diff --git a/DESCRIPTION b/DESCRIPTION index 6f5c3c81..f911c1c7 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -41,7 +41,7 @@ Imports: vctrs Suggests: covidcast, - delphi.epidata, + epidatr, ggplot2, knitr, outbreaks, @@ -52,7 +52,7 @@ Suggests: VignetteBuilder: knitr Remotes: - dajmcdon/delphi.epidata, + cmu-delphi/epidatr, reconverse/outbreaks Config/testthat/edition: 3 Encoding: UTF-8 diff --git a/data-raw/archive_cases_dv_subset.R b/data-raw/archive_cases_dv_subset.R index 36750b02..561bf35f 100644 --- a/data-raw/archive_cases_dv_subset.R +++ b/data-raw/archive_cases_dv_subset.R @@ -1,4 +1,4 @@ -library(delphi.epidata) +library(epidatr) library(epiprocess) library(data.table) library(dplyr) diff --git a/data-raw/incidence_num_outlier_example.R b/data-raw/incidence_num_outlier_example.R index 992e9d89..560edd2f 100644 --- a/data-raw/incidence_num_outlier_example.R +++ b/data-raw/incidence_num_outlier_example.R @@ -1,4 +1,4 @@ -library(delphi.epidata) +library(epidatr) library(epiprocess) library(dplyr) library(tidyr) diff --git a/data-raw/jhu_csse_county_level_subset.R b/data-raw/jhu_csse_county_level_subset.R index a5cacd83..350ba376 100644 --- a/data-raw/jhu_csse_county_level_subset.R +++ b/data-raw/jhu_csse_county_level_subset.R @@ -1,4 +1,4 @@ -library(delphi.epidata) +library(epidatr) library(covidcast) library(epiprocess) library(dplyr) diff --git a/data-raw/jhu_csse_daily_subset.R b/data-raw/jhu_csse_daily_subset.R index 5aae3402..7942d9a4 100644 --- a/data-raw/jhu_csse_daily_subset.R +++ b/data-raw/jhu_csse_daily_subset.R @@ -1,4 +1,4 @@ -library(delphi.epidata) +library(epidatr) library(epiprocess) library(dplyr) diff --git a/vignettes/advanced.Rmd b/vignettes/advanced.Rmd index 04c73af3..5514eaaa 100644 --- a/vignettes/advanced.Rmd +++ b/vignettes/advanced.Rmd @@ -192,7 +192,7 @@ to demonstrate the last point in a more realistic setting. First, we fetch the versioned data and build the archive. ```{r, message = FALSE, warning = FALSE, eval =FALSE} -library(delphi.epidata) +library(epidatr) library(data.table) library(ggplot2) theme_set(theme_bw()) diff --git a/vignettes/aggregation.Rmd b/vignettes/aggregation.Rmd index 617f0983..c3c71d3c 100644 --- a/vignettes/aggregation.Rmd +++ b/vignettes/aggregation.Rmd @@ -13,7 +13,7 @@ kinds of tasks with `epi_df` objects. We'll work with county-level reported COVID-19 cases in MA and VT. ```{r, message = FALSE, eval= FALSE, warning= FALSE} -library(delphi.epidata) +library(epidatr) library(covidcast) library(epiprocess) library(dplyr) @@ -41,7 +41,7 @@ x <- covidcast( The data contains 16,212 rows and 5 columns. ```{r, echo=FALSE, warning=FALSE, message=FALSE} -library(delphi.epidata) +library(epidatr) library(covidcast) library(epiprocess) library(dplyr) diff --git a/vignettes/archive.Rmd b/vignettes/archive.Rmd index 1b8d0622..11014755 100644 --- a/vignettes/archive.Rmd +++ b/vignettes/archive.Rmd @@ -26,7 +26,7 @@ on its [API documentation page](https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/doctor-visits.html). ```{r, message = FALSE, warning = FALSE, eval=FALSE} -library(delphi.epidata) +library(epidatr) library(epiprocess) library(data.table) library(dplyr) @@ -44,7 +44,7 @@ dv <- covidcast( ``` ```{r, echo=FALSE, message=FALSE, warning=FALSE} -library(delphi.epidata) +library(epidatr) library(epiprocess) library(data.table) library(dplyr) @@ -64,7 +64,7 @@ has (at least) the following columns: the data for January 14, 2022 that were available one day later. As we can see from the above, the data frame returned by -`delphi.epidata::covidcast()` has