The goal of discretewq is to integrate discrete water quality data from the San Francisco Estuary.
You can install the latest version from GitHub with:
# install.packages("devtools")
devtools::install_github("InteragencyEcologicalProgram/discretewq")To obtain the full integrated water quality dataset
library(discretewq)
Data <- wq(
Sources = c(
"20mm",
"Baystudy",
"DJFMP",
"DOP",
"EDSM",
"EMP",
"FMWT",
"NCRO",
"SDO",
"SKT",
"SLS",
"STN",
"Suisun",
"USBR",
"USGS_CAWSC",
"USGS_SFBS",
"YBFMP"
)
)
str(Data)
#> tibble [357,725 × 79] (S3: tbl_df/tbl/data.frame)
#> $ Source : chr [1:357725] "20mm" "20mm" "20mm" "20mm" ...
#> $ Station : chr [1:357725] "504" "519" "809" "901" ...
#> $ Latitude : num [1:357725] 38.1 38.1 38.1 38 38 ...
#> $ Longitude : num [1:357725] -122 -122 -122 -122 -122 ...
#> $ Field_coords : logi [1:357725] FALSE FALSE FALSE FALSE FALSE FALSE ...
#> $ Date : POSIXct[1:357725], format: "1997-05-03" "1997-05-03" ...
#> $ Datetime : POSIXct[1:357725], format: "1997-05-03 07:50:00" "1997-05-03 08:36:00" ...
#> $ Depth : num [1:357725] 7.62 3.05 12.19 2.44 7.62 ...
#> $ Tide : chr [1:357725] "Ebb" "Ebb" "Flood" "Flood" ...
#> $ Secchi : num [1:357725] 16 13 63 78 90 48 58 70 68 74 ...
#> $ Temperature : num [1:357725] 17.1 17.2 18.8 19.1 20 20.2 20.6 20.6 21.4 19.5 ...
#> $ Conductivity : num [1:357725] 1490 652 239 250 276 311 302 339 321 230 ...
#> $ Conductivity_bottom : num [1:357725] 1949 1174 248 251 275 ...
#> $ Notes : chr [1:357725] NA NA NA NA ...
#> $ Temperature_bottom : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ DissolvedOxygen : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ Salinity : num [1:357725] 0.747 0.316 0.113 0.118 0.131 ...
#> $ pH : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ TurbidityFNU : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ Chlorophyll : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ DissolvedOxygen_bottom : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ Microcystis : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ Chlorophyll_Sign : chr [1:357725] NA NA NA NA ...
#> $ DissolvedOxygenPercent : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ DissolvedOxygenPercent_bottom: num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ pH_bottom : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ TurbidityNTU : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ TurbidityNTU_bottom : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ TurbidityFNU_bottom : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ Pheophytin_Sign : chr [1:357725] NA NA NA NA ...
#> $ Pheophytin : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ TotAlkalinity_Sign : chr [1:357725] NA NA NA NA ...
#> $ TotAlkalinity : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ TotAmmonia_Sign : chr [1:357725] NA NA NA NA ...
#> $ TotAmmonia : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ DissAmmonia_Sign : chr [1:357725] NA NA NA NA ...
#> $ DissAmmonia : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ DissBromide_Sign : chr [1:357725] NA NA NA NA ...
#> $ DissBromide : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ DissCalcium_Sign : chr [1:357725] NA NA NA NA ...
#> $ DissCalcium : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ TotChloride_Sign : chr [1:357725] NA NA NA NA ...
#> $ TotChloride : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ DissChloride_Sign : chr [1:357725] NA NA NA NA ...
#> $ DissChloride : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ DissNitrateNitrite_Sign : chr [1:357725] NA NA NA NA ...
#> $ DissNitrateNitrite : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ DOC_Sign : chr [1:357725] NA NA NA NA ...
#> $ DOC : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ TOC_Sign : chr [1:357725] NA NA NA NA ...
#> $ TOC : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ DON_Sign : chr [1:357725] NA NA NA NA ...
#> $ DON : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ TON_Sign : chr [1:357725] NA NA NA NA ...
#> $ TON : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ DissOrthophos_Sign : chr [1:357725] NA NA NA NA ...
#> $ DissOrthophos : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ TotPhos_Sign : chr [1:357725] NA NA NA NA ...
#> $ TotPhos : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ DissSilica_Sign : chr [1:357725] NA NA NA NA ...
#> $ DissSilica : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ TDS_Sign : chr [1:357725] NA NA NA NA ...
#> $ TDS : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ TSS_Sign : chr [1:357725] NA NA NA NA ...
#> $ TSS : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ VSS_Sign : chr [1:357725] NA NA NA NA ...
#> $ VSS : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ TKN_Sign : chr [1:357725] NA NA NA NA ...
#> $ TKN : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ Secchi_estimated : logi [1:357725] NA NA NA NA NA NA ...
#> $ Sample_depth_surface : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ Sample_depth_bottom : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ Salinity_bottom : num [1:357725] 0.989 0.582 0.117 0.119 0.13 ...
#> $ Sample_depth_nutr_surface : num [1:357725] NA NA NA NA NA NA NA NA NA NA ...
#> $ MonthYear : POSIXct[1:357725], format: "1997-05-01" "1997-05-01" ...
#> $ Year : num [1:357725] 1997 1997 1997 1997 1997 ...
#> $ StationID : chr [1:357725] "20mm 504" "20mm 519" "20mm 809" "20mm 901" ...
#> $ Month : num [1:357725] 5 5 5 5 5 5 5 5 5 5 ...
#> $ Season : chr [1:357725] "Spring" "Spring" "Spring" "Spring" ...The dataset is also published on the Environmental Data Initiative, where you can find detailed metadata. This static version of the dataset corresponds to version 2.4.0 of the R package (archived on zenodo).
