diff --git a/DESCRIPTION b/DESCRIPTION index c7cfeb8..7918a4e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -49,7 +49,7 @@ Imports: rvest URL: https://github.com/InteragencyEcologicalProgram/zooper BugReports: https://github.com/InteragencyEcologicalProgram/zooper/issues -RoxygenNote: 7.3.2 +RoxygenNote: 7.3.3 Suggests: spelling, testthat (>= 2.1.0), diff --git a/NEWS.md b/NEWS.md index 292807c..e127eb7 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,7 @@ # zooper (development version) -- Added EMP data released in June 2025 (sampling from 1972–2023), **which no longer includes amphipods in the macro dataset**; see the [amphipods_notes (EDI 522)](https://portal.edirepository.org/nis/mapbrowse?scope=edi&identifier=522) for more information. +- Added EMP and FRP data released in May 2026 +- Added EMP data released in June 2025 (sampling from 1972–2023), **which no longer includes amphipods in the macro dataset**; see the [amphipods_notes (EDI 522)](https://portal.edirepository.org/nis/mapbrowse?scope=edi&identifier=522) for more information. - ~~Fixed issue where EMP macro amphipod counts from before 2014 were being converted to unidentified mysids instead of unidentified amphipods, since amphipods were not identified to species before 2014.~~ - Fixed issue with biomass conversion for macro and micro zooplankton. Previously it was not taking into account the count and instead providing the BPUE if 1 individual were present. - Added the biomass for the surveys and size classes with the appropriate conversation factors and length data. This feature is still experimental diff --git a/R/Download_utilities.R b/R/Download_utilities.R index 1812612..ab6f304 100644 --- a/R/Download_utilities.R +++ b/R/Download_utilities.R @@ -82,10 +82,10 @@ zoop_urls<-function(Sources){ EMP_name_urls <- paste("https://pasta.lternet.edu/package/name/eml/edi/522", EMP_latest_revision, EMP_entities, sep="/") names(EMP_entities) <- purrr::map_chr(EMP_name_urls, ~Tryer(n=3, fun=readLines, con=.x, warn = FALSE)) - out$EMP$Meso<-paste0(EMP_pkg_url, "/", EMP_entities["1972-2023_CBMatrix_EDI"]) - out$EMP$Micro<-paste0(EMP_pkg_url, "/", EMP_entities["1972-2023_PumpMatrix_EDI"]) - out$EMP$Macro<-paste0(EMP_pkg_url, "/", EMP_entities["1972-2023_MysidMatrix_EDI"]) - out$EMP$Lengths<-paste0(EMP_pkg_url, "/", EMP_entities["1972-2023_Mysid_Length_Data_EDI"]) + out$EMP$Meso<-paste0(EMP_pkg_url, "/", EMP_entities["1972-2024_CBMatrix_EDI"]) + out$EMP$Micro<-paste0(EMP_pkg_url, "/", EMP_entities["1972-2024_PumpMatrix_EDI"]) + out$EMP$Macro<-paste0(EMP_pkg_url, "/", EMP_entities["1972-2024_MysidMatrix_EDI"]) + out$EMP$Lengths<-paste0(EMP_pkg_url, "/", EMP_entities["1972-2024_Mysid_Length_Data_EDI"]) } @@ -159,3 +159,6 @@ zoop_urls<-function(Sources){ return(out) } + +#set options to allow access to EDI without signing in +#options(HTTPUserAgent="EDI_CodeGen") diff --git a/R/data.R b/R/data.R index e5c7a8b..b1a3d4d 100644 --- a/R/data.R +++ b/R/data.R @@ -2,7 +2,7 @@ #' #' A crosswalk table relating the taxonomic code used by each dataset to current scientific names, life stages, and taxonomic hierarchies. #' -#' @format a tibble with 404 rows and 34 variables +#' @format a tibble with 471 rows and 37 variables #' \describe{ #' \item{EMP_Micro}{Taxonomic codes used in the Environmental Monitoring Program microzooplankton (43 \eqn{\mu}m) mesh