the columns required for the `epi_archive` +`epidatr::covidcast()` has the columns required for the `epi_archive` format, with `issue` playing the role of `version`. We can now use `as_epi_archive()` to bring it into `epi_archive` format. For removal of redundant version updates in `as_epi_archive` using compactify, please refer diff --git a/vignettes/correlation.Rmd b/vignettes/correlation.Rmd index f1fbada5..003f2caa 100644 --- a/vignettes/correlation.Rmd +++ b/vignettes/correlation.Rmd @@ -16,7 +16,7 @@ state-level COVID-19 case and death rates, smoothed using 7-day trailing averages. ```{r, message = FALSE, warning = FALSE} -library(delphi.epidata) +library(epidatr) library(epiprocess) library(dplyr) ``` diff --git a/vignettes/epiprocess.Rmd b/vignettes/epiprocess.Rmd index 379423b0..c4a118da 100644 --- a/vignettes/epiprocess.Rmd +++ b/vignettes/epiprocess.Rmd @@ -50,12 +50,12 @@ A data frame or tibble that has `geo_value` and `time_value` columns can be converted into an `epi_df` object, using the function `as_epi_df()`. As an example, we'll work with daily cumulative COVID-19 cases from four U.S. states: CA, FL, NY, and TX, over time span from mid 2020 to early 2022, and we'll use -the [`delphi.epidata`](https://github.com/cmu-delphi/delphi-epidata-r) package +the [`epidatr`](https://github.com/cmu-delphi/epidatr) package to fetch this data from the [COVIDcast API](https://cmu-delphi.github.io/delphi-epidata/api/covidcast.html). ```{r, message = FALSE} -library(delphi.epidata) +library(epidatr) library(epiprocess) library(dplyr) library(withr) @@ -72,7 +72,7 @@ cases <- covidcast( colnames(cases) ``` -As we can see, a data frame returned by `delphi.epidata::covidcast()` has the +As we can see, a data frame returned by `epidatr::covidcast()` has the columns required for an `epi_df` object (along with many others). We can use `as_epi_df()`, with specification of some relevant metadata, to bring the data frame into `epi_df` format. diff --git a/vignettes/growth_rate.Rmd b/vignettes/growth_rate.Rmd index 707243c1..d7383917 100644 --- a/vignettes/growth_rate.Rmd +++ b/vignettes/growth_rate.Rmd @@ -15,7 +15,7 @@ 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(delphi.epidata) +library(epidatr) library(epiprocess) library(dplyr) library(tidyr) diff --git a/vignettes/outliers.Rmd b/vignettes/outliers.Rmd index 9be62556..ba5f4c1f 100644 --- a/vignettes/outliers.Rmd +++ b/vignettes/outliers.Rmd @@ -15,7 +15,7 @@ apply them to `epi_df` objects. We'll demonstrate this using state-level daily reported COVID-19 case counts from FL and NJ. ```{r, message = FALSE, eval= FALSE} -library(delphi.epidata) +library(epidatr) library(epiprocess) library(dplyr) library(tidyr) @@ -37,7 +37,7 @@ x <- covidcast( The dataset has 730 rows and 3 columns. ```{r, echo=FALSE, warning=FALSE, message=FALSE} -library(delphi.epidata) +library(epidatr) library(epiprocess) library(dplyr) library(tidyr) diff --git a/vignettes/slide.Rmd b/vignettes/slide.Rmd index 8bb11eab..51170427 100644 --- a/vignettes/slide.Rmd +++ b/vignettes/slide.Rmd @@ -26,11 +26,11 @@ in this vignette. As in getting started guide, we'll fetch daily reported COVID-19 cases from CA, FL, NY, and TX (note: here we're using new, not cumulative cases) using the -[`delphi.epidata`](https://github.com/cmu-delphi/delphi-epidata-r) package, +[`epidatr`](https://github.com/cmu-delphi/epidatr) package, and then convert this to `epi_df` format. ```{r, message = FALSE, warning=FALSE} -library(delphi.epidata) +library(epidatr) library(epiprocess) library(dplyr) ```