Zoopdownloader: Downloads and combines zooplankton datasets collected by the...

In InteragencyEcologicalProgram/zooper: Download and Integrate Zooplankton Datasets from the Upper San Francisco Estuary

Downloads and combines zooplankton datasets collected by the Interagency Ecological Program from the Sacramento-San Joaquin Delta

Description

This function downloads all IEP zooplankton datasets from the internet, converts them to a consistent format, binds them together, and exports the combined dataset as .Rds R data files and/or an R object. Datasets currently include "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).

Usage

Zoopdownloader(
  Data_sets = c("EMP_Meso", "FMWT_Meso", "STN_Meso", "20mm_Meso", "FRP_Meso",
    "EMP_Micro", "FRP_Macro", "EMP_Macro", "FMWT_Macro", "STN_Macro", "DOP_Meso",
    "DOP_Macro"),
  Biomass = TRUE,
  Data_folder = tempdir(),
  Save_object = TRUE,
  Return_object = FALSE,
  Return_object_type = "List",
  Redownload_data = FALSE,
  Download_method = "auto",
  Zoop_path = file.path(Data_folder, "zoopforzooper"),
  Env_path = file.path(Data_folder, "zoopenvforzooper"),
  Crosswalk = zooper::crosswalk,
  Stations = zooper::stations
)

Arguments

Data_sets	Datasets to include in combined data. Choices include "EMP_Meso", "FMWT_Meso", "STN_Meso", "20mm_Meso", "FRP_Meso", "YBFMP_Meso", "EMP_Micro", "YBFMP_Micro", "FRP_Macro", "EMP_Macro", "FMWT_Macro", "STN_Macro", "DOP_Macro", and "DOP_Meso". Defaults to including all datasets except the two YBFMP datasets.
Biomass	Whether to add carbon biomass (carbon biomass per unit effort (\mug/ m3)) to the dataset (where conversion equations and required data are available). Defaults to Biomass = TRUE
Data_folder	Path to folder in which source datasets are stored, and to which you would like datasets to be downloaded if you set Redownload_data = TRUE. If you do not want to store every source dataset, you can leave this at the default tempdir(). If you do not wish to redownload these datasets every time you run the function, you can set this to a directory on your computer and run the function in the future with Redownload_data = FALSE, which will load the source datasets from Data_folder instead of downloading them again.
Save_object	Should the combined data be saved to disk? Defaults to Save_object = TRUE.
Return_object	Should data be returned as an R object? If TRUE, the function will return the full combined dataset. Defaults to 'Return_object = FALSE'.
Return_object_type	If Return_object = TRUE, should data be returned as a combined dataframe (Return_object_type = "Combined") or a list with component "Zooplankton" containing the zooplankton data and component "Environment" containing the environmental data (Return_object_type = "List", the default). A list is required to feed data into the Zoopsynther function without saving the combined dataset to disk.
Redownload_data	Should source datasets be redownloaded from the internet? Defaults to Redownload_data = FALSE.
Download_method	Method used to download files. See argument method options in download.file. Defaults to "curl".
Zoop_path	File path specifying the folder and filename of the zooplankton dataset. Defaults to Zoop_path = file.path(Data_folder, "zoopforzooper").
Env_path	File path specifying the folder and filename of the dataset with accessory environmental parameters. Defaults to Env_path = file.path(Data_folder, "zoopenvforzooper").
Crosswalk	Crosswalk table to be used for conversions. Must have columns named for each unique combination of source and size class with an underscore separator, as well as all taxonomic levels Phylum through Species, Taxname (full scientific name) and Lifestage. See crosswalk (the default) for an example.
Stations	Latitudes and longitudes for each unique station. See stations (the default) for an example.

Details

Note that EMP Macro samples with QAQC flags (any value of AmphipodCode other than "A") have had their Amphipod CPUE set to NA in this function. For more information on the source datasets see zooper.

Value

If Return_object = TRUE, returns the combined dataset as a list or tibble, depending on whether Return_object_type is set to "List" or "Combined". If Save_object = TRUE, writes 2 .Rds files to disk: one with the zooplankton catch data and another with accessory environmental parameters.

Author(s)

Sam Bashevkin

See Also

Zoopsynther, crosswalk, stations, zooper

Examples

## Not run: 
Data <- Zoopdownloader(Data_folder = tempdir(), Return_object = TRUE,
Save_object = FALSE, Redownload_data = TRUE)

## End(Not run)

InteragencyEcologicalProgram/zooper documentation built on Feb. 6, 2025, 9:01 a.m.