Merge pull request #44 from rosehartman/main

NCRO 2022 data

DESCRIPTION

@@ -1,49 +1,22 @@
 Package: discretewq
-Title: Integrated Dataset of Discrete Water Quality in the San Francisco Estuary
+Title: Integrated Dataset of Discrete Water Quality in the San Francisco
+    Estuary
 Version: 2.4.0.9000
-Authors@R: 
-   c(person(given = "Samuel M",
-           family = "Bashevkin",
-           role = c("aut", "cre"),
-           email = "sam.bashevkin@waterboards.ca.gov",
+Authors@R: c(
+    person("Samuel M", "Bashevkin", , "sam.bashevkin@waterboards.ca.gov", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-7406-7089")),
-     person(given = "Dave",
-           family = "Bosworth",
-           role = c("aut"),
-           email = "David.Bosworth@water.ca.gov",
+    person("Dave", "Bosworth", , "David.Bosworth@water.ca.gov", role = "aut",
            comment = c(ORCID = "0000-0003-0740-3390")),
-     person(given = "Sarah",
-           family = "Perry",
-           role = c("aut"),
-           email = "Sarah.Perry@water.ca.gov",
+    person("Sarah", "Perry", , "Sarah.Perry@water.ca.gov", role = "aut",
            comment = c(ORCID = "0000-0002-2561-8195")),
-     person(given = "Elizabeth B",
-           family = "Stumpner",
-           role = c("aut"),
-           email = "Elizabeth.Stumpner@water.ca.gov",
+    person("Elizabeth B", "Stumpner", , "Elizabeth.Stumpner@water.ca.gov", role = "aut",
            comment = c(ORCID = "0000-0003-2356-2244")),
-     person(given = "Rosemary",
-           family = "Hartman",
-           role = c("ctb"),
-           email = "Rosemary.Hartman@water.ca.gov",
-           comment = c(ORCID = "0000-0002-0642-183X")))
-Description: Produce an integrated dataset of discrete water quality measurements using any combination of the 16 source datasets included. 
+    person("Rosemary", "Hartman", , "Rosemary.Hartman@water.ca.gov", role = "ctb",
+           comment = c(ORCID = "0000-0002-0642-183X"))
+  )
+Description: Produce an integrated dataset of discrete water quality
+    measurements using any combination of the 17 source datasets included.
 License: GPL-3
-Encoding: UTF-8
-LazyData: true
-LazyDataCompression: xz
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
-Suggests: 
-    readr,
-    purrr,
-    spelling,
-    testthat,
-    covr,
-    tibble,
-    readxl,
-    hms,
-    dataRetrieval
 Depends: 
     R (>= 2.10)
 Imports: 
@@ -53,6 +26,22 @@ Imports:
     stringr,
     tidyr,
     wql
+Suggests: 
+    conflicted,
+    covr,
+    dataRetrieval,
+    hms,
+    purrr,
+    readr,
+    readxl,
+    spelling,
+    testthat,
+    tibble
 Remotes: 
     InteragencyEcologicalProgram/deltamapr
+Encoding: UTF-8
 Language: en-US
+LazyData: true
+LazyDataCompression: xz
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3

NEWS.md

@@ -1,5 +1,7 @@
 # discretewq (development version)
 
+* Added `DOP` water quality data.
+
 # discretewq 2.4.0
 
 * Added temperature and conductivity to `USGS_CAWSC`

R/data.R

@@ -82,6 +82,40 @@
 "DJFMP"
 
 
+# DOP -------------------------------------------------------------------
+
+#' Directed Outflow Project water quality data
+#'
+#' Water quality data from the ICF/USBR Directed Outflow Project.
+#'
+#' @encoding UTF-8
+#' @format a tibble with 3,473 rows and 16 variables
+#' \describe{
+#'   \item{Source}{Name of the source dataset.}
+#'   \item{Station}{Station where sample was collected. Includes Station_Code
+#'   and Habitat from the source dataset because multiple habitats are collected
+#'   at each station.}
+#'   \item{Latitude}{Latitude at start of zooplankton tow in decimal degrees.}
+#'   \item{Longitude}{Longitude at start of zooplankton tow in decimal degrees.}
+#'   \item{Field_coords}{Were lat/long coordinates collected in the field (TRUE), or do they represent the location of a fixed station (FALSE)?}
+#'   \item{Date}{Date sample was collected.}
+#'   \item{Datetime}{Date and time of sample collection.}
+#'   \item{Depth}{Bottom depth at start of trawl (m).}
+#'   \item{Secchi}{Secchi depth (cm).}
+#'   \item{Temperature}{Temperature (°C) at surface.}
+#'   \item{Salinity}{Salinity at surface.}
+#'   \item{Conductivity}{Specific conductance (\eqn{\mu}S \ifelse{html}{\out{cm<sup>-1</sup>}}{\eqn{cm^{-1}}}) at surface.}
+#'   \item{DissolvedOxygen}{Dissolved oxygen (mg/L) at surface.}
+#'   \item{pH}{pH (dimensionless) at surface.}
+#'   \item{TurbidityFNU}{Turbidity (FNU) at surface.}
+#'   \item{Chlorophyll}{Chlorophyll-a concentration (\eqn{\mu}g \ifelse{html}{\out{L<sup>-1</sup>}}{\eqn{L^{-1}}}) at surface.}
+#'   }
+#'
+#' @details More metadata and information on methods are available \href{https://portal.edirepository.org/nis/metadataviewer?packageid=edi.1187.4}{here}.
+#' @seealso \code{\link{wq}}
+"DOP"
+
+
 # EDSM --------------------------------------------------------------------
 
