Skip to contents

Class for stock-recruitment models.

Usage

FLSR(model, ...)

# S4 method for class 'ANY'
FLSR(model, ...)

# S4 method for class 'missing'
FLSR(model, ...)

Details

A series of commonly-used stock-recruitment models are already available, including the corresponding likelihood functions and calculation of initial values. See SRModels for more details and the exact formulation implemented for each of them.

Slots

name

Name of the object (character).

desc

Description of the object (character).

range

Range (numeric).

rec

Recruitment series (FLQuant).

ssb

Index of reproductive potential, e.g. SSB or egg oor egg production (FLQuant).

fitted

Estimated values for rec (FLQuant).

residuals

Residuals obtained from the model fit (FLArray).

covar

Covariates for SR model (FLQuants).

model

Model formula (formula).

gr

Function returning the gradient of the likelihood (function).

logl

Log-likelihood function (function).

initial

Function returning initial parameter values for the optimizer (function).

params

Estimated parameter values (FLPar).

logLik

Value of the log-likelihood (logLik).

vcov

Variance-covariance matrix (array).

details

Extra information on the model fit procedure (list).

logerror

Is the error on a log scale (logical).

distribution

(factor).

hessian

Resulting Hessian matrix from the fit (array).

See also

Author

The FLR Team

Examples


  # Create an empty FLSR object.
  sr1 <- FLSR()

  # Create an  FLSR object using the existing SR models.
  sr2 <- FLSR(model = 'ricker')
  sr2@model
#> rec ~ a * ssb * exp(-b * ssb)
#> <environment: 0x55fb4b461c48>
  sr2@initial
#> function(rec, ssb) {
#> 		# The function to provide initial values
#>     res  <-coefficients(lm(log(c(rec)/c(ssb))~c(ssb)))
#>     return(FLPar(a=max(exp(res[1])), b=-max(res[2])))}
#> <bytecode: 0x55fb4b45a3b8>
#> <environment: 0x55fb4b461c48>
#> attr(,"lower")
#> [1] -Inf -Inf
#> attr(,"upper")
#> [1] Inf Inf
  sr2@logl
#> function(a, b, rec, ssb)
#>       loglAR1(log(rec), log(a*ssb*exp(-b*ssb)))
#> <bytecode: 0x55fb4b458968>
#> <environment: 0x55fb4b461c48>

  sr3 <- FLSR(model = 'bevholt')
  sr3@model
#> rec ~ a * ssb/(b + ssb)
#> <environment: 0x55fb4b902d80>
  sr3@initial
#> function(rec, ssb) {
#>     a <- max(quantile(c(rec), 0.75, na.rm = TRUE))
#>     b <- max(quantile(c(rec)/c(ssb), 0.9, na.rm = TRUE))
#>     return(FLPar(a = a, b = a/b))}
#> <bytecode: 0x55fb4b8fb8e0>
#> <environment: 0x55fb4b902d80>
#> attr(,"lower")
#> [1] -Inf -Inf
#> attr(,"upper")
#> [1] Inf Inf
  sr3@logl
#> function(a, b, rec, ssb)
#>       loglAR1(log(rec), log(a*ssb/(b+ssb)))
#> <bytecode: 0x55fb4b8f4808>
#> <environment: 0x55fb4b902d80>

  # Create an FLSR using a function.
  mysr1 <- function(){
    model <- rec ~ a*ssb^b
    return(list(model = model))}

  sr4 <- FLSR(model = mysr1)

  # Create an FLSR using a function and check that it works.
  mysr2 <- function(){
    formula <- rec ~ a+ssb*b

    logl <- function(a, b, sigma, rec, ssb) sum(dnorm(rec,
      a + ssb*b, sqrt(sigma), TRUE))

   initial <- structure(function(rec, ssb) {
      a   <- mean(rec)
      b   <- 1
      sigma <- sqrt(var(rec))

      return(list(a=a, b=b, sigma=sigma))},
        lower = c(0, 1e-04, 1e-04), upper = rep(Inf, 3))

   return(list(model = formula, initial = initial, logl = logl))
  }

  ssb <- FLQuant(runif(10, 10000, 100000))
  rec <- 10000 + 2*ssb + rnorm(10,0,1)
  sr5 <- FLSR(model = mysr2, ssb = ssb, rec = rec)

