vignettes/convert_DO.Rmd
convert_DO.RmdDifferent oxygen probe systems output oxygen values in many different units of concentration or partial pressure, or even in a proportional unit such as relative percentage of dissolved air or oxygen. For example, it is very common to use water that has been 100% saturated with air through vigorous bubbling, mixing or stirring as the starting value of 100%, with percent saturation recorded as it declines, the assumption being this is the oxygen being removed by the specimen.
The convert_DO() function allows you to convert between
any commonly used unit of oxygen concentration, partial pressure, or
percent air or oxygen saturation.
Some unit conversions require temperature, salinity, and atmospheric
pressure inputs in order to do conversions. The first two of these must
be entered if they are required. For the atmospheric pressure input
(P), a default value of 1.013 bar (standard pressure at sea
level) is applied if not entered. In most locations which have a normal
range (outside of extreme weather events) of around 20 millibars, any
variability in pressure will have a relatively minor effect on dissolved
oxygen, and even less on calculated rates. However, we would encourage
users to enter the true value if they know it, or use historical weather
data to find out what it was on the day of the experiment.
Concentration units should be formatted as oxygen amount per unit
volume or mass in SI units (L or kg) for the denominator. For example,
ml/kg or mg/L. A range of different pressure
units are also available. See unit_args() for the various
units that are accepted.
The sardine.rd dataset has oxygen values in percent air
saturation, and the accompanying help file,
help("sardine.rd"), contains the temperature, salinity and
atmospheric pressure inputs to allow it to be converted.
sardine.rd
#> Time Oxygen Temperature
#> <int> <num> <num>
#> 1: 0 95.6 15.192
#> 2: 1 95.6 15.199
#> 3: 2 95.6 15.203
#> 4: 3 95.6 15.193
#> 5: 4 95.6 15.200
#> ---
#> 7509: 7508 90.0 15.106
#> 7510: 7509 90.1 15.106
#> 7511: 7510 90.1 15.106
#> 7512: 7511 90.2 15.109
#> 7513: 7512 90.3 15.099We will convert it to umol/kg. In
convert_DO, the t, S and
P inputs must be in °C, ppt (‰), and bar.
conv <- convert_DO(sardine.rd$Oxygen, # data to convert
from = "%Air", # oxygen unit to convert from
to = "umol/kg", # oxygen unit to convert to
t = 15, # in C
S = 35, # in ppt
P = 1.013) # in bar
head(conv)
#> [1] 236.5437 236.5437 236.5437 236.5437 236.5437 236.5437By default the function outputs a numeric vector of converted values, which can be saved as it’s own object. In this case we will add it to the original data frame.
sardine_new <- cbind(sardine.rd,
umol_kg = conv)
sardine_new
#> Time Oxygen Temperature umol_kg
#> <int> <num> <num> <num>
#> 1: 0 95.6 15.192 236.5437
#> 2: 1 95.6 15.199 236.5437
#> 3: 2 95.6 15.203 236.5437
#> 4: 3 95.6 15.193 236.5437
#> 5: 4 95.6 15.200 236.5437
#> ---
#> 7509: 7508 90.0 15.106 222.6876
#> 7510: 7509 90.1 15.106 222.9350
#> 7511: 7510 90.1 15.106 222.9350
#> 7512: 7511 90.2 15.109 223.1824
#> 7513: 7512 90.3 15.099 223.4299Alternatively, if simplify = FALSE the output is a
list object which can be used with print for a
convenient summary output.
conv <- convert_DO(sardine.rd$Oxygen, # data to convert
from = "%Air", # oxygen unit to convert from
to = "umol/kg", # oxygen unit to convert to
t = 15, # in C
S = 35, # in ppt
P = 1.013, # in bar
simplify = FALSE) # output vector of values
print(conv)
#>
#> # print.convert_DO # --------------------
#> Showing only the first 20 conversions:
#>
#> Input values:
#> [1] 95.6 95.6 95.6 95.6 95.6 95.6 95.6 95.5 95.5 95.5 95.6 95.6 95.5 95.5 95.6 95.6 95.6 95.4 95.6 95.6
#> Output values:
#> [1] 236.5437 236.5437 236.5437 236.5437 236.5437 236.5437 236.5437 236.2963 236.2963 236.2963 236.5437 236.5437 236.2963 236.2963 236.5437 236.5437 236.5437 236.0488 236.5437 236.5437
#>
#> Input unit: %Air
#> Output unit: umol/kg
#> -----------------------------------------Note the difference between percent air saturation
(%Air), where air saturated water is ~100%, and percent
oxygen saturation (%Oxy), where air saturated water is
~20.946% oxygen saturated. In other words,
%Oxy = %Air * 0.20946. Some oxygen probe systems output in
both units, or tend to use one over the other, so take care not to
confuse them.
