Convert rate value to absolute and/or mass-specific

Source: R/convert_rate.R

This is a conversion function. It can convert a dimensionless unit of rate, derived from calc_rate, calc_rate.ft, calc_rate.bg, auto_rate, or adjust_rate into volume-adjusted (i.e. to the container), VO2 or mass-specific (i.e. to the specimen mass), MO2 rate.

convert_rate(
  x,
  o2.unit = NULL,
  time.unit = NULL,
  output.unit = NULL,
  volume = NULL,
  mass = NULL,
  S = NULL,
  t = NULL,
  P = NULL
)

Arguments

x

numeric, or objects of class calc_rate(), calc_rate.ft(), auto_rate() or adjust_rate().
o2.unit

string. The dissolved oxygen unit of the data used to determine rate. Check unit_args().
time.unit

string. The time unit of the data used to determine rate. Check unit_args().
output.unit

string. The output unit to convert rate to. Check unit_args().
volume

numeric. Volume in litres. This is the volume of fluid in the respirometry chamber, not the specimen volume.
mass

numeric. Mass/weight in kg. This is the mass of the specimen if you wish to calculate mass-specific rates.
S

numeric. Salinity (ppt). Defaults to NULL. Used only in conversion of some units. See unit_args() for details.
t

numeric. Temperature(°C). Defaults to NULL. Used only in conversion of some units. See unit_args() for details.
P

numeric. Pressure (bar). Defaults to NULL. Used only in conversion of some units. If left NULL, default value of 1.013253 is applied in conversions. See unit_args() for details.

Value

A list object.

Details

Unless other values are specifically called as x, the function converts the primary $rate from calc_rate and auto_rate objects, the $corrected rate from adjust_rate objects, and the $mean rate from calc_rate.ft and calc_rate.bg objects. Values or vectors of other rates within these obects can be converted by calling them as x using $.

Note, for rates from flowthrough experiments, the volume and time inputs should be set with reference to the flow rate in L per unit time. E.g. for a flow rate in L/s volume = 1, time = "s". With these rates volume does NOT represent the volume of the respirometer, and time does NOT represent the resolution of the original data."

The function uses an internal database and a fuzzy string matching algorithm to accept various unit formatting styles.

For example, 'mg/l', 'mg/L', 'mgL-1', 'mg l-1', 'mg.l-1' are all the same. Use unit_args() to view a list of usable unit strings.

Output units (output.unit) must be in the sequence O2-Time (e.g. mg/h, mg-h) for absolute rates, and for mass-specific rates O2-Time-Mass (e.g. mg/h/kg).

Some units also require temperature (t), salinity (S), and atmospheric pressure (P) to be specified. See unit_args() for details. For freshwater experiments, salinity should be set to zero (i.e. S = 0).

Examples

# Manually enter values
convert_rate(7.5, o2.unit = 'mg/l', time.unit = 's',
  output.unit = 'mg/min/kg', volume = 1.2, mass = 0.5)

#> Error in convert_rate(7.5, o2.unit = "mg/l", time.unit = "s", output.unit = "mg/min/kg",     volume = 1.2, mass = 0.5): could not find function "convert_rate"

# Use example data
data("sardine.rd")

#> Warning: data set ‘sardine.rd’ not found
x <- calc_rate(sardine.rd, from = 200, to = 1800, by = "time")

#> Error in calc_rate(sardine.rd, from = 200, to = 1800, by = "time"): could not find function "calc_rate"
convert_rate(x, o2.unit = '%', time.unit = 's',
  output.unit = 'mg/h/g', volume = 12.3, mass = 0.05,
  S =35, t = 15, P = 1.013)

#> Error in convert_rate(x, o2.unit = "%", time.unit = "s", output.unit = "mg/h/g",     volume = 12.3, mass = 0.05, S = 35, t = 15, P = 1.013): could not find function "convert_rate"