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Overview

Source: vignettes/Overview.Rmd
Overview.Rmd
Marcus W. Beck,

Overview

The System Wide Monitoring Program (SWMP) was implemented by the National Estuarine Research Reserve System (NERRS) in 1995 to provide continuous monitoring data at over 140 continuous monitoring stations in 28 estuaries across the United States. SWMPr (pronounced “swamper”) is an R package for retrieving, organizing, and analyzing estuary monitoring data from SWMP. Please cite the package as follows:

Beck MW. 2016. SWMPr: An R package for retrieving, organizing, and analyzing environmental data for estuaries. The R Journal. 8(1):219-232. https://journal.r-project.org/archive/2016-1/beck.pdf

Installing the package

Install the package from CRAN as follows:

The development (unstable) version of this package can be installed from Github:

install.packages('devtools')
library(devtools)
install_github('fawda123/SWMPr', ref = 'development')
library(SWMPr)

Using the package

A manuscript describing full use of the package is available from the R Journal. All source materials for the manuscript are available here. A brief description of the available functions is provided below. See help documentation for more details on each function (e.g., ?all_params). All functions are grouped into respective categories that describe their use: retrieve, organize, and analyze. Help files for functions in each category can be viewed as follows:

help.search('retrieve', package = 'SWMPr')
help.search('organize', package = 'SWMPr')
help.search('analyze', package = 'SWMPr')

Retrieve

all_params Retrieve any number of records starting with the most recent at a given station, all parameters. Wrapper to exportAllParamsXMLNew function on web services.
all_params_dtrng Retrieve records of all parameters within a given date range for a station. Optional argument for a single parameter. Wrapper to exportAllParamsDateRangeXMLNew.
import_local Import files from a local path. The files must be in a specific format, specifically those returned from the CDMO using the zip downloads option for a reserve.
import_remote Import SWMP site data from a remote independent server. These files have been downloaded from CDMO, processed using functions in this package, and uploaded to an Amazon server for quicker import into R.
single_param Retrieve any number of records for a single parameter starting with the most recent at a given station. Wrapper to exportSingleParamXMLNew function on web services.
site_codes Metadata for all stations, wrapper to exportStationCodesXMLNew function on web services.
site_codes_ind Metadata for all stations at a single site, wrapper to NERRFilterStationCodesXMLNew function on web services.

Organize

cens_id Creates additional columns in a swmpr object that identify observations below, within, or above the detection limit.
comb Combines swmpr objects to a common time series using setstep, such as combining the weather, nutrients, and water quality data for a single station. Only different data types can be combined.
qaqc Remove QAQC columns and remove data based on QAQC flag values for a swmpr object. Only applies if QAQC columns are present.
qaqcchk View a summary of the number of observations in a swmpr object that are assigned to different QAQC flags used by CDMO. The output is used to inform further processing but is not used explicitly.
rem_reps Remove replicate nutrient data that occur on the same day. The default is to average replicates.
setstep Format data from a swmpr object to a continuous time series at a given timestep. The function is used in comb and can also be used with individual stations.
subset Subset by dates and/or columns for a swmpr object. This is a method passed to the generic `subset’ function provided in the base package.

Analyze

aggreswmp Aggregate swmpr objects for different time periods - years, quarters, months, weeks, days, or hours. Aggregation function is user-supplied but defaults to mean.
aggremetab Aggregate metabolism data from a swmpr object. This is primarily used within plot_metab but may be useful for simple summaries of raw daily data.
ecometab Estimate ecosystem metabolism for a combined water quality and weather dataset using the open-water method.
decomp Decompose a swmpr time series into trend, seasonal, and residual components. This is a simple wrapper to decompose. Decomposition of monthly or daily trends is possible.
decomp_cj Decompose a swmpr time series into grandmean, annual, seasonal, and events components. This is a simple wrapper to decompTs in the wq package. Only monthly decomposition is possible.
hist Plot a histogram for a swmpr object.
lines Add lines to an existing swmpr plot.
map_reserve Create a map of all stations in a reserve using the ggmap package.
na.approx Linearly interpolate missing data (NA values) in a swmpr object. The maximum gap size that is interpolated is defined as a maximum number of records with missing data.
overplot Plot multiple SWMP time series on the same y-axis.
plot Plot a univariate time series for a swmpr object. The parameter name must be specified.
plot_metab Plot ecosystem metabolism estimates after running ecometab on a swmpr object.
plot_summary Create summary plots of seasonal/annual trends and anomalies for a water quality or weather parameter.
plot_wind Create a wind rose using weather data.
smoother Smooth swmpr objects with a moving window average. Window size and sides can be specified, passed to filter.

Miscellaneous

calcKL Estimate the reaeration coefficient for air-sea gas exchange. This is only used within the ecometab function.
metab_day Identify the metabolic day for each approximate 24 period in an hourly time series. This is only used within the ecometab function.
param_names Returns column names as a list for the parameter type(s) (nutrients, weather, or water quality). Includes QAQC columns with ‘f_’ prefix. Used internally in other functions.
parser Parses html returned from CDMO web services, used internally in retrieval functions.
swmpr Creates object of swmpr class, used internally in retrieval functions.
time_vec Converts time vectors to POSIX objects with correct time zone for a site/station, used internally in retrieval functions.