Package 'zooper' reference manual

Title:	Download and Integrate Zooplankton Datasets from the Upper San Francisco Estuary
Description:	This package downloads and integrates zooplankton datasets from the Sacramento San Joaquin Delta. Datasets are manipulated into a consistent format and bound together, then differences in taxonomic resolution among datasets are resolved using one of two methods, depending on whether the user wishes to analyze community or taxa-specific trends. Ancillary environmental data are retained in the final dataset. Users can also filter the dataset by a number of parameters.
Authors:	Samuel M Bashevkin [aut, cre] , Rosemary Hartman [aut] , Karrin Alstad [aut], Catarina Pien [aut]
Maintainer:	Samuel M Bashevkin <[email protected]>
License:	GPL-3
Version:	2.5.0.9000
Built:	2024-11-25 21:33:14 UTC
Source:	https://github.com/InteragencyEcologicalProgram/zooper

Macro zooplankton length-weight equations

Description

Length-weight equations for macro zooplankton to be used for biomass conversions. The equations relate length in mm to dry mass in milligrams. Dry mass can be converted to carbon mass by assuming 40 Uye, S. 1982. Length-weight relationships of important zooplankton from the Inland Sea of Japan. Journal of the Oceanographical Society of Japan 38:149–158.

Usage

biomass_macro
biomass_macro

Format

a tibble with 23 rows and 9 columns.

Taxname: Current scientific name.
Level: Taxonomic level of the taxa.
Preservative: Preservative used to store sample before individuals were measured to develop the equations.
Weight_type: The type of weight measurement.
N: The number of individuals used in developing the equation.
Min_length: Minimum length (mm) of individuals used in developing the equation.
Max_length: Maximum length (mm) of individuals used in developing the equation.
a: Coefficient a in the equation Weight (mg) = a * Length (mm) ^ b.
b: Coefficient b in the equation Weight (mg) = a * Length (mm) ^ b.

Meso and Micro zooplankton average biomass values

Description

Average carbon biomass values for meso and micro zooplankton to be used for biomass conversions

Usage

biomass_mesomicro
biomass_mesomicro

Format

a tibble with 44 rows and 4 columns.

Taxname: Current scientific name.
Level: Taxonomic level of the taxa.
Lifestage: Plankton lifestage.
Carbon_mass_micrograms: Average carbon mass of an individual in micrograms.

Detect common taxonomic names across all source datasets

Description

Calculates taxa by life stage combos present in all source datasets

Usage

Commontaxer(Source_taxa_key, Taxa_level, Size_class)
Commontaxer(Source_taxa_key, Taxa_level, Size_class)

Arguments

`Source_taxa_key`	A dataframe with columns named Source, Lifestage, SizeClass, and the value provided to the parameter `Taxa_level`. This dataframe should list all `Taxa_level` by `Lifestage` combinations present for each source dataset. You can provide it with the output of `SourceTaxaKeyer`.
`Taxa_level`	Taxonomic level you would like to perform this calculation for. E.g., if you wish to determine all Genus x lifestage combinations present in all datasets, provide `Taxa_level = "Genus"`. The value provided here must be the name of a column in the dataset provided to `Source_taxa_key`.
`Size_class`	The size class(es) you would like this function to consider. You should generally only supply 1 size class.

Details

This function is designed to work on just one size class. To apply to multiple size classes, use map or apply functions to apply across size classes.

Value

A tibble with a column for Taxa_level and another for Lifestage representing all combinations of these values present in all source datasets.

Author(s)

Sam Bashevkin

Examples

## Not run: 
library(rlang)
library(purrr)
SourceTaxaKey <- SourceTaxaKeyer(zoopComb, crosswalk)
Size_classes <- set_names(c("Micro", "Meso", "Macro"))
Commontax <- map(Size_classes, ~ Commontaxer(SourceTaxaKey, "Taxname", .))

## End(Not run)
## Not run: 
library(rlang)
library(purrr)
SourceTaxaKey <- SourceTaxaKeyer(zoopComb, crosswalk)
Size_classes <- set_names(c("Micro", "Meso", "Macro"))
Commontax <- map(Size_classes, ~ Commontaxer(SourceTaxaKey, "Taxname", .))

## End(Not run)

All taxonomic names

Description

A complete list of all valid taxonomic names included in the full dataset. Used to limit choices for filtering by taxa.

Usage

completeTaxaList
completeTaxaList

Format

a character vector of length 454.

Taxonomic crosswalk among datasets

Description

A crosswalk table relating the taxonomic code used by each dataset to current scientific names, life stages, and taxonomic hierarchies.

