diff --git a/NEWS.md b/NEWS.md index 41d55ea..430998f 100644 --- a/NEWS.md +++ b/NEWS.md @@ -12,6 +12,7 @@ - Jungbluth, M. J., J. Burns, L. Grimaldo, A. Slaughter, A. Katla, and W. Kimmerer. 2021. Feeding habits and novel prey of larval fishes in the northern San Francisco Estuary. Environmental DNA.1-22. - 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 # zooper 2.5.1 diff --git a/R/zoop_downloader.R b/R/zoop_downloader.R index b6a7bbf..b4ca3b1 100644 --- a/R/zoop_downloader.R +++ b/R/zoop_downloader.R @@ -1005,7 +1005,11 @@ Zoopdownloader <- function( Crangonyx_sp="d", Gammarus_daiberi="d", Grandidierella_japonica="d", Hyalella_sp="d", Unidentified_Amphipod="d", Unidentified_Corophium="d", Unidentified_Gammarus="d"))%>% - dplyr::mutate(ID=paste(.data$Year, .data$Project, .data$Survey, .data$Station)) + dplyr::mutate(ID=paste(.data$Year, .data$Project, .data$Survey, .data$Station)) %>% + dplyr::mutate(Datetime = lubridate::parse_date_time(dplyr::if_else(is.na(.data$Time), NA_character_, + paste(.data$Date, .data$Time)), "%Y-%m-%d %H:%M", tz="America/Los_Angeles"), + Date=lubridate::parse_date_time(.data$Date, "%Y-%m-%d", tz="America/Los_Angeles")) + #The 2025 data upload has a new date format for Macro (but not meso, and not SMSCG very annoying) zoo_SMSCG_Macro <- readr::read_csv(file.path(Data_folder, "SMSCG_Macro.csv"), col_types=readr::cols_only(Project="c", Year="d", Survey="d", @@ -1021,13 +1025,17 @@ Zoopdownloader <- function( Hyalella_sp="d", Unidentified_Amphipod="d", Unidentified_Corophium="d", Unidentified_Gammarus="d"))%>% dplyr::mutate(ID=paste(.data$Year, .data$Project, .data$Survey, .data$Station))%>% - dplyr::filter(!.data$ID%in%unique(zoo_FMWT_Macro$ID) & .data$Project%in%c("FMWT", "STN")) + dplyr::filter(!.data$ID%in%unique(zoo_FMWT_Macro$ID) & .data$Project%in%c("FMWT", "STN")) %>% + + #put date and time in the right format. Date first, tehn datetime to try and fix a problem where the date randomly came out wrong in the 'datetime' version + dplyr::mutate(Date=lubridate::parse_date_time(.data$Date, "%m/%d/%y", tz="America/Los_Angeles"), + Datetime = lubridate::parse_date_time(dplyr::if_else(is.na(.data$Time), NA_character_, + paste(.data$Date, .data$Time)), "%Y-%m-%d %H:%M:%S", tz="America/Los_Angeles")) data.list[["FMWT_Macro"]] <- dplyr::bind_rows(zoo_FMWT_Macro, zoo_SMSCG_Macro)%>% dplyr::select(-"ID")%>% - dplyr::mutate(Datetime = lubridate::parse_date_time(dplyr::if_else(is.na(.data$Time), NA_character_, paste(.data$Date, .data$Time)), "%m/%d/%Y %H:%M", tz="America/Los_Angeles"), - Date=lubridate::parse_date_time(.data$Date, "%m/%d/%Y", tz="America/Los_Angeles"), - Microcystis = as.character(.data$Microcystis))%>% #create a variable for datetime + distinct()%>% #remove any samples duplicated between the SMSCG datset and the FMWTdataset + dplyr::mutate(Microcystis = as.character(.data$Microcystis))%>% tidyr::pivot_longer(cols=c(-"Project", -"Year", -"Survey", -"Date", -"Datetime", -"Station", -"Time", -"TideCode", -"DepthBottom", -"CondSurf", -"CondBott", diff --git a/data-raw/crosswalk-zoopComb-zoopEnvComb-startDates.R b/data-raw/crosswalk-zoopComb-zoopEnvComb-startDates.R index 714fc00..0c5014a 100644 --- a/data-raw/crosswalk-zoopComb-zoopEnvComb-startDates.R +++ b/data-raw/crosswalk-zoopComb-zoopEnvComb-startDates.R @@ -31,6 +31,7 @@ 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 @@ -45,3 +46,4 @@ startDates<-zoopComb%>% dplyr::summarise(Startdate = min(Date), .groups="drop") usethis::use_data(zoopComb, zoopEnvComb, startDates, crosswalk, overwrite = TRUE) + diff --git a/data/crosswalk.rda b/data/crosswalk.rda index 9f01f6e..ad4451e 100644 Binary files a/data/crosswalk.rda and b/data/crosswalk.rda differ diff --git a/data/startDates.rda b/data/startDates.rda index 9f94dba..98a0937 100644 Binary files a/data/startDates.rda and b/data/startDates.rda differ diff --git a/data/zoopComb.rda b/data/zoopComb.rda index c920cff..6b7d266 100644 Binary files a/data/zoopComb.rda and b/data/zoopComb.rda differ diff --git a/data/zoopEnvComb.rda b/data/zoopEnvComb.rda index e233c54..ab9b915 100644 Binary files a/data/zoopEnvComb.rda and b/data/zoopEnvComb.rda differ