an1_gain_loss: Compute gains and losses

In McCannLab/HomogenFishOntario: Analysis for study described in DOI: 10.1111/gcb.14829

Description

Filter data and compute gains and losses

Usage

an1_gain_loss(x, nocc = 10, min_year_AHI = 1965, max_year_AHI = 1982,
  rm_outlier = TRUE, verbose = FALSE)

Arguments

x	data set of observation see ?df_bsm_ahi.
nocc	Only species that have more than nocc occurrence are considered .
min_year_AHI	First year for AHI (see details below).
max_year_AHI	Last year for AHI (see details below).
rm_outlier	a logical. Should outlier be removed? Default is set to TRUE.
verbose	a logical. Should extra information be reported on progress? Default is set to TRUE.

Details

min_year_AHI and max_year_AHI are used to reproduce the analysis with a subset of the dataset as used in Fig. S3.

Value

A list of six elements:

• sf_bsm_ahi: a sf object including filtered data,

• gain_loss: gains and losses for all lakes,

• beta_AHI: beta diversity measure in AHI (historical survey),

• beta_BSM: beta diversity measure in BSM (contempory survey),

• nm_ahi: column names of ahi presence/absence columns in AHI,

• nm_bsm: column names of bsm presence/absence columns in BSM.

Examples

res0 <- an1_gain_loss(sf_bsm_ahi)

McCannLab/HomogenFishOntario documentation built on Nov. 20, 2021, 1:25 a.m.