Merge pull request #319 from cmu-delphi/lcb/update-for-latest-epidatr

Update to use latest `epidatr` (`fetch_tbl` -> `fetch`)

Author: brookslogan

data-raw/archive_cases_dv_subset.R

@@ -12,7 +12,7 @@ dv_subset <- covidcast(
   geo_values = "ca,fl,ny,tx",
   issues = epirange(20200601, 20211201)
 ) %>%
-  fetch_tbl() %>%
+  fetch() %>%
   select(geo_value, time_value, version = issue, percent_cli = value) %>%
   # We're using compactify=FALSE here and below to avoid some testthat test
   # failures on tests that were based on a non-compactified version.
@@ -27,7 +27,7 @@ case_rate_subset <- covidcast(
   geo_values = "ca,fl,ny,tx",
   issues = epirange(20200601, 20211201)
 ) %>%
-  fetch_tbl() %>%
+  fetch() %>%
   select(geo_value, time_value, version = issue, case_rate_7d_av = value) %>%
   as_epi_archive(compactify=FALSE)
 

data-raw/incidence_num_outlier_example.R

@@ -12,7 +12,7 @@ incidence_num_outlier_example <- covidcast(
   geo_values = "fl,nj",
   as_of = 20211028
 ) %>%
-  fetch_tbl() %>%
+  fetch() %>%
   select(geo_value, time_value, cases = value) %>%
   as_epi_df()
 

data-raw/jhu_csse_county_level_subset.R

@@ -17,7 +17,7 @@ jhu_csse_county_level_subset <- covidcast(
   time_values = epirange(20200601, 20211231),
   geo_values = paste(y$geo_value, collapse = ",")
 ) %>%
-  fetch_tbl() %>%
+  fetch() %>%
   select(geo_value, time_value, cases = value) %>%
   full_join(y, by = "geo_value") %>%
   as_epi_df()

data-raw/jhu_csse_daily_subset.R

@@ -10,7 +10,7 @@ confirmed_7dav_incidence_prop <- covidcast(
   time_values = epirange(20200301, 20211231),
   geo_values = "ca,fl,ny,tx,ga,pa"
 ) %>%
-  fetch_tbl() %>%
+  fetch() %>%
   select(geo_value, time_value, case_rate_7d_av = value) %>%
   arrange(geo_value, time_value) 
 
@@ -22,7 +22,7 @@ deaths_7dav_incidence_prop <- covidcast(
   time_values = epirange(20200301, 20211231),
   geo_values = "ca,fl,ny,tx,ga,pa"
 ) %>%
-  fetch_tbl() %>%
+  fetch() %>%
   select(geo_value, time_value, death_rate_7d_av = value) %>%
   arrange(geo_value, time_value) 
 
@@ -34,7 +34,7 @@ confirmed_incidence_num <- covidcast(
   time_values = epirange(20200301, 20211231),
   geo_values = "ca,fl,ny,tx,ga,pa"
 ) %>%
-  fetch_tbl() %>%
+  fetch() %>%
   select(geo_value, time_value, cases = value) %>%
   arrange(geo_value, time_value) 
 
@@ -46,7 +46,7 @@ confirmed_7dav_incidence_num <- covidcast(
   time_values = epirange(20200301, 20211231),
   geo_values = "ca,fl,ny,tx,ga,pa"
 ) %>%
-  fetch_tbl() %>%
+  fetch() %>%
   select(geo_value, time_value, cases_7d_av = value) %>%
   arrange(geo_value, time_value)
 

vignettes/advanced.Rmd

@@ -215,7 +215,7 @@ y1 <- covidcast(
   time_value = epirange(20200601, 20211201),
   geo_values = "ca,fl",
   issues = epirange(20200601, 20211201)
-) %>% fetch_tbl()
+) %>% fetch()
 
 y2 <- covidcast(
   data_source = "jhu-csse",
@@ -225,7 +225,7 @@ y2 <- covidcast(
   time_value = epirange(20200601, 20211201),
   geo_values = "ca,fl",
   issues = epirange(20200601, 20211201)
-) %>% fetch_tbl()
+) %>% fetch()
 
 x <- y1 %>%
   select(geo_value, time_value,

vignettes/aggregation.Rmd

@@ -32,7 +32,7 @@ x <- covidcast(
   time_values = epirange(20200601, 20211231),
   geo_values = paste(y$geo_value, collapse = ",")
 ) %>%
-  fetch_tbl() %>%
+  fetch() %>%
   select(geo_value, time_value, cases = value) %>%
   full_join(y, by = "geo_value") %>%
   as_epi_df()

vignettes/archive.Rmd

@@ -41,7 +41,7 @@ dv <- covidcast(
   time_values = epirange(20200601, 20211201),
   geo_values = "ca,fl,ny,tx",
   issues = epirange(20200601, 20211201)
-) %>% fetch_tbl()
+) %>% fetch()
 
 ```
 
@@ -252,7 +252,7 @@ y <- covidcast(
   geo_values = "ca,fl,ny,tx",
   issues = epirange(20200601, 20211201)
 ) %>%
-  fetch_tbl() %>%
+  fetch() %>%
   select(geo_value, time_value, version = issue, case_rate_7d_av = value) %>%
   as_epi_archive(compactify=TRUE)
 

vignettes/correlation.Rmd

@@ -31,7 +31,7 @@ x <- covidcast(
   time_values = epirange(20200301, 20211231),
   geo_values = "*"
 ) %>%
-  fetch_tbl() %>%
+  fetch() %>%
   select(geo_value, time_value, case_rate = value)
 
 y <- covidcast(
@@ -42,7 +42,7 @@ y <- covidcast(
   time_values = epirange(20200301, 20211231),
   geo_values = "*"
 ) %>%
-  fetch_tbl() %>%
+  fetch() %>%
   select(geo_value, time_value, death_rate = value)
 
 x <- x %>%

vignettes/epiprocess.Rmd

@@ -67,7 +67,7 @@ cases <- covidcast(
   geo_type = "state",
   time_values = epirange(20200301, 20220131),
   geo_values = "ca,fl,ny,tx"
-) %>% fetch_tbl()
+) %>% fetch()
 
 colnames(cases)
 ```

vignettes/growth_rate.Rmd

@@ -31,7 +31,7 @@ x <- covidcast(
   time_values = epirange(20200601, 20211231),
   geo_values = "ga,pa"
 ) %>%
-  fetch_tbl() %>%
+  fetch() %>%
   select(geo_value, time_value, cases = value) %>%
   arrange(geo_value, time_value) %>%
   as_epi_df()

vignettes/outliers.Rmd

@@ -29,7 +29,7 @@ x <- covidcast(
   geo_values = "fl,nj",
   as_of = 20211028
 ) %>%
-  fetch_tbl() %>%
+  fetch() %>%
   select(geo_value, time_value, cases = value) %>%
   as_epi_df()
 ```

vignettes/slide.Rmd

@@ -45,7 +45,7 @@ x <- covidcast(
   time_values = epirange(20200301, 20211231),
   geo_values = "ca,fl,ny,tx,ga,pa"
 ) %>%
-  fetch_tbl() %>%
+  fetch() %>%
   select(geo_value, time_value, cases = value) %>%
   arrange(geo_value, time_value) %>%
   as_epi_df()