Battey, M. and S. Perry. 2023. Interagency Ecological Program: Discrete water quality monitoring in the Sacramento-San Joaquin Bay-Delta, collected by the Environmental Monitoring Program, 1975-2022 ver 9. Environmental Data Initiative. doi:10.6073/pasta/a306956e3ebdc78348c2df8d05cd2ccb
CDFW. 2022. Bay Study data. https://filelib.wildlife.ca.gov/Public/BayStudy/Access_Database/.
CDFW. 2023a. Fall Midwater Trawl data. https://filelib.wildlife.ca.gov/public/TownetFallMidwaterTrawl/FMWT%20Data/.
CDFW. 2023b. Summer Townet data. https://filelib.wildlife.ca.gov/public/TownetFallMidwaterTrawl/TNS%20MS%20Access%20Data/TNS%20data/.
CDWR. 2023. Water Quality Evaluation Section, North Central Region Office. https://wdl.water.ca.gov/waterdatalibrary/WaterQualityDataLib.aspx.
Cloern, J. E., and T. S. Schraga. 2016. USGS Measurements of Water Quality in San Francisco Bay (CA), 1969-2015 (ver. 3.0 June 2017). U. S. Geological Survey data release. doi:https://doi.org/10.5066/F7TQ5ZPR
Interagency Ecological Program (IEP), S. Lesmeister, and J. Rinde. 2020. Interagency Ecological Program: Discrete dissolved oxygen monitoring in the Stockton Deep Water Ship Channel, collected by the Environmental Monitoring Program, 1997-2018. ver2. Environmental Data Initiative. doi:10.6073/PASTA/3268530C683726CD430C81894FFAD768
Interagency Ecological Program (IEP), L. Damon, and A. Chorazyczewski. 2021a. Interagency Ecological Program San Francisco Estuary 20mm Survey 1995 - 2021. ver 4. Environmental Data Initiative. doi:10.6073/pasta/32de8b7ffbe674bc6e79dbcd29ac1cc2
Interagency Ecological Program (IEP), L. Damon, and A. Chorazyczewski. 2021b. Interagency Ecological Program San Francisco Estuary Spring Kodiak Trawl Survey 2002 - 2021. ver 4. Environmental Data Initiative. doi:10.6073/pasta/f0e2916f4a026f3f812a0855cee74a8d
Interagency Ecological Program (IEP), L. Damon, T. Tempel, and A. Chorazyczewski. 2021c. Interagency Ecological Program San Francisco Estuary Smelt Larva Survey 2009 – 2021. ver 4. Environmental Data Initiative. doi:10.6073/pasta/8e1ceb1c02fbc8b0ba7a6b58229109f2
Interagency Ecological Program (IEP), C. Pien, J. Adams, and N. Kwan. 2021d. Interagency Ecological Program: Zooplankton catch and water quality data from the Sacramento River floodplain and tidal slough, collected by the Yolo Bypass Fish Monitoring Program, 1998-2018. ver 2. Environmental Data Initiative. doi:10.6073/pasta/baad532af96cba1d58d43b89c08ca081
Interagency Ecological Program (IEP), R. McKenzie, J. Speegle, A. Nanninga, J.R. Cook, J. Hagen, and B. Mahardja. 2022a. Interagency Ecological Program: Over four decades of juvenile fish monitoring data from the San Francisco Estuary, collected by the Delta Juvenile Fish Monitoring Program, 1976-2021. ver 9. Environmental Data Initiative. doi:10.6073/pasta/30a3232084be9c936c976fbb6b31c5a2
Interagency Ecological Program (IEP), C. Pien, and N. Kwan. 2022b. Interagency Ecological Program: Fish catch and water quality data from the Sacramento River floodplain and tidal slough, collected by the Yolo Bypass Fish Monitoring Program, 1998-2021. ver 3. Environmental Data Initiative. doi:10.6073/pasta/f5c4362f4a1f370723e2b9113432909f
O’Rear, T., J. Durand, and P. Moyle. 2022. Suisun Marsh Fish Study. https://watershed.ucdavis.edu/project/suisun-marsh-fish-study.
Schraga, T. S., E. S. Nejad, C. A. Martin, and J. E. Cloern. 2020. USGS measurements of water quality in San Francisco Bay (CA), beginning in 2016 (ver. 3.0, March 2020). U. S. Geological Survey data release. doi:https://doi.org/10.5066/F7D21WGF
Schultz, A. A. and A. J. Kalmbach. 2023. Directed Outflow Project Lower Trophic Study ver 4. Environmental Data Initiative. doi:10.6073/pasta/86a01140eb3bb756ee9f7f8dab8aefc4.
United States Fish and Wildlife Service, T. Senegal, R. Mckenzie, J. Speegle, B. Perales, D. Bridgman, K. Erly, S. Staiger, A. Arrambide, and M. Gilbert. 2022. Interagency Ecological Program and US Fish and Wildlife Service: San Francisco Estuary Enhanced Delta Smelt Monitoring Program data, 2016-2021 ver 8. Environmental Data Initiative. doi:10.6073/pasta/e1a540c161b7be56b941df50fd7b44c5
U.S. Geological Survey. 2022. USGS water data for the Nation: U.S. Geological Survey National Water Information System database, accessed October 21, 2022, at doi:10.5066/F7P55KJN
USBR, R. Dahlgren, L. Loken, and E. Van Nieuwenhuyse. 2020. Monthly vertical profiles of water quality in the Sacramento Deep Water Ship Channel 2012-2019. https://www.usbr.gov/mp/bdo/index.html