cmu-delphi · kenmawer · Jul 22, 2022 · Aug 8, 2022 · Aug 8, 2022 · Aug 10, 2022
diff --git a/R/growth_rate.R b/R/growth_rate.R
@@ -44,7 +44,8 @@
 #' * "rel_change": uses (B/A - 1) / h, where B is the average of `y` over the
 #'   second half of a sliding window of bandwidth h centered at the reference
 #'   point `x0`, and A the average over the first half. This can be seen as
-#'   using a first-difference approximation to the derivative.
+#'   using a first-difference approximation to the derivative. This is the
+#'   default method if `method` is not specified.
 #' * "linear_reg": uses the slope from a linear regression of `y` on `x` over a
 #'   sliding window centered at the reference point `x0`, divided by the fitted
 #'   value from this linear regression at `x0`.
@@ -145,7 +146,7 @@ growth_rate = function(x = seq_along(y), y, x0 = x,
 
   # Remove NAs if we need to
   if (na_rm) {
-    o = !(is.na(x) & is.na(y))
+    o = !(is.na(x) | is.na(y))
     x = x[o]
     y = y[o]
   }

diff --git a/man/as_epi_archive.Rd b/man/as_epi_archive.Rd
diff --git a/man/as_epi_df.Rd b/man/as_epi_df.Rd
diff --git a/man/epi_archive.Rd b/man/epi_archive.Rd
diff --git a/man/epi_slide.Rd b/man/epi_slide.Rd
diff --git a/man/epix_as_of.Rd b/man/epix_as_of.Rd
diff --git a/man/epix_slide.Rd b/man/epix_slide.Rd
diff --git a/man/growth_rate.Rd b/man/growth_rate.Rd
diff --git a/tests/testthat/test-growth_rate.R b/tests/testthat/test-growth_rate.R
@@ -0,0 +1,57 @@
+library(dplyr)
+
+test_that("Test error throwing",{
+  # Error cases
+  expect_error(growth_rate(x=1:3,y=1:4),
+               "`x` and `y` must have the same length.")
+  expect_error(growth_rate(x=1:20,y=1:20,x0=21),
+               "`x0` must be a subset of `x`.")
+
+  # This should produce no error
+  expect_error(growth_rate(x=1:20,y=1:20,x0=c(1,3)),NA)
+})
+
+test_that("Test throwing of warning of duplicates",{
+  # The warning that is prompted is as follows:
+  # "`x` contains duplicate values. (If being run on a column in an `epi_df`,
+  # did you group by relevant key variables?)"
+  # Note that putting it in the regexp of expect_warning doesn't seem to work
+  jhu_csse_daily_subset %>%
+    mutate(cases_gr = growth_rate(x = time_value,  y = cases, dup_rm=TRUE)) %>%
+    expect_warning() %>%
+    expect_error()
+})
+
+test_that("Simple example of growth rate that produces desired results",{
+  expect_equal(growth_rate(x=1:20,y=2^(1:20),h=1),
+               c(rep(1,19),NaN))
+})
+
+test_that("Running different methods won't fail",{
+  expect_error(
+    for (m in c("rel_change","linear_reg","smooth_spline","trend_filter")) {
+      growth_rate(x=1:25,y=sin(0:24)+0:24+1,method=m,h=3)
+    }, NA)
+})
+
+test_that("When using trend_filter, if `cv=FALSE`, then df must be an integer",{
+  expect_error(growth_rate(x=1:25,y=sin(0:24)+0:24+1,method="trend_filter",
+                           cv=FALSE,df=1.5,h=3),
+               "If `cv = FALSE`, then `df` must be an integer.")
+})
+
+test_that("log_scale works",{
+  expect_equal(growth_rate(x=1:20,y=exp(1:20),h=5,method="linear_reg",log_scale = TRUE),
+               rep(1,20))
+})
+
+test_that("na_rm works",{
+  X <- c(1:10,NA,12:19,NA)
+  Y <- c(1:9,NA,NA,12:20)
+
+  expect_false(NA %in% growth_rate(x=X,y=Y,na_rm = TRUE))
+  expect_equal(length(growth_rate(x=X,y=Y,na_rm = TRUE)),17)
+  expect_equal(growth_rate(x=X,y=Y,na_rm = FALSE),
+               # 1+NA gives an NA classified as a numeric
+               rep(1+NA,20))
+})