GR3Dfunction.R 12.8 KB
 Poulet Camille committed Feb 25, 2021 1 2 3 ``````#---------------------------------------------- # Temperature effect #---------------------------------------------- `````` patrick.lambert committed Dec 05, 2020 4 5 6 7 8 9 10 11 12 ``````# temperature effect in GR3D # from Rosso temperatureEffect = function(tempWater, Tmin, Topt, Tmax){ response = (tempWater - Tmin) * (tempWater - Tmax) / ((tempWater - Tmin) * (tempWater - Tmax) - (tempWater - Topt)^2) response[tempWater <= Tmin | tempWater >= Tmax] = 0 return(response) } `````` patrick.lambert committed Feb 17, 2021 13 14 15 16 17 18 19 20 21 ``````thermalRange = function(pct = 0.8, Tmin, Topt, Tmax){ lower = uniroot(function(x) temperatureEffect(x, Tmin, Topt, Tmax) - pct, interval = c(Tmin, Topt))\$root upper = uniroot(function(x) temperatureEffect(x, Tmin, Topt, Tmax) - pct, interval = c(Topt, Tmax))\$root return(c(lower = lower,upper = upper)) } #optimalThermalRange(Tmin = 3, Topt = 17, Tmax =27) `````` patrick.lambert committed Dec 05, 2020 22 `````` `````` Poulet Camille committed Feb 25, 2021 23 24 25 ``````#---------------------------------------------- # Growth simulation #--------------------------------------------- `````` patrick.lambert committed Dec 05, 2020 26 27 28 29 30 31 32 33 34 35 36 37 38 ``````# von Bertalaffy : L = f(age) vonBertalanffyGrowth = function(age, L0, Linf, K){ t0 = log(1 - L0 / Linf) / K return(Linf * (1 - exp(-K * (age - t0)))) } # von Bertalanffy inverse : age = f(L) # with L0 rather the usual t0 parameter vonBertalanffyInverse = function(L, L0, Linf, K){ t0 = log(1 - L0/Linf)/K return(t0 - log(1 - L/Linf)/K) } `````` Poulet Camille committed Mar 02, 2021 39 `````` `````` patrick.lambert committed Dec 05, 2020 40 41 ``````# von Bertalanffy increment # pas cohérent avec la temperature effet sur le coeff de croissance mais ca marche `````` patrick.lambert committed Apr 21, 2021 42 `````` `````` patrick.lambert committed Feb 17, 2021 43 ``````vonBertalanffyIncrement = function(nStep, L0, Linf, K, timeStepDuration, sigma, withTempEffect=FALSE, TrefAtSea = c(9.876946, 13.489854, 15.891487, 11.554104) ){ `````` patrick.lambert committed Dec 05, 2020 44 45 46 47 `````` tempEffect = temperatureEffect( TrefAtSea , 3, 17, 26) L = matrix(nrow = nStep + 1) L[1] = L0 for (i in 1:nStep) { `````` patrick.lambert committed Feb 17, 2021 48 `````` mu = log((Linf - L[i]) * (1 - exp(-K * timeStepDuration))) - sigma * sigma / 2 `````` patrick.lambert committed Dec 05, 2020 49 50 51 52 53 54 55 56 57 `````` increment = exp(rnorm(1, mu, sigma)) if (withTempEffect) { increment = increment * tempEffect[((i - 1) %% 4) + 1] } L[i + 1] = L[i] + increment } return(L) } `````` patrick.lambert committed Apr 20, 2021 58 ``````vonBertalanffyWithNextIncrement = function(L, Linf, K, timeStepDuration, sigma, tempEffect ){ `````` patrick.lambert committed Dec 05, 2020 59 `````` if (sigma == 0) { `````` patrick.lambert committed Feb 17, 2021 60 `````` mu = log((Linf - L) * (1 - exp(-K * timeStepDuration))) `````` patrick.lambert committed Dec 05, 2020 61 62 63 `````` increment = exp(mu) } else { `````` patrick.lambert committed Feb 17, 2021 64 `````` mu = log((Linf - L) * (1 - exp(-K * timeStepDuration))) - (sigma * sigma) / 2 `````` patrick.lambert committed Mar 16, 2021 65 `````` increment = exp(rnorm(length(mu), mu, sigma)) `````` patrick.lambert committed Dec 05, 2020 66 67 68 69 70 `````` } L = L + increment * tempEffect return(L) } `````` patrick.lambert committed Apr 20, 2021 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 ``````# generate a cohort of length trajectories computeMultipleLengthTrajectories = function(temperaturePattern, Nind = 10, growPar){ ages = temperaturePattern\$age res <- expand_grid(ind = seq.int(Nind), age = ages) %>% inner_join(temperaturePattern, by = 'age') %>% arrange(age, ind) %>% mutate(temperatureEffect = temperatureEffect(temperature, growPar\$tempMinGrow, growPar\$tempOptGrow, growPar\$tempMaxGrow), L = if_else(age == 0, growPar\$lengthAtHatching, 0)) for (i in 2:length(ages)) { previousAge = ages[i - 1] currentAge = ages[i] tempEffect = res %>% filter(age == currentAge) %>% select(temperatureEffect) %>% unlist(use.names = FALSE) previousL <- res %>% filter(age == previousAge) %>% select(L) %>% unlist(use.names = FALSE) currentL <- vonBertalanffyWithNextIncrement(L = previousL, Linf = growPar\$Linf, K = growPar\$kOpt, timeStepDuration = currentAge - previousAge, sigma = growPar\$sigmaDeltaLVonBert, tempEffect = tempEffect) res = res %>% mutate(L =replace(L, age == ages[i], currentL) ) } return(res) } computeMultipleLengthTrajectoriesWithRandomSeed = function(temperaturePattern, Nind = 10, growPar, RNGseed =1){ set.seed(RNGseed) ages = temperaturePattern %>% distinct(age) %>% unlist(use.names = FALSE) res <- expand_grid(ind = seq.int(Nind), age = ages) %>% mutate(random = rnorm(Nind * length(ages))) %>% inner_join(temperaturePattern, by = 'age') %>% arrange(age, ind) %>% mutate(temperatureEffect = temperatureEffect(temperature, growPar\$tempMinGrow, growPar\$tempOptGrow, growPar\$tempMaxGrow), L = if_else(age == 0, growPar\$lengthAtHatching, 0)) for (i in 2:length(ages)) { previousAge = ages[i - 1] currentAge = ages[i] tempEffect <- res %>% filter(age == currentAge) %>% select(temperatureEffect) %>% unlist(use.names = FALSE) previousL <- res %>% filter(age == previousAge) %>% select(L) %>% unlist(use.names = FALSE) rnd <- res %>% filter(age == currentAge) %>% select(random) %>% unlist(use.names = FALSE) currentL <- vonBertalanffyWithRandomVector(L = previousL, Linf = growPar\$Linf, K = growPar\$kOpt, timeStepDuration = currentAge - previousAge, randomVector = rnd, sigma = growPar\$sigmaDeltaLVonBert, tempEffect = tempEffect) res = res %>% mutate(L = replace(L, age == ages[i], currentL) ) } return(res) } #computeMultipleLengthTrajectoriesWithRandomSeed(temperaturePattern, Nind = 10, #growPar = growParUnisex, # RNGseed = 1) vonBertalanffyWithRandomVector = function(L, Linf, K, timeStepDuration, randomVector, sigma, tempEffect ){ if (sigma == 0) { mu = if_else(L < Linf, log((Linf - L) * (1 - exp(-K * tempEffect * timeStepDuration))),-Inf) #mu = log((Linf - L) * (1 - exp(-K * tempEffect * timeStepDuration))) increment = exp(mu) } else { mu = if_else(L < Linf, log((Linf - L) * (1 - exp(-K * tempEffect * timeStepDuration))) - (sigma * sigma) / 2, -Inf) # mu = log((Linf - L) * (1 - exp(-K * tempEffect * timeStepDuration))) - (sigma * sigma) / 2 increment = exp(randomVector * sigma + mu) } L = pmin(Linf, L + increment) return(L) } `````` patrick.lambert committed Apr 21, 2021 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 ``````computeOgive = function(lengthTrajectories, lengthAtMaturity){ ogive <- lengthTrajectories %>% group_by(age) %>% summarise(nTotal = n()) %>% left_join(lengthTrajectories %>% group_by(age) %>% filter(L >= lengthAtMaturity) %>% summarise(taller = n(), .groups = 'drop'), by = 'age') %>% replace_na(list(taller = 0)) %>% mutate(mature = c(0,diff(taller)), immature = nTotal - cumsum(mature), p = if_else(mature + immature > 0 , mature / (mature + immature), 1)) %>% select(age, p) return(ogive) } `````` patrick.lambert committed Apr 20, 2021 175 `````` `````` patrick.lambert committed Apr 21, 2021 176 177 ``````# deprecated computeOgive3 = function(lengthTrajectories, lengthAtMaturity) { `````` patrick.lambert committed Apr 20, 2021 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 `````` ogive <- lengthTrajectories %>% group_by(age) %>% summarise(nTotal=n()) %>% left_join(lengthTrajectories %>% group_by(age) %>% filter(L > lengthAtMaturity) %>% summarise(mature = n(), .groups = 'drop'), by = 'age') %>% replace_na(list(mature = 0)) %>% mutate(p = mature/nTotal) %>% select(age, p) return(ogive) } `````` patrick.lambert committed Dec 05, 2020 193 194 195 196 197 198 199 200 201 202 203 ``````# ------------------------------------------------------- # Dispersal # see see (Chapman et al., 2007; Holloway et al., 2016) # ------------------------------------------------------- logitKernel = function(distance, alpha0, alpha1, meanInterDistance, standardDeviationInterDistance, basinSurface = 0, alpha2 = 0, meanBasinSurface = 0, standardDeviationBasinSurface = 1, fishLength = 0, alpha3 = 0, meanLengthAtRepro = 0, standardDeviationLengthAtRepro = 1) { logitW = alpha0 - alpha1 * (distance - meanInterDistance) / standardDeviationInterDistance + alpha2 * (basinSurface - meanBasinSurface) / standardDeviationBasinSurface + alpha3 * (fishLength - meanLengthAtRepro) / standardDeviationInterDistance; `````` patrick.lambert committed Dec 18, 2020 204 205 206 207 208 209 210 211 212 213 214 215 216 `````` W = 1 / (1+ exp(-logitW)) return(W) } # extended negative exponential kernel eneKernel = function(distance, alpha_D, beta_D){ W = exp(-alpha_D * distance ^ beta_D) return(W) } strayerSurvival = function(distance, m ){ # m: extra mortality rate for strayers (L-1) return(exp(-m * distance)) } `````` Poulet Camille committed Feb 25, 2021 217 218 219 220 221 `````` #------------------------------------------------------- # Spwaner survival before reproduction # Dome-shape curve with temperature effect #------------------------------------------------------- `````` Poulet Camille committed Mar 30, 2021 222 ``````spawnerSurvivalPreReproduction <- function(Triver,Tmin, Topt, Tmax, parSurv){ `````` Poulet Camille committed Feb 25, 2021 223 224 `````` #River survival `````` Poulet Camille committed Mar 30, 2021 225 `````` survProbOptRiver = parSurv\$survProbOptRiver `````` Poulet Camille committed Feb 25, 2021 226 `````` `````` Poulet Camille committed Mar 24, 2021 227 `````` spRiver = survProbOptRiver * temperatureEffect(Triver, Tmin, Topt, Tmax) `````` Poulet Camille committed Feb 25, 2021 228 229 230 231 232 233 234 235 236 237 238 239 `````` #StockAfterSurv = S * SpRiver return(spRiver) } #---------------------------------------------- # Stock Recruitement relationship #See Rougier et al, 2014; 2015 and Jatteau et al., 2017 #---------------------------------------------- #survival of larvae 14dph from Jatteau et al, 2017 `````` Poulet Camille committed Mar 30, 2021 240 241 242 243 244 245 246 247 248 249 ``````stockRecruitementRelationship <- function(Triver,Tmin, Topt, Tmax, survivalStock, parRep, parSurv, surfaceWatershed = 84810) { #surfaceWatershed = 84810 Surface de la Garonne lambda = parRep\$lambda deltaT = parRep\$deltaT survOptRep = parRep\$survOptRep eta = parRep\$eta #simule l'effet allee ratioS95_S50 = parRep\$ratioS95_S50 alpha = parRep\$a #species fecundity survProbOptRiver = parSurv\$survProbOptRiver `````` Poulet Camille committed Feb 25, 2021 250 251 252 253 `````` periodAtSea = 5 - deltaT ###--------------------- SR relationship ----------------- `````` Poulet Camille committed Mar 02, 2021 254 `````` #parametre c de la RS de BH int?grant un effet du BV consid?r? `````` Poulet Camille committed Feb 25, 2021 255 256 `````` cj = lambda/surfaceWatershed `````` Poulet Camille committed Mar 02, 2021 257 `````` #parametre b repr?sentant la mortalit? densit? d?pendante de la RS de BH int?grant un effet de la temperature `````` Poulet Camille committed Feb 25, 2021 258 259 260 261 262 `````` # bj = (-(1/deltaTrecruitement))* # log(survOptRep * temperatureEffect(temp, 9.8, 20.0, 26.0)) bj = -log(survOptRep * temperatureEffect(Triver, Tmin , Topt , Tmax)) / deltaT `````` Poulet Camille committed Mar 02, 2021 263 `````` #parametre a (f?condit? de l'esp?ce) de la RS de BH int?grant un effet de la temperature `````` Poulet Camille committed Feb 25, 2021 264 265 266 `````` alphaj = (bj * exp(-bj * deltaT)) / (cj * (1 - exp(-bj * deltaT))) alphaj[is.na(alphaj)] <- 0 `````` Poulet Camille committed Mar 02, 2021 267 `````` #Bj = param?tre de la relation SR int?grant l'effet de la temp?rature `````` Poulet Camille committed Feb 25, 2021 268 269 `````` betaj = bj/(alpha*cj*(1 - exp(-bj*deltaT))) `````` Poulet Camille committed Mar 02, 2021 270 `````` #p = proportion de g?niteurs participant ? la reproduction en focntion de la quantit? de g?niteur total `````` Poulet Camille committed Feb 25, 2021 271 272 `````` #p = 1/(1+exp(-log(19)*(S-n)/(Ratio*surfaceWatershed))) `````` Poulet Camille committed Mar 30, 2021 273 `````` S95 = eta * surfaceWatershed `````` Poulet Camille committed Feb 25, 2021 274 275 276 277 `````` S50 = S95/ratioS95_S50 p = 1/(1 + exp(-log(19)*(survivalStock - S50)/(S95 - S50))) `````` Poulet Camille committed Mar 02, 2021 278 `````` #relation Stock Recrutement ie calcul le nombre de recrues en fonction du nombre de g?niteurs et de la T en int?grant l'effet Allee `````` Poulet Camille committed Feb 25, 2021 279 280 281 `````` #R0 = aj * S * p `````` Poulet Camille committed Mar 30, 2021 282 `````` alleeEffect = 1/(1 + exp(-log(19)*(survivalStock - eta/ratioS95_S50*surfaceWatershed)/(eta*surfaceWatershed - eta/ratioS95_S50*surfaceWatershed))) `````` Poulet Camille committed Feb 25, 2021 283 284 `````` `````` Poulet Camille committed Mar 24, 2021 285 `````` Rj = (alphaj * survivalStock * alleeEffect)/(betaj + survivalStock * alleeEffect) `````` Poulet Camille committed Feb 25, 2021 286 287 288 289 290 291 292 293 294 295 296 297 `````` #Rj = ((aj * S) * p)/(Bj +S * p) stockRecruitement = as.vector(Rj) return(stockRecruitement) } # ---------------------------------------------- # Spawner survival after reproduction #---------------------------------------------- `````` Poulet Camille committed Apr 14, 2021 298 299 300 301 302 303 304 305 306 307 308 ``````#Logit with temperature effect depending on a Triver spawnerSurvivalPostReproductionTempRiver <- function(Triver, coeffa, coeffb){ spRiverPostSpawn = (coeffb/ (1 + exp(coeffa*(Triver)))) return(spRiverPostSpawn) } #Logit with temperature effect depending on the difference between the river temperature and Tref spawnerSurvivalPostReproductionTempRef <- function(Triver,Tref, coeffa, coeffb){ `````` Poulet Camille committed Feb 25, 2021 309 310 311 312 313 314 315 `````` spRiverPostSpawn = (coeffb/ (1 + exp(coeffa*(Triver-Tref)))) return(spRiverPostSpawn) } `````` Poulet Camille committed Apr 19, 2021 316 317 318 319 320 321 322 ``````#Logit for survival after reproduction with log19 #similar to spawnerSurvivalPostReproductionWithTempRef which include a logit2 = function(Triver, Tref,minTempForIteroparity){ return( 1/ (1+exp((log(19)/(minTempForIteroparity-Tref))*(Triver-Tref)))) } `````` Poulet Camille committed Feb 25, 2021 323 ``````#Dome-shape curve with temperature effect `````` Poulet Camille committed Apr 19, 2021 324 ``````spawnerSurvivalPostReproductionWithBellCurve <- function(Triver, Tmin, Topt, Tmax, coeffb){ `````` Poulet Camille committed Feb 25, 2021 325 326 327 328 329 330 331 332 333 334 335 `````` #P1: #SpRiverPostSpawn = probSurvAfterRepro/(probSurvAfterRepro + (1 - probSurvAfterRepro)*exp(-coeffLogit*(TemperatureEffect(Triver, Tmin, Topt, Tmax)))) #P2: #SpRiverPostSpawn = probSurvAfterRepro/(probSurvAfterRepro + (1 - probSurvAfterRepro)*exp(-coeffLogit)) #SpRiverPostSpawnTempEffect = (probSurvAfterRepro/(probSurvAfterRepro + (1 - probSurvAfterRepro)*exp(-coeffLogit))) * TemperatureEffect(Triver, Tmin, Topt, Tmax) #P3: spRiverPostSpawn = coeffb * temperatureEffect(Triver, Tmin, Topt, Tmax) `````` Poulet Camille committed Mar 30, 2021 336 `````` #stockAfterSpawn = S * spRiverPostSpawn `````` Poulet Camille committed Feb 25, 2021 337 338 339 340 341 342 `````` return(spRiverPostSpawn) } `````` Poulet Camille committed Apr 19, 2021 343