dataset} #' \item{EMP_Meso}{Taxonomic codes used in the Environmental Monitoring Program mesozooplankton (160 \eqn{\mu}m) mesh dataset} @@ -36,6 +36,8 @@ #' \item{twentymmstart2}{First year the 20mm Survey restarted counting this taxa} #' \item{DOPstart}{First year DOP starting counting this taxa} #' \item{DOPend}{Last year DOP counted this taxa} +#' \item{FRPstart}{First year FRP starting counting this taxa} +#' \item{FRPend}{Last year FRP counted this taxa} #' } #' @seealso \code{\link{Zoopdownloader}}, \code{\link{Zoopsynther}}, \code{\link{zooper}} "crosswalk" @@ -57,7 +59,7 @@ #' #' Latitudes and longitudes for each zooplankton station. #' -#' @format a tibble with 387 rows and 4 columns +#' @format a tibble with 399 rows and 4 columns #' \describe{ #' \item{Source}{Abbreviated name of the source dataset} #' \item{Station}{Sampling station name} @@ -71,7 +73,7 @@ #' #' Latitudes and longitudes for EMP EZ stations on each sampling date from 2004 to present. #' -#' @format a tibble with 491 rows and 4 columns +#' @format a tibble with 575 rows and 4 columns #' \describe{ #' \item{Date}{Date sample was collected} #' \item{Station}{Sampling station name} @@ -85,7 +87,7 @@ #' #' All source zooplankton datasets combined into one tibble. #' -#' @format a tibble with 3,615,105 rows and 14 columns. +#' @format a tibble with 3,833,994 rows and 14 columns. #' \describe{ #' \item{Source}{Abbreviated name of the source dataset. "EMP"=Environmental Monitoring Program, "FRP"=Fish Restoration Program, "FMWT"= Fall Midwater Trawl, "STN"= Townet Survey, "20mm" =20mm survey, "DOP" = Directed Outflow Project Lower Trophic Study, and "YBFMP"= Yolo Bypass Fish Monitoring Program.} #' \item{SizeClass}{Net size class. Micro corresponds to 43-50 \eqn{\mu}m mesh, Meso corresponds to 150-160 \eqn{\mu}m mesh, and Macro corresponds to 500-505 \eqn{\mu}m mesh. However, prior to 1974 EMP macrozooplankton were sampled with a 930 \eqn{\mu}m mesh net.} @@ -112,7 +114,7 @@ #' Accessory environmental data from the combined zooplankton dataset. Not all datasets report all environmental parameters. #' #' @encoding UTF-8 -#' @format a tibble with 44,690 rows and 20 columns +#' @format a tibble with 48,933 rows and 20 columns #' \describe{ #' \item{Source}{Abbreviated name of the source dataset. "EMP"=Environmental Monitoring Program, "FRP"=Fish Restoration Program, "FMWT"= Fall Midwater Trawl, "STN"= Townet Survey, "20mm" =20mm survey, "DOP" = Directed Outflow Project Lower Trophic Study, and "YBFMP"= Yolo Bypass Fish Monitoring Program.} #' \item{Year}{Year sample was collected} diff --git a/R/zoop_downloader.R b/R/zoop_downloader.R index 0b56e62..b613c68 100644 --- a/R/zoop_downloader.R +++ b/R/zoop_downloader.R @@ -134,7 +134,7 @@ Zoopdownloader <- function( dplyr::filter(!is.na(.data$SampleDate))%>% dplyr::mutate(SampleDate=lubridate::parse_date_time(.data$SampleDate, "%m/%d/%Y", tz="America/Los_Angeles"), Datetime=lubridate::parse_date_time(dplyr::if_else(is.na(.data$Time), NA_character_, paste(.data$SampleDate, .data$Time)), - c("%Y-%m-%d %I:%M %p"), tz="Etc/GMT+8"), #create a variable for datetime + c("%Y-%m-%d %H:%M"), tz="Etc/GMT+8"), #create a variable for datetime Datetime=lubridate::with_tz(.data$Datetime, "America/Los_Angeles"))%>% # Ensure everything ends up in local time tidyr::pivot_longer(cols=c(-"SampleDate", -"StationNZ", -"Time", -"Secchi", -"Chl_a", -"Temperature", -"ECSurfacePreTow", -"ECBottomPreTow", -"Volume", -"Datetime", -"Depth"), @@ -823,7 +823,6 @@ Zoopdownloader <- function( CommonName == "Palaemonetes" ~ "Palaemon", CommonName == "Hymenoptera UNID" ~ "Hymenoptera Other", CommonName == "Asellidae UNID" ~ "Asellidae", - CommonName == "Diptera adult" ~ "Diptera Adult", CommonName == "Coleoptera other" ~ "Coleoptera Other", CommonName == "Tricoptera larvae UNID"~"Trichoptera larvae Other", TRUE ~ CommonName)) @@ -903,7 +902,7 @@ Zoopdownloader <- function( data.list[["EMP_Macro"]] <- zoo_EMP_Macro%>% dplyr::mutate(SampleDate=lubridate::parse_date_time(.data$SampleDate, "%m/%d/%Y", tz="America/Los_Angeles"), Datetime=lubridate::parse_date_time(dplyr::if_else(is.na(.data$Time), NA_character_, paste(.data$SampleDate, .data$Time)), - c("%Y-%m-%d %I:%M %p"), tz="Etc/GMT+8"), #create a variable for datetime + c("%Y-%m-%d %H:%M"), tz="Etc/GMT+8"), #create a variable for datetime Datetime=lubridate::with_tz(.data$Datetime, "America/Los_Angeles"))%>% # Ensure everything ends up in local time tidyr::pivot_longer(cols=c(-"SampleDate", -"Time", -"Datetime", -"StationNZ", -"Secchi", -"Chl_a", -"Temperature", -"ECSurfacePreTow", -"ECBottomPreTow", -"Volume", -"Depth"), diff --git a/data-raw/EZ_stations.csv b/data-raw/EZ_stations.csv index c9be347..10cc6dd 100644 --- a/data-raw/EZ_stations.csv +++ b/data-raw/EZ_stations.csv @@ -557,3 +557,23 @@ NZEZ6SJR,12/4/2023,38.02171,-121.8073 NZEZ2SJR,12/4/2023,38.04548,-121.6952 NZEZ2,12/6/2023,38.12078,-121.7008 NZEZ6,12/6/2023,38.07955,-121.7616 +NZEZ2SJR,2024-01-03,38.03355,-121.7176 +NZEZ6,2024-01-05,38.06473,-121.8441 +NZEZ2,2024-01-05,38.06417,-121.7917 +NZEZ2,2024-02-06,38.04848,-121.9154 +NZEZ6,2024-02-06,38.05835,-121.9602 +NZEZ6,2024-04-19,38.0598,-122.0023 +NZEZ2,2024-04-19,38.05653,-121.9664 +NZEZ6,2024-05-17,38.06454,-122.0364 +NZEZ2,2024-06-17,38.0596,-121.9812 +NZEZ6,2024-06-17,38.0596,-121.9812 +NZEZ6,2024-07-16,38.04959,-121.9249 +NZEZ2,2024-07-16,38.06318,-121.8238 +NZEZ6,2024-08-16,38.04704,-121.8993 +NZEZ2,2024-08-16,38.06195,-121.8165 +NZEZ2,2024-09-13,38.0625,-121.8186 +NZEZ6,2024-09-13,38.05059,-121.8825 +NZEZ6,2024-10-10,38.06509,-121.8346 +NZEZ2,2024-10-10,38.07302,-121.775 +NZEZ6,2024-12-11,38.06281,-121.8228 +NZEZ2,2024-12-11,38.07899,-121.7615 diff --git a/data-raw/crosswalk-zoopComb-zoopEnvComb-startDates.R b/data-raw/crosswalk-zoopComb-zoopEnvComb-startDates.R index 7779304..f5515bf 100644 --- a/data-raw/crosswalk-zoopComb-zoopEnvComb-startDates.R +++ b/data-raw/crosswalk-zoopComb-zoopEnvComb-startDates.R @@ -35,6 +35,8 @@ zoopComb <- zoop$Zooplankton zoopEnvComb <- zoop$Environment + + startDates<-zoopComb%>% dplyr::left_join(zoopEnvComb%>% dplyr::select(Date, SampleID), @@ -46,3 +48,4 @@ startDates<-zoopComb%>% usethis::use_data(zoopComb, zoopEnvComb, startDates, crosswalk, overwrite = TRUE) + diff --git a/data-raw/crosswalk.csv b/data-raw/crosswalk.csv index 27004f3..431047c 100644 --- a/data-raw/crosswalk.csv +++ b/data-raw/crosswalk.csv @@ -92,6 +92,7 @@ BARNNAUP,BARNNAUP,,,BARNNAUP,,BARNNAUP,,Barnacle nauplii,Barnacle Nauplii,Barnac ,,,,,,,,,,Cnidaria Other,,,,,,Undifferentiated,Cnidaria,Phylum,Cnidaria,,,,,,,,,,,,,,,,2016, ,,,,,,,,,Jellyfish UNID,Jellyfish UNID,,,,,,Undifferentiated,Cnidaria,Phylum,Cnidaria,,,,,,,,,,,,,,,,2016, ,,,,,,,,,Coccidae adult,Coccidae