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README.Rmd
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---
output:
html_document:
keep_md: yes
toc: no
self_contained: no
pdf_document:
toc: yes
---
[](https://travis-ci.org/LimnoTech/SWMPrExtension)[](https://cran.r-project.org/package=SWMPrExtension)[](http://cran.rstudio.com/package=SWMPrExtension)
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "README-"
)
```
# Overview
The System Wide Monitoring Program ([SWMP](http://nerrs.noaa.gov/RCDefault.aspx?ID=18)) was implemented by the National Estuarine Research Reserve System ([NERRS](http://nerrs.noaa.gov/)) in 1995 to provide continuous monitoring data at over 140 continuous monitoring stations in 28 estuaries across the United States. SWMPrExtension (pronounced "swamper extension") is an R package that provides additional functions to organize and analyze SWMP data and is intended as a companion package for [SWMPr](https://github.com/fawda123/SWMPr) (pronounced "swamper"). Currently, there is no citation for SWMPrExtension.
[SWMPr](https://github.com/fawda123/SWMPr) is an R package for retrieving, organizing, and analyzing estuary monitoring data from SWMP. SWMPr can be cited 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:
```{r eval = F, message = F}
install.packages('SWMPrExtension')
library(SWMPrExtension)
```
Install the development (unstable) version from Github:
```{r eval = F, message = F}
install.packages('devtools')
library(devtools)
install_github('NOAA-OCM/SWMPrExtension')
library(SWMPrExtension)
```
# Using the package
Documentation for SWMPrExtension is currently in development.
A quick summary of the SWMPr package can be found [here](https://github.com/fawda123/SWMPr). A detailed manuscript describing full use of the SWMPr package is available from the [R Journal](https://journal.r-project.org/archive/accepted/beck.pdf). All source materials for the manuscript are available [here](https://github.com/fawda123/swmpr_manu).
SWMPrExtension adds several functions to existing concepts in SWMPr and introduces a new concept called "Reporting".
<h3>Analyze</h3>
The core analyses available within the SWMPrExtension R package and used to create the reserve level annual report fall into four general categories: boxplots and barplots, range plots, threshold plots, and trend plots. There is also an additional category called “mapping” which contains functions that generate many of maps associated with the reserve-level reports. The analyses, methods, and maps in this section were selected by and approved by a technical advisory committee composed of NERR research coordinators, SWMP technicians and CDMO staff.
<h4>Core Analyses</h4>
<table>
<tr><td><code>annual_range.swmpr</code></td><td>For a user-specified year, calculate averages, average ranges, and min/max observed ranges the on a monthly or seasonal basis.</td></tr>
<tr><td><code>historical_daily_range.swmpr</code></td><td>Compare a user-specified year against historical data on a daily basis.</td></tr>
<tr><td><code>historical_range.swmpr</code></td><td>Compare a user-specified year against historical data on a monthly/seasonal basis.</td></tr>
<tr><td><code>raw_boxplot.swmpr</code></td><td>Generate a monthly/seasonal boxplots of raw data for a target year.</td></tr>
<tr><td><code>seasonal_barplot.swmpr</code></td><td>Generate monthly/seasonal barplot for parameters that are better viewed in on a cumulative basis (e.g. precipitation).</td></tr>
<tr><td><code>seasonal_boxplot.swmpr</code></td><td>Generate monthly/seasonal boxplots for daily average statistics (min/average/max) across a user-specified time period.Includes the option to calculate a median value for a target year and include a line for a water quality threshold.</td></tr>
<tr><td><code>seasonal_dot.swmpr</code></td><td>Plot average/min/max seasonal values faceted by season.</td></tr>
<tr><td><code>sk_seasonal.swmpr</code></td><td>Seasonal Kendall non-parametric test for monotonic seasonal trends.</td></tr>
<tr><td><code>threshold_criteria_plot.swmpr</code></td><td>Compare raw data against user-specified water quality thresholds</td></tr>
<tr><td><code>threshold_identification.swmpr</code></td><td>Identify dates and times that a user-specified water quality threshold is exceeded. For continuous monitoring data, the user can also specify the length of time the threshold must be exceeded for the event to be included (e.g. DO must be < 2 mg/L for at least 2 hours).</td></tr>
