calc_iphc_ser_EF: Calculate Series EF and test if the scaled E and F are...

In pbs-assess/gfiphc: Data Extraction and Analysis for Groundfish Data from the IPHC Longline Survey in BC

Calculate Series EF and test if the scaled E and F are significantly different

Description

Calculate Series EF (Series E with 1995 and 1996 appropriately scaled from Series F)

Usage

calc_iphc_ser_EF(series_all, return_F_if_same_length = TRUE)

Arguments

series_all	List of tibbles, one for each of Series E and F, resulting from calc_iphc_ser_E_and_F()
return_F_if_same_length	logical to return Series F if Series E and F have the same number of years. User should check which is more suitable and then change this value if necessary (F uses all hooks but E includes 1995 and 1996)

Value

List containing

ser_longest: the longest time series possible from Series E and F,

test_EF: the results from the paired t-test, NULL if Series F is longest.

G_E, G_F: geometric means of nonzero values in Series E and Series F (based on bootstrapped means).

type: which type the longest series is, either EF, E, or F, based on the descriptions below.

Longest series is either

(i) Series EF (Series E with 1995 and 1996 appropriately scaled from Series F) if test_EF$p.value >= 0.05, because the p-value means that we cannot reject the null hypothesis that the true difference in means of the rescaled (by their geometric means) Series E and F equals 0,

(ii) Series E, which is the longest series available if the rescaled series are significantly different.

(iii) Series F, if the years for which only the first 20 hooks are enumerated never caught the species (but other years do). Then Series EF becomes Series E plus some zeros, so we may as well use Series F that uses all the hooks and so is more likely to catch the species. This is a rare situation (and likely arises because not all species were specifically identified in earlier years (or 2013?), but seems to occur for China Rockfish for Series AB analysis. Return NULL for t_EF (to then use later to identify that Series F is the longest series).

(iv) Series F (since all hooks) if E and F contain the same number of years, but user can change return_F_if_same_length as Series E may make more sense (since goes back to 1995). If E and F contain the same exact years then F is always returned.

See vignette for example.

Author(s)

Andrew Edwards

pbs-assess/gfiphc documentation built on July 4, 2023, 1:13 p.m.