adult,,,,,,Adult,Coccidae,Family,Arthropoda,Hexapoda,Hemiptera,Coccidae,,,,,,,,,,,,,2018, +,,,,,,,,,,Coccinellidae larvae,,,,,,Adult,Coccinellidae,Family,Arthropoda,Insecta,Coleoptera,Coccinellidae,,,,,,,,,,,,,2024, ,,,,,,,,,,Coccinellidae adult,,,,,,Adult,Coccinellidae,Family,Arthropoda,Insecta,Coleoptera,Coccinellidae,,,,,,,,,,,,,2016, ,,,,,,,,,Coenagrionidae larvae,Coenagrionidae larvae,,,,,,Larva,Coenagrionidae,Family,Arthropoda,Insecta,Odonata,Coenagrionidae,,,,,,,,,,,,,2016, ,,,,,,,,,Coleoptera adult UNID,Coleoptera adult UNID,,,,,,Adult,Coleoptera,Order,Arthropoda,Insecta,Coleoptera,,,,,,,,,,,,,,2018, @@ -171,7 +172,7 @@ OTHCYCADPUMP,,,,,,,,,,,,,,,,Adult,Cyclopoida,Order,Arthropoda,Copepoda,Cyclopoid ,,,,,,,,,,,Eucyclops elegans adult,,,,,Adult,Eucyclops elegans,Species,Arthropoda,Copepoda,Cyclopoida,Cyclopidae,Eucyclops,Eucyclops elegans,,,,,,,,,,,, ,,,,,,,,,,,Eucyclops pectinifer adult,,,,,Adult,Eucyclops pectinifer,Species,Arthropoda,Copepoda,Cyclopoida,Cyclopidae,Eucyclops,Eucyclops pectinifer,,,,,,,,,,,, ,,,,,,,,,,,Eucyclops prionophorus adult,,,,,Adult,Eucyclops prionophorus,Species,Arthropoda,Copepoda,Cyclopoida,Cyclopidae,Eucyclops,Eucyclops prionophorus,,,,,,,,,,,, -,,,,,,,,,,,Eurycercus sp. undifferentiated,,,,,Adult,Eurycercus,Genus,Arthropoda,Branchiopoda,Anomopoda,Chydoridae,Eurycercus,,,,,,,,,,,,, +,,,,,,,,,Eurycercus,,Eurycercus sp. undifferentiated,,,,,Adult,Eurycercus,Genus,Arthropoda,Branchiopoda,Anomopoda,Chydoridae,Eurycercus,,,,,,,,,,,,2023, ,,,,,,,,Eurytemora nauplii,Eurytemora nauplii,,,,,Eurytemora_spp_nauplii,,Larva,Eurytemora,Genus,Arthropoda,Copepoda,Calanoida,Temoridae,Eurytemora,,,,,,,2006,,,2017,,2016, ,,,,,,,,,,,Eurytemora sp. adult,,,,,Adult,Eurytemora,Genus,Arthropoda,Copepoda,Calanoida,Temoridae,Eurytemora,,,,,,,,,,,,, ,EURYTEM,,,EURYTEM,,EURYTEM,,Eurytemora spp_,Eurytemora affinis,,Eurytemora affinis adult,,,Eurytemora_affinis_adult,,Adult,Eurytemora carolleeae,Species,Arthropoda,Copepoda,Calanoida,Temoridae,Eurytemora,Eurytemora carolleeae,,1972,,2005,,1995,,,2017,,2016, @@ -207,6 +208,7 @@ EURYNAUP,EURYNAUP,,,EURYNAUP,,EURYNAUP,,,,,,,,,,Larva,Eurytemora carolleeae,Spec ,,,,,,,,,Gyraulus,Gyraulus,,,,,,Adult,Gyraulus,Genus,Mollusca,Gastropoda,Hygrophila,Planorbidae,Gyraulus,,,,,,,,,,,,2016, ,,,,,,,,,,Gyrinidae larvae,,,,,,Larva,Gyrinidae,Family,Arthropoda,Insecta,Coleoptera,Gyrinidae,,,,,,,,,,,,,2016, ,,,,,,,,,Halicyclops,,,,,,,Adult,Halicyclops,Genus,Arthropoda,Copepoda,Cyclopoida,Cyclopidae,Halicyclops,,,,,,,,,,,,2016, +,,,,,,,,,,Haliplidae larvae,,,,,,Larva,Haliplidae,Family,Arthropoda,Insecta,Coleoptera,Haliplidae,,,,,,,,,,,,,2024, ,,,,,,,,,,Haliplidae adult,,,,,,Adult,Haliplidae,Family,Arthropoda,Insecta,Coleoptera,Haliplidae,,,,,,,,,,,,,2018, HARPACT,HARPACT,,,HARPACT,,HARPACT,,Harpacticoids,Harpacticoids,Harpacticoids,Harpacticoida undifferentiated,,,Harpacticoid_UNID,,Undifferentiated,Harpacticoida,Order,Arthropoda,Copepoda,Harpacticoida,,,,,1972,,2005,,1995,,,2017,,2016, ,,,,,,,,,,Hebridae,,,,,,Adult,Hebridae,Family,Arthropoda,Insecta,Hemiptera,Hebridae,,,,,,,,,,,,,2016, @@ -217,7 +219,7 @@ HARPACT,HARPACT,,,HARPACT,,HARPACT,,Harpacticoids,Harpacticoids,Harpacticoids,Ha ,,,,,,,,,,,Hesperodiaptomus cf. californiensis adult,,,,,Adult,Hesperodiaptomus californiensis,Species,Arthropoda,Copepoda,Calanoida,Diaptomidae,Hesperodiaptomus,Hesperodiaptomus