<tr><td><code>threshold_percentile_plot.swmpr</code></td><td>Compare raw data against user-specified percentiles calculated from historical data. User has the option to calculate percentiles on a monthly basis.</td></tr>
<tr><td><code>threshold_summary.swmpr</code></td><td>Summarize the results from <code>threshold_identification</code> in either a plot or tabular format. Results can be aggregated on a monthly, seasonal, or annual basis.</td></tr>
</table>
<h4>Mapping</h4>
<table>
<tr><td><code>national_sk_map</code></td><td>Create a base map for NERRS reserves in ggplot with seasonal kendall results.</td></tr>
<tr><td><code>res_custom_map</code></td><td>Create a stylized reserve-level map of custom station locations for use with the reserve level reporting template.</td></tr>
<tr><td><code>res_custom_sk_map</code></td><td>Create a stylized reserve-level map of seasonal kendall results from custom station locations for use with the reserve level reporting template.</td></tr>
<tr><td><code>res_local_map</code></td><td>Create a stylized reserve-level map for use with the reserve level reporting template.</td></tr>
<tr><td><code>res_national_map</code></td><td>Create a base map for NERRS reserves in ggplot.</td></tr>
<tr><td><code>res_sk_map</code></td><td>Create a stylized reserve-level map of seasonal kendall results for use with the reserve level reporting template.</td></tr>
</table>
<h3>Retrieve</h3>
in the <code>SWMPr</code> package, retrieve functions help the user load SWMP data into R.
</br>
<table>
<tr><td><code>import_local_nut</code></td><td>A modified version of <code>import_local</code> from the <code>SWMPr</code> package. This version allows the user to specify the collection method (<code>CollMethd</code>) argument to separate monthly nutrient sampling data from monthly 24-hr nutrient sampling data.</td></tr>
</table>
<h3>Reporting</h3>
The new concept of reporting refers to functions that were specifically developed for use with NERRS reserve-level & national-level reporting scripts that are used to generate the reserve-level and national-level annual reports. They are included as part of this package in case users find them useful for their own purposes.
<h4>Reserve Level Template</h4>
<table>
<tr><td><code>create_sk_flextable_list</code></td><td>Create a list of <code>flextable</code> objects to display Seasonal Kendall results in the NERRS reserve level template.</td></tr>
<tr><td><code>geographic_unique_stations</code></td><td>Creates an alphabetically sorted, vector of geographically unique stations for mapping. Intended for use with <code>res_local_map</code>.</td></tr>
<tr><td><code>get_reserve</code></td><td>Return the full name of the reserve associated with the data files in the 'data' folder of the reserve level template.</td></tr>
<tr><td><code>get_shp_name</code></td><td>Return the name of the shape file associated with the data files in the 'data' folder of the reserve level template.</td></tr>
<tr><td><code>get_site_code</code></td><td>Return the 3 letter reserve code associated with the reserve.</td></tr>
<tr><td><code>get_site_coordinates</code></td><td>Return the station coordinates for stations associated with the data files in the 'data' folder of the reserve level template.</td></tr>
<tr><td><code>get_sites</code></td><td>Return the stations associated with the data files in 'data' folder of the reserve level template.</td></tr>
<tr><td><code>load_shp_file</code></td><td>Load and format shapefile for use with res_local_map.</td></tr>
</table>
<h4>National Level Template</h4>
<table>
<tr><td><code>create_sk_national_ft_reserves</code></td><td>Create a <code>flextable</code> of reserve names for use with the NERRS national level template.</td></tr>
<tr><td><code>create_sk_national_ft_results</code></td><td>Create a <code>flextable</code> object to display Seasonal Kendall results for each reserve in the NERRS national level template.</td></tr>
<tr><td><code>summarise_handoff_files</code></td><td>Summarise the seasonal kendall results from reserve level report hand-off files.</td></tr>
</table>
<h3>Miscellaneous</h3>
Miscellaneous functions are generally helper functions that are called internally by other analysis functions.
