specify timezones to avoid unit test errors

If these are run in other locales the unit tests will fail due to timezones altering model outputs
PaulMelloy · Nov 15, 2024 · 44926d2 · 44926d2
1 parent 9290751
commit 44926d2
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Showing 4 changed files with 25 additions and 29 deletions.
diff --git a/R/calc_DIV.R b/R/calc_DIV.R
@@ -68,8 +68,8 @@ calc_DIV <- function(date_time, Tm,RH, rain,dat){
           "moist_ind") := list(temperature_index(temp),
                               moisture_index(rh,rain,70))]
 
-  DIV <- dat[, list(DIV = mean(fifelse(test = Tm_index == 0 | moist_ind == 0,
-                                  yes = 0, no = (Tm_index * moist_ind)))),
+  DIV <- dat[, list(DIV = round(mean(fifelse(test = Tm_index == 0 | moist_ind == 0,
+                                  yes = 0, no = Tm_index * moist_ind)),digits = 7)),
              by = c("Year", "Month", "Day")]
 
   return(DIV)

diff --git a/R/sysdata.rda b/R/sysdata.rda
diff --git a/tests/testthat/test-calc_DIV.R b/tests/testthat/test-calc_DIV.R
@@ -6,9 +6,9 @@ test_that("calc_DIV works", {
     RH = RH1,
     rain = rain1
   )
-  expect_equal(DIV1$DIV, c(0.8445079, 0.8196010 ,0.8513760), tolerance = 0.00001)
+  expect_equal(DIV1$DIV, c(0.7845169, 0.8551818), tolerance = 0.00001)
   expect_type(DIV1,"list")
-  expect_equal(dim(DIV1), c(3,4))
+  expect_equal(dim(DIV1), c(2,4))
   expect_equal(colnames(DIV1), c("Year","Month","Day","DIV"))
 
   in_dat <- data.frame(
@@ -21,23 +21,18 @@ test_that("calc_DIV works", {
   expect_error(calc_DIV(dat = in_dat),
                regexp = "'dat' data.frame must have colnames 'times','temp','rh','rain'")
 
+  # accept a data.frame as input
   in_dat <- data.frame(
     times = date_t,
     temp = Tm1,
     rh = RH1,
     rain = rain1
   )
-  #calc_DIV(dat = in_dat)
+  dat_out <- calc_DIV(dat = in_dat)
 
-})
-
-# define DIV calculation
+  expect_equal(dat_out$DIV, c(0.7845169, 0.8551818), tolerance = 0.00001)
+  expect_type(dat_out,"list")
+  expect_equal(dim(dat_out), c(2,4))
+  expect_equal(colnames(dat_out), c("Year","Month","Day","DIV"))
 
-# dat <- data.table(Tm = rep(0:49, times = 50),
-#                   Rh = rep (51:100, each = 50))
-#
-# dat[, DIV := list(temperature_index(Tm)*
-#                     moisture_index(Rh))]
-# library(ggplot2)
-# ggplot(dat, aes(x = Tm, y = Rh, z = DIV))+
-#   geom_contour_filled()
+})
diff --git a/tests/testthat/test-calc_epidemic_onset.R b/tests/testthat/test-calc_epidemic_onset.R
@@ -1,5 +1,6 @@
 # load the weather data to be formatted
 # import BOM data file
+set.seed(321)
 brisvegas <-
   system.file("extdata", "bris_weather_obs.csv", package = "epiphytoolR")
 bris <- data.table::fread(brisvegas)
@@ -74,14 +75,14 @@ test_that("epidemic onset produces expected outcome", {
                                rh)]
 
   # susceptible cultivar
-  sus_out <- calc_epidemic_onset(c_closure = as.POSIXct("2023-06-01"),
+  sus_out <- calc_epidemic_onset(c_closure = as.POSIXct("2023-06-01", tz = "UTC"),
                       weather = bris_formated,
                       cultivar_sus = 3)
   expect_type(sus_out,"double")
   expect_equal(sus_out, as.POSIXct("2023-06-07",tz = "UTC"))
 
   # resistant cultivar
-  res_out <- calc_epidemic_onset(c_closure = as.POSIXct("2023-06-01"),
+  res_out <- calc_epidemic_onset(c_closure = as.POSIXct("2023-06-01", tz = "UTC"),
                       weather = bris_formated,
                       cultivar_sus = 5)
   expect_type(res_out,"double")
@@ -99,7 +100,7 @@ test_that("different start dates provide different epidemic dates",{
   # set NA wind direction values to 20 degrees. Wind is not important for this model
   w_dat[,WR200 := runif(.N,min = 0,359)]
   # remove all data after September as it contains missing data
-  w_dat <- w_dat[Datum < as.POSIXct("2022-10-01")]
+  w_dat <- w_dat[Datum < as.POSIXct("2022-10-01",tz = "UTC")]
   # set NA wind speed values to zero
   w_dat[is.na(WG200),WG200 := 0]
 
@@ -125,21 +126,21 @@ test_that("different start dates provide different epidemic dates",{
     }
     out <- calc_epidemic_onset(start = as.POSIXct("2022-04-25",tz = "UTC"),
                                end = as.POSIXct("2022-09-30",tz = "UTC"),
-                               c_closure = as.POSIXct("2022-05-01")+(i*3*86400), # 86400 is the number of seconds in a day
+                               c_closure = as.POSIXct("2022-05-01",tz = "UTC")+(i*3*86400), # 86400 is the number of seconds in a day
                                weather = w_dat,
                                cultivar_sus = 3)
 
     out2 <- c(out2,as.character(out))
 
   }
-  # cat(out2,sep = "\", \"")
-  expect_equal(out2, c("2022-05-20", "2022-05-20", "2022-05-21", "2022-05-24",
-                       "2022-05-24", "2022-05-29", "2022-06-05", "2022-06-08",
-                       "2022-06-09", "2022-06-11", "2022-06-12", "2022-06-13",
-                       "2022-06-20", "2022-06-24", "2022-06-26", "2022-06-27",
-                       "2022-06-30", "2022-07-01", "2022-07-04", "2022-07-08",
-                       "2022-07-11", "2022-07-13", "2022-07-17", "2022-07-22",
-                       "2022-07-25", "2022-07-26", "2022-07-29", "2022-08-01",
-                       "2022-08-01", "2022-08-04"))
+
+  expect_equal(out2, c("2022-05-20", "2022-05-21", "2022-05-22", "2022-05-24",
+                       "2022-05-25", "2022-05-31", "2022-06-06", "2022-06-08",
+                       "2022-06-09", "2022-06-11", "2022-06-12", "2022-06-17",
+                       "2022-06-22", "2022-06-25", "2022-06-26", "2022-06-27",
+                       "2022-06-30", "2022-07-01", "2022-07-07", "2022-07-09",
+                       "2022-07-11", "2022-07-13", "2022-07-20", "2022-07-23",
+                       "2022-07-26", "2022-07-26", "2022-07-29", "2022-08-01",
+                       "2022-08-03", "2022-08-05"))
 })