| Title: | Data for the IEP Long Term Monitoring Survey Review |
|---|---|
| Description: | Integration of the Fall Midwater Trawl, Bay Study, and Suisun Marsh Fish Study data for use in the IEP long-term monitoring survey review. |
| Authors: | Sam Bashevkin [aut, cre] (ORCID: <https://orcid.org/0000-0001-7406-7089>) |
| Maintainer: | Sam Bashevkin <[email protected]> |
| License: | GPL-3 |
| Version: | 2.2.1 |
| Built: | 2026-10-18 11:17:02 UTC |
| Source: | https://github.com/sbashevkin/LTMRdata |
California Department of Fish and Wildlife Bay Study data.
BaystudyBaystudy
a tibble with 868,814 and 23 variables
Name of source dataset.
Station where sample was collected.
May not be accurate, see details.
May not be accurate, see details.
Date sample was collected.
Date and time sample was collected.
Survey number, roughly corresponding to month.
Bottom depth (m).
Unique sample identifier.
Sampling method (Otter Trawl or Midwater Trawl).
Tidal stage.
Surface salinity.
Surface temperature in °C.
Secchi depth (cm).
Duration of tow (minutes).
Area towed (m2).
Volume towed (m3).
Tow direction relative to current.
Scientific name.
Fork length, total length if there's no fork or heterocercal tail (sturgeon, shark). Bat Ray wing widths starting around 1989-1992 to present. (mm).
Estimated count for each sample, taxa, and length.
Why is the length NA?
Notes or comments on the trawl.
@details Some station locations have moved over time due to shoals filling in, trees, etc.
Only measured lengths from the Baystudy data
Baystudy_measured_lengthsBaystudy_measured_lengths
a tibble with 864,599 rows and 5 variables
Unique sample identifier.
Scientific name.
When two different size groups of a species are collected, Bay study may split them into size groups and subsample from each size group separately for fish to measure.
Fork length, total length if there's no fork or heterocercal tail (sturgeon, shark). Bat Ray wing widths starting around 1989-1992 to present. (mm).
Number of fish measured to this length.
Integrate datasets, add zeroes, divide into fish and survey tables, and export to csv and/or rda.
data_integrate( data_path, sources = c("Baystudy", "Suisun", "FMWT", "SKT", "DJFMP", "EDSM", "TMM", "SLS", "STN", "Salvage"), format = "rda", write = TRUE, quiet = FALSE )data_integrate( data_path, sources = c("Baystudy", "Suisun", "FMWT", "SKT", "DJFMP", "EDSM", "TMM", "SLS", "STN", "Salvage"), format = "rda", write = TRUE, quiet = FALSE )
data_path |
Path to the folder where you wish the csv/rda files to be saved. |
sources |
Character vector of data sources to include |
format |
Should the fish and survey tables be saved as a csv alone, a combined .rda file, or both? Defaults to 'rda' and other options are 'csv' or 'both'. |
write |
Logical. Should the files be written to disk, or would you just like them returned as an R object? Defaults to TRUE. |
quiet |
Logical. Set to TRUE if you wish to hide all status messages. |
Invisibly returns a list with the survey and fish tables.
## Not run: data_integrate(data_path=file.path("data-raw", "EDI", "data_objects")) ## End(Not run)## Not run: data_integrate(data_path=file.path("data-raw", "EDI", "data_objects")) ## End(Not run)
US Fish and Wildlife Service Delta Juvenile Fish Monitoring Program data.
DJFMPDJFMP
a tibble with 2,336,862 rows and 23 variables
Name of source dataset.
Station where sample was collected.
Latitude (decimal degrees).
Longitude (decimal degrees).
Date sample was collected.
Date and time sample was collected.
Bottom depth (m).
Unique sample identifier.
Sampling method (Otter Trawl or Midwater Trawl).
Surface salinity.
Surface temperature in °C.
Turbidity (NTU).
Turbidity (FNU).
Secchi depth (cm).
Volume towed (m3).
Tow direction relative to current.
Scientific name.
Fork length from tip of the snout to a point at the fork of the caudal fin (mm).
Estimated count for each sample, taxa, and length.
Why is the length NA?
Some station locations have moved over time due to shoals filling in, trees, etc. More metadata and information on methods are available here.
US Fish and Wildlife Service Enhanced Delta Smelt Monitoring (EDSM) data.
EDSMEDSM
a tibble with 294,773 rows and 23 number of variables
Name of source dataset.
Station where sample was collected.
Average of start and end Latitude.
Average of start and end Longitude.
Date sample was collected.
Date and time sample was collected.
Bottom depth (m). Start depth as noted in survey.
Unique sample identifier.
Sampling method (Otter Trawl or Midwater Trawl).
Tidal stage.
Surface salinity.
Surface temperature in °C.
Turbidity (NTU).
Turbidity (FNU).
Secchi depth (cm).
Volume towed (m3).
Tow direction relative to current.
Scientific name.
Fish fork length from point of mouth to fork of the caudal fin.
Estimated count for each sample, taxa, and length.
Why is the length NA?