<h4>Analyze</h4>
<table>
<tr><td><code>assign_season</code></td><td>Assign seasons to SWMPr sampling data on a monthly basis or user-defined basis. Used by multiple analysis functions to group sampling data into user-defined seasons.</td></tr>
<tr><td><code>lm_p_labs</code></td><td>Generate a dataframe of p-value labels based on p-values from linear regression. Used internally by <code>seasonal_dot.swmpr</code> to add linear regression results to the plot.</td></tr>
<tr><td><code>set_date_break_labs</code></td><td>Select reasonable labels for breaks used in <code>scale_x_datetime</code>. Used internally by several analysis functions.</td></tr>
<tr><td><code>set_date_breaks</code></td><td>A helper function to select reasonable breaks for <code>scale_x_datetime</code>. Used internally by several analysis functions.</td></tr>
<tr><td><code>sk_tidy</code></td><td>Tidy results from <code>EnvStats::kendallSeasonalTrendTest</code>. Used by <code>sk_seasonal.swmpr</code> to tidy seasonal kendall test results.</td></tr>
<tr><td><code>std_param_check</code></td><td>Determine if a parameter is one of the standard SWMP parameters.</td></tr>
<tr><td><code>title_labeler</code></td><td>Generate a plot title based on SWMP station abbreviation. Used internally by several analysis functions.</td></tr>
<tr><td><code>y_count_labeler</code></td><td>Generate a y-axis label based on SWMP parameter abbreviation. Used internally by several analysis functions.</td></tr>
<tr><td><code>y_labeler</code></td><td>Generate a y-axis label based on SWMP parameter abbreviation and threshold criteria. Used internally by several analysis functions.</td></tr>
</table>
<h4>Mapping</h4>
<table>
<tr><td><code>reserve_locs</code></td><td>Create a dataframe of selected NERRS locations for plotting with <code>res_national_map</code>.</td></tr>
</table>
<h4>Reporting</h4>
<table>
<tr><td><code>ft_col_names</code></td><td>Convert <code>SWMPr</code> parameter abbreviations into formats appropriate for use with NERRS reserve level template <code>flextable</code>. Used internally by <code>create_sk_flextable_list</code>.</td></tr>
<tr><td><code>generate_results_table</code></td><td>Filters a <code>data.frame</code> of user-specified results for display in the NERRS reserve level report. Used internally by <code>create_sk_flextable_list</code>.</td></tr>
<tr><td><code>generate_station_table</code></td><td>Filters a <code>data.frame</code> of user-specified results for display in the NERRS reserve level report. Used internally by <code>create_sk_flextable_list</code>.</td></tr>
</table>
<h3>Datasets</h3>
The following data sets are included within the <code>SWMPrExtension</code> package. They are used for examples and for mapping.
</br>
<table>
<tr><td><code>cbm_spatial</code></td><td>A shapefile of the reserve boundary for Chesapeake Bay-Maryland NERR. Available from: <code>http://cdmo.baruch.sc.edu/</code>.</td></tr>
<tr><td><code>elk_spatial</code></td><td>A shapefile of the reserve boundary for Elkhorn Slough NERR. Available from: <code>http://cdmo.baruch.sc.edu/</code>.</td></tr>
<tr><td><code>elknmnut</code></td><td>Nutrient data (2007-2016) from North Marsh station at Elkhorn Slough NERR.</td></tr>
<tr><td><code>elksmwq</code></td><td>Water quality data (2007-2016) from South Marsh station at Elkhorn Slough NERR.</td></tr>
<tr><td><code>sampling_stations</code></td><td>Metadata on NERRS stations provided by the Central Data Management Office (CDMO) when data is downloaded. Additional formatting applied in order to make the dataset useful to several <code>SWMPrExtension</code> functions.</td></tr>
<tr><td><code>us_aea</code></td><td>US County boundaries from the US Census Bureau's MAF/TIGER geographic database, modified to remove non-ASCII characters. Reprojected using Albers Equal Area. Used to create national-level maps.</td></tr>
</table>