InteragencyEcologicalProgram · sbashevkin · Aug 4, 2025 · Jun 16, 2025 · Jun 23, 2025 · Jun 23, 2025
diff --git a/NEWS.md b/NEWS.md
@@ -13,6 +13,8 @@
 -   Fixed issue where macrozoop biomass was being incorrectly converted to micrograms, resulting in 100X higher biomass values. 
 -   Added FRP 2022 data and adjusted crosswalk to reflect changes to their taxonomic table. 
 -   Added 2023 FMWT/STN data and adjusted zoopdownloader to reflect new date format
+-   Added FRP 2023 data and adjusted crosswalk to reflect changes to their table. 
+-   Adjusted crosswalk table to reflect the order "Cladocera" being split into several orders. 
 
 # zooper 2.5.1
 

diff --git a/R/Download_utilities.R b/R/Download_utilities.R
@@ -76,7 +76,8 @@ zoop_urls<-function(Sources){
 
   if("EMP"%in%Sources){
     EMP_revision_url <- "https://pasta.lternet.edu/package/eml/edi/522"
-    EMP_latest_revision <- utils::tail(Tryer(n=3, fun=readLines, con=EMP_revision_url, warn = FALSE), 1)
+    #EMP_latest_revision <- utils::tail(Tryer(n=3, fun=readLines, con=EMP_revision_url, warn = FALSE), 1)
+    EMP_latest_revision = 11 #Keeping the old EMP dataset until I can go through and do a full update - next pull request.
     EMP_pkg_url <- paste0("https://pasta.lternet.edu/package/data/eml/edi/522/", EMP_latest_revision)
     EMP_entities <- Tryer(n=3, fun=readLines, con=EMP_pkg_url, warn = FALSE)
     EMP_name_urls <- paste("https://pasta.lternet.edu/package/name/eml/edi/522", EMP_latest_revision, EMP_entities, sep="/")

diff --git a/R/zoop_downloader.R b/R/zoop_downloader.R
@@ -1034,7 +1034,7 @@ Zoopdownloader <- function(
 
     data.list[["FMWT_Macro"]] <- dplyr::bind_rows(zoo_FMWT_Macro, zoo_SMSCG_Macro)%>%
       dplyr::select(-"ID")%>%
-      distinct()%>% #remove any samples duplicated between the SMSCG datset and the FMWTdataset
+      dplyr::distinct()%>% #remove any samples duplicated between the SMSCG datset and the FMWTdataset
       dplyr::mutate(Microcystis = as.character(.data$Microcystis))%>%
       tidyr::pivot_longer(cols=c(-"Project", -"Year", -"Survey", -"Date", -"Datetime",
                                  -"Station", -"Time", -"TideCode",

diff --git a/R/zoop_synthesizer.R b/R/zoop_synthesizer.R
@@ -149,7 +149,7 @@ Zoopsynther<-function(
   }
 
   if(!is.null(Taxa) & !purrr::every(Taxa, ~.%in%CompleteTaxaList)){
-    warning("Check spelling of Taxa, some are not present in the completeTaxaList and are likely misspelled.")
+    warning("Check spelling of Taxa, some are not present in the completeTaxaList and are likely misspelled. If you want information on Cladocera, note that the Order Cladocera has been revised to reflect several different orders, three of which are found in our estuary: Anomopoda, Ctenopoda, and Onychopoda. 'Branchiopoda' (Class) will select all of these orders.")
   }
 
   #Make it possible to re-download data if desired

diff --git a/data-raw/crosswalk-zoopComb-zoopEnvComb-startDates.R b/data-raw/crosswalk-zoopComb-zoopEnvComb-startDates.R
@@ -31,7 +31,6 @@ zoop<-Zoopdownloader(Data_sets=c("EMP_Meso", "FMWT_Meso", "STN_Meso",
                      Data_folder=tempdir(), Save_object=FALSE, Return_object=TRUE,
                      Redownload_data=TRUE, Crosswalk=crosswalk, Biomass=TRUE)
 
-
 zoopComb <- zoop$Zooplankton
 
 zoopEnvComb <- zoop$Environment

diff --git a/data-raw/crosswalk.csv b/data-raw/crosswalk.csv
diff --git a/data/crosswalk.rda b/data/crosswalk.rda
diff --git a/data/startDates.rda b/data/startDates.rda
diff --git a/data/zoopComb.rda b/data/zoopComb.rda
diff --git a/data/zoopEnvComb.rda b/data/zoopEnvComb.rda
diff --git a/tests/testthat/test-Crosswalk.R b/tests/testthat/test-Crosswalk.R
@@ -88,3 +88,4 @@ taxname_level<-zooper::crosswalk%>%
 test_that("Taxnames are entered with a consistent taxonomic level", {
   expect_equal(length(taxname_level), 0)
 })
+
diff --git a/tests/testthat/test-Source_datasets.R b/tests/testthat/test-Source_datasets.R
@@ -212,7 +212,7 @@ test_that("20mm Meso column names have not changed", {
 
 test_that("FRP Meso column names have not changed", {
   expect_setequal(names_FRP_Meso, c( "SampleID_key","SampleID_frp","CommonName", "VisitNo","Location", "Date",
-                                     "subsample" ,
+                                     "subsample" , "DragMethod",
                                      "Count" , "AdjCount" ,"CPUE","Flagged_Data_zoops", "StartTime",
                                      "EndTime",  "LatitudeStart", "LatitudeEnd", "LongitudeStart", "LongitudeEnd",
                                     "DepthOfWater", "NetMeterEnd", "TowDirection", "NetMeterStart",
@@ -242,6 +242,7 @@ test_that("EMP Micro column names have not changed", {
 
 test_that("FRP Macro column names have not changed", {
   expect_setequal(names_FRP_Macro, c("SampleID_key","SampleID_frp", "CommonName", "VisitNo", "subsample",
+                                     "DragMethod",
                                      "Count", "AdjCount", "Flagged_Data_macroinvert", "StartTime", "EndTime",
                                      "LatitudeStart", "LatitudeEnd", "LongitudeStart", "LongitudeEnd",  "DepthOfSample",
                                      "DepthOfWater", "NetMeterEnd", "TowDirection", "NetMeterStart",        "Boulder",
@@ -253,7 +254,7 @@ test_that("FRP Macro column names have not changed", {
 test_that("FRP site data column names have not changed", {
   expect_setequal(names_FRP_sites, c('VisitNo', 'Location', 'Date', 'Temp', 'SC', 'pH', 'DO',
                                      'Turbidity', 'Chlorophyll', 'Phycocyanin', 'FDOM', 'Secchi',
-                                     'Microcystis', 'Tide', 'Weather', 'WindWaves', 'Flagged_Data'))
+                                     'Microcystis', 'Tide', 'Weather', 'WindWaves', 'Flagged_Data', "SiteComments"))
 
 })
 

diff --git a/zooper.Rproj b/zooper.Rproj
@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: e55d72fd-fe3f-4bf5-9b19-6df88f448b78
 
 RestoreWorkspace: No
 SaveWorkspace: No
Original file line number	Diff line number	Diff line change
Expand Up		@@ -88,3 +88,4 @@ taxname_level<-zooper::crosswalk%>%
		test_that("Taxnames are entered with a consistent taxonomic level", {
		expect_equal(length(taxname_level), 0)
		})