import_local_nut: Import local CDMO data

In padilla410/SWMPrExtension: Functions for Analyzing and Plotting Estuary Monitoring Data

Description

Import local data that were obtained from the CDMO through the zip downloads feature

Usage

import_local_nut(path, station_code, collMethd = c(1, 2), trace = FALSE)

Arguments

path	chr string of full path to .csv files with raw data, can be a zipped or unzipped directory where the former must include the .zip extension
station_code	chr string of station to import, typically 7 or 8 characters including wq, nut, or met extensions, may include full name with year, excluding file extension
collMethd	chr string of nutrient data to subset. 1 indicates monthly, 2 indicates diel. Default is both diel and monthly data.
trace	logical indicating if progress is sent to console, default FALSE

Details

The function is designed to import local data that were downloaded from the CDMO outside of R. This approach works best for larger data requests, specifically those from the zip downloads feature in the advanced query section of the CDMO. The function may also work using data from the data export system, but this feature has not been extensively tested. The downloaded data will be in a compressed folder that includes multiple .csv files by year for a given data type (e.g., apacpwq2002.csv, apacpwq2003.csv, apacpnut2002.csv, etc.). The import_local function can be used to import files directly from the compressed folder or after the folder is decompressed. In the former case, the requested files are extracted to a temporary directory and then deleted after they are loaded into the current session. An example dataset is available online to illustrate the format of the data provided through the zip downloads feature. See the link below to access these data. All example datasets included with the package were derived from these raw data.

Occasionally, duplicate time stamps are present in the raw data. The function handles duplicate entries differently depending on the data type (water quality, weather, or nutrients). For water quality and nutrient data, duplicate time stamps are simply removed. Note that nutrient data often contain replicate samples with similar but not duplicated time stamps within a few minutes of each other. Replicates with unique time stamps are not removed but can be further processed using rem_reps. Weather data prior to 2007 may contain duplicate time stamps at frequencies for 60 (hourly) and 144 (daily) averages, in addition to 15 minute frequencies. Duplicate values that correspond to the smallest value in the frequency column (15 minutes) are retained.

This function differs from import_local in that it allows for special handling of nutrient data. Using this function, the user can separate diel sampling data from low-tide sampling data using the collMthd argument.

Zip download request through CDMO: http://cdmo.baruch.sc.edu/aqs/zips.cfm

Example dataset: https://s3.amazonaws.com/swmpexdata/zip_ex.zip

Value

Returns a swmpr object with all parameters and QAQC columns for the station. The full date range in the raw data are also imported.

Author(s)

Marcus Beck, Julie Padilla (additional of codecollMthd argument) maintainer: Julie Padilla

See Also

all_params, all_params_dtrng, rem_reps, single_param

padilla410/SWMPrExtension documentation built on Dec. 29, 2021, 5:48 a.m.