BUG FIX: correct classification of "super" endemic areas

need **both** pe_obs_p and pe_alt_obs_p to be highly significant (> 0.99)

R/cpr_classify_endem.R

@@ -52,7 +52,7 @@ cpr_classify_endem <- function(df) {
 		#         (PE_orig is consistently higher than PE_alt across the random realisations)
 		#   b)    Else if RPE is significantly low then we have neo-endemism
 		#         (PE_orig is consistently lower than PE_alt across the random realisations)
-		#     c)    Else we have mixed age endemism in which case
+		#   c)    Else we have mixed age endemism in which case
 		#        i)    If both PE_orig and PE_alt are highly significant (p<0.01) then we
 		#              have super endemism (high in both palaeo and neo)
 		#        ii)   Else we have mixed (some mixture of palaeo, neo and non endemic)
@@ -61,7 +61,7 @@ cpr_classify_endem <- function(df) {
 		endem_type = dplyr::case_when(
 			(pe_obs_p_upper %greater% 0.95 | pe_alt_obs_p_upper %greater% 0.95) & rpe_obs_p_upper %greater% 0.975 ~ "paleo",
 			(pe_obs_p_upper %greater% 0.95 | pe_alt_obs_p_upper %greater% 0.95) & rpe_obs_p_lower %greater% 0.975 ~ "neo",
-			pe_obs_p_upper %greater% 0.99 | pe_alt_obs_p_upper %greater% 0.99 ~ "super",
+			pe_obs_p_upper %greater% 0.99 & pe_alt_obs_p_upper %greater% 0.99 ~ "super",
 			pe_obs_p_upper %greater% 0.95 | pe_alt_obs_p_upper %greater% 0.95 ~ "mixed",
 			TRUE ~ "not significant"
 		)

tests/testthat/test-cpr_classify_endem.R

@@ -14,6 +14,22 @@ test_that("Input is valid", {
 	)
 })
 
+#' @srrstats {G5.4a} Correctness tests on trivial examples for new implementations
+test_that("Calculations work", {
+  dummy_res <- data.frame(
+  	pe_obs_p_upper =     c(0.99, 0.10, 0.999, 0.999, 0.10, 0.10),
+  	pe_alt_obs_p_upper = c(0.10, 0.99, 0.999, 0.10,  0.10, 0.10),
+  	rpe_obs_p_upper =    c(0.99, 0.10, 0.10,  0.10,  0.10, 0.99),
+  	rpe_obs_p_lower =    c(0.10, 0.99, 0.10,  0.10,  0.10, 0.10)
+  ) %>% cpr_classify_endem()
+  expect_equal(dummy_res$endem_type[[1]], "paleo")
+  expect_equal(dummy_res$endem_type[[2]], "neo")
+  expect_equal(dummy_res$endem_type[[3]], "super")
+  expect_equal(dummy_res$endem_type[[4]], "mixed")
+  expect_equal(dummy_res$endem_type[[5]], "not significant")
+  expect_equal(dummy_res$endem_type[[6]], "not significant")
+})
+
 test_that("Output is formatted as expected", {
 	expect_s3_class(
 		cpr_classify_endem(rand_test),