Usage

crosswalk
crosswalk

Format

a tibble with 404 rows and 34 variables

EMP_Micro: Taxonomic codes used in the Environmental Monitoring Program microzooplankton (43 $\mu$ m) mesh dataset
EMP_Meso: Taxonomic codes used in the Environmental Monitoring Program mesozooplankton (160 $\mu$ m) mesh dataset
EMP_Macro: Taxonomic codes used in the Environmental Monitoring Program macrozooplankton (505 $\mu$ m mesh) dataset
STN_Meso: Taxonomic codes used in the Townet Survey mesozooplankton (160 $\mu$ m mesh) dataset
STN_Macro: Taxonomic codes used in the Townet Survey macrozooplankton (505 $\mu$ m mesh) dataset
FMWT_Meso: Taxonomic codes used in the Fall Midwater Trawl mesozooplankton (160 $\mu$ m mesh) dataset
FMWT_Macro: Taxonomic codes used in the Fall Midwater Trawl macrozooplankton (505 $\mu$ m mesh) dataset
twentymm_Meso: Taxonomic codes used in the 20mm Survey mesozooplankton (160 $\mu$ m mesh) dataset
FRP_Meso: Taxonomic codes used in the Fish Restoration Program mesozooplankton (150 $\mu$ m mesh) dataset
FRP_Macro: Taxonomic codes used in the Fish Restoration Program macrozooplankton (500 $\mu$ m mesh) dataset
DOP_Meso: Taxonomic codes used in the Directed Outflow Project mesozooplankton (150 $\mu$ m mesh) dataset
DOP_Macro: Taxonomic codes used in the Directed Outflow Project macrozooplankton (500 $\mu$ m mesh) dataset
YBFMP: Taxonomic codes used in the Yolo Bypass Fish Monitoring Program zooplankton dataset)
Lifestage: Plankton lifestage
Taxname: Current scientific name
Level: Taxonomic level of the taxa
Phylum: Phylum
Class: Class
Order: Order
Family: Family
Genus: Genus
Species: Species
Intro: Introduction year for non-native species
EMPstart: First year the Environmental Monitoring Program starting counting this taxa
EMPend: Last year the Environmental Monitoring Program counted this taxa
FMWTstart: First year the Fall Midwater Trawl starting counting this taxa
FMWTend: Last year the Fall Midwater Trawl counted this taxa
twentymmstart: First year the 20mm Survey starting counting this taxa
twentymmend: Last year the 20mm Survey counted this taxa
twentymmstart2: First year the 20mm Survey restarted counting this taxa
DOPstart: First year DOP starting counting this taxa
DOPend: Last year DOP counted this taxa

Apply LCD approach for "Taxa" option

Description

Sums to least common denominator taxa, one taxonomic level at a time

Usage

LCD_Taxa(
  Data,
  Taxalevel,
  Groupers = c("Genus_g", "Family_g", "Order_g", "Class_g", "Phylum_g"),
  Response = "CPUE"
)
LCD_Taxa(
  Data,
  Taxalevel,
  Groupers = c("Genus_g", "Family_g", "Order_g", "Class_g", "Phylum_g"),
  Response = "CPUE"
)

Arguments

`Data`	Zooplankton dataset including columns named the same as the `Groupers`, a `Taxname` column, "CPUE", and no other taxonomic identifying columns.
`Taxalevel`	The value of Groupers on which to apply this function.
`Groupers`	A character vector of names of additional taxonomic levels to be removed in this step. This vector can include `Taxalevel` and, if so, it will be removed from the vector within the function so `Taxalevel` is preserved.
`Response`	Which response variable(s) would you like for the zooplankton data? Choices are "CPUE" (catch per unit effort) and "BPUE" (carbon biomass per unit effort ( $\mu$ g/ m³)). Defaults to `Response = "CPUE"`.

Details

This function is designed to work on just one Taxalevel at a time. To apply to multiple Taxalevels, use map or apply functions to apply across taxonomic levels.

Value

A tibble with sums calculated for each unique value in Data$Taxalevel. Sums will be excluded for grouping taxa that only contain 1 unique Taxname.