californiensis,,,,,,,,,,,, ,,,,,,,,,,,Hesperodiaptomus franciscanus adult,,,,,Adult,Hesperodiaptomus franciscanus,Species,Arthropoda,Copepoda,Calanoida,Diaptomidae,Hesperodiaptomus,Hesperodiaptomus franciscanus,,,,,,,,,,,, ,,,,,,,,,,Heteroceridae adult,,,,,,Adult,Heteroceridae,Family,Arthropoda,Insecta,Coleoptera,Heteroceridae,,,,,,,,,,,,,2018, -,,,,,,,,,,Heteroceridae larvae,,,,,,Larva,Heteroceridae,Family,Arthropoda,Insecta,Coleoptera,Heteroceridae,,,,,,,,,,,,,2018, +,,,,,,,,,Heteroceridae larvae,Heteroceridae larvae,,,,,,Larva,Heteroceridae,Family,Arthropoda,Insecta,Coleoptera,Heteroceridae,,,,,,,,,,,,,2018, ,,,,,,,,,Leech,Leech,,,,,,Undifferentiated,Hirudinea,Class,Annelida,Hirudinea,,,,,,,,,,,,,,,2016, ,,,,,,,,,Holopedium,,,,,,,Adult,Holopedium,Genus,Arthropoda,Branchiopoda,Ctenopoda,Holopedidae,Holopedium,,,,,,,,,,,,2016, ,,,,,,,,,,,,,,Holopedium_gibberum,,Adult,Holopedium gibberum,Species,Arthropoda,Branchiopoda,Ctenopoda,Holopedidae,Holopedium,Holopedium gibberum,,,,,,,,,2020,,, @@ -230,7 +232,9 @@ HARPACT,HARPACT,,,HARPACT,,HARPACT,,Harpacticoids,Harpacticoids,Harpacticoids,Ha ,,,,,,,,,,Hydrometridae,,,,,,Adult,Hydrometridae,Family,Arthropoda,Insecta,Hemiptera,Hydrometridae,,,,,,,,,,,,,2016, ,,,,,,,,,Hydrophilidae adult Beetle,Hydrophilidae adult Beetle,,,,,,Adult,Hydrophilidae,Family,Arthropoda,Insecta,Coleoptera,Hydrophilidae,,,,,,,,,,,,,2016, ,,,,,,,,,Hydrophilidae larvae Beetle,Hydrophilidae larvae Beetle,,,,,,Larva,Hydrophilidae,Family,Arthropoda,Insecta,Coleoptera,Hydrophilidae,,,,,,,,,,,,,2016, +,,,,,,,,,,Hydroptilidae adult Caddisfly,,,,,,Adult,Hydroptilidae,Family,Arthropoda,Insecta,Trichoptera,Hydroptilidae,,,,,,,,,,,,,2024, ,,,,,,,,,Hydroptilidae larvae Caddisfly,Hydroptilidae larvae Caddisfly,,,,,,Larva,Hydroptilidae,Family,Arthropoda,Insecta,Trichoptera,Hydroptilidae,,,,,,,,,,,,,2016, +,,,,,,,,,,Trichoptera pupae UNID,,,,,,Pupa,Trichoptera,Order,Arthropoda,Insecta,Trichoptera,,,,,,,,,,,,,,2024, ,,,,,,,,,,Hydroptilidae pupae Caddisfly,,,,,,Pupa,Hydroptilidae,Family,Arthropoda,Insecta,Trichoptera,Hydroptilidae,,,,,,,,,,,,,2016, ,,,,,,,,,,Hydroscaphidae adult,,,,,,Adult,Hydroscaphidae,Family,Arthropoda,Insecta,Coleoptera,Hydroscaphidae,,,,,,,,,,,,,2016, ,,,,,,,,,Hydrozoa,Hydrozoa,,,,,,Undifferentiated,Hydrozoa,Class,Cnidaria,Hydrozoa,,,,,,,,,,,,,,,2018, @@ -257,6 +261,7 @@ KERATELA,KERATELA,,,KERATELA,,KERATELA,,Keratella,Keratella,,,,,Keratella_spp,,A ,,,,,,,,,Latona,,,,,,,Adult,Latona,Genus,Arthropoda,Branchiopoda,Ctenopoda,Sididae,Latona,,,,,,,,,,,,2016, ,,,,,,,,,,Hitch,,,,,,Juvenile,Lavinia exilicauda,Species,Chordata,Actinopterygii,,Cyprinidae,Lavinia,Lavinia exilicauda,,,,,,,,,,,2016, ,,,,,,,,,Lecane,,,,,,,Adult,Lecane,Genus,Rotifera,Eurotatoria,Ploima,Lecanidae,Lecane,,,,,,,,,,,,2018, +,,,,,,,,,,Lepidoptera adult,,,,,,Adult,Lepidoptera,Order,Arthropoda,Insecta,Lepidoptera,,,,,,,,,,,,,,2024, ,,,,,,,,,Lepidoptera larvae,Lepidoptera larvae,,,,,,Larva,Lepidoptera,Order,Arthropoda,Insecta,Lepidoptera,,,,,,,,,,,,,,2016, ,,,,,,,,,,Green Sunfish,,,,,,Juvenile,Lepomis cyanellus,Species,Chordata,Actinopterygii,,Centrarchidae,Lepomis,Lepomis cyanellus,,,,,,,,,,,2016, ,,,,,,,,,,Bluegill,,,,,,Juvenile,Lepomis macrochirus,Species,Chordata,Actinopterygii,,Centrarchidae,Lepomis,Lepomis macrochirus,,,,,,,,,,,2016, @@ -285,12 +290,12 @@ LIMNOTET,LIMNOTET,,,LIMNOTET,,LIMNOTET,,Limnoithona tetraspina,Limnoithona tetra ,,,,,,,,,Macrothricidae,,,,,,,Adult,Macrothricidae,Family,Arthropoda,Branchiopoda,Anomopoda,Macrothricidae,,,,,,,,,,,,,2016, ,,,,,,,,,,,Macrothrix sp. undifferentiated,,,Macrothrix_spp,,Adult,Macrothrix,Genus,Arthropoda,Branchiopoda,Anomopoda,Macrothricidae,Macrothrix,,,,,,,,,,2017,,, ,,,,,,,,,Maeotias,Maeotias,,,,,,Undifferentiated,Maeotias,Genus,Cnidaria,Hydrozoa,Limnomedusae,Olindiidae,Maeotias,,,,,,,,,,,,2016, -,,,,,,,,,,Melanoides tuberculata,,,,,,Adult,Melanoides tuberculata,Species,Mollusca,Gastropoda,Caenogastropoda,Thiaridae,Melanoides,Melanoides tuberculata,,,,,,,,,,,2016, +,,,,,,,,,Melanoides tuberculata,Melanoides tuberculata,,,,,,Adult,Melanoides tuberculata,Species,Mollusca,Gastropoda,Caenogastropoda,Thiaridae,Melanoides,Melanoides tuberculata,,,,,,,,,,,2016, ,,,,,,,,,,Melita,,,,,,Adult,Melita,Genus,Arthropoda,Malacostraca,Amphipoda,Hadzioidea,Melita,,1938,,,,,,,,,,2016, ,,,,,,,,,Mississippi Silverside,Mississippi Silverside,,,,,,Juvenile,Menidia audens,Species,Chordata,Actinopterygii,,Atherinidae,Menidia,Menidia audens,,,,,,,,,,,2016, ,,,,,,,,,Mesocyclops,,,,,,,Adult,Mesocyclops,Genus,Arthropoda,Copepoda,Cyclopoida,Cyclopidae,Mesocyclops,,,,,,,,,,,,2016, ,,,,,,,,,,,Mesocyclops edax adult,,,,,Adult,Mesocyclops edax,Species,Arthropoda,Copepoda,Cyclopoida,Cyclopidae,Mesocyclops,Mesocyclops edax,,,,,,,,,,,, -,,,,,,,,,,Mesoveliidae,,,,,,Adult,Mesoveliidae,Family,Arthropoda,Insecta,Hemiptera,Mesoveliidae,,,,,,,,,,,,,2016, +,,,,,,,,,Mesoveliidae,Mesoveliidae,,,,,,Adult,Mesoveliidae,Family,Arthropoda,Insecta,Hemiptera,Mesoveliidae,,,,,,,,,,,,,2016, ,,,,,,,,,Microcyclops,,,,,,,Adult,Microcyclops,Genus,Arthropoda,Copepoda,Cyclopoida,Cyclopidae,Microcyclops,,,,,,,,,,,,2018, ,,,,,,,,,,,Microcyclops sp. adult,,,,,Adult,Microcyclops,Genus,Arthropoda,Copepoda,Cyclopoida,Cyclopidae,Microcyclops,,,,,,,,,,,,, ,,,,,,,,,,,Microcyclops rubellus adult,,,,,Adult,Microcyclops rubellus,Species,Arthropoda,Copepoda,Cyclopoida,Cyclopidae,Microcyclops,Microcyclops rubellus,,,,,,,,,,,, @@ -408,13 +413,13 @@ SINONAUP,SINONAUP,,,SINONAUP,,SINONAUP,,,Sinocalanus nauplii,,,,,Sinocalanus_doe ,,,,,,,,,,,Sinocalanus doerrii copepodid,,,Sinocalanus_doerrii_copepodid,,Juvenile,Sinocalanus doerrii,Species,Arthropoda,Copepoda,Calanoida,Centropagidae,Sinocalanus,Sinocalanus doerrii,1978,,,,,,,,2017,,, ,,,,,,,,,,,Sinoclanus doerii adult,,,,,Adult,Sinocalanus doerrii,Species,Arthropoda,Copepoda,Calanoida,Centropagidae,Sinocalanus,Sinocalanus doerrii,1978,,,,,,,,,,, ,,,,,,,,,,,,Sinocalanus doerrii,Sinocalanus doerrii,,,Undifferentiated,Sinocalanus doerrii,Species,Arthropoda,Copepoda,Calanoida,Centropagidae,Sinocalanus,Sinocalanus doerrii,1978,,,,,,,,,,, -,,C_alienense,,,Corophium alienense,,Corophium_alienense,,,Corophium alienense,,,,,Sinocorophium_alienense,Adult,Sinocorophium alienense,Species,Arthropoda,Malacostraca,Amphipoda,Corophiidae,Sinocorophium,Sinocorophium alienense,1973,2014,,2013,,,,,2017,,2016, +,,C_alienense,,,Corophium alienense,,Corophium_alienense,,Corophium alienense,Corophium alienense,,,,,Sinocorophium_alienense,Adult,Sinocorophium alienense,Species,Arthropoda,Malacostraca,Amphipoda,Corophiidae,Sinocorophium,Sinocorophium alienense,1973,2014,,2013,,,,,2017,,2016, ,,,,,,,,,,,,,,,Sinocorophium_heteroceratum,Adult,Sinocorophium heteroceratum,Species,Arthropoda,Malacostraca,Amphipoda,Corophiidae,Sinocorophium,Sinocorophium