  sr5.mle <- fmle(sr5)
#>   Nelder-Mead direct search function minimizer
#> function value for initial parameters = 163406.701688
#>   Scaled convergence tolerance is 0.00243495
#> Stepsize computed as 7496.820439
#> BUILD              4 9181163641994.675781 141540.160296
#> LO-REDUCTION       6 2129977522396.011719 141540.160296
#> HI-REDUCTION       8 538828068094.632690 141540.160296
#> HI-REDUCTION      10 135471725247.814880 141540.160296
#> HI-REDUCTION      12 33943657773.507915 141540.160296
#> HI-REDUCTION      14 8485095365.236800 141540.160296
#> HI-REDUCTION      16 2116059492.850708 141540.160296
#> HI-REDUCTION      18 525861882.708607 141540.160296
#> HI-REDUCTION      20 129877061.405528 141540.160296
#> HI-REDUCTION      22 31729980.268444 141540.160296
#> HI-REDUCTION      24 7626132.270864 141540.160296
#> HI-REDUCTION      26 1817676.813873 141540.160296
#> HI-REDUCTION      28 474446.919157 141540.160296
#> HI-REDUCTION      30 219409.298128 141540.160296
#> REFLECTION        32 193097.769001 128665.987280
#> LO-REDUCTION      34 163406.701688 128665.987280
#> EXTENSION         36 141540.160296 86398.126977
#> LO-REDUCTION      38 136930.633178 86398.126977
#> HI-REDUCTION      40 128665.987280 86398.126977
#> EXTENSION         42 99061.935418 57313.041709
#> LO-REDUCTION      44 97008.208272 57313.041709
#> EXTENSION         46 86398.126977 31904.956474
#> REFLECTION        48 61527.247440 31099.754288
#> HI-REDUCTION      50 57313.041709 31099.754288
#> EXTENSION         52 41725.116784 9994.304172
#> LO-REDUCTION      54 31904.956474 9994.304172
#> EXTENSION         56 31099.754288 7899.295274
#> EXTENSION         58 16622.579730 2362.855801
#> REFLECTION        60 9994.304172 865.531551
#> HI-REDUCTION      62 7899.295274 865.531551
#> LO-REDUCTION      64 2362.855801 697.123217
#> LO-REDUCTION      66 2061.396804 131.370456
#> HI-REDUCTION      68 865.531551 131.370456
#> LO-REDUCTION      70 697.123217 131.370456
#> HI-REDUCTION      72 300.924786 131.370456
#> HI-REDUCTION      74 157.736501 121.566363
#> HI-REDUCTION      76 141.827460 73.447339
#> LO-REDUCTION      78 131.370456 72.115881
#> HI-REDUCTION      80 121.566363 72.115881
#> LO-REDUCTION      82 86.968056 72.115881
#> HI-REDUCTION      84 80.304614 72.115881
#> LO-REDUCTION      86 74.328873 72.115881
#> HI-REDUCTION      88 73.447339 71.407375
#> HI-REDUCTION      90 72.905934 70.943981
#> LO-REDUCTION      92 72.115881 70.785005
#> HI-REDUCTION      94 71.407375 70.785005
#> HI-REDUCTION      96 71.092687 70.785005
#> HI-REDUCTION      98 70.943981 70.785005
#> HI-REDUCTION     100 70.917673 70.763889
#> LO-REDUCTION     102 70.829585 70.752861
#> HI-REDUCTION     104 70.785005 70.752861
#> HI-REDUCTION     106 70.763889 70.749545
#> REFLECTION       108 70.761302 70.748467
#> REFLECTION       110 70.752861 70.744787
#> HI-REDUCTION     112 70.749545 70.740893
#> EXTENSION        114 70.748467 70.724123
#> HI-REDUCTION     116 70.744787 70.724123
#> LO-REDUCTION     118 70.740893 70.724123
#> EXTENSION        120 70.734920 70.722481
#> LO-REDUCTION     122 70.734458 70.722481
#> EXTENSION        124 70.724123 70.695721
#> LO-REDUCTION     126 70.723645 70.695721
#> LO-REDUCTION     128 70.722481 70.695721
#> EXTENSION        130 70.715444 70.676064
#> EXTENSION        132 70.703208 70.637697
#> LO-REDUCTION     134 70.695721 70.637697
#> EXTENSION        136 70.676064 70.611820
#> EXTENSION        138 70.644578 70.541271
#> LO-REDUCTION     140 70.637697 70.541271
#> LO-REDUCTION     142 70.611820 70.541271
#> EXTENSION        144 70.563786 70.443727
