Here we describe the various functions within the
afscISS package that obtain results provided from the
surveyISS package.
The primary result that is provided by the afscISS
package is the annual input sample size (ISS) for age, length, or
conditional age-at-length composition data by survey region; this is
provided by the afscISS::get_ISS() function. The following
is an example for standard age composition ISS for GOA Pacific cod:
afscISS::get_ISS(species = 21720,
region = 'goa',
comp = 'age',
sex_cat = 4,
spec_case = NULL)The species argument in the
afscISS::get_ISS() function is the RACE species code for
your species.
The region argument in the
afscISS::get_ISS() function is the survey region for which
you desire the ISS. Currently there are 5 survey regions, described in
the following table:
| region | Description |
|---|---|
| ai | Aleutian Islands survey region |
| ebs | Eastern Bering Sea survey region |
| ebs_slope | Eastern Bering Sea slope survey region |
| goa | Gulf of Alaska survey region |
| nebs | Combined Northern and Eastern Bering Sea survey regions |
The comp argument in the afscISS::get_ISS()
function is the composition type for which you desire ISS. There are 3
options: age for age composition, length for
length composition, and caal for conditional age-at-length
composition.
The sex_cat argument in the
afscISS::get_ISS() function is the sex category for the
specific composition data for which you are obtaining ISS output. There
are 5 options, described in the following table:
| sex_cat | Description |
|---|---|
| 0 | Combined sex categories (females + males + unsexed) that are combined prior to computation of composition |
| 1 | Male composition |
| 2 | Female composition |
| 12 | Female-Male composition that sums to 1 across both sexes (rather than sum to 1 across Females or Males only) |
| 4 | Combined sex categories (females + males + unsexed) that are combined after the computation of composition. Note that this is the historical standard for combined sex composition data at AFSC. Also note that there is no sex category of 4 for conditional age-at-length data, as it is equivalent to sex category 0. |
Finally, the spec_case argument in the
afscISS::get_ISS() function specifies whether you desire
ISS for a special case function within the surveyISS
package. There are three general categories of special cases: (1) stock
complex special cases, (2) spatially-explicit special cases, and (3)
length binning special case (note that the first two special cases only
pertain the the AI and GOA survey regions). The stock complex special
cases include:
| spec_case | Description |
|---|---|
| bsre | Provides output for the AI Blackspotted-Rougheye stock complex (where length pop’n computed for each individual species but age pop’n computed for the complex as a whole). |
| dr | Provides output for the GOA dusky rockfish stock. |
| rebs | Provides output for the GOA Rougheye-Blackspotted stock complex (where length and age pop’n are computed for each individual species and summed post-expansion). |
Note that for the bsre, dr, and
rebs special cases, the species argument is
not needed (so you can either leave this argument out or define it as
NULL), as a special species code has already been defined (as an
agglomeration of the individual species codes). Also note for that these
stock complex special cases are not included in the spatially-explicit
special cases. The spatially-explicit special cases are as follows:
| spec_case | Description |
|---|---|
| ai_subreg | Provides output for age/length composition (but not caal) computed at the sub-region scale within the AI survey region (and will also provide output for the combined values at the overall AI region). |
| w140 | Provides output for age/length composition (but not caal) computed for the GOA survey region west of 140 longitude (currently only computed for the GOA walleye pollock stock). |
| w_c_egoa | Provides output computed for the Western, Central, and Eastern GOA survey regions (and will also provide output for the combined values at the overall GOA region). |
| wc_egoa | Provides output computed for the Western-Central GOA (combined), and Eastern GOA survey regions (and will also provide output for the combined values at the overall GOA region). |
Finally, the length binning special case allows for custom length bins other than at 1 cm (which is the default setting). Note that providing output for this case is still under construction (in terms of providing standard output from this package) and if you want to explore alternative length bins please contact us and we’ll set up custom output for you.
