Merge pull request #159 from dajmcdon/km-test-archive

Updated testing for instatiation of an epi_archive

Author: brookslogan

man/as_epi_archive.Rd

@@ -0,0 +1,129 @@
+library(dplyr)
+
+test_that("first input must be a data.frame",{
+  expect_error(as_epi_archive(c(1,2,3),compactify=FALSE),
+               regexp="`x` must be a data frame.")
+})
+
+dt <- archive_cases_dv_subset$DT
+
+test_that("data.frame must contain geo_value, time_value and version columns",{
+  expect_error(as_epi_archive(select(dt,-geo_value), compactify=FALSE),
+               regexp="`x` must contain a `geo_value` column.")
+  expect_error(as_epi_archive(select(dt,-time_value), compactify=FALSE),
+               regexp="`x` must contain a `time_value` column.")
+  expect_error(as_epi_archive(select(dt,-version), compactify=FALSE),
+               regexp="`x` must contain a `version` column.")
+})
+
+test_that("other_keys can only contain names of the data.frame columns",{
+  expect_error(as_epi_archive(dt,other_keys = "xyz", compactify=FALSE),
+               regexp="`other_keys` must be contained in the column names of `x`.")
+  expect_error(as_epi_archive(dt,other_keys = "percent_cli", compactify=FALSE),NA)
+})
+
+test_that("other_keys cannot contain names geo_value, time_value or version",{
+  expect_error(as_epi_archive(dt,other_keys = "geo_value", compactify=FALSE),
+               regexp="`other_keys` cannot contain \"geo_value\", \"time_value\", or \"version\".")
+  expect_error(as_epi_archive(dt,other_keys = "time_value", compactify=FALSE),
+               regexp="`other_keys` cannot contain \"geo_value\", \"time_value\", or \"version\".")
+  expect_error(as_epi_archive(dt,other_keys = "version", compactify=FALSE),
+               regexp="`other_keys` cannot contain \"geo_value\", \"time_value\", or \"version\".")
+})
+
+test_that("Warning thrown when other_metadata contains overlapping names with geo_type or time_type fields",{
+  expect_warning(as_epi_archive(dt,additional_metadata = list(geo_type = 1), compactify=FALSE),
+                 regexp="`additional_metadata` names overlap with existing metadata fields\n\"geo_type\", \"time_type\".")
+  expect_warning(as_epi_archive(dt,additional_metadata = list(time_type = 1), compactify=FALSE),
+                 regexp="`additional_metadata` names overlap with existing metadata fields\n\"geo_type\", \"time_type\".")
+})
+
+test_that("epi_archives are correctly instantiated with a variety of data types",{
+  # Data frame
+  df <- data.frame(geo_value="ca",
+                   time_value=as.Date("2020-01-01"),
+                   version = as.Date("2020-01-01") + 0:19,
+                   value=1:20)
+  
+  ea1 <- as_epi_archive(df, compactify=FALSE)
+  expect_equal(key(ea1$DT),c("geo_value","time_value","version"))
+  expect_equal(ea1$additional_metadata,list())
+  
+  ea2 <- as_epi_archive(df, other_keys="value", additional_metadata=list(value=df$value), compactify=FALSE)
+  expect_equal(key(ea2$DT),c("geo_value","time_value","value","version"))
+  expect_equal(ea2$additional_metadata,list(value=df$value))
+  
+  # Tibble
+  tib <- tibble::tibble(df, code="x")
+  
+  ea3 <- as_epi_archive(tib, compactify=FALSE)
+  expect_equal(key(ea3$DT),c("geo_value","time_value","version"))
+  expect_equal(ea3$additional_metadata,list())
+  
+  ea4 <- as_epi_archive(tib, other_keys="code", additional_metadata=list(value=df$value), compactify=FALSE)
+  expect_equal(key(ea4$DT),c("geo_value","time_value","code","version"))
+  expect_equal(ea4$additional_metadata,list(value=df$value))
+  
+  # Keyed data.table
+  kdt <- data.table::data.table(geo_value="ca",
+                                time_value=as.Date("2020-01-01"),
+                                version = as.Date("2020-01-01") + 0:19,
+                                value = 1:20,
+                                code = "CA",
+                                key = "code")
+  
+  ea5 <- as_epi_archive(kdt, compactify=FALSE)
+  # Key from data.table isn't absorbed when as_epi_archive is used
+  expect_equal(key(ea5$DT),c("geo_value","time_value","version")) 
+  expect_equal(ea5$additional_metadata,list())
+  
+  ea6 <- as_epi_archive(kdt,other_keys="value", additional_metadata=list(value=df$value), compactify=FALSE)
+  # Mismatched keys, but the one from as_epi_archive overrides
+  expect_equal(key(ea6$DT),c("geo_value","time_value","value","version"))
+  expect_equal(ea6$additional_metadata,list(value=df$value))
+  
+  # Unkeyed data.table
+  udt <- data.table::data.table(geo_value="ca",
+                                time_value=as.Date("2020-01-01"),
+                                version = as.Date("2020-01-01") + 0:19,
+                                value=1:20,
+                                code = "CA")
+  
+  ea7 <- as_epi_archive(udt, compactify=FALSE)
+  expect_equal(key(ea7$DT),c("geo_value","time_value","version"))
+  expect_equal(ea7$additional_metadata,list())
+  
+  ea8 <- as_epi_archive(udt,other_keys="code", additional_metadata=list(value=df$value), compactify=FALSE)
+  expect_equal(key(ea8$DT),c("geo_value","time_value","code","version"))
+  expect_equal(ea8$additional_metadata,list(value=df$value))
+  
+  # epi_df
+  edf1 <- jhu_csse_daily_subset %>%
+    select(geo_value,time_value,cases) %>%
+    mutate(version = max(time_value), code = "USA")
+  
+  ea9 <- as_epi_archive(edf1, compactify=FALSE)
+  expect_equal(key(ea9$DT),c("geo_value","time_value","version"))
+  expect_equal(ea9$additional_metadata,list())
+  
+  ea10 <- as_epi_archive(edf1,other_keys="code", additional_metadata=list(value=df$value), compactify=FALSE)
+  expect_equal(key(ea10$DT),c("geo_value","time_value","code","version"))
+  expect_equal(ea10$additional_metadata,list(value=df$value))
+  
+  # Keyed epi_df
+  edf2 <- data.frame(geo_value = "al",
+                     time_value = rep(as.Date("2020-01-01") + 0:9,2),
+                     version = c(rep(as.Date("2020-01-25"),10),
+                                 rep(as.Date("2020-01-26"),10)),
+                     cases = 1:20,
+                     misc = "USA") %>%
+    as_epi_df(additional_metadata = list(other_keys = "misc"))
+  
+  ea11 <- as_epi_archive(edf2, compactify=FALSE)
+  expect_equal(key(ea11$DT),c("geo_value","time_value","version"))
+  expect_equal(ea11$additional_metadata,list())
+  
+  ea12 <- as_epi_archive(edf2,other_keys="misc", additional_metadata=list(value=df$misc), compactify=FALSE)
+  expect_equal(key(ea12$DT),c("geo_value","time_value","misc","version"))
+  expect_equal(ea12$additional_metadata,list(value=df$misc))
+})