8 changed files with 28 additions and 13 deletions.
diff --git a/R/reexports.R b/R/reexports.R
@@ -93,7 +93,9 @@ ggplot2::autoplot
 #' cases_deaths_subset
 #'
 #' # fails
-#' data(cases_deaths_subset, package = "epiprocess")
+#' \dontrun{
+#'   data(cases_deaths_subset, package = "epiprocess")
+#' }
 #' @export
 delayedAssign("cases_deaths_subset", epidatasets::cases_deaths_subset)
 
@@ -111,7 +113,9 @@ delayedAssign("cases_deaths_subset", epidatasets::cases_deaths_subset)
 #' covid_incidence_county_subset
 #'
 #' # fails
-#' data(covid_incidence_county_subset, package = "epiprocess")
+#' \dontrun{
+#'   data(covid_incidence_county_subset, package = "epiprocess")
+#' }
 #' @export
 delayedAssign("covid_incidence_county_subset", epidatasets::covid_incidence_county_subset)
 
@@ -129,7 +133,9 @@ delayedAssign("covid_incidence_county_subset", epidatasets::covid_incidence_coun
 #' covid_incidence_outliers
 #'
 #' # fails
-#' data(covid_incidence_outliers, package = "epiprocess")
+#' \dontrun{
+#'   data(covid_incidence_outliers, package = "epiprocess")
+#' }
 #' @export
 delayedAssign("covid_incidence_outliers", epidatasets::covid_incidence_outliers)
 
@@ -147,7 +153,9 @@ delayedAssign("covid_incidence_outliers", epidatasets::covid_incidence_outliers)
 #' jhu_confirmed_cumulative_num
 #'
 #' # fails
-#' data(jhu_confirmed_cumulative_num, package = "epiprocess")
+#' \dontrun{
+#'   data(jhu_confirmed_cumulative_num, package = "epiprocess")
+#' }
 #' @export
 delayedAssign("jhu_confirmed_cumulative_num", epidatasets::jhu_confirmed_cumulative_num)
 
@@ -165,7 +173,9 @@ delayedAssign("jhu_confirmed_cumulative_num", epidatasets::jhu_confirmed_cumulat
 #' archive_cases_dv_subset
 #'
 #' # fails
-#' data(archive_cases_dv_subset, package = "epiprocess")
+#' \dontrun{
+#'   data(archive_cases_dv_subset, package = "epiprocess")
+#' }
 #'
 #' @export
 delayedAssign("archive_cases_dv_subset", epidatasets::archive_cases_dv_subset)
diff --git a/vignettes/aggregation.Rmd b/vignettes/aggregation.Rmd
@@ -15,8 +15,6 @@ COVID-19 cases in MA and VT.
 The data is included in this package (via the [`epidatasets` package](https://cmu-delphi.github.io/epidatasets/)) and can be loaded with:
 
 ```{r, warning = FALSE, message = FALSE}
-library(epidatr)
-library(covidcast)
 library(epiprocess)
 library(dplyr)
 
@@ -25,6 +23,9 @@ x <- covid_incidence_county_subset
 
 The data can also be fetched from the Delphi API with the following query:
 ```{r, message = FALSE, eval = FALSE, warning = FALSE}
+library(epidatr)
+library(covidcast)
+
 d <- as.Date("2024-03-20")
 
 # Use covidcast::county_census to get the county and state names

diff --git a/vignettes/archive.Rmd b/vignettes/archive.Rmd
@@ -28,7 +28,6 @@ page](https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/doctor-v
 The data is included in this package (via the [`epidatasets` package](https://cmu-delphi.github.io/epidatasets/)) and can be loaded with:
 
 ```{r, message = FALSE, warning = FALSE}
-library(epidatr)
 library(epiprocess)
 library(data.table)
 library(dplyr)
@@ -41,6 +40,8 @@ dv <- archive_cases_dv_subset$DT
 
 The data can also be fetched from the Delphi API with the following query:
 ```{r, message = FALSE, warning = FALSE, eval = FALSE}
+library(epidatr)
+
 dv <- pub_covidcast(
   source = "doctor-visits",
   signals = "smoothed_adj_cli",

diff --git a/vignettes/correlation.Rmd b/vignettes/correlation.Rmd
@@ -16,7 +16,6 @@ state-level COVID-19 case and death rates, smoothed using 7-day trailing
 averages.
 
 ```{r, message = FALSE, warning = FALSE}
-library(epidatr)
 library(epiprocess)
 library(dplyr)
 ```
@@ -30,6 +29,8 @@ x <- cases_deaths_subset %>%
 
 The data can also be fetched from the Delphi API with the following query:
 ```{r, eval = FALSE}
+library(epidatr)
+
 d <- as.Date("2024-03-20")
 
 x <- pub_covidcast(

diff --git a/vignettes/epiprocess.Rmd b/vignettes/epiprocess.Rmd
@@ -104,7 +104,6 @@ to fetch this data from the [COVIDcast
 API](https://cmu-delphi.github.io/delphi-epidata/api/covidcast.html).
 
 ```{r, message = FALSE}
-library(epidatr)
 library(epiprocess)
 library(dplyr)
 library(tidyr)

diff --git a/vignettes/growth_rate.Rmd b/vignettes/growth_rate.Rmd
@@ -15,7 +15,6 @@ current vignette, applied to state-level daily reported COVID-19 cases from GA
 and PA, smoothed using a 7-day trailing average.
 
 ```{r, message = FALSE, warning = FALSE}
-library(epidatr)
 library(epiprocess)
 library(dplyr)
 library(tidyr)
@@ -32,7 +31,10 @@ x <- cases_deaths_subset %>%
 
 The data can also be fetched from the Delphi API with the following query:
 ```{r, message = FALSE, eval = FALSE}
+library(epidatr)
+
 d <- as.Date("2024-03-20")
+
 x <- pub_covidcast(
   source = "jhu-csse",
   signals = "confirmed_7dav_incidence_num",

diff --git a/vignettes/outliers.Rmd b/vignettes/outliers.Rmd
@@ -17,7 +17,6 @@ reported COVID-19 case counts from FL and NJ.
 The dataset has 730 rows and 3 columns.
 
 ```{r, echo=FALSE, warning=FALSE, message=FALSE}
-library(epidatr)
 library(epiprocess)
 library(dplyr)
 library(tidyr)

diff --git a/vignettes/slide.Rmd b/vignettes/slide.Rmd
@@ -29,7 +29,6 @@ FL, NY, and TX (note: here we're using new, not cumulative cases) using the
 and then convert this to `epi_df` format.
 
 ```{r, message = FALSE, warning = FALSE}
-library(epidatr)
 library(epiprocess)
 library(dplyr)
 ```
@@ -44,7 +43,10 @@ x <- cases_deaths_subset %>%
 
 The data can also be fetched from the Delphi API with the following query:
 ```{r, message = FALSE, eval = FALSE}
+library(epidatr)
+
 d <- as.Date("2024-03-20")
+
 x <- pub_covidcast(
   source = "jhu-csse",
   signals = "confirmed_incidence_num",