@details Stations change randomly due to random stratified sampling. More metadata and information on methods are available here.
California Department of Fish and Wildlife Fall Midwater Trawl data.
FMWTFMWT
a tibble with 274,096 rows and 23 variables
Name of source dataset.
Station where sample was collected.
Latitude (decimal degrees).
Longitude (decimal degrees).
Date sample was collected.
Date and time sample was collected.
Survey number, roughly corresponding to month.
Bottom depth (m).
Unique sample identifier.
Sampling method (Otter Trawl or Midwater Trawl).
Tidal stage.
Surface salinity.
Surface temperature in °C.
Turbidity (NTU).
Secchi depth (cm).
Was Secchi depth estimated?
Volume towed (m3).
Tow direction relative to current.
Length of cable released when net deployed (m).
Scientific name.
Fork length from tip of the snout to a point at the fork of the caudal fin (mm).
Estimated count for each sample, taxa, and length.
Why is the length NA?
More metadata and information on methods are available here.
Only measured lengths from the FMWT data
FMWT_measured_lengthsFMWT_measured_lengths
a tibble with 240,495 rows and 4 variables
Unique sample identifier.
Scientific name.
Sampling survey (loosely corresponds to month).
Number of fish measured to this length.
Intercepts and slopes for equations to convert Standard Length to Fork Length (or Total Length if no fork). Equations derived from the CDFW length-weight study (2005) and Jereme Gaeta, unpublished.
Length_conversionsLength_conversions
a tibble with 20 rows and 3 variables
Scientific name.
Intercept in the equation FL = Intercept + Slope * SL.
Slope in the equation FL = Intercept + Slope * SL.
This package contains internal datasets and a function (data_integrate) to bind them all together.
Maintainer: Sam Bashevkin [email protected] (ORCID)
Authors:
Sam Bashevkin [email protected] (ORCID)
Useful links:
California Department of Fish and Wildlife Fish Salvage dataset.
SalvageSalvage
a tibble with 2,734,547 rows and 15 variables
Name of source dataset.
State or federal facility buildings (of the SWP or CVP).
Latitude (decimal degrees) of the full facility.
Longitude (decimal degrees) of the full facility.
Date sample was collected.
Date and time sample was collected.
Unique sample identifier.
Sampling period (0000 = Normal count, 9999 = Second flush)
Daily export volume for the sampled facility(m3).
Surface temperature in °C.
Scientific name.
Fork length from tip of the snout to a point at the fork of the caudal fin (mm) or total length for species without a forked tail.
Estimated count for each sample, taxa, and length.
Comments or notes of the sampling period.
Why is the length NA?
More metadata and information on methods are available here.
Only measured lengths from the Salvage data
Salvage_measured_lengthsSalvage_measured_lengths
a tibble with 1,904,345 rows and 4 variables
Unique sample identifier.
Scientific name.
Fork length from tip of the snout to a point at the fork of the caudal fin (mm) or total length for species without a forked tail.
Number of fish measured to this length.
California Department of Fish and Wildlife Spring Kodiac Trawl (SKT) data.
SKTSKT
a tibble with 42,909 rows and 22 variables
Name of source dataset.
Station where sample was collected.
Latitude of Station
Longitude of Station
Date sample was collected.
Date and time sample was collected.
Survey number, roughly corresponding to month.
Bottom depth (m).
Unique sample identifier.
Sampling method (Otter Trawl or Midwater Trawl).
Tidal stage.
Surface salinity.
Surface temperature in °C.
Turbidity (NTU).
Turbidity (FNU).
Secchi depth (cm).
Volume towed (m3).
Tow direction relative to current.
Scientific name.
Fork length, total length if there's no fork or heterocercal tail (sturgeon, shark).
Estimated count for each sample, taxa, and length.
Why is the length NA?
More metadata and information on methods are available here.
Only measured lengths from the SKT data
SKT_measured_lengthsSKT_measured_lengths
a tibble with 41,295 rows and 4 variables
Unique sample identifier.
Scientific name.
Fork length, total length if there's no fork or heterocercal tail (sturgeon, shark).
Estimated count for each sample, taxa, and length.
California Department of Fish and Wildlife Smelt Larva Survey data.
SLSSLS
a tibble with 34,227 rows and 26 variables
Name of source dataset.
Station where sample was collected.
Latitude (decimal degrees).
Longitude (decimal degrees).
Date sample was collected.
Date and time sample was collected.
Survey number, roughly corresponding to month.
Bottom depth (m).
Unique sample identifier.
Sampling method.
Tidal stage.
Surface salinity.
Bottom salinity.
Surface temperature in °C.
Secchi depth (cm).
Turbidity (NTU).
Turbidity (FNU).
Volume towed (m3).
Length of cable released when net deployed (m).
Duration of tow (minutes).
Scientific name.
Fork length (mm).
Estimated count for each sample, taxa, and length.
Why is the length NA?
Notes or comments on the trawl.
Notes or comments on the flowmeter reading.
More metadata and information on methods are available here.
Crosswalk table of species codes to common and scientific names
SpeciesSpecies
a tibble with 322 rows and 13 variables
Scientific Name.