 #' EDSM water quality data
@@ -234,7 +268,7 @@
 #' Water quality data from the California Department of Water Resources North Central Region Office.
 #'
 #' @encoding UTF-8
-#' @format a tibble with 10,250 rows and 49 variables
+#' @format a tibble with 10,652 rows and 49 variables
 #' \describe{
 #'   \item{Source}{Name of the source dataset.}
 #'   \item{Station}{Station where sample was collected.}

R/wq.R

@@ -5,6 +5,7 @@
 #'   Choices include "20mm" (20mm Survey, \code{\link{twentymm}}),
 #'   "Baystudy" (Bay Study, \code{\link{baystudy}}),
 #'   "DJFMP" (Delta Juvenile Fish Monitoring Program, \code{\link{DJFMP}}),
+#'   "DOP" (Directed Outflow Project \code{\link{DOP}})),
 #'   "EDSM" (Enhanced Delta Smelt Monitoring, \code{\link{EDSM}}),
 #'   "EMP" (Environmental Monitoring Program, \code{\link{EMP}}),
 #'   "FMWT" (Fall Midwater Trawl, \code{\link{FMWT}}),
@@ -29,6 +30,7 @@
 #'     "20mm",
 #'     "Baystudy",
 #'     "DJFMP",
+#'     "DOP",
 #'     "EDSM",
 #'     "EMP",
 #'     "FMWT",
@@ -60,6 +62,7 @@ wq <- function(Sources = NULL,
     "20mm",
     "Baystudy",
     "DJFMP",
+    "DOP",
     "EDSM",
     "EMP",
     "FMWT",
@@ -105,6 +108,10 @@ wq <- function(Sources = NULL,
     WQ_list[["DJFMP"]] <- discretewq::DJFMP
   }
 
+  if ("DOP" %in% Sources) {
+    WQ_list[["DOP"]] <- discretewq::DOP
+  }
+
   if ("EDSM" %in% Sources) {
     WQ_list[["EDSM"]] <- discretewq::EDSM
   }

README.Rmd

@@ -46,6 +46,7 @@ Data <- wq(
     "20mm",
     "Baystudy",
     "DJFMP",
+    "DOP",
     "EDSM",
     "EMP",
     "FMWT",
@@ -81,7 +82,7 @@ CDFW. 2023a. Fall Midwater Trawl data. [https://filelib.wildlife.ca.gov/public/T
 
 CDFW. 2023b. Summer Townet data. [https://filelib.wildlife.ca.gov/public/TownetFallMidwaterTrawl/TNS%20MS%20Access%20Data/TNS%20data/](https://filelib.wildlife.ca.gov/public/TownetFallMidwaterTrawl/TNS%20MS%20Access%20Data/TNS%20data/).
 
-CDWR. 2022. Water Quality Evaluation Section, North Central Region Office. [https://wdl.water.ca.gov/waterdatalibrary/WaterQualityDataLib.aspx](https://wdl.water.ca.gov/waterdatalibrary/WaterQualityDataLib.aspx). 
+CDWR. 2023. Water Quality Evaluation Section, North Central Region Office. [https://wdl.water.ca.gov/waterdatalibrary/WaterQualityDataLib.aspx](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](https://doi.org/10.5066/F7TQ5ZPR)
 
@@ -103,6 +104,8 @@ O’Rear, T., J. Durand, and P. Moyle. 2022. Suisun Marsh Fish Study. [https://w
 
 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](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](https://portal.edirepository.org/nis/metadataviewer?packageid=edi.1187.4).
+
 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](https://portal.edirepository.org/nis/metadataviewer?packageid=edi.415.8)
 
 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