SWMPr 2.1.0 on CRAN

I’ve just released an updated version of my package for estuary monitoring data, SWMPr, available on CRAN. I’ve made several additions to the package since it’s initial release – nothing too crazy but enough to warrant another push to CRAN and blog post. I’ve been pretty bad about regular updates but I’ve added a few features to make some of the functions easier to use in addition to some new functions for plotting SWMP data. I’ll start with a brief overview of the package then describe some of the major changes since the last release (2.0.0). As always, please keep a close watch on the GitHub repository for progress on the development version of the package.

What is SWMPr? SWMPr is an R package for estuary monitoring data from the National Estuarine Research Reserve System (NERRS). NERRS is a collection of reserve programs located at 28 estuaries in the United States. The System-Wide Monitoring Program (SWMP) was established by NERRS in 1995 as a long-term monitoring program to collect water quality, nutrient, and weather data at over 140 stations (more info here). To date, over 58 million records have been collected and are available online through the Centralized Data Management Office (CDMO). The SWMPr package provides a bridge between R and the data provided by SWMP (which explains the super clever name). The package is meant to augment existing CDMO services and to provide more generic features for working with water quality time series. The initial release included functions to import SWMP data from the CDMO directly into R, functions for data organization, and some basic analysis functions. The original release also included functions for estimating rates of ecosystem primary production using the open-water method.

# installing and loading the package
install.packages('SWMPr')
library(SWMPr)

What’s new in 2.1? A full list of everything that’s changed can be viewed here. Not all these changes are interesting (bugs mostly), but they are worth viewing if you care about the nitty gritty. The most noteworthy changes include the following.

• The overplot function can be used to plot multiple variables with identical scaling on the y-axis. I think this is generally discouraged under sound plotting theory (see the rants here), but overplotting is an often-requested feature regardless of popular opinion. I had to use the base graphics to write this function since it’s not possible with ggplot. I actually borrowed most of the code from a colleague at NERRS, shouts to the Grand Bay office. To illustrate ease of use…

# import data and do some initial clean up
data(apacpwq)
dat <- qaqc(apacpwq)

# a truly heinous plot
overplot(dat, select = c('depth', 'do_mgl', 'ph', 'turb'),
  subset = c('2013-01-01 0:0', '2013-02-01 0:0'), lwd = 2)

• The qaqc function now has more flexible filtering of QAQC data flags by using regular expression matching, rather than searching by integer flags as in the previous version. What this means is that observations can be filtered with greater control over what flags and errors are removed. This example shows how to remove flags using the old method as integer flags and using the new method. The second example will keep all flags that are annotated with the ‘CSM’ comment code (meaning check the metadata). The value with this approach is that not all integer flags are coded the same, i.e., QAQC flags with the same integer may not always have the same error code. The user may not want to remove all flags of a single type if only certain error codes are important.

# import data
data(apadbwq)
dat <- apadbwq

# retain only '0' and '-1' flags, as in the older version
newdat <- qaqc(dat, qaqc_keep = c('0', '-1'))

# retain observations with the 'CSM' error code
newdat <- qaqc(dat, qaqc_keep = 'CSM')

• Several of the data import functions were limited in the total number of records that could be requested from the CDMO. I made some dirty looping hacks so that most of these rate limitations, although technically still imposed, can be ignored when making large data requests to the CDMO. Previously, the single_param, all_params, and all_params_dtrng functions were limited to 100 records in a single request – not very useful for time series taken every 15 minutes. The new version lets you download any number of records using these functions, although be warned that the data request can take a long time for larger requests. As before, your computer’s IP address must be registered with the CDMO to use these functions.

• Although it’s now theoretically possible to retrieve all the SWMP data with the above functions, using the import_local function is still much, much easier. The main advantage of this function is that local data can be imported into R, which allows the user to import large amounts of data from a single request. The new release of SWMPr makes this process even easier by allowing data to be imported directly from the compressed, zipped data folder returned from the CDMO data request. The syntax is the same, but the full path including the .zip file extension must be included. As before, this function is designed to be used with data from the zip downloads feature of the CDMO.

# this is the path for the downloaded data files, zipped folder
path <- 'C:/this/is/my/data/path.zip'

# import the data
dat <- import_local(path, 'apaebmet')

• A nice feature in R documentation that I recently discovered is the ability to search for functions by ‘concept’ or ‘alias’ tags. I’ve described the functions in SWMPr as being in one of three categories based on their intended use in the data workflow: retrieve, organize, and analyze. The new version of SWMPr uses these categories as search terms for finding the help files for each function. The package includes additional functions not in these categories but they are mostly intended as helpers for the primary functions. As always, consult the manual for full documentation.

