New in CatDyn 1.1.1

1 Expand model types to 25 perturbations for single fleet and two-fleet models

2 Fix error message, max. number of par is 50, not 208

3 Add error message when abundance is NaN in catdynexp (NA when TRUE/FALSE needed in Results[,4]

4 Some double ;; in likelihood models

5 Correct error in 2P2P, naming pars with “P3.” and missing two lines after hessian in the call to optimx.

6 Correct error in naming pars “P8,” intead of “P8.”

7 Make Biom.tstep in plot.CatDynExp the same as in plot.CatDynMod and correct help pages.

8 Allow to plot just the fit for results (not the residuals nor the quantiles) in plot.CatDynMod and allow option to change the sizing of panels

9 Change names in data.frame catdynexp$Model$Results to eliminate spaces, replace with short version with dots

10 Correct error in AIC 2par-2loglik, loglik is actually the minimized negative, so formula should be 2par+2loglik.

11 Add robust lognormal likelihood

12 Add Gumbel likelihood

13 Correct as.CatDynData by allowing 0 catch time steps without causing NaN in catch in numbers

14 Add CatDynPar function, for neat table of parameter estimates, with effort to present the timing of perturbations in ISO8601 format

15 Add error message when fleet 1 has more perts than fleet 2

16 Put aggregated catch over user-specified number of time steps in weight in predictive plot

17 Add M.Hoenig function for mortality rate and its prediction error to get a good initial value for M from longevity data when starting the stock assessment for a new stock

18 Add the catch by time step in fixed kg units to CatDynPred and fix units of biomass to tons

19 Add caclulation of explotation rates by time steps to CatDynPred. 
Observed exploitation rate = observed catch in weight/predicted biomass
Expected exploitation rate = predicted catch in weight/predicted biomass

20 Add estimation of fishing mortality F from exploitation rate  to CatDynPred
Solve for F in Baranov exploitation rate (F/(F+M))(1-exp(-F-M)) using uniroot().
Observed F = using observed exploitation rate
Expected F = using expected exploitation rate

21 Add function CatDynBSD for annual biomass and its standard error for hierarchical estimation of surplus production model

22 Add function mobw.kg to calculate mean weight and its standard error by month using timeless length and weight data and sequential length and month data.

23 Add length and weight, length and month data from gay hake to use in mobw.kg example

25 Add m.hoenig data of natural mortality (1/yr) and longevity (yr) as published in Hoenig (2005)

26 Create newmodel type, resident stock with partial emigration, inspired by fishery for octpus in Asturias, northern Spain, set with p negative and partial = TRUE.

27 Add partial=TRUE to CatDynFit, CatDynPred, candynexp and all internal functions called by these to accommodate the new model type in 26. Only transit models need to be set by making partial=FALSE overriding default.