This vignette describes summarizing and reporting dissolved
oxygen (DO) data for the Peconic Estuary. Three continuous USGS
monitoring stations collect DO data at locations in the Peconic Estuary:
USGS stations 01304562 in the Peconic River, 01304200 in Orient Harbor,
and 01304650 in Shelter Island Sound. Data at these stations can be
downloaded using the read_pepdo()
function.
exdat <- read_pepdo(site = c('01304562', '01304200', '01304650'),
nms = c('Peconic River', 'Orient Harbor', 'Shelter Island'),
startDate = '2020-06-01', endDate = '2020-06-30')
The dodat
data object included with the package provides
DO data from 2013 to 2023 at the three sites. This takes several minutes
to download using the read_pepdo()
function, so it is
included with the package for ease of use.
head(dodat)
#> site DateTime do_mgl
#> 1 Orient Harbor 2013-01-01 00:00:00 11.2
#> 2 Orient Harbor 2013-01-01 00:06:00 11.2
#> 3 Orient Harbor 2013-01-01 00:12:00 11.2
#> 4 Orient Harbor 2013-01-01 00:18:00 11.2
#> 5 Orient Harbor 2013-01-01 00:24:00 11.2
#> 6 Orient Harbor 2013-01-01 00:30:00 11.2
A plot of the raw data:
ggplot(dodat, aes(x = DateTime, y = do_mgl)) +
geom_point(size = 0.7) +
geom_hline(yintercept = 4.8, linetype = 'dashed', colour = 'red') +
geom_hline(yintercept = 3, linetype = 'dashed', colour = 'red') +
facet_wrap(~site, ncol = 1) +
theme_minimal() +
labs(
y = 'Dissolved oxygen (mg/L)',
x = NULL,
title = 'Dissolved oxygen at Orient Harbor, Peconic River, and Shelter Island',
subtitle = 'Dashed lines are chronic and acute threhsolds (4.8, 3 mg/L)'
)
Dissolved oxygen data typically show daily and seasonal variation. Summaries of condition should account for variation at both temporal scales. Further, the impact of low dissolved oxygen concentrations on biota can vary depending on both magnitude and duration of hypoxia/anoxia. As such, condition assessment should consider how often concentrations fall below a threshold and for how long. The assessments below speak to each of these needs.
First, the data can be summarized from the continuous (~6 minute
observations) to daily averages using the anlz_dodlpep()
function. A user-specified threshold can be supplied to the
thr
argument to summarize the data relative to a value of
interest, the default value being the acute threshold of 3 mg/L (an
alternative may be the chronic threshold of 4.8 mg/L, [1]).
# 3 mg/l is acute, 4.8 mg/l is chronic
dlysum <- anlz_dodlypep(dodat, thr = 3)
dlysum
#> # A tibble: 8,503 × 7
#> site Date yr mo do_mgl below below_cumsum
#> <fct> <date> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 Peconic River 2013-01-01 2013 1 11.0 0 0
#> 2 Peconic River 2013-01-02 2013 1 11.3 0 0
#> 3 Peconic River 2013-01-03 2013 1 11.6 0 0
#> 4 Peconic River 2013-01-04 2013 1 11.6 0 0
#> 5 Peconic River 2013-01-05 2013 1 11.7 0 0
#> 6 Peconic River 2013-01-06 2013 1 11.8 0 0
#> 7 Peconic River 2013-01-07 2013 1 12.0 0 0
#> 8 Peconic River 2013-01-08 2013 1 12.1 0 0
#> 9 Peconic River 2013-01-09 2013 1 12.0 0 0
#> 10 Peconic River 2013-01-10 2013 1 11.7 0 0
#> # ℹ 8,493 more rows
The last three columns show the daily summarized data. The
do_mgl
column shows the average DO concentration for each
day, the below
column shows a 1 (yes) or 0 (no) if the
concentration was below the threshold value at any point during a day,
and the below_cumsum
column shows a cumulative tally of the
number of days in each month at which dissolved oxygen fell below the
threshold at any point during a day. By default, the
anlz_dodlypep()
function will impute missing daily
dissolved oxygen values to the average for the year, month, site
combination. This is often necessary to create summary values that make
sense. For example, if a month has incomplete data, the maximum
below_cumsum
value will not show 30 or 31 days even if
every day in the observed record is below the threshold.
The data can also be summarized by month using the
anlz_domopep()
function. Summarizing by month distills the
information into a simple format for plotting. Internally, the
anlz_domopep()
function uses the
anlz_dodlypep()
function to first summarize results by day,
which are then summarized by month.
mosum <- anlz_domopep(dodat, thr = 3)
mosum
#> # A tibble: 280 × 6
#> site yr mo do_mgl below_ave below_maxrun
#> <fct> <dbl> <ord> <dbl> <dbl> <dbl>
#> 1 Peconic River 2013 Jan 11.6 0 0
#> 2 Peconic River 2013 Feb 11.9 0 0
#> 3 Peconic River 2013 Mar 11.7 0 0
#> 4 Peconic River 2013 Apr 9.55 0 0
#> 5 Peconic River 2013 May 7.90 0 0
#> 6 Peconic River 2013 Jun 5.73 0.3 5
#> 7 Peconic River 2013 Jul 3.12 0.871 11
#> 8 Peconic River 2013 Aug 3.13 0.774 15
#> 9 Peconic River 2013 Sep 4.81 0.633 6
#> 10 Peconic River 2013 Oct 6.03 0.258 7
#> # ℹ 270 more rows
The last three columns show the monthly summarized data, where
do_mgl
is the average of all daily DO averages across the
month, below_ave
is the proportion of days in a month when
concentrations in a given day fell below the threshold (1 would mean all
days had an instance of DO below the threshold, 0 would mean none), and
below_maxrun
is the maximum number of sequential days in a
month when concentrations in a given day fell below the threshold (30 or
31, depending on month, would indicate all days in a month had an
instance of DO below the threshold).
The below_ave
and below_maxrun
columns
summarize the DO data differently depending on how hypoxia/anoxia
conditions can be described relative to potential impacts on biological
resources. The below_ave
column summarizes undersaturation
relative to only the number of times hypoxia conditions occurred,
whereas the below_maxrun
column summarizes undersaturation
relative to both the number of instances and duration of hypoxia. In
other words, biota may be stressed differently depending on the number
of times hypoxia occurs vs how long it may persist. The two measures may
indicate similar information, but not always depending on
characteristics of the DO time series.
The summarized monthly data for a station can be plotted with the
show_domatrix()
function. In this example, the default plot
shows the proportion of days in a month when concentrations in a given
day fell below a threshold of 3 mg/L for the Peconic River station.
The maximum number of sequential days in a month when concentrations
in a given day fell below the threshold can also be plotted by changing
the show
argument.
The threshold can also be changed. For example, the chronic threshold of 4.8 mg/L shows conditions relative to a more conservative threshold.
Plotting the results provides insights into hypoxia patterns at the site depending on how under-saturated conditions were summarized. Additional considerations may include: