Commit aa29aae7 authored by patrick.lambert's avatar patrick.lambert
Browse files

identification of metapopulation

based on code developed during Tomas Niarfex intership
parent 18ff1042
library(tidyverse)
computeAutochtonousRate = function(data){
data %>% filter(migrationBasin == originBasin) %>%
select(-originBasin) %>%
inner_join(data %>% group_by(year, migrationBasin) %>%
summarise(totalRun = sum(effective), .groups = 'drop'), by = c('migrationBasin', 'year')) %>%
mutate(autochtonousRate = effective / totalRun) %>%
select(year, migrationBasin, autochtonousRate)
}
computeHomingRate = function(data){
data %>% filter(migrationBasin == originBasin) %>%
select(-migrationBasin) %>%
inner_join(data %>% group_by(year, originBasin) %>%
summarise(production = sum(effective), .groups = 'drop'), by = c('originBasin', 'year')) %>%
mutate(homingRate = effective / production) %>%
select(year, originBasin, homingRate)
}
# comparison between autochtonous rate and homing rate
# computeAutochtonousRate(exchangesData) %>%
# inner_join(computeHomingRate(data = exchangesData), by = c('migrationBasin' = 'originBasin', 'year'))
identyMetapopulation = function(exchangesData, threshold = .95, verbose = FALSE) {
exchangesDataUpdated = exchangesData
# initialise the connection table between basin and metapopulation
metapopulation = exchangesDataUpdated %>%
distinct(year, basin = migrationBasin) %>%
mutate(metapop = basin)
iteration = 1
# find the basin with the minimum autochtonous rate for the first time,
basinWithMinAutochtonousRate = computeAutochtonousRate(data = exchangesDataUpdated) %>%
group_by(year) %>%
slice(which.min(autochtonousRate))
# loop while autochtonousRate is still < 0.95
while (basinWithMinAutochtonousRate$autochtonousRate < threshold ) {
# while (iteration <= 4 ) {
if (verbose) cat(iteration, ": ", basinWithMinAutochtonousRate$autochtonousRate, '\n' )
# basinWithMinAutochtonousRate will be merged with origin basin sending the maximum number of fish in this basin
metapopsToBeMerged <- exchangesDataUpdated %>%
inner_join(basinWithMinAutochtonousRate %>% select(-autochtonousRate),
by = c('year', 'migrationBasin' )) %>%
filter(migrationBasin != originBasin) %>% # to avoid self merging
group_by(year) %>%
slice(which.max(effective)) %>%
ungroup() %>%
select(year, migrationBasin, originBasin)
# update the connection table between basin and metapopulation by merging metapopulation
for (i in 1:nrow(metapopsToBeMerged)) {
mergedName = paste0("M", iteration, '_',i)
metapopsToBeMerged_i <- metapopsToBeMerged %>% slice(i)
if (verbose) cat("\t", metapopsToBeMerged_i$migrationBasin, ' + ', metapopsToBeMerged_i$originBasin, ' = ', mergedName, "\n")
metapopulation <- metapopulation %>%
mutate(metapop = if_else(year == metapopsToBeMerged_i$year &
metapop %in% (metapopsToBeMerged_i %>% select(ends_with("Basin")) %>% unlist(use.names = FALSE)),
mergedName,
metapop))
}
# sum by migration and origin basins according to updated metapopulations
# computed with initial exchangesData
exchangesDataUpdated <- exchangesData %>%
#sum up on migration basins
inner_join(metapopulation,
by = c('year', 'migrationBasin' = 'basin')) %>%
group_by(year, metapop, originBasin) %>%
summarise(effective = sum(effective), .groups = 'drop') %>%
rename(migrationBasin = metapop) %>%
# sum on origine basins
inner_join(metapopulation,
by = c('year', 'originBasin' = 'basin')) %>%
group_by(year, metapop, migrationBasin) %>%
summarise(effective = sum(effective), .groups = 'drop') %>%
rename(originBasin = metapop)
# minimum of autochtonous rate
basinWithMinAutochtonousRate = computeAutochtonousRate(data = exchangesDataUpdated) %>%
group_by(year) %>%
slice(which.min(autochtonousRate))
iteration = iteration + 1
}
return(list(metapopulation = metapopulation, exchangesData = exchangesDataUpdated))
}
# upload data =====
# longer table of effective of different origin basins in each migration basin
exchangesData <- read_csv("../../data/output/northeastamerica/effectiveFluxes_1-observed.csv")
exchangesData %>% group_by(year, basin = originBasin) %>%
summarise(production = sum(effective), .groups = 'drop') %>%
inner_join(exchangesData %>% group_by(year, basin = migrationBasin) %>%
summarise(totalRun = sum(effective), .groups = 'drop'), by = c('year', 'basin')) %>%
arrange(totalRun, production) %>% print(n = Inf)
#TODO explain how it is possible to have a production >0 and spawners run = 0: PB in JAVA or
# no reproductive success some years
exchangesData %>% filter(migrationBasin == 'Musquodoboit' ) %>% print(n = Inf)
exchangesData %>% filter(originBasin == 'Musquodoboit') %>% print(n = Inf)
# remove basin with no run of spawner
selectedBasins <- exchangesData %>% group_by(year, basin = originBasin) %>%
summarise(production = sum(effective), .groups = 'drop') %>%
inner_join(exchangesData %>% group_by(year, basin = migrationBasin) %>%
summarise(totalRun = sum(effective), .groups = 'drop'), by = c('year', 'basin')) %>%
filter(totalRun > 0) %>% select(year, basin)
selectedExchangesData <- exchangesData %>%
inner_join(selectedBasins, by = c('year', 'migrationBasin' = 'basin')) %>%
inner_join(selectedBasins, by = c('year', 'originBasin' = 'basin'))
# results ====
metapopulations = identyMetapopulation(selectedExchangesData, threshold = .95)
metapopulations$metapopulation %>% group_by(metapop) %>% summarise(n_basin = n(), .groups = 'drop') %>% arrange(desc(n_basin)) %>%
mutate(nb_basin = sum(n_basin)) %>%
print(n = Inf)
computeAutochtonousRate(exchangesData)
computeAutochtonousRate(metapopulations$exchangesData) %>% print(n = Inf)
# =================================
# idées abandonnées
# =================================
# # compute ratio strayer-from over production
# # the basin with the minimum of autochonous (maximum of allotochnous) in the spawner run is merged with the origin basin that sends
# # the maximum strayers accornding to its production
# metapopsToBeMerged <- exchangesData %>%
# inner_join(basinWithMinAutochtonousRate, by = c('year', 'migrationBasin')) %>%
# #joint with production in each catchment
# inner_join(exchangesData %>% group_by(year, originBasin) %>%
# summarise(production = sum(effective))
# , by = c('year', 'originBasin')) %>%
# filter(migrationBasin != originBasin) %>%
# mutate(ratioStrayerProdution = effective / production) %>%
# group_by(year) %>%
# slice(which.max(ratioStrayerProdution)) %>%
# ungroup() %>%
# mutate(mergedName = paste0("M", iteration, '_',row_number()))
\ No newline at end of file
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