Author(s)

Sam Bashevkin

Examples

## Not run: 
library(dplyr)
df <- zoopComb%>%
  mutate(dplyr::across(tidyselect::all_of(c("Genus", "Family", "Order", "Class", "Phylum")),
                   list(g=~if_else(.%in%completeTaxaList, ., NA_character_))))%>%
  select(-Phylum, -Class, -Order, -Family, -Genus, -Species, -Taxlifestage)
family_sums <- LCD_Taxa(df, "Family_g")

## End(Not run)

## Not run: 
library(dplyr)
df <- zoopComb%>%
  mutate(dplyr::across(tidyselect::all_of(c("Genus", "Family", "Order", "Class", "Phylum")),
                   list(g=~if_else(.%in%completeTaxaList, ., NA_character_))))%>%
  select(-Phylum, -Class, -Order, -Family, -Genus, -Species, -Taxlifestage)
family_sums <- LCD_Taxa(df, "Family_g")

## End(Not run)

Unique taxa by lifestage combinations present in each source and size class

Description

Computes a dataframe with all unique taxa by lifestage combinations present in each source and size class

Usage

SourceTaxaKeyer(Data, Crosswalk)
SourceTaxaKeyer(Data, Crosswalk)

Arguments

`Data`	Zooplankton dataset. Must have a column named `Source` with the names of the source datasets and a column named `SizeClass` with the names of the zooplankton size classes.
`Crosswalk`	Crosswalk table (e.g., `crosswalk`) with columns named "Phylum", "Class", "Order", "Family", "Genus", "Taxname", "Lifestage", and column names corresponding to each unique value of `paste(data$Source, data$SizeClass, sep="_")`.

Value

a tibble with the complete taxonomic information for each combination of source and size class.

Author(s)

Sam Bashevkin

Examples

SourceTaxaKey <- SourceTaxaKeyer(Data = dplyr::filter(zoopComb, Source!="YBFMP"),
Crosswalk = crosswalk)
SourceTaxaKey <- SourceTaxaKeyer(Data = dplyr::filter(zoopComb, Source!="YBFMP"),
Crosswalk = crosswalk)

Start dates

Description

First dates sampled by each survey and size class

Usage

startDates
startDates

Format

a tibble with 14 rows and 3 columns.

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.
SizeClass: Net size class. Micro corresponds to 43 (EMP) or 50 (YBFMP) $\mu$ m mesh, Meso corresponds to 150 (FRP and DOP) or 160 (EMP, FMWT, STN, 20mm, YBFMP) $\mu$ m mesh, and Macro corresponds to 500 (FRP and DOP) - 505 (EMP, FMWT, STN) $\mu$ m mesh. However, prior to 1974 EMP macrozooplankton were sampled with a 930 $\mu$ m mesh net.
Startdate: Date first sample was collected.

Station locations

Description

Latitudes and longitudes for each zooplankton station.

Usage

stations
stations

Format

a tibble with 387 rows and 4 columns

Source: Abbreviated name of the source dataset
Station: Sampling station name
Latitude: Latitude in decimal degrees
Longitude: Longitude in decimal degrees

EMP EZ Station locations

Description

Latitudes and longitudes for EMP EZ stations on each sampling date from 2004 to present.

Usage

stationsEMPEZ
stationsEMPEZ

Format

a tibble with 491 rows and 4 columns

Date: Date sample was collected
Station: Sampling station name
Latitude: Latitude in decimal degrees
Longitude: Longitude in decimal degrees

Finds all of the lowest-level (i.e. counted) taxonomic names within a vector of taxa

Description

Helps filter the zooplankton dataset by returning a set of lowest-level taxa (i.e. the level taxa were recorded at when counted in plankton samples) within a vector of taxa (which can include taxa from any taxonomic level).

Usage

Taxnamefinder(Crosswalk, Taxa)
Taxnamefinder(Crosswalk, Taxa)

Arguments

`Crosswalk`	Crosswalk table (such as `crosswalk`) with columns named "Phylum", "Class", "Order", "Family", "Genus", "Species", and "Taxname." "Taxname" corresponds to the full scientific name of the taxonomic level assigned to the plankter when recorded in the dataset.
`Taxa`	A character vector of taxa you wish to select. These taxa can be from any taxonomic level present in the list above. If using the built-in data and crosswalk, they should be present in the `completeTaxaList`.

Value

A character vector of scientific names contained within the vector of Taxa provided.

Author(s)

Sam Bashevkin

Examples

Taxnames <- Taxnamefinder(crosswalk, c("Calanoida", "Cyclopoida"))
Taxnames <- Taxnamefinder(crosswalk, c("Calanoida", "Cyclopoida"))

Detect dates when a species was not counted

Description

Detects years when a species was present in the system (i.e., post-invasion for invasive species) but not counted in each zooplankton survey

Usage

Uncountedyears(Source, Size_class, Crosswalk, Start_year, Intro_lag)
Uncountedyears(Source, Size_class, Crosswalk, Start_year, Intro_lag)

Arguments

`Source`	String with the name of the source dataset (e.g., `Source="EMP"`).
`Size_class`	String with the name of the desired zooplankton size class (e.g., `Source="Meso"`).
`Crosswalk`	Crosswalk table like `crosswalk` or another table in the same format.
`Start_year`	First year the `Source` survey started sampling zooplankton.
`Intro_lag`	Number of years buffer after a species is introduced when we expect surveys to start recording them. Effectively adds `Intro_lag` years to the introduction year of each species.

