bias_correct_regurgitated: Bias correct due to regurgitated stomachs

In MortenVinther/FishStomachs: Compilation of stomach contents data

Bias correct due to regurgitated stomachs

Description

Regurgitated stomachs are from feeding fish, but their actual absolute stomach contents (in the sea) are not known. Stomach contents from regurgitated stomachs are not analysed or included as data, however the number of regurgitated stomachs (n_regur) should be noted together with the number of stomachs with skeletal remains only (n_nskel) and the number of empty stomachs (n_empty). The bias correction assumes that the regurgitated stomachs have had the same stomach contents as the observed feeding fish (n_food).

Usage

bias_correct_regurgitated(
  stom,
  delete_just_regurgitated = TRUE,
  drop_variables,
  update_n_food_with_n_regur = TRUE
)

Arguments

stom	stomach contents data of class STOMobs.
delete_just_regurgitated	Delete stomachs where all stomachs within a sample_id and predator size class are regurgitated.
drop_variables	Names of variables for number of stomachs to be deleted from dataset. This includes combinations of 'n_food', 'n_regur', 'n_skel' and 'n_empty'. By default the variables 'n_food', 'n_regur', 'n_skel' and 'n_empty' will be deleted.
update_n_food_with_n_regur	Update number of stomachs with food (n_food) by the number of regurgitated stomachs (n_regur).

Details

Ideally each stomach should be classified as: with food, with food but regurgitated, with skeletal remains only or empty. This information is included in the presently used exchange format.

Variable	Comments
n_food	Stomachs with (recently ingested) food
n_regur	Stomach with food, but evidence of regurgitation of parts or all the stomach contents
n_skel	Stomachs with practically indigestible remains and the fish is not considered feeding recently
n_empt	No stomach contents

Stomach contents from regurgitated (or everted) stomachs should not be included in the estimation of diet as the proportion regurgitated is unknown. The number of fish with regurgitated stomachs may however be recorded ('n_regur'). With the assumption that the regurgitated stomachs sampled within 'sample_id' have had the same stomach contents as the feeding (non-regurgitated) fish each observed prey item weight and number can be corrected by a factor to calculate the mean stomach contents of a predator within a 'sample_id'.

The bias correction makes sense for stomach that have been pooled during sampling (e.g. the 1981 and 1991 North Sea sampling) or if several individually processed stomachs are aggregated into a group of stomachs to get the stomach contents for a group of fish (see aggregate_within_sample).

factor = \frac{(N_{food} + N_{regur})}{N_{food}*(N_{food} + N_{skel} + N_{regur} + N_{empt})}

Value

stomach contents data of class STOMobs, where the stomach contents per sample have been raised as it is assumed that the regurgitated stomach had the same stomach contents as the one with food (and no regurgitation).

Examples

## Not run: a <- bias_correct_regurgitated(stom=a,delete_just_regurgitated=TRUE,
          drop_variables=c('n_skel','n_empty', 'n_regur'))
## End(Not run)

MortenVinther/FishStomachs documentation built on Feb. 14, 2025, 7:33 a.m.