# Retrieving, Organizing, and Analyzing Estuary Monitoring Data

## Documentation for package ‘SWMPr’ version 2.5.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

aggremetab | Aggregate metabolism data
aggremetab.swmpr | Aggregate metabolism data
aggreswmp | Aggregate swmpr data
aggreswmp.swmpr | Aggregate swmpr data
all_params | Import current station records from the CDMO
all_params_dtrng | Get CDMO records within a date range
apacpnut | Example nutrient data for Apalachicola Bay Cat Point station.
apacpwq | Example water quality data for Apalachicola Bay Cat Point station.
apadbwq | Example water quality data for Apalachicola Bay Dry Bar station.
apaebmet | Example weather data for Apalachicola Bay East Bay station.
calckl | Calculate oxygen mass transfer coefficient
cens_id | Flag observations above/below detection limits
cens_id.swmpr | Flag observations above/below detection limits
comb | Combine swmpr data
comb.default | Combine swmpr data
comb.swmpr | Combine swmpr data
decomp | Simple trend decomposition
decomp.default | Simple trend decomposition
decomp.swmpr | Simple trend decomposition
decompTs | Decompose a time series
decomp_cj | Simple trend decomposition of monthly swmpr data
decomp_cj.default | Simple trend decomposition of monthly swmpr data
decomp_cj.swmpr | Simple trend decomposition of monthly swmpr data
ecometab | Ecosystem metabolism
ecometab.default | Ecosystem metabolism
ecometab.swmpr | Ecosystem metabolism
gradcols | Get colors for plots
hist.swmpr | Plot swmpr using a histogram
import_local | Import local CDMO data
lines.swmpr | Plot swmpr data
map_reserve | Map a reserve
metab_day | Identify metabolic days in a time series
metab_day.default | Identify metabolic days in a time series
na.approx.swmpr | Linearly interpolate gaps
overplot | Plot multiple SWMP time series on the same y-axis
overplot.default | Plot multiple SWMP time series on the same y-axis
overplot.swmpr | Plot multiple SWMP time series on the same y-axis
oxySol | Dissolved oxygen at saturation
param_names | Get parameters of a given type
parser | Parse web results for swmpr
plot.swmpr | Plot swmpr data
plot_metab | Plot ecosystem metabolism for a swmpr object
plot_metab.swmpr | Plot ecosystem metabolism for a swmpr object
plot_quants | Create a plot of data for a single year overlaid on historical data.
plot_quants.swmpr | Create a plot of data for a single year overlaid on historical data.
plot_summary | Plot graphical summaries of SWMP data
plot_summary.swmpr | Plot graphical summaries of SWMP data
plot_wind | Create a wind rose
plot_wind.swmpr | Create a wind rose
qaqc | QAQC filtering for SWMP data
qaqc.swmpr | QAQC filtering for SWMP data
qaqcchk | Summary of QAQC flags in SWMP data
qaqcchk.swmpr | Summary of QAQC flags in SWMP data
rem_reps | Remove replicates in nutrient data
rem_reps.swmpr | Remove replicates in nutrient data
setstep | Format a swmpr time vector
setstep.default | Format a swmpr time vector
setstep.swmpr | Format a swmpr time vector
single_param | Get CDMO records for a single parameter
site_codes | Obtain metadata for all stations
site_codes_ind | Obtain metadata for a single reserve
smoother | Smooth swmpr data
smoother.default | Smooth swmpr data
smoother.swmpr | Smooth swmpr data
stat_locs | Locations of NERRS sites
subset.swmpr | Subset a swmpr object
swmpr | Create a swmpr object
time_vec | Format SWMP datetimestamp