Details

This function is designed to work on one source and size class at a time. To apply across multiple IDs, use the map or apply functions.

Value

A tibble with columns for the Taxlifestage, Taxname, Lifestage, Source, Sizeclass, and then a list-column of years in which that particular taxon was not counted in the specified study and size class. Taxa that were counted in all applicable years are not included in the tibble.

Author(s)

Sam Bashevkin

Examples

require(purrr)
require(dplyr)
require(lubridate)

datasets<-zooper::zoopComb%>%
 mutate(names=paste(Source, SizeClass, sep="_"))%>%
 select(names, Source, SizeClass)%>%
 filter(Source%in%c("EMP", "FMWT", "twentymm"))%>%
 distinct()

BadYears<-map2_dfr(datasets$Source, datasets$SizeClass, ~ Uncountedyears(Source = .x,
Size_class = .y,
Crosswalk = zooper::crosswalk,
Start_year = zooper::startDates%>%
 filter(Source==.x & SizeClass==.y)%>%
 pull(Startdate)%>%
 year(),
 Intro_lag=2))
require(purrr)
require(dplyr)
require(lubridate)

datasets<-zooper::zoopComb%>%
 mutate(names=paste(Source, SizeClass, sep="_"))%>%
 select(names, Source, SizeClass)%>%
 filter(Source%in%c("EMP", "FMWT", "twentymm"))%>%
 distinct()

BadYears<-map2_dfr(datasets$Source, datasets$SizeClass, ~ Uncountedyears(Source = .x,
Size_class = .y,
Crosswalk = zooper::crosswalk,
Start_year = zooper::startDates%>%
 filter(Source==.x & SizeClass==.y)%>%
 pull(Startdate)%>%
 year(),
 Intro_lag=2))

Taxa undersampled in each size class

Description

A table listing the taxonomic names and life stages of plankton undersampled by each net mesh size (i.e. size class)

Usage

undersampled
undersampled

Format

a tibble with 27 rows and 3 columns

SizeClass: The size class of zooplankton intended to be capture be each net mesh size. Micro corresponds to 43 $\mu$ m mesh and Meso corresponds to 150-160 $\mu$ m mesh.
Taxname: The scientific name of taxa undersampled by the corresponding mesh size class
Lifestage: The lifestage of each taxa undersampled by the corresponding mesh size class

Extract latest EDI files This function extracts the latest version of a zooplankton EDI package and the list of files from that package

Description

Extract latest EDI files This function extracts the latest version of a zooplankton EDI package and the list of files from that package

Usage

zoop_urls(Sources)
zoop_urls(Sources)

Arguments

Sources

Source datasets to be included. Choices include "EMP" (Environmental Monitoring Program), "FRP" (Fish Restoration Program), "FMWT" (Fall Midwater Trawl), "STN" (Townet Survey), "DOP" (Directed Outflow Project), and "20mm" (20mm survey). The YBFMP datasets cannot be used in this function due to taxonomic and life stage issues with that dataset. Defaults to Sources = c("EMP", "FRP", "FMWT", "STN", "20mm", "DOP").

Value

A list with the files and/or URLs for each source dataset

Author(s)

Sam Bashevkin

Convert CPUE to biomass This function converts zooplankton CPUE to carbon biomass (Carbon biomass per unit effort ( $\mu$ g/ m³)) for taxa with conversion equations.

Description

Convert CPUE to biomass This function converts zooplankton CPUE to carbon biomass (Carbon biomass per unit effort ( $\mu$ g/ m³)) for taxa with conversion equations.

Usage

Zoopbiomass(
  Zoop,
  ZoopLengths,
  Biomass_mesomicro = zooper::biomass_mesomicro,
  Biomass_macro = zooper::biomass_macro
)
Zoopbiomass(
  Zoop,
  ZoopLengths,
  Biomass_mesomicro = zooper::biomass_mesomicro,
  Biomass_macro = zooper::biomass_macro
)

Arguments

`Zoop`	Zooplankton count dataset
`ZoopLengths`	Zooplankton length dataset for macrozooplankton.
`Biomass_mesomicro`	The micro and meso zooplankton biomass conversion table. The default is `biomass_mesomicro`
`Biomass_macro`	The macro zooplankton biomass conversion table. The default is `biomass_macro`

Combined zooplankton dataset

Description

All source zooplankton datasets combined into one tibble.

