Description Usage Arguments Details Value See Also Examples
Get the aggregated kinetic data or the aggregation
settings used. (See do_aggr
for generating
aggregated data.)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ## S4 method for signature 'MOPMX'
aggr_settings(object, join = NULL)
## S4 method for signature 'OPMA'
aggr_settings(object, join = NULL)
## S4 method for signature 'OPMS'
aggr_settings(object, join = NULL)
## S4 method for signature 'MOPMX'
aggregated(object, ...)
## S4 method for signature 'OPMA'
aggregated(object, subset = NULL, ci = TRUE,
trim = c("no", "full", "medium"), full = FALSE, in.parens = TRUE,
max = opm_opt("max.chars"), ...)
## S4 method for signature 'OPMS'
aggregated(object, ...)
|
object |
|
subset |
Character vector. If not |
ci |
Logical scalar. Include the estimates of confidence intervals (CIs) in the output? |
trim |
Character scalar. Parameter estimates from intrinsically negative reactions (i.e., no respiration) are sometimes biologically unreasonable because they are too large or too small, and some corrections might be appropriate.
Currently the other parameters are not checked, and all
|
full |
Logical scalar passed to |
in.parens |
Logical scalar also passed to that function. |
max |
Numeric scalar also passed to that function. |
join |
Empty or character scalar. If empty, a list
is returned; a nested list in the case of
All other
values of |
... |
Optional arguments passed between the methods
or to |
Note that the conversion of the settings list to a matrix
or data frame might not work for all combinations of
object
and join
, mainly because the options
entry can hold arbitrary content. For similar conversions
of the metadata, see the OPMX
methods of
to_metadata
.
aggregated
yields a numeric matrix of aggregated
values (a.k.a. the curve parameters). If bootstrapping
was used, their CIs are included. The columns
represent the wells, the rows the estimated parameters
and their CIs.
aggr_settings
returns a named list if join
is empty. Other values yield a matrix or data frame (or
an error). See the description of the argument above and
the examples below for further details.
Other getter-functions: anyDuplicated
,
anyNA
, contains
,
csv_data
, dim
,
disc_settings
, discretized
,
duplicated
, has_aggr
,
has_disc
, hours
,
max
, measurements
,
minmax
, seq
,
subset
, thin_out
,
well
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 | # 'OPMA' methods
# Get full matrix
(x <- aggregated(vaas_1))[, 1:3]
stopifnot(is.matrix(x), dim(x) == c(12, 96))
(y <- aggregated(vaas_1, full = TRUE))[, 1:3] # full names
stopifnot(x == y, nchar(colnames(x)) < nchar(colnames(y)))
# Subsetting
(x <- aggregated(vaas_1, "lambda"))[, 1:3]
stopifnot(is.matrix(x), dim(x) == c(3, 96), any(x < 0))
# Now with lambda correction
(x <- aggregated(vaas_1, "lambda", trim = "full"))[, 1:3]
stopifnot(is.matrix(x), dim(x) == c(3, 96), !any(x < 0))
# settings
(x <- aggr_settings(vaas_1)) # yields named list
stopifnot(is.list(x), !is.null(names(x)))
(x <- aggr_settings(vaas_1, join = "json")) # yields a matrix
stopifnot(is.matrix(x), is.character(x), nrow(x) == 1)
# 'OPMS' methods
summary(x <- aggregated(vaas_4)) # => one matrix per OPM object
stopifnot(is.list(x), length(x) == length(vaas_4), sapply(x, is.matrix))
# settings
summary(x <- aggr_settings(vaas_4)) # list of named lists, one per plate
stopifnot(is.list(x), length(x) == length(vaas_4), sapply(x, is.list))
(x <- aggr_settings(vaas_4, join = "yaml")) # matrix, one row per plate
stopifnot(is.matrix(x), is.character(x), nrow(x) == 4)
|
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