Caribou Population Forecasting
Try the Shiny app or run
locally as shiny::runGitHub("bcgov/CaribouBC", subdir = "inst/shiny/matpen").
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.
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
## Create projection matrices
s <- caribou_settings()
caribou_matrix(s, wild=TRUE) # wild
#> [0,1) [1,2) [2,3) [3,Inf]
#> [0,1) 0.000 0.000 0.000 0.39238
#> [1,2) 0.163 0.000 0.000 0.00000
#> [2,3) 0.000 0.853 0.000 0.00000
#> [3,Inf] 0.000 0.000 0.853 0.85300
caribou_matrix(s, wild=FALSE) # captive
#> [0,1) [1,2) [2,3) [3,Inf]
#> [0,1) 0.00 0.000 0.000 0.41538
#> [1,2) 0.54 0.000 0.000 0.00000
#> [2,3) 0.00 0.903 0.000 0.00000
#> [3,Inf] 0.00 0.000 0.903 0.90300
## Compare scenarios for captive breeding
## out.prop = 0: move only N[t]-in.max youngs
x0 <- caribou_breeding(s,
tmax = 20, # projection horizon
in.inds = rep(10, 5),
out.prop = 0.5)
x0
#> Caribou captive breeding:
#>
#> - tmax :20
#> - pop.start :100
#> - f.surv.trans:1
#> - j.surv.trans:1
#> - j.surv.red :1
#>
#> capt recip wild
#> N 67.242 56.3459 16.539
#> lambda 1.004 0.9914 0.914
summary(x0)
#> Years Nin Nout Ncapt Nrecip Nwild
#> 0 0 10 0 10.00000 100.00000 100.00000
#> 1 1 10 0 23.18380 91.39560 91.39560
#> 2 2 10 1 36.33182 84.53156 83.53156
#> 3 3 10 2 49.22996 79.19717 76.34417
#> 4 4 10 3 61.70599 75.20883 69.77522
#> 5 5 0 3 65.04446 71.69185 63.77148
#> 6 6 0 4 64.97138 69.65794 58.28433
#> 7 7 0 4 64.68270 67.96027 53.26931
#> 8 8 0 4 64.67842 66.32655 48.68581
#> 9 9 0 4 64.94646 65.05482 44.49669
#> 10 10 0 4 65.17513 63.87539 40.66802
#> 11 11 0 4 65.32882 62.79033 37.16878
#> 12 12 0 4 65.46682 61.78874 33.97063
#> 13 13 0 4 65.64046 60.87521 31.04766
#> 14 14 0 4 65.83908 60.04108 28.37620
#> 15 15 0 4 66.04654 59.27907 25.93460
#> 16 16 0 4 66.25912 58.58247 23.70308
#> 17 17 0 4 66.48284 57.94576 21.66357
#> 18 18 0 4 66.72118 57.36382 19.79955
#> 19 19 0 4 66.97435 56.83197 18.09592
#> 20 20 0 4 67.24185 56.34588 16.53888
## out.prop = 1: move all youngs
x1 <- update(x0, out.prop = 1)
x1
#> Caribou captive breeding:
#>
#> - tmax :20
#> - pop.start :100
#> - f.surv.trans:1
#> - j.surv.trans:1
#> - j.surv.red :1
#>
#> capt recip wild
#> N 17.8090 61.2520 16.539
#> lambda 0.9674 0.9494 0.914
## Visualize the 2 scenarios
op <- par(mfrow=c(1, 2))
plot(x0, main="out.prop = 0")
plot(x1, main="out.prop = 1")
par(op)To report bugs/issues/feature requests, please file an issue.
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.
Copyright 2018 Province of British Columbia
Licensed under the Apache License, Version 2.0 (the "License");
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 "AS IS" 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.
![repo-mountie[bot] avatar](https://avatars.githubusercontent.com/in/19327?v=4 "repo-mountie[bot]")
React
Typescript
Django
Laravel
Facebook
Microsoft
Google
Alibaba
D3
Tencent