Convert age, length, or generalized size composition data from wide to long format.
Usage
comp2long(x, ...)
age2long(x, expand = FALSE, zero = TRUE)
size2long(x, measure = NULL, zero = TRUE)Arguments
- x
A data frame containing age, length, generalized size composition data, or a list containing such a data frame.
- ...
Passed to
age2longorsize2long.- expand
Whether to repeat recurring entries in the resulting data frame, so that the
freqcolumn is1for every entry.- zero
Whether zero frequencies should be included in the output.
- measure
An optional string indicating the type of measurement, e.g.,
"weight".
Details
The age2long function converts age compositions and size2long
converts length or generalized size compositions. Alternatively, the wrapper
function comp2long converts any composition data and will call either
age2long or size2long, depending on the data type of x.
If x is not a data frame, the function will look for a data frame
inside the list: first lencomp, then agecomp, and then
sizefreq_data_list[[1]].
The expand = TRUE option is mainly useful for accessing conditional
age-at-length, e.g., to produce a data frame that has the same number of rows
as the number of otoliths.
Note
In r4ss input data objects, age composition data are stored as
agecomp, length composition data as lencomp, and generalized
size composition data as sizefreq_data_list[[i]].
See also
SS_read and SS_readdat read composition data from
files into r4ss list objects.
Examples
# Read composition data from example model
path <- system.file("extdata", "simple_small", package = "r4ss")
inputs <- SS_read(path)
dat <- SS_readdat(file.path(path, "data.ss"), verbose = FALSE)
x <- dat[["lencomp"]]
y <- dat[["agecomp"]]
# Main argument can be a list or data frame
head(comp2long(inputs))
#> year month fleet sex part Nsamp length freq
#> 1 2011 7 1 f 0 50 26 0
#> 2 2011 7 1 f 0 50 28 0
#> 3 2011 7 1 f 0 50 30 0
#> 4 2011 7 1 f 0 50 32 0
#> 5 2011 7 1 f 0 50 34 0
#> 6 2011 7 1 f 0 50 36 0
head(comp2long(dat))
#> year month fleet sex part Nsamp length freq
#> 1 2011 7 1 f 0 50 26 0
#> 2 2011 7 1 f 0 50 28 0
#> 3 2011 7 1 f 0 50 30 0
#> 4 2011 7 1 f 0 50 32 0
#> 5 2011 7 1 f 0 50 34 0
#> 6 2011 7 1 f 0 50 36 0
head(comp2long(x))
#> year month fleet sex part Nsamp length freq
#> 1 2011 7 1 f 0 50 26 0
#> 2 2011 7 1 f 0 50 28 0
#> 3 2011 7 1 f 0 50 30 0
#> 4 2011 7 1 f 0 50 32 0
#> 5 2011 7 1 f 0 50 34 0
#> 6 2011 7 1 f 0 50 36 0
head(comp2long(y))
#> year month fleet sex part ageerr Lbin_lo Lbin_hi Nsamp age freq
#> 1 2011 7 1 f 0 2 1 -1 25 1 0
#> 2 2011 7 1 f 0 2 1 -1 25 2 1
#> 3 2011 7 1 f 0 2 1 -1 25 3 0
#> 4 2011 7 1 f 0 2 1 -1 25 4 0
#> 5 2011 7 1 f 0 2 1 -1 25 5 0
#> 6 2011 7 1 f 0 2 1 -1 25 6 2
# Rename second to last column
head(comp2long(x, measure = "weight"))
#> year month fleet sex part Nsamp weight freq
#> 1 2011 7 1 f 0 50 26 0
#> 2 2011 7 1 f 0 50 28 0
#> 3 2011 7 1 f 0 50 30 0
#> 4 2011 7 1 f 0 50 32 0
#> 5 2011 7 1 f 0 50 34 0
#> 6 2011 7 1 f 0 50 36 0
# Shrink output by omitting zero frequencies
nrow(comp2long(x))
#> [1] 800
nrow(comp2long(x, zero = FALSE))
#> [1] 418
nrow(comp2long(y))
#> [1] 480
nrow(comp2long(y, zero = FALSE))
#> [1] 256
# Expand output by repeating recurring entries
nrow(comp2long(y, expand = TRUE))
#> [1] 400
# Aggregate by sex
aggregate(freq~sex, comp2long(x), sum)
#> sex freq
#> 1 f 408
#> 2 m 392
aggregate(freq~sex, comp2long(y), sum)
#> sex freq
#> 1 f 216
#> 2 m 184