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Apply basic QAQC procedures to a survey dataset

Source: R/qaqcData.R
qaqcData.Rd

Apply basic QAQC procedures to a survey dataset

Usage

qaqcData(
  data,
  year,
  survey = c("ybfmp", "djfmp", "frp", "edsm", "sls", "20mm", "stn", "fmwt", "skt", "sms"),
  convertNames = F,
  officialGPS = NULL,
  gpsDistance = 0.5,
  startingGPSFormat = c("dms", "ddm"),
  towSchedule = NULL,
  meterSchedule = NULL,
  waterQualityVariables = c("BottomDepth", "WaterTemperature", "WaterTemperatureTop",
    "WaterTemperatureBottom", "SpecificConductance", "SpecificConductanceTop",
    "SpecificConductanceBottom", "Secchi", "TurbidityNTU", "TurbidityTopNTU",
    "TurbidityBottomNTU", "Salinity", "SalinityTop", "SalinityBottom"),
  stdev = 2,
  waterQualityGroupings = list("StationCode", c("StationCode", "Month"))
)

Arguments

data

A data frame with the required data, dependent on what QAQC procedures you want to run. It is advised to provide the fully joined/merged dataset.

year

A filtering year. This can support custom year labels if desired, e.g., your sampling season extends across two years.

survey

Name of a qualifying IEP survey name. Currently explicit support only for sls, 20mm, stn, fmwt, and bs.

convertNames

T/F. Should the names be changed to their respective IEP recommended names

officialGPS

Calculate outlying gps points if provided, defaulting to NULL. A data frame containing the official GPS coordinates of the sampling stations. Required to have at least three columns: station, lat, and lon. Coordinates should be provided in degree decimals.

gpsDistance

A value in miles indicating the threshold distance beyond which is an outlier. Defaults to 0.5 miles

startingGPSFormat

Either degrees, minutes, and seconds (dms) or degrees and decimal minutes (ddm). Format of your GPS coordinates. This will be convert to decimal degrees

towSchedule

Calculate outlying cable length values if provided. A data frame containing the tow schedule. Several tow schedules are provided in the package within the towSchedule list. See details.

meterSchedule

Calculate outlying flow meter readings if provided. A data frame containing the expected range for a meter reading based on the duration of the tow. Several meter schedules are provided in the package within the meterSchedule list. You can provide your own data frame following the format.

waterQualityVariables

Calculate outlying water quality variables.

stdev

Defaults to 2. The number of standard deviation away from the mean to flag as an outlying water quality value

waterQualityGroupings

A list of grouping variables to iterate through the water quality check. By default, calculates per station and per station and month.

Value

A list of objects containing identified outliers or rows with missing data points

Details

For the towSchedule and meterSchedule arguments, you can use a schedules recorded in the package (towSchedule or meterSchedule), currently available only for center surveys, which were based on protocol documentation. If not available, you can provide your own schedule. See the example on how to create such a table.

Examples