#> LO-REDUCTION     146 70.552506 70.443727
#> EXTENSION        148 70.541271 70.403008
#> EXTENSION        150 70.455309 70.266001
#> LO-REDUCTION     152 70.443727 70.266001
#> LO-REDUCTION     154 70.403008 70.266001
#> LO-REDUCTION     156 70.347710 70.266001
#> EXTENSION        158 70.325720 70.207409
#> EXTENSION        160 70.281998 70.174752
#> EXTENSION        162 70.266001 69.966123
#> LO-REDUCTION     164 70.207409 69.966123
#> LO-REDUCTION     166 70.174752 69.966123
#> EXTENSION        168 70.102607 69.665746
#> EXTENSION        170 70.010629 69.402631
#> LO-REDUCTION     172 69.966123 69.402631
#> EXTENSION        174 69.665746 68.343674
#> LO-REDUCTION     176 69.467717 68.343674
#> EXTENSION        178 69.402631 67.340172
#> EXTENSION        180 68.578834 63.479393
#> LO-REDUCTION     182 68.343674 63.479393
#> Warning: NaNs produced
#> HI-REDUCTION     184 67.340172 63.479393
#> Warning: NaNs produced
#> REFLECTION       186 66.915483 61.301086
#> Warning: NaNs produced
#> HI-REDUCTION     188 65.241403 61.301086
#> HI-REDUCTION     190 64.548113 61.301086
#> LO-REDUCTION     192 64.162698 61.301086
#> EXTENSION        194 63.479393 58.547281
#> Warning: NaNs produced
#> REFLECTION       196 62.922467 58.529138
#> Warning: NaNs produced
#> HI-REDUCTION     198 61.301086 58.529138
#> LO-REDUCTION     200 61.266886 58.529138
#> Warning: NaNs produced
#> HI-REDUCTION     202 59.761060 58.529138
#> Warning: NaNs produced
#> REFLECTION       204 58.630956 56.896382
#> LO-REDUCTION     206 58.547281 56.896382
#> Warning: NaNs produced
#> HI-REDUCTION     208 58.529138 56.896382
#> REFLECTION       210 57.675235 56.452485
#> Warning: NaNs produced
#> REFLECTION       212 57.185361 56.267132
#> HI-REDUCTION     214 56.896382 56.267132
#> EXTENSION        216 56.452485 55.396118
#> LO-REDUCTION     218 56.429536 55.260150
#> EXTENSION        220 56.267132 51.721751
#> LO-REDUCTION     222 55.396118 51.721751
#> HI-REDUCTION     224 55.260150 51.721751
#> LO-REDUCTION     226 54.477910 51.721751
#> EXTENSION        228 53.896320 47.475276
#> HI-REDUCTION     230 52.586416 47.475276
#> LO-REDUCTION     232 52.326430 47.475276
#> Warning: NaNs produced
#> HI-REDUCTION     234 51.721751 47.475276
#> EXTENSION        236 50.948154 47.004641
#> Warning: NaNs produced
#> HI-REDUCTION     238 49.353867 47.004641
#> LO-REDUCTION     240 49.073246 47.004641
#> HI-REDUCTION     242 47.760300 47.004641
#> HI-REDUCTION     244 47.612588 47.004641
#> EXTENSION        246 47.475276 46.317208
#> REFLECTION       248 47.262919 45.622102
#> LO-REDUCTION     250 47.004641 45.027214
#> LO-REDUCTION     252 46.317208 44.861974
#> HI-REDUCTION     254 45.622102 44.861974
#> HI-REDUCTION     256 45.329985 44.861974
#> REFLECTION       258 45.088177 44.810057
#> REFLECTION       260 45.027214 44.266724
#> REFLECTION       262 44.861974 44.138604
#> HI-REDUCTION     264 44.810057 44.138604
#> HI-REDUCTION     266 44.427386 44.138604
#> REFLECTION       268 44.337632 44.032394
#> REFLECTION       270 44.266724 43.951003
#> REFLECTION       272 44.138604 43.800632
#> LO-REDUCTION     274 44.032394 43.774492
#> HI-REDUCTION     276 43.951003 43.774492
#> EXTENSION        278 43.840938 43.473799
#> EXTENSION        280 43.800632 43.313788
#> REFLECTION       282 43.774492 43.281572
#> EXTENSION        284 43.473799 42.844823
#> EXTENSION        286 43.313788 42.373266
#> EXTENSION        288 43.281572 42.182610
#> LO-REDUCTION     290 42.844823 42.182610
#> EXTENSION        292 42.373266 40.670656
#> LO-REDUCTION     294 42.207204 40.670656
