spp_master: Master Species-Level Data

In rBatt/trawlDiversity: Long-term changes in species richness along the North American coastline

Description

Master data set of species time series related to colonization, extinction, richness, MSOM results, and environmental values.

Usage

spp_master

Format

data.table

Details

reg	character	region code
spp	character	species scientific name
year	integer	sampling year
detect_mu	numeric	mean of posterior of species-specific detection parameter for the current year-model
detect_sd	numeric	standard deviation of posterior of species-specific detection parameter
col	integer	0 or 1, 1 indicates that the species colonized the region this year (was absent in previou sampling year)
ext	integer	0 or 1, 1 indicates that the species will be absent in following sampling year
present	integer	0 or 1, 1 indicates that the species is present in the region in current year
now_ext	integer	0 or 1, 1 indicates that the species is absent this year, but was present in previous sampling year
cumm_yrs_pres	integer	number of sampling years that the species has been seen up to (and including) this year
consec_yrs_pres	integer	number of consecutive sampling years that the species has been observed
yrs_since_1st	integer	number of sampling events (including current) since species was first observed
ext_dist, ext_dist_sign, ext_dist_samp	integer (possibly numeric)	see event_distance; _samp is sampling years elapsed, others are actual years elapsed
propStrata	numeric	proportion of strata that the species was observed to occupy in current sampling year
bt_ann	numeric	cross-stratum average of bottom temperature in current sampling year; not a species-specific value (is same for all species in that region-year)
has_stretches	logical	indicates whether or not this spp-year-reg is part of a stretch of presences that is flanked (on at least 1 side) by an absence
stretch_id, hybrid_part	integer	see event_stretches
stretch_type	character	"post_col" for post-colonization stretch, "pre_ext" for pre-extinction stretch
event_year	integer	the year of the closest absence, all years in the same stretch have the same event_year
stretch_length	integer	number of sampling years included in the current stretch
bt_opt, bt_tol, prob_max	numeric	optimum bottom temperature and bottom temperature tolerance; presence probability at optimum (see response_metrics)
depth_base_opt	numeric	median depth of strata that are in the top 95% of strata ranked by estimated probabilities of occurrence for the species; needed so that prob_max can be calculated, as depth needs to be part of the intercept
btemp_ODS	numeric	ODS is optimal depth strata; average bottom temperature in the strata used in depth_base_opt
nODS	integer	number of ODS
bt_opt_avg, bt_tol_avg, detect_mu_avg	numeric	cross-year average of this species' (in this region) bt_opt, bt_tol, detect_mu
ce_categ	character	colonization/extinction category; neither means present every year, colonizer means colonized only, leaver means went extinct only, both means has both types of events

See Also

comm_master, mapDat

rBatt/trawlDiversity documentation built on Aug. 14, 2021, 1:01 p.m.