Usage

zoopComb
zoopComb

Format

a tibble with 3,615,105 rows and 14 columns.

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.
SizeClass: Net size class. Micro corresponds to 43-50 $\mu$ m mesh, Meso corresponds to 150-160 $\mu$ m mesh, and Macro corresponds to 500-505 $\mu$ m mesh. However, prior to 1974 EMP macrozooplankton were sampled with a 930 $\mu$ m mesh net.
Volume: Volume (m³) of water sampled
Lifestage: Zooplankton life stage
Taxname: Scientific name
Phylum: Phylum
Class: Class
Order: Order
Family: Family
Genus: Genus
Species: Species
Taxlifestage: Combined Taxname and Lifestage
SampleID: Unique ID of the zooplankton sample. This key and SizeClass link to the zoopEnvComb dataset
CPUE: Catch per unit effort (number m^-3)
BPUE: Carbon biomass per unit effort ( $\mu$ g/ m³)

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 integrated dataset. For more information on the source datasets see zooper.

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
)
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 ( $\mu$ g/ 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

Examples

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

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

## End(Not run)

Environmental data

Description

Accessory environmental data from the combined zooplankton dataset. Not all datasets report all environmental parameters.

Usage

zoopEnvComb
zoopEnvComb

Format

a tibble with 44,690 rows and 20 columns

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.
Year: Year sample was collected
Date: Date sample was collected
Datetime: Date and time sample was collected, if time was provided
TowType: Sample collection method identifying whether each tow was a surface, bottom, oblique, or vertical pump sample
Tide: Tidal stage
Station: Station where sample was collected. This is the key that links to the stations dataset
Chl: Chlorophyll concentration in $\mu$ g/L
Secchi: Secchi depth in cm
Temperature: Temperature in °C.
BottomDepth: Total depth of the water column in m
TurbidityNTU: Water turbidity in Nephelometric Turbidity Units
TurbidityFNU: Water turbidity in Formazin Nephelometric Units
Microcystis: Intensity of Microcystis bloom coded qualitatively from 1-5 where 1 = absent, 2 = low, 3 = medium, 4 = high, 5 = very high
pH: Water pH
DO: Dissolved oxygen in mg/L
SalSurf: Surface salinity in PPT
SalBott: Bottom salinity in PPT
Latitude: Latitude in decimal degrees
Longitude: Longitude in decimal degrees
AmphipodCode: Code indicating sample quality for EMP macro amphipod samples (A=valid, B=questionable [veg/algal bloom in net], C=not valid [error in lab], D=suspect [possible missing data])
SampleID: Unique ID of the zooplankton sample. This is the key that links to the zoopComb dataset

zooper: A package for integrating zooplankton datasets from the Sacramento San Joaquin Delta

Description

This package contains functions, lookup tables, and 2 built-in pre-combined datasets (one with the zooplankton data and another with the environmental data).

zooper lookup tables

crosswalk
undersampled
stations
completeTaxaList
startDates

zooper pre-combined (with the `Zoopdownloader` function) zooplankton datasets. These may be out of date

