fix to no c score in transect summary

ifoxfoot · Sep 25, 2023 · eb1f799 · eb1f799
1 parent bbe306b
commit eb1f799
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Showing 3 changed files with 52 additions and 4 deletions.
diff --git a/R/cover_metrics.R b/R/cover_metrics.R
@@ -156,14 +156,16 @@ transect_summary <- function(x, key = "name", db, cover_class = "percent_cover",
   entries_c <- entries %>%
     dplyr::group_by(!!as.name(key)) %>%
     dplyr::mutate(mean = mean(.data$cover)) %>%
-    dplyr::distinct(!!as.name(key), mean, c)
+    dplyr::distinct(!!as.name(key), mean, c) %>%
+    dplyr::filter(!is.na(c))
 
   #get native entries c
   entries_n <- entries %>%
     dplyr::filter(.data$nativity == "native") %>%
     dplyr::group_by(!!as.name(key)) %>%
     dplyr::mutate(mean = mean(.data$cover)) %>%
-    dplyr::distinct(!!as.name(key), mean, c)
+    dplyr::distinct(!!as.name(key), mean, c) %>%
+    dplyr::filter(!is.na(c))
 
 
   #create list of all metrics that will be included in the output

diff --git a/R/helper.R b/R/helper.R
@@ -31,7 +31,8 @@ transect <- data.frame(acronym  = c("ABEESC", "ABIBAL", "AMMBRE", "ANTELE", "ABE
                       cover = c(50, 4, 20, 30, 40, 7, 60),
                       quad_id = c(1, 1, 1, 1, 2, 2, 2))
 #na C Value
-no_c_test <- data.frame(name = c("ABRONIA FRAGRANS", "ACER GLABRUM", "ACER GRANDIDENTATUM", "BOOP", "ACER PLATANOIDES"))
+no_c_test <- data.frame(name = c("ABRONIA FRAGRANS", "ACER GLABRUM", "ACER GRANDIDENTATUM", "BOOP", "ACER PLATANOIDES"),
+                        cover = c(1, 2, 3, 4, 62))
 
 #cover method test
 cover_test <- data.frame(acronym  = c("ABEESC", "ABIBAL", "AMMBRE", "ANTELE"),

diff --git a/tests/testthat/test-cover_metrics.R b/tests/testthat/test-cover_metrics.R
@@ -114,7 +114,6 @@ test_that("transect_summary() works in with synonyms (diff names, same ID)", {
                           )))
 })
 
-
 test_that("transect_summary() works in with duplicates", {
   expect_equal(transect_summary(accepted_dup, "acronym", "michigan_2014"),
 
@@ -161,6 +160,52 @@ test_that("transect_summary() works in with duplicates", {
                           )))
 })
 
+test_that("transect_summary() works in with no c score", {
+  expect_equal(transect_summary(no_c_test, "name", "montana_2017"),
+
+               data.frame(metrics = c("Total Species Richness",
+                                      "Native Species Richness",
+                                      "Introduced Species Richness",
+                                      "% of Species with no C Value",
+                                      "% of Species with 0 C Value",
+                                      "% of Species with 1-3 C Value",
+                                      "% of Species with 4-6 C Value",
+                                      "% of Species with 7-10 C Value",
+                                      "Mean C",
+                                      "Native Mean C",
+                                      "Cover-Weighted Mean C",
+                                      "Cover-Weighted Native Mean C",
+                                      "Total FQI",
+                                      "Native FQI",
+                                      "Cover-Weighted FQI",
+                                      "Cover-Weighted Native FQI",
+                                      "Adjusted FQI",
+                                      "Mean Wetness",
+                                      "Native Mean Wetness",
+                                      "% Hydrophytes"),
+                          values = c(species_richness(no_c_test, "name", "montana_2017", allow_no_c = T),
+                                     species_richness(no_c_test, "name", "montana_2017", native = TRUE, allow_no_c = T),
+                                     1, #introduced
+                                     50.00, #no c score
+                                     0.0, #0 score
+                                     25.0, #1-3 score
+                                     25.0, #4-6 score
+                                     0, #7-10 score
+                                     mean_c(no_c_test, "name", "montana_2017"),
+                                     mean_c(no_c_test, "name", "montana_2017", native = TRUE),
+                                     cover_mean_c(no_c_test, "name", "montana_2017", allow_duplicates = T),
+                                     cover_mean_c(no_c_test, "name", "montana_2017", native = TRUE, allow_duplicates = T),
+                                     FQI(no_c_test, "name", "montana_2017"),
+                                     FQI(no_c_test, "name", "montana_2017", native = TRUE),
+                                     cover_FQI(no_c_test, "name", "montana_2017", allow_duplicates = T),
+                                     cover_FQI(no_c_test, "name", "montana_2017", allow_duplicates = T, native = TRUE),
+                                     adjusted_FQI(no_c_test, "name", "montana_2017"),
+                                     mean_w(no_c_test, "name", "montana_2017", allow_no_c = T),
+                                     mean_w(no_c_test, "name", "montana_2017", native = TRUE, allow_no_c = T),
+                                     NA #hydro
+                          )))
+})
+
 
 #-------------------------------------------------------------------------------
 #testing plot_summary()