In sjbonner/shinyRMark: Shiny Interface for RMark

Preliminaries

## Load packages
library(RMark)
library(tidyverse)
library(devtools)

## Load package
devtools::load_all()

## Load data
data(wtsp)

Data Manipulations

1) Create capture histories

## Create capture histories
wtsp <- collapseCH(data=wtsp,prefix = "Time")

## Drop time variables
wtsp <- select(wtsp,-starts_with("Time"))

2) Process Data

## Process data
wtsp.processed <- process.data(wtsp, model="CJS", groups=c("SEX","TREATMENT"))

3) Generate Design Data

## Create default design data
wtsp.ddl <- make.design.data(wtsp.processed,
                             parameters = list(Phi=list(pim.type="time"),
                                               p=list(pim.type="time")))

Modelling

## Define formulas
fdot <- list(formula=~1)
ftreat <- list(formula=~TREATMENT)
ftime <- list(formula=~time)
ftreat.sex <- list(formula=~TREATMENT * SEX)

## Fit models

## 1) Phi{.},p{.}
model1 <- mark(wtsp.processed,
               ddl=wtsp.ddl,
               model.parameters = list(Phi=fdot,p=fdot),
               model.name = "Phi{.},p{.}")

model1$results$real

## 2) Phi{t},p{.}
model2 <- mark(wtsp.processed,
               ddl=wtsp.ddl,
               model.parameters = list(Phi=ftime,p=fdot),
               model.name = "Phi{time},p{.}")

model2$results$real

## 3) Phi{TREATMENT},p{.}
model3 <- mark(wtsp.processed,
               ddl=wtsp.ddl,
               model.parameters = list(Phi=ftreat,p=fdot),
               model.name = "Phi{TREATMENT},p{.}")

model3$results$real

## 4) Phi{TREATMENT*SEX},p{.}
model4 <- mark(wtsp.processed,
               ddl=wtsp.ddl,
               model.parameters = list(Phi=ftreat.sex,p=fdot),
               model.name = "Phi{TREATMENT*SEX},p{.}")

model4$results$real

## Compare models
collect.models()

sjbonner/shinyRMark documentation built on May 3, 2019, 9:39 p.m.