heteroceratum,,,,,,,,,2018,,, ,,,,,,,,,,Sisyridae larvae,,,,,,Larva,Sisyridae,Family,Arthropoda,Insecta,Neuroptera,Sisyridae,,,,,,,,,,,,,2016, ,,,,,,,,,,,Skistodiaptomus sp. adult,,,,,Adult,Skistodiaptomus,Genus,Arthropoda,Copepoda,Calanoida,Diaptomidae,Skistodiaptomus,,,,,,,,,,,,, ,,,,,,,,,,,Skistodiaptomus pallidus adult,,,,,Adult,Skistodiaptomus pallidus,Species,Arthropoda,Copepoda,Calanoida,Diaptomidae,Skistodiaptomus,Skistodiaptomus pallidus,,,,,,,,,,,, ,,,,,,,,,,Longfin Smelt,,,,,,Juvenile,Spirinchus thaleichthys,Species,Chordata,Actinopterygii,,Osmeridae,Spirinchus,Spirinchus thaleichthys,,,,,,,,,,,2016, -,,,,,,,,,,Longfin Smelt (Yolk-Sac),,,,,,Larva,Spirinchus thaleichthys,Species,Chordata,Actinopterygii,,Osmeridae,Spirinchus,Spirinchus thaleichthys,,,,,,,,,,,2016, +,,,,,,,,,Longfin Smelt (Yolk-Sac),Longfin Smelt (Yolk-Sac),,,,,,Larva,Spirinchus thaleichthys,Species,Chordata,Actinopterygii,,Osmeridae,Spirinchus,Spirinchus thaleichthys,,,,,,,,,,,2016, ,,,,,,,,,Staphylinidae adult,Staphylinidae adult,,,,,,Adult,Staphylinidae,Family,Arthropoda,Insecta,Coleoptera,Staphylinidae,,,,,,,,,,,,,2016, ,,,,,,,,,,Stratiomyidae,,,,,,Undifferentiated,Stratiomyidae,Family,Arthropoda,Insecta,Diptera,Stratiomyidae,,,,,,,,,,,,,2018, ,,,,,,,,,Stylaria,Stylaria,,,,,,Undifferentiated,Stylaria,Genus,Annelida,Oligochaeta,Haplotaxida,Naididae,Stylaria,,,,,,,,,,,,2016, @@ -451,4 +456,17 @@ TRICHO,TRICHO,,,TRICHO,,TRICHO,,Trichocerca,Trichocerca,,,,,Trichocerca_spp,,Adu ,,,,,,,,,,Eggs UNID,,,,,,Egg,Unknown,,Unknown,,,,,,,,,,,,,,,,2016, ,,,,,,,,,Veliidae,Veliidae,,,,,,Adult,Veliidae,Family,Arthropoda,Insecta,Hemiptera,Veliidae,,,,,,,,,,,,,2016, ,,,,,,,,,Wolga,,,,,,,Adult,Wolga,Genus,Rotifera,Eurotatoria,Ploima,Trichotriidae,Wolga,,,,,,,,,,,,2023, -,,,,,,,,,,,,,,,,,,,Arthropoda,Anomopoda,Eurycercidae,NA,Eurycercus,,,,,,,,,,,,, \ No newline at end of file +,,,,,,,,,Cephalodella,,,,,,,Adult,Cephalodella,Genus,Rotifera,Eurotatoria,Ploima,Notommatidae,Cephalodella,,,,,,,,,,,,2024, +,,,,,,,,,Filinia,,,,,,,Adult,Filinia,Genus,Rotifera,Eurotatoria,Flosculariaceae,Trochosphaeridae,Filinia,,,,,,,,,,,,2024, +,,,,,,,,,Conochiloides,,,,,,,Adult,Conochiloides,Genus,Rotifera,Eurotatoria,Flosculariaceae,Conochilidae,Conochiloides,,,,,,,,,,2017,,2024, +,,,,,,,,,Collotheca,,,,,,,Adult,Collotheca,Genus,Rotifera,Eurotatoria,Collothecaceae,Collothecidae,Collotheca,,,,,,,,,,,,2024, +,,,,,,,,,,Macoma,,,,,,Adult,Macoma,Genus,Mollusca,Bivalvia,Cardiida,Tellinidae,Macoma,,,,,,,,,,,,2024, +,,,,,,,,,,White Catfish,,,,,,Larva,Ameiurus catus,Species,Chordata,Actinopterygii,Siluriformes,Ictaluridae,Ameiurus,Ameiurus catus,,,,,,,,,,,2024, +,,,,,,,,,,Sponge Freshwater,,,,,,Adult,Spongillida,Order,Porifera,Demospongiae,Spongillida,,,,,,,,,,,,,,2024, +,,,,,,,,,,Musculium,,,,,,Adult,Sphaerium,Genus,Mollusca,Bivalvia,Sphaeriida,Sphaeriidae,Sphaerium,,,,,,,,,,,,2024, +,,,,,,,,,,Planthopper,,,,,,Adult,Hemiptera,Order,Arthropoda,Insecta,Hemiptera,,,,,,,,,,,,,,2024, +,,,,,,,,,,Tingidae,,,,,,Adult,Tingidae,Family,Arthropoda,Insecta,Hemiptera,Tingidae,,,,,,,,,,,,,2024, +,,,,,,,,,,Leptoceridae larvae,,,,,,Larva,Leptoceridae,Family,Arthropoda,Insecta,Trichoptera,Leptoceridae,,,,,,,,,,,,,2024, +,,,,,,,,,,Harris Mud Crab,,,,,,Adult,Rhithropanopeus harrisii,Species,Arthropoda,Malacostraca,Decapoda,Panopeidae,Rhithropanopeus,Rhithropanopeus harrisii,,,,,,,,,,,2024, +,,,,,,,,,,Chinook