#> LO-REDUCTION     296 42.182610 40.670656
#> EXTENSION        298 41.638092 39.458445
#> EXTENSION        300 41.153727 36.769684
#> LO-REDUCTION     302 40.670656 36.769684
#> LO-REDUCTION     304 39.458445 36.769684
#> Warning: NaNs produced
#> REFLECTION       306 37.921832 35.200274
#> HI-REDUCTION     308 37.448116 35.200274
#> EXTENSION        310 37.010754 33.039041
#> Warning: NaNs produced
#> REFLECTION       312 36.769684 29.418643
#> Warning: NaNs produced
#> HI-REDUCTION     314 35.200274 29.418643
#> LO-REDUCTION     316 34.772622 29.418643
#> Warning: NaNs produced
#> REFLECTION       318 33.039041 26.451462
#> Warning: NaNs produced
#> REFLECTION       320 32.651520 24.329467
#> Warning: NaNs produced
#> HI-REDUCTION     322 30.273241 24.329467
#> Warning: NaNs produced
#> HI-REDUCTION     324 29.418643 24.329467
#> LO-REDUCTION     326 28.501430 24.208132
#> Warning: NaNs produced
#> HI-REDUCTION     328 26.551550 24.208132
#> Warning: NaNs produced
#> REFLECTION       330 26.451462 19.349720
#> Warning: NaNs produced
#> HI-REDUCTION     332 24.329467 19.349720
#> HI-REDUCTION     334 24.208132 19.349720
#> Warning: NaNs produced
#> REFLECTION       336 24.021515 14.604988
#> Warning: NaNs produced
#> HI-REDUCTION     338 21.734688 14.604988
#> Warning: NaNs produced
#> HI-REDUCTION     340 21.122190 14.604988
#> Warning: NaNs produced
#> HI-REDUCTION     342 20.117199 14.604988
#> Warning: NaNs produced
#> HI-REDUCTION     344 19.469040 14.604988
#> HI-REDUCTION     346 19.349720 14.604988
#> LO-REDUCTION     348 18.821741 14.604988
#> LO-REDUCTION     350 18.286990 14.604988
#> LO-REDUCTION     352 18.228687 14.604988
#> Warning: NaNs produced
#> HI-REDUCTION     354 16.729009 14.604988
#> Warning: NaNs produced
#> REFLECTION       356 15.451851 13.780624
#> Warning: NaNs produced
#> REFLECTION       358 14.672805 11.868968
#> HI-REDUCTION     360 14.604988 11.868968
#> Warning: NaNs produced
#> HI-REDUCTION     362 13.780624 11.868968
#> LO-REDUCTION     364 13.604789 11.868968
#> EXTENSION        366 13.377487 10.876970
#> LO-REDUCTION     368 13.143379 10.807862
#> Warning: NaNs produced
#> HI-REDUCTION     370 12.008277 10.807862
#> HI-REDUCTION     372 11.868968 10.807862
#> LO-REDUCTION     374 11.419716 10.807862
#> REFLECTION       376 10.876970 10.432530
#> REFLECTION       378 10.836609 10.333558
#> LO-REDUCTION     380 10.807862 10.275494
#> REFLECTION       382 10.432530 10.076943
#> LO-REDUCTION     384 10.333558 10.076943
#> LO-REDUCTION     386 10.275494 10.007425
#> REFLECTION       388 10.081922 9.871004
#> HI-REDUCTION     390 10.076943 9.871004
#> REFLECTION       392 10.007425 9.832550
#> EXTENSION        394 9.906016 9.608536
#> EXTENSION        396 9.871004 9.477899
#> REFLECTION       398 9.832550 9.431202
#> REFLECTION       400 9.608536 9.391317
#> EXTENSION        402 9.477899 9.064771
#> LO-REDUCTION     404 9.431202 9.064771
#> LO-REDUCTION     406 9.391317 9.064771
#> EXTENSION        408 9.208730 8.588939
#> EXTENSION        410 9.081577 8.388029
#> LO-REDUCTION     412 9.064771 8.388029
#> REFLECTION       414 8.588939 8.109063
#> LO-REDUCTION     416 8.432654 8.109063
#> HI-REDUCTION     418 8.388029 8.109063
#> REFLECTION       420 8.241052 8.094280
#> LO-REDUCTION     422 8.165604 8.080601
#> HI-REDUCTION     424 8.109063 8.080601
#> REFLECTION       426 8.094280 8.069875
#> HI-REDUCTION     428 8.093345 8.069875
#> HI-REDUCTION     430 8.080601 8.069875
#> Exiting from Nelder Mead minimizer
#>     432 function evaluations used
  sr5.nls <- nls(sr5)

