#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# dataCensored ####
#' @title Chesapeake Bay Program Monitoring Data, 1985-2016
#'
#' @description Selected 1985-2016 data for eight (8) stations from the
#' Chesapeake Bay Monitoring Program. Water quality variables are stored as
#' either class 'num' for variables with no censoring or class 'Surv'
#' (see survival::Surv) that allows for left- and interval-censored data.
#'
#' @format A data frame with 13,062 rows and 17 variables:
#' \describe{
#' \item{station}{station identifier}
#' \item{date}{sample date}
#' \item{layer}{sample layer}
#' \item{secchi}{Secchi depth [m]}
#' \item{salinity}{Salinity [ppt]}
#' \item{do}{Dissolved Oxygen [mg/L]}
#' \item{wtemp}{Water Temperature [deg C]}
#' \item{chla}{Corrected Chlorophyll-a [ug/L]}
#' \item{tn}{Total Nitrogen [mg/L]}
#' \item{tp}{Total Phosphorus [mg/L]}
#' \item{tss}{Total Suspended Solids [mg/L]}
#' \item{din}{Dissolved Inorganic Nitrogen [mg/L]}
#' \item{po4}{Orthophosphorus [mg/L]}
#' \item{tdn}{Total Dissolved Nitrogen [mg/L]}
#' \item{tdp}{Total Dissolved Phosphorus [mg/L]}
#' \item{nh4}{Ammonium [mg/L]}
#' \item{no23}{Nitrite + Nitrate [mg/L]}
#' }
"dataCensored"
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# layerLukup ####
#' @title Layer List
#'
#' @description A lookup table of layer abbreviations and the corresponding
#' names.
#'
#' @format A data frame with 10 rows and 3 variables:
#' \describe{
#' \item{layers}{Layer codes}
#' \item{order}{Analysis order}
#' \item{name}{Layer name}
#' }
"layerLukup"
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# parameterList ####
#' @title Parameter List
#'
#' @description A lookup table of water quality parameters
#'
#' @format A data frame with 82 rows and 13 variables:
#' \describe{
#' \item{parm}{"preferred" parameter ID}
#' \item{parmSource}{parmamter field as may be found in sample data sets}
#' \item{parmCat}{Parameter Group Header}
#' \item{parmName}{Full parameter name}
#' \item{parmCalc}{indicator if parameter is calculated}
#' \item{parmNamelc}{parameter name in lower case}
#' \item{parmUnits}{units}
#' \item{parmRecensor}{numerical value used in log plots if data are reported
#' as <= 0}
#' \item{parmRO1}{Parameter sort order level 1}
#' \item{parmRO2}{Parameter sort order level 2}
#' \item{parmTrend}{TRUE/FALSE for whether parameter should be analyzed for
#' trend}
#' \item{logTrans}{TRUE/FALSE for whether parameter should be analyzed in log
#' transposed}
#' \item{trendIncrease}{Should an increase in conccentration be interpreted
#' as 'improving', 'degrading', 'increasing', or 'decreasing'}
#' }
"parameterList"
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# stationMasterList ####
#' @title Chesapeake Bay Program long-term tidal monitoring stations
#'
#' @description Chesapeake Bay Program long-term tidal monitoring stations
#'
#' @format A data frame with 145 rows and 19 variables:
#' \describe{
#' \item{station}{Water quality station code}
#' \item{state}{State location}
#' \item{locationType}{As identified in the state trend reports, whether this
#' station is in the mainstem or tributary monitoring}
#' \item{waterbody}{Location as identified in the CBP CIMS database}
#' \item{latitude}{From the CBP CIMS database, and verified in a GIS map}
#' \item{longitude}{From the CBP CIMS database, and verified in a GIS map}
#' \item{cbSeg92}{Match to CB 92 Segmentation scheme (for 303d list)}
#' \item{usgsGageName}{Manual match to a USGS fall-line monitoring station
#' (See usgsGages$siteName)}
#' \item{usgsGageID}{USGS station code (See usgsGages$siteNumber)}
#' \item{usgsGageMatch}{Identifies how the USGS-to-TribStation match was
#' made. Direct: If the station falls within a tributary with a USGS station,
#' or in the mainstem. Indirect: If the station is in a small sub-tributary
#' of one of the major tributaries. The USGS station may not be that
#' representative, but it is better than matching to the Susquehanna.
#' SusDefault: If there was no clear match, the tidal station was matched to
#' the Susquehanna River.}
#' \item{stationRO1}{Station sort order level 1}
#' \item{stationRO2}{Station sort order level 2}
#' \item{stationGrpName}{Station group header}
#' \item{stationMethodGroup}{Foreign key to methodsList table}
#' \item{hydroTerm}{"flow" or "salinity" to indicate whether to model flow or
#' salinity effects (if missing, "flow" assumed)}
#' \item{flwAvgWin}{list of averaging windows if flow is selected in
#' hydroTerm (options are: 1, 5, 10, 15, 20, 30, 40, 50, 60, 90, 120, 150,
#' 180, 210)}
#' \item{flwParms}{list of parameters to model with flow (regardless of
#' hydroTerm value), each parameter separated by a space}
#' \item{salParms}{list of parameters to model with salinity (regardless of
#' hydroTerm value), each parameter separated by a space}
#' \item{notes}{Optional note to track updates}
#' }
"stationMasterList"
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# usgsGages ####
#' @title USGS Gages
#'
#' @description List of core USGS gages for CBP trend analyses
#'
#' @format A data frame with 9 rows and 2 variables:
#' \describe{
#' \item{usgsGageID}{USGS Gage ID}
#' \item{siteName}{USGS Site Name}
#' }
"usgsGages"
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# sal ####
#' @title Salinity data
#'
#' @description Salinity data, 1984 to 2016, for 8 stations.
#'
#' @format A data frame with 51,092 rows and 4 variables:
#' \describe{
#' \item{station}{CBP Station ID}
#' \item{date}{date, YYYY-MM-DD}
#' \item{layer}{sample layer}
#' \item{salinity}{Measured salinity}
#' }
"sal"
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