The output that will return from the afscISS::get_ISS()
function will include the following columns:
| Column | Description |
|---|---|
| year | Survey year. |
| species_code | RACE species code. |
| sex | Numerical value for sex category (described in table above). |
| sex_desc | Text string with short description of sex category. |
| iss | Input sample size. |
| sd_iss | Standard deviation of input sample size (derived as the SD of a harmonic mean using the delta method). |
| nss* | Nominal sample size (the number of age/length samples collected). |
| nhl | Number of hauls from which samples were collected. |
*in the eastern bering sea survey region there is a juvenile/adult expansion that occurs within the length frequency data prior to the design-based expansion (further details can be found in this gapindex issue), thus, the nominal sample size in some cases (e.g., pollock) reported in this output will not be the actual numbers of fish lengthed, but will be much larger. We note that this will have minimal (if any) impact on the resulting input sample size as previous experiments (Hulson et al. 2024) have shown that (1) length samples greater than 250 per haul have little influence on the resulting length composition input sample size (i.e., reducing from 10k expanded length samples to 500 actual samples withing a haul will have negligible impact), and (2) age composition input sample size was stable across a range of lengths sampled within a haul.
The afscISS::get_popn() function obtains the
design-based expanded population at age or length values (will also
provide the design-based mean and sd in length-at-age when obtaining age
output). This output replicates what is provided in the GAP_PRODUCTS
tables, with the exception of the special cases implemented in the
surveyISS package that are not available in the
gapindex package. Note that the sex_cat
arguments for this function are 0 (sexes combined pre-expansion), 1
(males), 2 (females), 3 (unsexed), and 4 (sexes combined post-expansion)
and does not include sex_cat argument of 12 (as those
results are provided in this case for sex_cat 1 and 2
individually). The output that will return from the
afscISS::get_popn() function for comp = 'age'
will include the following columns:
| Column | Description |
|---|---|
| year | Survey year. |
| species_code | RACE species code. |
| sex | Numerical value for sex category. |
| age | Age. |
| agepop | Design-based expanded population numbers for age. |
| mean_length | Design-based computed mean length-at-age. |
| sd_length | Design-based computed standard deviation in length-at-age. |
The output that will return from the afscISS::get_popn()
function for comp = 'length' will include the following
columns:
| Column | Description |
|---|---|
| year | Survey year. |
| species_code | RACE species code. |
| length | Length in cm. |
| sex | Numerical value for sex category. |
| abund | Design-based expanded population numbers for length. |
The afscISS::get_comp() function obtains the computed
age, length, and conditional age-at-length composition from design-based
population estimates (i.e., the proportions that would be used in a
stock assessment model). The output that will return from the
afscISS::get_comp() function for comp = 'age'
and comp = 'length' will include the following columns:
| Column | Description |
|---|---|
| year | Survey year. |
| species_code | RACE species code. |
| sex | Numerical value for sex category. Note that when
sex_cat = 12 this will return values of 1 (males) and 2
(females) in the sex column where the proportions will sum to 1 across
both sexes. |
| age/length | Age or length (in cm). |
| prop | Proportion at age or length. |
| q2_5th | 2.5th percentile in the bootstrapped proportion at age or length. |
| q97_5th | 97.5th percentile in the bootstrapped proportion at age or length. |
The output that will return from the afscISS::get_comp()
function for comp = 'caal' will include the following
columns:
| Column | Description |
|---|---|
| year | Survey year. |
| species_code | RACE species code. |
| sex | Numerical value for sex category. Note that the only
sex_cat arguments available for comp = 'caal'
are 0 (combined sexes), 1 (males), and 2 (females). |
| length | Length in cm. |
| age | Age. |
| caal | Proportion at age within given length. |
| q2_5th | 2.5th percentile in the bootstrapped proportion at age within given length. |
| q97_5th | 97.5th percentile in the bootstrapped proportion at age within given length. |
The afscISS::get_bias() function obtains the average
bias in the bootstrap simulated age/length/conditional age-at-length.
The output that will return from the afscISS::get_bias()
function for comp = 'age' and comp = 'length'
will include the following columns:
| Column | Description |
|---|---|
| year | Survey year. |
| species_code | RACE species code. |
| sex | Numerical value for sex category. |
| bias | Average bias in composition across age/length. |
The output that will return from the afscISS::get_bias()
function for comp = 'caal' will include the same columns as
comp = 'age' or comp = 'length', with an
additional column for length (in cm) to reflect that the bias column is
the average bias in composition across age within given length. Note
that the only sex_cat arguments available for
comp = 'caal' are 0 (combined sexes), 1 (males), and 2
(females).