convert_DO(100, "%Air", "%Oxy",
t = 15,
S = 35,
P = 1.013)
#> [1] 20.946convert_DO can also convert between units of oxygen
partial pressure. We will add a column of the same oxygen values in
hectopascals, converting from the umol/kg column we just
added.
sardine_new$hPa <- convert_DO(sardine_new$umol_kg,
from = "umol per kg",
to = "hPa",
t = 15,
S = 35,
P = 1.013)
sardine_new
#> Time Oxygen Temperature umol_kg hPa
#> <int> <num> <num> <num> <num>
#> 1: 0 95.6 15.192 236.5437 202.1883
#> 2: 1 95.6 15.199 236.5437 202.1883
#> 3: 2 95.6 15.203 236.5437 202.1883
#> 4: 3 95.6 15.193 236.5437 202.1883
#> 5: 4 95.6 15.200 236.5437 202.1883
#> ---
#> 7509: 7508 90.0 15.106 222.6876 190.3446
#> 7510: 7509 90.1 15.106 222.9350 190.5561
#> 7511: 7510 90.1 15.106 222.9350 190.5561
#> 7512: 7511 90.2 15.109 223.1824 190.7676
#> 7513: 7512 90.3 15.099 223.4299 190.9791Note how the from unit is formatted differently but
still recognised. Unit conversions in respR use a
forgiving, fuzzy algorithm to recognise different variations of unit
strings.
For quick conversions, convert_DO also accepts single
values. These particular units here do not require temperature, salinity
and pressure.
convert_DO(8,
"mg/L",
"mmol/L")
#> [1] 0.2500094respR has a convenient helper function to assist with
convert_DO (and convert_rate()) where certain
inputs such as temperature or atmospheric pressure have to be in
specific units.
convert_val() will convert between units of temperature,
volume, mass, area, and atmospheric pressure. The utility of using it
here is that it will by default convert to the required units for the
relevant convert_DO input.
Let’s say we have been reading an old paper and want to convert an
oxygen value in ml/L to mg/L, and the
temperature and atmospheric pressure values are in Fahrenheit and Torr.
For the t and P inputs in
convert_DO these must be in °C and bar. We could easily go
to an online converter to do this, but convert_val can help
do it right within the convert_DO function call.
convert_DO(4.6,
from = "ml/L",
to = "mg/L",
t = convert_val(65, from = "F"), # needs to be in C
S = 30,
P = convert_val(775, from = "Torr"), # needs to be in bar
simplify = FALSE)
#>
#> # print.convert_DO # --------------------
#>
#> Input values:
#> [1] 4.6
#> Output values:
#> [1] 6.282206
#>
#> Input unit: mL/L
#> Output unit: mg/L
#> -----------------------------------------Notice two convenient aspects:
We don’t need to tell convert_val what parameter
(temperature, pressure, etc.) the value is a measurement of -
it is recognised automatically using the from
unit.
We don’t need to specify a to unit (although it’s
possible to). The defaults for these are the required input units, that
is °C and bar.
The convert_val() function can also be used for general
conversions of temperature, volume, mass, area, and atmospheric pressure
in many common units:
convert_val(0, from = "C", to = "K")
#> [1] 273.15
convert_val(1, from = "L", to = "ml")
#> [1] 1000
convert_val(10000, from = "mg", to = "kg")
#> [1] 0.01
convert_val(0.0077, from = "m2", to = "mm2")
#> [1] 7700
convert_val(775, from = "Torr", to = "mbar")
#> [1] 1033.251See also convert_rate() where convert_val
can be used in a similar way with the volume,
mass, and area inputs.