Bay Study code.
Common name.
EDSM and DJFMP codes.
Spring Kodiak Trawl code.
Summer Townet Survey code.
Suisun Marsh Fish Study code.
Fall Midwater Trawl code.
20-mm Survey code.
SLS Survey code.
Salvage Survey code.
Lifestage if specified.
Scientific name and life stage.
California Department of Fish and Wildlife Summer Townet Survey (STN) data.
STNSTN
a tibble with 198,359 rows and 22 variables
Name of source dataset.
Station where sample was collected.
Latitude (decimal degrees).
Longitude (decimal degrees).
Date sample was collected.
Date and time sample was collected.
Survey number, roughly corresponding to month.
Bottom depth (m).
Unique sample identifier.
Sampling method (STN trawl).
Tidal stage.
Surface salinity.
Surface temperature in °C.
Turbidity (NTU).
Secchi depth (cm).
Volume towed (m3).
Tow direction relative to current.
Length of cable released when net deployed (feet).
Scientific name.
Fork length from the most anterior part of the fish to the median caudal fin rays (mm).
Estimated count for each sample, taxa, and length.
Why is the length NA?
More metadata and information on methods are available here.
Only measured lengths from the STN data
STN_measured_lengthsSTN_measured_lengths
a tibble with 179,641 rows and 4 variables
Unique sample identifier.
Scientific name.
Fork length from the most anterior part of the fish to the median caudal fin rays (mm).
Number of fish measured to this length.
UC Davis Suisun Marsh Fish Study data.
SuisunSuisun
a tibble with 220,146 rows and 21 variables
Name of source dataset.
Station where sample was collected.
Latitude (decimal degrees).
Longitude (decimal degrees).
Date sample was collected.
Date and time sample was collected.
Bottom depth (m).
Unique sample identifier.
Sampling method (Otter Trawl or Midwater Trawl).
Tidal stage.
Surface salinity.
Surface temperature in °C.
Secchi depth (cm).
Duration of tow (minutes).
Area towed (m2).
Scientific name.
Standard length for all species except sturgeon, which are fork length (mm).
Estimated count for each sample, taxa, and length.
Why is the length NA?
Notes or comments on the fish catch.
Notes or comments on the trawl.
Only measured lengths from the Suisun data
Suisun_measured_lengthsSuisun_measured_lengths
a tibble with 182,940 rows and 5 variables
Unique sample identifier.
Scientific name.
Was fish dead?
Standard length for all species except sturgeon, which are fork length (mm).
Number of fish measured to this length.
Applies the standard suite of integration tests to a dataset. This is the same suite of tests as the ones in the 'test' folder. Useful for catching issues before binding datasets together. Salvage-specific test logic is handled automatically when 'source_name' is "Salvage".
test_dataset(data, source_name = NULL, return_failures = FALSE)test_dataset(data, source_name = NULL, return_failures = FALSE)
data |
A data frame — typically one of the LTMRdata survey objects (e.g. LTMRdata::Baystudy). |
source_name |
Optional character string naming the source (e.g. "Baystudy"). If NULL and a 'Source' column is present, the unique value(s) are used. Affects test labels and Salvage-specific logic. |
return_failures |
Logical. If FALSE (default), runs testthat assertions. If TRUE, skips assertions and returns a named list containing the rows that failed each check. |
If 'return_failures = FALSE', invisibly returns 'data' and is called for its side-effect of running testthat assertions. If 'return_failures = TRUE', returns a named list of data frames representing failed checks (returns an empty list if all checks pass).
## Not run: test_dataset(LTMRdata::Baystudy) fails <- test_dataset(LTMRdata::Salvage, return_failures = TRUE) ## End(Not run)## Not run: test_dataset(LTMRdata::Baystudy) fails <- test_dataset(LTMRdata::Salvage, return_failures = TRUE) ## End(Not run)
California Department of Fish and Wildlife 20-mm Survey data.
TMMTMM
a tibble with 390,248 rows and 23 variables
Name of source dataset.
Station where sample was collected.
Latitude (decimal degrees).
Longitude (decimal degrees).
Date sample was collected.
Date and time sample was collected.
Survey number, roughly corresponding to month.
Bottom depth (m).
Unique sample identifier.
Sampling method (20mm Net).
Tidal stage.
Surface salinity.
Surface temperature in °C.
Turbidity (NTU).
Turbidity (FNU).
Secchi depth (cm).
Volume towed (m3).
Tow direction relative to current. Not recorded but field is included here for consistency.
Length of cable released when net deployed (m).
Scientific name.
Fork length from tip of the snout to a point at the fork of the caudal fin (mm).
Estimated count for each sample, taxa, and length.
Why is the length NA?
More metadata and information on methods are available here.
Only measured lengths from the 20-mm Survey data
TMM_measured_lengthsTMM_measured_lengths
a tibble with 386,777 rows and 4 variables
Unique sample identifier.
Scientific name.
Fork length from tip of the snout to a point at the fork of the caudal fin (mm).
Number of fish measured to this length.