Merge pull request #325 from cmu-delphi/r/fix-imports

Fix imports from dplyr and lubridate

Author: capnrefsmmat

R-packages/covidcast/DESCRIPTION

@@ -43,7 +43,6 @@ Imports:
   grDevices,
   httr,
   jsonlite,
-  lubridate,
   maptools,
   purrr,
   rlang,

R-packages/covidcast/R/covidcast.R

@@ -438,9 +438,9 @@ covidcast_meta <- function() {
   }
 
   meta <- meta$epidata %>%
-    dplyr::mutate(min_time = as.Date(as.character(.data$min_time), format = "%Y%m%d"),
-                  max_time = as.Date(as.character(.data$max_time), format = "%Y%m%d"),
-                  max_issue = as.Date(as.character(.data$max_issue), format = "%Y%m%d"))
+    dplyr::mutate(min_time = api_to_date(.data$min_time),
+                  max_time = api_to_date(.data$max_time),
+                  max_issue = api_to_date(.data$max_issue))
 
   class(meta) <- c("covidcast_meta", "data.frame")
   return(meta)
@@ -589,15 +589,18 @@ covidcast_days <- function(data_source, signal, start_day, end_day, geo_type,
     }
     if (dat[[i]]$message == "success") {
       desired_geos <- tolower(unique(geo_value))
+
       returned_epidata <- dat[[i]]$epidata
       returned_geo_array <- returned_epidata %>%
-        select(geo_value, time_value) %>%
-        group_by(time_value) %>%
-        summarize(geo_value = list(geo_value))
+        dplyr::select(geo_value, time_value) %>%
+        dplyr::group_by(time_value) %>%
+        dplyr::summarize(geo_value = list(geo_value))
       returned_time_values <- returned_geo_array$time_value
+
       if (length(returned_time_values) != length(time_values)) {
         missing_time_values <- setdiff(time_values, returned_time_values)
-        missing_dates <- ymd(missing_time_values)
+        missing_dates <- api_to_date(missing_time_values)
+
         warn(sprintf("Data not fetched for the following days: %s",
                      paste(missing_dates, collapse = ", ")),
              data_source = data_source,
@@ -611,6 +614,7 @@ covidcast_days <- function(data_source, signal, start_day, end_day, geo_type,
       if (!identical("*", geo_value)) {
         missing_geo_array <- returned_geo_array[
           lapply(returned_geo_array$geo_value, length) < length(desired_geos), ]
+
         if (nrow(missing_geo_array) > 0) {
           missing_geo_array$warning <-
             unlist(apply(returned_geo_array,
@@ -620,7 +624,7 @@ covidcast_days <- function(data_source, signal, start_day, end_day, geo_type,
           warn(missing_geo_array$warning,
                data_source = data_source,
                signal = signal,
-               day = ymd(missing_geo_array$time_value),
+               day = api_to_date(missing_geo_array$time_value),
                geo_value = geo_value,
                api_msg = dat[[i]]$message,
                class = "covidcast_missing_geo_values")
@@ -647,8 +651,8 @@ covidcast_days <- function(data_source, signal, start_day, end_day, geo_type,
 
   if (nrow(df) > 0) {
     # If no data is found, there is no time_value column to report
-    df$time_value <- as.Date(as.character(df$time_value), format = "%Y%m%d")
-    df$issue <- as.Date(as.character(df$issue), format = "%Y%m%d")
+    df$time_value <- api_to_date(df$time_value)
+    df$issue <- api_to_date(df$issue)
     df$data_source <- data_source
     df$signal <- signal
 
@@ -668,7 +672,7 @@ geo_warning_message <- function(row, desired_geos) {
   if (length(missing_geos) > 0) {
     missing_geos_str <- paste0(missing_geos, collapse = ", ")
     err_msg <- sprintf("Data not fetched for some geographies on %s: %s",
-                   ymd(row$time_value), missing_geos_str)
+                       api_to_date(row$time_value), missing_geos_str)
     return(err_msg)
   }
 }
@@ -755,3 +759,8 @@ covidcast <- function(data_source, signal, time_type, geo_type, time_values,
 date_to_string <- function(mydate) {
   format(mydate, "%Y%m%d")
 }
+
+# Convert dates from API to Date objects
+api_to_date <- function(str) {
+  as.Date(as.character(str), format = "%Y%m%d")
+}

R-packages/covidcast/tests/testthat/test-covidcast.R

@@ -1,7 +1,6 @@
 library(covidcast)
 library(httptest)
 library(mockery)
-library(lubridate)
 library(dplyr)
 
 # Many of these tests use mockery::with_mock_api. This replaces calls to the
@@ -145,7 +144,7 @@ test_that("covidcast_days does not treat \"*\" as a missing geo_value", {
          signal = "signal",
          time_value = c(20201030, 20201031),
          direction = NA,
-         issue = ymd("2020-11-04"),
+         issue = as.Date("2020-11-04"),
          lag = 2,
          value = 3,
          stderr = NA,
@@ -156,8 +155,8 @@ test_that("covidcast_days does not treat \"*\" as a missing geo_value", {
     covidcast_days(
       data_source = "fb-survey",
       signal = "raw_cli",
-      start_day = ymd("2020-10-30"),
-      end_day = ymd("2020-10-31"),
+      start_day = as.Date("2020-10-30"),
+      end_day = as.Date("2020-10-31"),
       geo_type = "county",
       geo_value = c("*"),
       as_of = NULL,
@@ -174,7 +173,7 @@ test_that("covidcast_days does not raise warnings for full response", {
          signal = "signal",
          time_value = c(20201030, 20201031),
          direction = NA,
-         issue = ymd("2020-11-04"),
+         issue = as.Date("2020-11-04"),
          lag = 2,
          value = 3,
          stderr = NA,
@@ -185,8 +184,8 @@ test_that("covidcast_days does not raise warnings for full response", {
     covidcast_days(
       data_source = "fb-survey",
       signal = "raw_cli",
-      start_day = ymd("2020-10-30"),
-      end_day = ymd("2020-10-31"),
+      start_day = as.Date("2020-10-30"),
+      end_day = as.Date("2020-10-31"),
       geo_type = "county",
       geo_value = c("geoa"),
       as_of = NULL,
@@ -202,7 +201,7 @@ test_that("covidcast_days batches calls to covidcast", {
     signal = "signal",
     time_value = rep(NA, 3),
     direction = NA,
-    issue = ymd("2020-11-04"),
+    issue = as.Date("2020-11-04"),
     lag = 2,
     value = 3,
     stderr = NA,
@@ -217,8 +216,8 @@ test_that("covidcast_days batches calls to covidcast", {
       covidcast_days(
         data_source = "fb-survey",
         signal = "raw_cli",
-        start_day = ymd("2020-10-01"),
-        end_day = ymd("2020-10-06"),
+        start_day = as.Date("2020-10-01"),
+        end_day = as.Date("2020-10-06"),
         geo_type = "county",
         geo_value = "*",
         as_of = NULL,