zoopComb
zoopEnvComb

Source datasets

Environmental Monitoring Program (EMP): The EMP zooplankton survey is run by the California Department of Fish and Wildlife. Zooplankton were first collected in 1972. It samples monthly at 17 fixed stations, 2 floating entrapment zone stations, and 3 stations in Carquinez Strait and San Pablo Bay that are only sampled during high outflow and low salinity conditions. EMP samples using micro (43 $\mu$ m), meso (160 $\mu$ m), and macro (505 $\mu$ m) zooplankton nets. Note that additional Amphipod data with quality issues (e.g., vegetation in net) are available in the EMP data publication. Data are available here.
20-mm Survey: The 20-mm survey is run by the California Department of Fish and Wildlife. Zooplankton were first collected in 1995. Zooplankton are collected concurrently with fish samples at 41-55 fixed open-channel stations per year. Samples are collected twice per month between March and July. Only Mesozooplankton are collected with a 160 $\mu$ m mesh net. Data are available here.
Fall Midwater Trawl (FMWT) and Summer Townet Survey (STN): The FMWT and STN are run by the California Department of Fish and Wildlife. FMWT samples are collected monthly between September and December from a subset of the 122 fixed open-channel stations. STN samples are collected monthly between June and August from 40 fixed open-channel stations. Macrozooplankton have been collected since 2007 with a 505 $\mu$ m mesh net while mesozooplankton have been collected since 2005 with a 160 $\mu$ m mesh net. Data are available here.. Supplemental sampling from the Suisun Marsh Salinity Control Gate study data are also included and those data can be found here.
Fish Restoration Program (FRP): FRP is run by the California Department of Fish and Wildlife. Zooplankton were first collected in 2015. Samples are collected monthly between March and December in shallow-water habitats near marshes. FRP samples with meso (150 $\mu$ m) and macro (500 $\mu$ m) zooplankton nets. Data are available here.
Directed Outflow Project Lower Trophic Study (DOP): The Directed Outflow Project Lower Trophic Study is run by ICF for the United States Bureau of Reclamation. Zooplankton were first collected in fall 2017. Samples were collected once every two weeks in 2017 and weekly thereafter. Sampling is conducted in the fall and, starting in 2019, spring and summer seasons have also been sampled. Three sampling stations per region are randomly selected for 5 regions (Suisun Bay, Suisun Marsh, Lower Sac. River, Cache Slough, Sac Ship Channel). In 2017, stations were sampled in 3 additional regions: West of the Benicia Bridge, Lower San Joaquin, and Upper Sac River. At each station, sample collection is attempted at both shoal (<=10 feet) and channel (>10 feet) habitat. Channels are sampled at the surface and, if deeper than 20 feet, also at the bottom 1/2 to 1/3 of the water column. DOP samples with meso (150 $\mu$ m) and macro (500 $\mu$ m) zooplankton nets. Data are available here.
Yolo Bypass Fish Monitoring Program (YBFMP): YBFMP is run by the California Department of Water Resources. Zooplankton were first collected in 1999. Samples are from 2 sites, one in the Yolo Bypass and one in the Sacramento River. In 1999 and 2000, samples were collected for a couple of months each year, and then it increased to roughly winter/spring from 2001-2010. Since 2011, samples are collected twice monthly during most of the year, and weekly when the bypass is inundated. YBFMP samples with micro (50 $\mu$ m) and meso (150 $\mu$ m) zooplankton nets. Data are available here.

Author(s)

Maintainer: Samuel M Bashevkin [email protected] (ORCID)

Authors:

Rosemary Hartman [email protected] (ORCID)
Karrin Alstad [email protected]
Catarina Pien [email protected] (ORCID)

Integrates zooplankton datasets collected by the Interagency Ecological Program from the Sacramento-San Joaquin Delta

Description

This function returns an integrated zooplankton dataset with taxonomic issues resolved, according to user-specifications, along with important caveats about the data. It requires the output of the Zoopdownloader function to run. This can be provided either as a list or paths to saved .Rds files generated by the Zoopdownloader function. The function defaults to loading pre-packaged combined datasets (which may be outdated).

Usage

Zoopsynther(
  Data_type = NULL,
  Zoop = zooper::zoopComb,
  ZoopEnv = zooper::zoopEnvComb,
  Zoop_path = NULL,
  Env_path = NULL,
  Sources = c("EMP", "FRP", "FMWT", "STN", "20mm", "DOP"),
  Size_class = c("Micro", "Meso", "Macro"),
  Time_consistency = FALSE,
  Intro_lag = 2,
  Response = "CPUE",
  Taxa = NULL,
  Date_range = c(NA, NA),
  Months = NA,
  Years = NA,
  Sal_bott_range = NA,
  Sal_surf_range = NA,
  Temp_range = NA,
  Lat_range = NA,
  Long_range = NA,
  Reload_data = F,
  Redownload_data = F,
  All_env = T,
  Shiny = F,
  Crosswalk = zooper::crosswalk,
  Undersampled = zooper::undersampled,
  CompleteTaxaList = zooper::completeTaxaList,
  StartDates = zooper::startDates,
  ...
)
Zoopsynther(
  Data_type = NULL,
  Zoop = zooper::zoopComb,
  ZoopEnv = zooper::zoopEnvComb,
  Zoop_path = NULL,
  Env_path = NULL,
  Sources = c("EMP", "FRP", "FMWT", "STN", "20mm", "DOP"),
  Size_class = c("Micro", "Meso", "Macro"),
  Time_consistency = FALSE,
  Intro_lag = 2,
  Response = "CPUE",
  Taxa = NULL,
  Date_range = c(NA, NA),
  Months = NA,
  Years = NA,
  Sal_bott_range = NA,
  Sal_surf_range = NA,
  Temp_range = NA,
  Lat_range = NA,
  Long_range = NA,
  Reload_data = F,
  Redownload_data = F,
  All_env = T,
  Shiny = F,
  Crosswalk = zooper::crosswalk,
  Undersampled = zooper::undersampled,
  CompleteTaxaList = zooper::completeTaxaList,
  StartDates = zooper::startDates,
  ...
)

Arguments

`Data_type`	What type of data are you looking for? This option allows you to to choose a final output dataset for either community (`Data_type = "Community"`; the default) or Taxa-specific (`Data_type = "Taxa"`) analyses. NOTE: If you set `Data_type="Community"` we do not recommend utilizing the `Taxa` argument. See below for more explanation of this argument.
`Zoop`	Zooplankton data. You must provide the "Zooplankton" element from the list returned from `Zoopdownloader(Save_object = FALSE, Return_object = TRUE, Return_object_type="List")`. The default argument provides the built-in (and possibly outdated) version of this combined dataset. If you instead wish to provide paths to saved datasets from the `Zoopdownloader` function, set `Data_list = NULL` and provide `Zoop_path`.
`ZoopEnv`	Accessory environmental data. You must provide the "Environment" element from the list returned from `Zoopdownloader(Save_object = FALSE, Return_object = TRUE, Return_object_type="List")`. The default argument provides the built-in (and possibly outdated) version of this combined dataset. If you instead wish to provide paths to saved datasets from the `Zoopdownloader` function, set `Data_list = NULL` and provide `Env_path`.
`Zoop_path`	If you wish to save time by saving the combined zooplankton datasets returned from the `zoopdatadownloader` to disk, provider here the path to the combined zooplankton dataset on disk. You must also set `Data_list = NULL`.
`Env_path`	If you wish to save time by saving the combined zooplankton datasets returned from the `zoopdatadownloader` to disk, provider here the path to the combined accessory environmental data on disk. You must also set `Data_list = NULL`.
`Sources`	Source datasets to be included. Choices include "EMP" (Environmental Monitoring Program), "FRP" (Fish Restoration Program), "FMWT" (Fall Midwater Trawl), "STN" (Townet Survey), "DOP" (Directed Outflow Project), and "20mm" (20mm survey). The YBFMP datasets cannot be used in this function due to taxonomic and life stage issues with that dataset. Defaults to `Sources = c("EMP", "FRP", "FMWT", "STN", "20mm", "DOP")`.
`Size_class`	Zooplankton size classes (as defined by net mesh sizes) to be included in the integrated dataset. Choices include "Micro" (43 $\mu$ m), "Meso" (150 - 160 $\mu$ m), and "Macro" (500-505 $\mu$ m). Defaults to `Size_class = c("Micro", "Meso", "Macro")`.
`Time_consistency`	Would you like to apply a fix to enforce consistent taxonomic resolution over time? Only available for the Community option.
`Intro_lag`	Only applicable if `Time_consistency = TRUE`. How many years after a species is introduced should we expect surveys to start counting them? Defaults to 2.
`Response`	Which response variable(s) would you like for the zooplankton data? Choices are "CPUE" (catch per unit effort) and "BPUE" (carbon biomass per unit effort ( $\mu$ g/ m³)). Defaults to `Response = "CPUE"`.
`Taxa`	If you only wish to include a subset of taxa, provide a character vector of the taxa you wish included. This can include taxa of any taxonomic level (e.g., `Taxa = "Calanoida"`) to include only calanoids. NOTE: we do not recommend you use this feature AND set `Data_type="Community"`. This is better suited to selecting higher-level taxa. If you wish to just include one or a few species, it would be faster to just filter the output of `Zoopdownloader` to include those taxa. Defaults to `NULL`, which includes all taxa.
`Date_range`	Range of dates to include in the final dataset. To filter within a range of dates, include a character vector of 2 dates formatted in the yyyy-mm-dd format exactly, specifying the upper and lower bounds. To specify an infinite upper or lower bound (to include all values above or below a limit) input `NA` for that infinite bound. Defaults to `Date_range = c(NA, NA)`, which includes all dates.
`Months`	Months (as integers) to be included in the integrated dataset. If you wish to only include data from a subset of months, input a vector of integers corresponding to the months you wish to be included. Defaults to `Months = NA`, which includes all months.
`Years`	Years to be included in the integrated dataset. If you wish to only include data from a subset of years, input a vector of years you wish to be included. Defaults to `Years = NA`, which includes all months.
`Sal_bott_range`	Filter the data by bottom salinity values. Include a vector of length 2 specifying the minimum and maximum values you wish to include. To include all values above or below a limit, utilize Inf or -Inf for the upper or lower bound respectively. Defaults to `Sal_bott_range = NA`, which includes all bottom salinities.
`Sal_surf_range`	Same as previous, but for surface salinity.
`Temp_range`	Same as `Sal_bott_range` but for surface temperature.
`Lat_range`	Latitude range to include in the final dataset. Include a vector of length 2 specifying the minimum and maximum values you wish to include, in decimal degree format. Defaults to `Lat_range = NA`, which includes all latitudes.
`Long_range`	Same as previous, but for longitude. Don't forget that Longitudes should be negative in the Delta!
`Reload_data`	If set to `Reload_data = T` runs the `Zoopdownloader` function to re-combine source datasets. To include local versions of the datasets without redownloading them from online, set `Reload_data = TRUE` and `Redownload_data = FALSE`. Defaults to `Reload_data= FALSE`
`Redownload_data`	Should data be re-downloaded from the internet? If set to `Redownload_data = TRUE`, runs `Zoopdownloader(Redownload_data=Redownload_data, Zoop_path=Zoop_path, Env_path=Env_path, ...)`. Defaults to `Redownload_data = FALSE`.
`All_env`	Should all environmental parameters be included? Defaults to `All_env = TRUE`.
`Shiny`	Is this function being used within the shiny app? If set to `Shiny = TRUE`, outputs a list with the integrated dataset as one component and the caveats as the other component. Defaults to `Shiny = FALSE`.
`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.
`Undersampled`	A table listing the taxonomic names and life stages of plankton undersampled by each net mesh size (i.e. size class). See `undersampled` (the default) for an example.
`CompleteTaxaList`	Character vector of all taxonomic names in source datasets. Defaults to `completeTaxaList`.
`StartDates`	Tibble with the starting dates of each source dataset. Defaults to `startDates`.
`...`	Arguments passed to `Zoopdownloader`.

