CaribouBC

Caribou Population Forecasting

This fork is retired.

Please now refer to Wildlift application and Nagy-Reis et al. 2020.

Try the Shiny app or run locally as shiny::runGitHub("bcgov/CaribouBC", subdir = "inst/shiny/matpen").

Installation

Stable version:

remotes::install_github("bcgov/CaribouBC")

Development version is available as this fork:

remotes::install_github("psolymos/CaribouBC")

See user visible changes in the NEWS file.

Usage

library(CaribouBC)
#> Loading required package: popbio
#> CaribouBC 0.2.2   2019-10-17

## Predefined settings
(s1 <- caribou_settings("mat.pen"))
#> Caribou settings - pen type: mat.pen 
#> 
#>  - c.surv.wild   :0.163
#>  - c.surv.capt   :0.54
#>  - f.surv.wild   :0.853
#>  - f.surv.capt   :0.903
#>  - f.preg.wild   :0.92
#>  - f.preg.capt   :0.92
#>  - pen.cap       :35
#>  - pen.cost.setup:500
#>  - pen.cost.proj :80
#>  - pen.cost.maint:300
#>  - pen.cost.capt :250
#>  - pen.cost.pred :0
(s2 <- caribou_settings("pred.excl"))
#> Caribou settings - pen type: pred.excl 
#> 
#>  - c.surv.wild   :0.163
#>  - c.surv.capt   :0.72
#>  - f.surv.wild   :0.853
#>  - f.surv.capt   :0.95
#>  - f.preg.wild   :0.92
#>  - f.preg.capt   :0.92
#>  - pen.cap       :35
#>  - pen.cost.setup:1868
#>  - pen.cost.proj :80
#>  - pen.cost.maint:600
#>  - pen.cost.capt :200
#>  - pen.cost.pred :80

## Modifying predefined settings
caribou_settings("mat.pen", c.surv.capt=0.65, pen.cap=30)
#> Caribou settings - pen type: mat.pen 
#> 
#>  - c.surv.wild   :0.163
#>  - c.surv.capt   :0.65
#>  - f.surv.wild   :0.853
#>  - f.surv.capt   :0.903
#>  - f.preg.wild   :0.92
#>  - f.preg.capt   :0.92
#>  - pen.cap       :30
#>  - pen.cost.setup:500
#>  - pen.cost.proj :80
#>  - pen.cost.maint:300
#>  - pen.cost.capt :250
#>  - pen.cost.pred :0

## Forecast based on settings for 75% females penned
f1 <- caribou_forecast(s1, fpen.prop = 0.75)
f2 <- caribou_forecast(s2, fpen.prop = 0.75)

## Most important results summarized
summary(f1)
#> Caribou forecast - pen type: mat.pen 
#> 
#>  - tmax     :20
#>  - pop.start:100
#>  - fpen.prop:0.75
#> 
#>  - npens      :5
#>  - lam.pen    :1.02
#>  - lam.nopen  :0.914
#>  - Nend.nopen :17
#>  - Nend.pen   :163
#>  - Nend.diff  :146
#>  - Cost.total :56
#>  - Cost.percap:0.384
summary(f2)
#> Caribou forecast - pen type: pred.excl 
#> 
#>  - tmax     :20
#>  - pop.start:100
#>  - fpen.prop:0.75
#> 
#>  - npens      :16
#>  - lam.pen    :1.09
#>  - lam.nopen  :0.914
#>  - Nend.nopen :17
#>  - Nend.pen   :556
#>  - Nend.diff  :539
#>  - Cost.total :192
#>  - Cost.percap:0.356

## Plot the results
plot(f2)
lines(f1, col = 2)
legend("topleft", col = c(1,1,2), lty = c(2,1,1),
    legend = c("No pen", "Mat pen", "Pred excl"))


## Find 'breakeven' proportion of females penned where lambda=1
(b1 <- caribou_breakeven(f1, lambda = 1))
#> [1] 0.5669914
(b2 <- caribou_breakeven(f2, lambda = 1))
#> [1] 0.3441178
f3 <- caribou_forecast(s1, fpen.prop = b1)
f4 <- caribou_forecast(s2, fpen.prop = b2)
## See that lines are truly flat
op <- par(mfrow = c(1, 2))
plot(f3, main = "Mat pen")
plot(f4, main = "Pred excl")

par(op)

## Forecast using number of penned females
## - it can be an initial number
## - or a vector of individuals for subsequent years
caribou_forecast(s1, fpen.inds = 5)
#> Caribou forecast - pen type: mat.pen 
#> 
#>  - tmax     :20
#>  - pop.start:100
#>  - fpen.inds:5
caribou_forecast(s2, fpen.inds = c(5, 0, 4, 6))
#> Caribou forecast - pen type: pred.excl 
#> 
#>  - tmax     :20
#>  - pop.start:100
#>  - fpen.inds:5 0 4 6

Getting Help or Reporting an Issue

To report bugs/issues/feature requests, please file an issue.

How to Contribute

If you would like to contribute to the package, please see our CONTRIBUTING guidelines.

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

License

Copyright 2018 Province of British Columbia

Licensed under the Apache License, Version 2.0 (the &quot;License&quot;);
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an &quot;AS IS&quot; BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and limitations under the License.

This project was created using the bcgovr package.

bcgov / CaribouBC