ta_skeleton {adapt3}R Documentation

Create Skeleton Data Frame for Trait Variation for Invasion Analysis

Description

Function ta_skeleton() creates a core data frame that can be modified by users to provide the core variation in transition elements and vital rates to use in invasion analysis. The resulting data frame should be used as input in function invade3().

Usage

ta_skeleton(rows = 10L)

Arguments

rows

The number of rows needed in the data frame. Defaults to 10.

Value

A data frame of class adaptAxis, with the following columns:

variant

Denotes each variant in order, with each row corresponding to a novel variant.

stage3

Stage at occasion t+1 in the transition to be replaced.

stage2

Stage at occasion t in the transition to be replaced.

stage1

Stage at occasion t-1 in the transition to be replaced.

age3

Age at occasion t+1 in the transition to be replaced.

age2

Age at occasion t in the transition to be replaced.

eststage3

Stage at occasion t+1 in the transition to replace the transition designated by stage3, stage2, and stage1.

eststage2

Stage at occasion t in the transition to replace the transition designated by stage3, stage2, and stage1.

eststage1

Stage at occasion t-1 in the transition to replace the transition designated by stage3, stage2, and stage1.

estage3

Age at occasion t+1 in the transition to replace the transition designated by age2.

estage2

Age at occasion t in the transition to replace the transition designated by age2.

givenrate

A constant to be used as the value of the transition.

offset

A constant value to be added to the transition or proxy transition.

multiplier

A multiplier for proxy transitions or for fecundity.

convtype

Designates whether the transition from occasion t to occasion t+1 is a survival transition probability (1), a fecundity rate (2), or a fecundity multiplier (3).

convtype_t12

Designates whether the transition from occasion t-1 to occasion t is a survival transition probability (1), a fecundity rate (2).

surv_dev

A numeric vector giving the deviations to the y-intercept of the vital rate model for survival probability.

obs_dev

A numeric vector giving the deviations to the y-intercept of the vital rate model for observation probability.

size_dev

A numeric vector giving the deviations to the y-intercept of the vital rate model for primary size transition.

sizeb_dev

A numeric vector giving the deviations to the y-intercept of the vital rate model for secondary size transition.

sizec_dev

A numeric vector giving the deviations to the y-intercept of the vital rate model for tertiary size transition.

repst_dev

A numeric vector giving the deviations to the y-intercept of the vital rate model for reproduction probability.

fec_dev

A numeric vector giving the deviations to the y-intercept of the vital rate model for fecundity.

jsurv_dev

A numeric vector giving the deviations to the y-intercept of the vital rate model for juvenile survival probability.

jobs_dev

A numeric vector giving the deviations to the y-intercept of the vital rate model for juvenile observation probability.

jsize_dev

A numeric vector giving the deviations to the y-intercept of the vital rate model for juvenile primary size transition.

jsizeb_dev

A numeric vector giving the deviations to the y-intercept of the vital rate model for juvenile secondary size transition.

jsizec_dev

A numeric vector giving the deviations to the y-intercept of the vital rate model for juvenile tertiary size transition.

jrepst_dev

A numeric vector giving the deviations to the y-intercept of the vital rate model for juvenile reproduction probability.

jmatst_dev

A numeric vector giving the deviations to the y-intercept of the vital rate model for maturity status.

Examples


current_traits <- ta_skeleton(4)
current_traits$stage3 <- c("Dorm", "Dorm", "Sdl1", NA)
current_traits$stage2 <- c("cut", "V0r", "rep", NA)
current_traits$convtype <- c(1, 1, 2, NA)
current_traits$offset <- c(0.1, 0.2, 0.3, NA)
current_traits$surv_dev <- c(NA, NA, NA, 0.1)


[Package adapt3 version 1.0.1 Index]