Details

This function combines any combination of the zooplankton datasets (included as parameters) and calculates least common denominator taxa to facilitate comparisons across datasets with differing levels of taxonomic resolution. For more information on the source datasets see zooper.

Value

An integrated zooplankton dataset.

Data type

The Data_type parameter toggles between two approaches to resolving differences in taxonomic resolution. If you want all available data on given Taxa, use Data_type="Taxa" but if you want to conduct a community analysis, use Data_type = "Community".

Briefly, Data_type = "Community" optimizes for community-level analyses by taking all taxa x life stage combinations that are not measured in every input dataset, and summing them up taxonomic levels to the lowest taxonomic level they belong to that is covered by all datasets. Remaining Taxa x life stage combos that are not covered in all datasets up to the phylum level (usually something like Annelida or Nematoda or Insect Pupae) are removed from the final dataset. However, some taxa x life stage combos are retained if they are taxonomic levels higher than species that are counted in some surveys, and a lower taxonomic level within this group is counted in all surveys. For example, if we had 3 surveys where surveys A and B count Pseudodiaptomus forbesi, Pseudodiaptomus marinus, and Pseudodiaptomus spp. (UnID) but survey C only counts P. forbesi and P. marinus then the Pseudodiaptomus spp. (UnID) category would be retained after applying the community approach.

Data_type = "Taxa" optimizes for the Taxa-level user by maintaining all data at the original taxonomic level (but it outputs warnings for taxa not measured in all datasets, which we call "orphans"). To facilitate comparisons across datasets, this option also sums data into general categories that are comparable across all datasets and years: "summed groups." The new variable "Taxatype" identifies which taxa are summed groups (Taxatype = "Summed group"), which are measured to the species level (Taxatype = "Species"), and which are higher taxonomic groupings with the species designation unknown: (Taxatype = "UnID species").

Author(s)

Sam Bashevkin

Examples

MyZoops <- Zoopsynther(Data_type = "Community",
Sources = c("EMP", "FRP", "FMWT"),
Size_class = "Meso",
Date_range = c("1990-10-01", "2000-09-30"))
MyZoops <- Zoopsynther(Data_type = "Community",
Sources = c("EMP", "FRP", "FMWT"),
Size_class = "Meso",
Date_range = c("1990-10-01", "2000-09-30"))

Package 'zooper'

Help Index

Macro zooplankton length-weight equations

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Meso and Micro zooplankton average biomass values

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Detect common taxonomic names across all source datasets

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All taxonomic names

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Taxonomic crosswalk among datasets

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Apply LCD approach for "Taxa" option

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Unique taxa by lifestage combinations present in each source and size class

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Start dates

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Station locations

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EMP EZ Station locations

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Finds all of the lowest-level (i.e. counted) taxonomic names within a vector of taxa

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Detect dates when a species was not counted

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Examples

Convert CPUE to biomass This function converts zooplankton CPUE to carbon biomass (Carbon biomass per unit effort ( $\mu$ g/ m³)) for taxa with conversion equations.

zooper pre-combined (with the `Zoopdownloader` function) zooplankton datasets. These may be out of date