README.md

In ianjonsen/simsmolt: simulate Atlantic salmon smolt migration and detections on acoustic arrays

simsmolt

Simulate salmon smolt migration and potential for acoustic detection

Roadmap:

while focused on a specific project, this code will be generalised so detections of acoustically-tagged animals can be simulated under a variety of ecological scenarios

tidy simulation

simulate a single smolt's migration for 50 d (1200 h)

d <- sim_setup() out <- sim_move(N=1200, data=d) %>% sim_detect(., data = d) summary(out, d) plot(out)

simulate multiple, independent smolts

d <- sim_setup() out <- data.frame(id=1:5) %>% group_by(id) %>% do(rep = try(sim_move(id = .$id, N=1200, data = d, mpar=list(surv=1)) %>% sim_detect(., data = d))) class(out) <- append(class(out), "simsmolt", 0) summary(out, d) plot(out)

simulate multiple smolts across multiple processor cores

d <- sim_setup() cls <- multidplyr::create_cluster(11) multidplyr::cluster_library(cls, c("simsmolt", "dplyr")) multidplyr::cluster_copy(cls, d) out <- data.frame(id = 1:100) %>% multidplyr::partition(id, cluster = cls) %>% do(rep = try(sim_move(id=.$id, N=1200, data = d, mpar=list(rho=0.8), pb=FALSE) %>% sim_detect(., data = d))) %>% collect() class(out) <- append(class(out), "simsmolt", 0) plot(out) summary(out, d)

ianjonsen/simsmolt documentation built on July 11, 2022, 12:29 p.m.