Salmon (fall),,,,,,Juvenile,Oncorhynchus tshawytscha,Species,Chordata,Actinopterygii,Salmoniformes,Salmonidae,Oncorhynchus,Oncorhynchus tshawytscha,,,,,,,,,,,2024, +,,,,,,,,,,Bristletail,,,,,,Adult,Archaeognatha,Order,Arthropoda,Insecta,Archaeognatha,,,,,,,,,,,,,,2024, diff --git a/data-raw/stations.R b/data-raw/stations.R index 3ccb664..94200ff 100644 --- a/data-raw/stations.R +++ b/data-raw/stations.R @@ -12,7 +12,7 @@ stations <- read_csv(file.path("data-raw", "stations.csv"), stationsEMPEZ<-read_csv(file.path("data-raw", "EZ_stations.csv"), col_types = cols_only(SampleDate="c", StationCode="c", Lat="d", Long="d"))%>% select(Date=SampleDate, Station=StationCode, Latitude=Lat, Longitude=Long)%>% - mutate(Date=parse_date_time(Date, "%m/%d/%Y", tz="America/Los_Angeles"), + mutate(Date=parse_date_time(Date, c("%m/%d/%Y", "%Y-%m-%d"), tz="America/Los_Angeles"), Station=recode(Station, EZ2="NZEZ2", EZ6="NZEZ6", EZ6SJR="NZEZ6SJR", EZ2SJR="NZEZ2SJR"))%>% drop_na() diff --git a/data/crosswalk.rda b/data/crosswalk.rda index 580cfda..3500d90 100644 Binary files a/data/crosswalk.rda and b/data/crosswalk.rda differ diff --git a/data/startDates.rda b/data/startDates.rda index 61e8a62..cc0ffa1 100644 Binary files a/data/startDates.rda and b/data/startDates.rda differ diff --git a/data/stations.rda b/data/stations.rda index 23995ee..bca1ccb 100644 Binary files a/data/stations.rda and b/data/stations.rda differ diff --git a/data/stationsEMPEZ.rda b/data/stationsEMPEZ.rda index d8189bd..fd9e775 100644 Binary files a/data/stationsEMPEZ.rda and b/data/stationsEMPEZ.rda differ diff --git a/data/zoopComb.rda b/data/zoopComb.rda index 11c4d88..8c9d6cd 100644 Binary files a/data/zoopComb.rda and b/data/zoopComb.rda differ diff --git a/data/zoopEnvComb.rda b/data/zoopEnvComb.rda index 4e5c3c6..5d3f492 100644 Binary files a/data/zoopEnvComb.rda and b/data/zoopEnvComb.rda differ diff --git a/tests/testthat/test-Source_datasets.R b/tests/testthat/test-Source_datasets.R index cc178f1..6f05b3f 100644 --- 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" , "DragMethod", + "subsample" , "DragMethod","SiteType", "Count" , "AdjCount" ,"CPUE","Flagged_Data_zoops", "StartTime", "EndTime", "LatitudeStart", "LatitudeEnd", "LongitudeStart", "LongitudeEnd", "DepthOfWater", "NetMeterEnd", "TowDirection", "NetMeterStart", @@ -244,7 +244,7 @@ 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", + "LatitudeStart", "LatitudeEnd","SiteType", "LongitudeStart", "LongitudeEnd", "DepthOfSample", "DepthOfWater", "NetMeterEnd", "TowDirection", "NetMeterStart", "Boulder", "Cobble", "Gravel", "Organics", "Sand", "Silt", "DetritalVolume", "GearTypeAbbreviation", "LAB_NAME", "Location", diff --git a/tests/testthat/test-Zoopdownloader.R b/tests/testthat/test-Zoopdownloader.R index 878173b..33f2e93 100644 --- a/tests/testthat/test-Zoopdownloader.R +++ b/tests/testthat/test-Zoopdownloader.R @@ -41,7 +41,8 @@ test_that("Only the expected stations are missing coordinates", { }) test_that("Only the expected EZ stations are missing coordinates", { - expect_setequal(unique(No_coords_EZ$Station), c("NZEZ6 2004-12-21", "NZEZ2 2007-08-21", "NZEZ6 2007-08-21")) + expect_setequal(unique(No_coords_EZ$Station), c("NZEZ6 2004-12-21", "NZEZ2 2007-08-21", "NZEZ6 2007-08-21", + "NZEZ6 2024-11-08", "NZEZ2 2024-11-08")) }) test_that("All rowshave station names", {