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

• Finally, I’ve added several default methods to existing SWMPr functions to make them easier to use outside of the normal SWMPr workflow. For example, combining time series with different time steps is a common challenge prior to data analysis. The comb function achieves this task for SWMP data, although using the previous release of the package on generic data was rather clunky. The new default method makes it easier to combine data objects with a generic format (data frames), provided a few additional arguments are provided so the function knows how to handle the information. Default methods were also added for the setstep, decomp, and decomp_cj functions.

I guarantee there are some bugs in this new release and I gladly welcome bug reports on the issues tab of the development repo. Ideas for additional features can also be posted. Please check out our SWMPrats web page for other SWMP-related analysis tools.

Cheers,

Marcus

SWMPr 2.0.0 now on CRAN

I’m pleased to announce that my second R package, SWMPr, has been posted on CRAN. I developed this package to work with water quality time series data from the System Wide Monitoring Program (SWMP) of the National Estuarine Research Reserve System (NERRS). SWMP was established in 1995 to provide continuous environmental data at over 300 fixed stations in 28 estuaries of the United States (more info here). SWMP data are collected with the general objective of describing dynamics of estuarine ecosystems to better inform coastal management. However, simple tools for processing and evaluating the increasing quantity of data provided by the monitoring network have complicated broad-scale comparisons between systems and, in some cases, simple trend analysis of water quality parameters at individual sites. The SWMPr package was developed to address common challenges of working with SWMP data by providing functions to retrieve, organize, and analyze environmental time series data.

The development version of this package lives on GitHub. It can be installed from CRAN and loaded in R as follows:

install.packages('SWMPr')
library(SWMPr)

SWMP data are maintained online by the Centralized Data Management Office (CDMO). Time series data describing water quality, nutrient, or weather observations can be downloaded for any of the 28 estuaries. Several functions are provided by the SWMPr package that allow import of data from CDMO into R, either through direct download through the existing web services or by local (import_local) or remote (import_remote) sources. Imported data are loaded as swmpr objects with several attributes following standard S3 object methods. The remaining functions in the package are used to organize and analyze the data using a mix of standard methods for time series and more specific approaches developed for SWMP. This blog concludes with a brief summary of the available functions, organized by category. As always, be sure to consult the help documentation for more detailed information.

I’ve also created two shiny applications to illustrate the functionality provided by the package. The first shiny app evaluates trends in SWMP data within and between sites using an interactive map. Trends between reserves can be viewed using the map, whereas trends at individual sites can be viewed by clicking on a map location. The data presented on the map were imported and processed using the import_local, qaqc, and aggregate functions. The second app provides graphical summaries of water quality, weather, or nutrient data at individual stations using the plot_summary function. Data were also processed with the import_local, qaqc, and aggregate functions.

SWMP trends map (click to access):

SWMP summary map (click to access):

SWMPr functions

Below is a brief description of each function in the SWMPr package. I’m currently working on a manuscript to describe use of the package in much greater detail. For now, please visit our website that introduced version 1.0.0 of the SWMPr package (check the modules tab).

Retrieve

all_params	Retrieve up to 100 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. Maximum of 1000 records. 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 up to 100 records for a single parameter starting with the most recent at a given station. Wrapper to exportSingleParamXMLNew function on web services.

Organize

comb.swmpr	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.swmpr	Remove QAQC columns and remove data based on QAQC flag values for a swmpr object. Only applies if QAQC columns are present.
qaqcchk.swmpr	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.swmpr	Remove replicate nutrient data that occur on the same day. The default is to average replicates.
setstep.swmpr	Format data from a swmpr object to a continuous time series at a given timestep. The function is used in comb.swmpr and can also be used with individual stations.
subset.swmpr	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.swmpr	Aggregate swmpr objects for different time periods – years, quarters, months, weeks, days, or hours. Aggregation function is user-supplied but defaults to mean.
aggremetab.swmpr	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.swmpr	Estimate ecosystem metabolism for a combined water quality and weather dataset using the open-water method.
decomp.swmpr	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.swmpr	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.swmpr	Plot a histogram for a swmpr object.
lines.swmpr	Add lines to an existing swmpr plot.
na.approx.swmpr	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.
plot.swmpr	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.
smoother.swmpr	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.
map_reserve	Create a map of all stations in a reserve using the ggmap package.
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.
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.
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.

Cheers,

Marcus