The System Wide Monitoring Program (SWMP) wasimplemented by the National Estuarine Research Reserve System (NERRS) in 1995 to providecontinuous monitoring data at over 140 continuous monitoring stations in28 estuaries across the United States. SWMPr (pronounced “swamper”) isan R package for retrieving, organizing, and analyzing estuarymonitoring 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
Install the package from CRAN as follows:
The development (unstable) version of this package can be installedfrom Github:
A manuscript describing full use of the package is available from theRJournal. All source materials for the manuscript are availablehere. A briefdescription of the available functions is provided below. See helpdocumentation for more details on each function (e.g.,?all_params). All functions are grouped into respectivecategories 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')all_params | Retrieve any number of records starting with the most recent at a givenstation, all parameters. Wrapper toexportAllParamsXMLNewfunction on web services. |
all_params_dtrng | Retrieve records of all parameters within a given date range for astation. Optional argument for a single parameter. Wrapper toexportAllParamsDateRangeXMLNew. |
import_local | Import files from a local path. The files must be in a specific format,specifically those returned from the CDMO using thezip downloadsoption for a reserve. |
import_remote | Import SWMP site data from a remote independent server. These files havebeen 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 themost recent at a given station. Wrapper toexportSingleParamXMLNew function on web services. |
site_codes | Metadata for all stations, wrapper toexportStationCodesXMLNew function on web services. |
site_codes_ind | Metadata for all stations at a single site, wrapper toNERRFilterStationCodesXMLNew function on web services. |
cens_id | Creates additional columns in a swmpr object that identify observationsbelow, within, or above the detection limit. |
comb | Combines swmpr objects to a common time series using setstep, such ascombining the weather, nutrients, and water quality data for a singlestation. Only different data types can be combined. |
qaqc | Remove QAQC columns and remove data based on QAQC flag values for aswmpr object. Only applies if QAQC columns are present. |
qaqcchk | View a summary of the number of observations in a swmpr object that areassigned to different QAQC flags used by CDMO. The output is used toinform further processing but is not used explicitly. |
rem_reps | Remove replicate nutrient data that occur on the same day. The defaultis to average replicates. |
setstep | Format data from a swmpr object to a continuous time series at a giventimestep. The function is used incomb and can also be usedwith individual stations. |
subset | Subset by dates and/or columns for a swmpr object. This is a methodpassed to the generic `subset’ function provided in the base package. |
aggreswmp | Aggregate swmpr objects for different time periods - years, quarters,months, weeks, days, or hours. Aggregation function is user-supplied butdefaults to mean. |
aggremetab | Aggregate metabolism data from a swmpr object. This is primarily usedwithinplot_metab but may be useful for simple summaries ofraw daily data. |
ecometab | Estimate ecosystem metabolism for a combined water quality and weatherdataset using the open-water method. |
decomp | Decompose a swmpr time series into trend, seasonal, and residualcomponents. This is a simple wrapper todecompose.Decomposition of monthly or daily trends is possible. |
decomp_cj | Decompose a swmpr time series into grandmean, annual, seasonal, andevents components. This is a simple wrapper todecompTs inthe 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 swmprobject. The maximum gap size that is interpolated is defined as amaximum 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 namemust be specified. |
plot_metab | Plot ecosystem metabolism estimates after runningecometabon a swmpr object. |
plot_summary | Create summary plots of seasonal/annual trends and anomalies for a waterquality or weather parameter. |
plot_wind | Create a wind rose using weather data. |
smoother | Smooth swmpr objects with a moving window average. Window size and sidescan be specified, passed tofilter. |
calcKL | Estimate the reaeration coefficient for air-sea gas exchange. This isonly used within theecometab function. |
metab_day | Identify the metabolic day for each approximate 24 period in an hourlytime series. This is only used within theecometabfunction. |
param_names | Returns column names as a list for the parameter type(s) (nutrients,weather, or water quality). Includes QAQC columns with ‘f_’ prefix. Usedinternally in other functions. |
parser | Parses html returned from CDMO web services, used internally inretrieval 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 asite/station, used internally in retrieval functions. |