| gasfluxes {gasfluxes} | R Documentation |
Flux calculation
Description
A wrapper function for convenient flux calculation.
Usage
gasfluxes(
dat,
.id = "ID",
.V = "V",
.A = "A",
.times = "time",
.C = "C",
methods = c("linear", "robust linear", "HMR", "NDFE"),
k_HMR = log(1.5),
k_NDFE = log(0.01),
verbose = TRUE,
plot = TRUE,
select,
maxiter = 100,
...
)
Arguments
dat |
a data.frame or data.table with data from flux measurements. |
.id |
character vector specifying the columns to be used as ID, multiple ID columns are possible. |
.V |
character specifying the column containing chamber volume values. |
.A |
character specifying the column containing chamber area values. |
.times |
character specifying the column containing chamber closing time values. |
.C |
character specifying the column containing concentration values. |
methods |
character; which methods to use for flux estimation. See details for available methods. |
k_HMR |
starting value for |
k_NDFE |
starting value for |
verbose |
logical; print progress messages? |
plot |
create a PDF with plots in the working directory if |
select |
deprecated; please use function |
maxiter |
see |
... |
further parameters |
Details
Available methods are
| "linear": | lin.fit |
| "robust linear": | rlin.fit |
| "HMR": | HMR.fit |
| "NDFE": | NDFE.fit |
Specifying other methods results in an error.
The default starting values for "HMR" and "NDFE", k = log(\kappa) and k = log(\tau), resp., assume that time is in hours. If you use a different time unit, you should adjust them accordingly.
Note that nls is used internally by these functions and thus they should not be used with artificial "zero-residual" data.
The input data.frame or data.table should be in the following format:
serie V A time C 1: ID1 0.522625 1 0.0000000 0.3317823 2: ID1 0.522625 1 0.3333333 0.3304053 3: ID1 0.522625 1 0.6666667 0.3394311 4: ID1 0.522625 1 1.0000000 0.4469102 5: ID2 0.523625 1 0.0000000 0.4572708
However, more than one ID column are possible. E.g., the first ID column could be the plot and a second ID column could be the date. Keep in mind that the combination of IDs must be a unique identifier for each flux measurement.
Units of the output depend on input units. It's recommended to use [V] = m^3, [A] = m^2, [time] = h, [C] = [mass or mol]/m^3, which results in [f0] = [mass or mol]/m^2/h. Since all algorithms use V/A, A can be input as 1 and V as the chamber height.
Value
A data.table with the results of the flux calculation. See the documentation of the fitting functions for details. If a selection algorithm has been specified, the last columns are the selected flux estimate, the corresponding standard error and p-value and the method with which the selected flux was estimated.
See Also
selectfluxes for flux selection
Examples
## Not run:
#compare result of original HMR with plinear HMR
data(fluxMeas)
res <- gasfluxes(fluxMeas[1:400,],
.id = "serie", .V = "V", .A = "A",
.times = "time", .C = "C",
methods = c("HMR"), verbose = TRUE)
#number of successful fits
res[, sum(!is.na(HMR.kappa))]
res <- gasfluxes(fluxMeas,
.id = "serie", .V = "V", .A = "A",
.times = "time", .C = "C",
methods = "HMR", verbose = TRUE)
# Error: time not sorted in flux ID ID556.
# Investigate the problem:
fluxMeas[serie %in% c("ID555", "ID556", "ID557")]
# serie V A time C
# 1: ID555 0.551625 1 0.0000000 0.3884388
# 2: ID555 0.551625 1 0.3333333 0.4125270
# 3: ID555 0.551625 1 0.6666667 0.3714207
# 4: ID555 0.551625 1 1.0000000 0.3735092
# 5: ID556 0.524250 1 0.0000000 0.3638239
# 6: ID556 0.524250 1 0.3333333 0.3520481
# 7: ID556 0.524250 1 0.6666667 0.3551644
# 8: ID557 0.528375 1 0.0500000 0.3954601
# 9: ID556 0.524250 1 0.0000000 0.3839834
#10: ID557 0.528375 1 0.3333333 0.3967269
#11: ID557 0.528375 1 0.6666667 0.3764967
#12: ID557 0.528375 1 1.0000000 0.3973055
# some mixup of IDs and times
# usually an input or Excel error during data preparation
# investigate and fix
## End(Not run)