# NS Herring stock-recruitment dataset
data(nsher)

# already fitted with a Ricker SR model
summary(nsher)
#> An object of class "FLSR"
#> 
#> Name:  
#> Description:  
#> Quant: age 
#> Dims:  age 	year	unit	season	area	iter
#> 	1	45	1	1	1	1	
#> 
#> Range:  min	minyear	max	maxyear 
#> 	0	1960	0	2004	
#> 
#> 
#> Model: 	rec ~ a * ssb * exp(-b * ssb)
#> An object of class "FLPar"
#> params
#>        a        b 
#> 1.19e+02 9.45e-03 
#> units:  NA 
#> Log-likelihood:  15.862(0) 
#> Variance-covariance:    
#>               a            b
#>   a 255.3388181 1.808870e-02
#>   b   0.0180887 1.992659e-06

plot(nsher)


# change model
model(nsher) <- bevholt()

# fit through MLE
nsher <- fmle(nsher)
#>   Nelder-Mead direct search function minimizer
#> function value for initial parameters = -10.336211
#>   Scaled convergence tolerance is 1.54022e-07
#> Stepsize computed as 501.110000
#> BUILD              3 44.842344 -11.603908
#> Warning: NaNs produced
#> HI-REDUCTION       5 31.685209 -11.603908
#> Warning: NaNs produced
#> HI-REDUCTION       7 17.913114 -11.603908
#> Warning: NaNs produced
#> HI-REDUCTION       9 5.415279 -11.603908
#> Warning: NaNs produced
#> HI-REDUCTION      11 -3.412974 -11.603908
#> HI-REDUCTION      13 -8.018030 -11.603908
#> LO-REDUCTION      15 -10.336211 -11.603908
#> LO-REDUCTION      17 -11.081040 -11.603908
#> EXTENSION         19 -11.295930 -12.061705
#> LO-REDUCTION      21 -11.603908 -12.061705
#> REFLECTION        23 -11.813826 -12.087620
#> REFLECTION        25 -12.061705 -12.199591
#> LO-REDUCTION      27 -12.087620 -12.199591
#> LO-REDUCTION      29 -12.158184 -12.199591
#> LO-REDUCTION      31 -12.191726 -12.199591
#> HI-REDUCTION      33 -12.192269 -12.199591
#> HI-REDUCTION      35 -12.197784 -12.199591
#> LO-REDUCTION      37 -12.198015 -12.199591
#> HI-REDUCTION      39 -12.199555 -12.199776
#> REFLECTION        41 -12.199591 -12.200058
#> HI-REDUCTION      43 -12.199776 -12.200092
#> HI-REDUCTION      45 -12.200058 -12.200142
#> HI-REDUCTION      47 -12.200092 -12.200155
#> HI-REDUCTION      49 -12.200142 -12.200160
#> HI-REDUCTION      51 -12.200155 -12.200177
#> HI-REDUCTION      53 -12.200160 -12.200177
#> LO-REDUCTION      55 -12.200171 -12.200179
#> HI-REDUCTION      57 -12.200177 -12.200179
#> HI-REDUCTION      59 -12.200178 -12.200179
#> HI-REDUCTION      61 -12.200179 -12.200179
#> HI-REDUCTION      63 -12.200179 -12.200179
#> HI-REDUCTION      65 -12.200179 -12.200179
#> Exiting from Nelder Mead minimizer
#>     67 function evaluations used

plot(nsher)