qaqc: QAQC filtering for SWMP data

Description

QAQC filtering for SWMP data obtained from retrieval functions, local and remote

Usage

qaqc(swmpr_in, ...)
# S3 method for swmpr
qaqc(swmpr_in, qaqc_keep = "0", trace = FALSE, ...)

Value

Returns a swmpr object with NA values for records that did not match qaqc_keep. QAQC columns are also removed.

Arguments

swmpr_in: input swmpr object
...: arguments passed to or from other methods
qaqc_keep: character string of qaqc flags to keep, default '0', any number of flag codes can be supplied including three character error codes (see examples)
trace: logical for progress output on console, default FALSE

Details

The qaqc function is a simple screen to retain values from the data with specified QAQC flags, described online: https://cdmo.baruch.sc.edu/data/qaqc.cfm. Each parameter in the swmpr data typically has a corresponding QAQC column of the same name with the added prefix 'f_'. Values in the QAQC column specify a flag from -5 to 5. Generally, only data with the '0' QAQC flag should be used, which is the default option for the function. Data that do not satisfy QAQC criteria are converted to NA values. Additionally, simple filters are used to remove obviously bad values, e.g., wind speed values less than zero or pH values greater than 12. Erroneous data entered as -99 are also removed. Processed data will have QAQC columns removed, in addition to removal of values in the actual parameter columns that do not meet the criteria.

The data are filtered by matching the flag columns with the character string provided by qaqc_keep. A single combined string is created by pasting each element together using the '|' operator, then using partial string matching with grepl to compare the actual flags in the QAQC columns. Values that can be passed to the function are those described online: https://cdmo.baruch.sc.edu/data/qaqc.cfm.

Examples

Run this code

if (FALSE) {
## get data
data(apadbwq)
dat <- apadbwq

## retain only '0' and '-1' flags
qaqc(dat, qaqc_keep = c('0', '-1'))

## retain observations with the 'CSM' error code
qaqc(dat, qaqc_keep = 'CSM')
}