New features
Added function calc.process.resid()
that calculates the process residuals for
the biomass and fishing mortality processes. The residuals are added to the
fitted spict object in the data frame called rep$process.resid
. The
residuals can be summarised with the function sumspict.diagnostics()
and
visualised with the function plotspict.diagnostic.process()
. Note, that the
process residuals have mainly been tested for scenarios without seasonal fishing patterns.
Added function plotspict.compare
that shows estimates from multiple
fits, of B, F, catch, F/Fmsy, B/Bmsy and the production curve on the same plot. The
fits can be given separately, like plotspict.compare(fit1, fit2)
or in a list, like
plotspict.compare(list(fit1, fit2))
.
Bug fixes
make.man.inp
now checks all fractiles to be between 0 and 0.5 (closes #167)add.manlines
correctly reports shorter management periods than 1 year (closes #168)add.manlines
checks for errflag for multiple management scenariosannual
function was rewritten to accommodate cases where intime
does not include full years. This happens when the first data point is not on a full year (closes #170, thanks to Paz Sampedro)man.select
checks for NA
s for multiple management scenariossummary
now respects the CI
argument. Added CI argument for sumspict.*
functionsMinor changes
New features
hindcast()
and plotspict.hindcast
.Bug fixes:
Bug fixes:
sim.spict
saves the dtc (and dte) (closes #159)New features:
use.tmb = TRUE
in sim.spict()
function to use TMB
SIMULATE{}
.parallel::mclapply()
have the argument mc.cores
to
specify the number of cores to be used. By default mc.cores
is equal to 1.Bug fixes
intermediatePeriodCatch
in
manage()
is used, the intermediate period was calculated incorrectly, using
the argument inp$indpred
rather than inp$indCpred
. This also led to an
error message in plotspict.catch()
with these management scenarios.Minor changes:
sim.spict()
check.inp
):
sim.random.effects
that allows to turn the simulation of random effects on
and off, and sim.fit
that allows to define whether the estimated parameters from the
last fit or initial values should be used for simulation.mc.cores=1
to circumvent multithread MKL and parallel problems.New features:
Blim
in the hockey-stick HCR to anything else than 0, by
specifying two values in breakpointB
, e.g. breakpointB = c(0.3,0.5)
.evalBreakpointB
.plotspict.hcr
that visualises management scenariosnews(package = "spict")
Bug fixes
Minor changes:
Minor changes:
sumspict.manage
control what is returned (uncertainty, absolute states)sumspict.manage
shows informative messages when scenarios are not comparable due to assumption differencescabs
) or fishing mortality (fabs
). Absolute catch scenarios are based on finding the fishing mortalirt (ffac
) that leads to the target catch using a simple optimisation.Bug fixes:
include.Ebinf
in sumspict.manage
Minor changes:
TMB
version 1.7.1 is requiredellipse
is now importedplyr
dependencyBug fixes:
test.spict
to work with the management updatesNew features:
plotspict.retro.fixed
. Plots parameter estimates (and confidence intervals) in each of the retrospective runsMinor changes:
plotspict.retro
returns Mohn's rho if add.mohn
is TRUEplotspict.retro
was polished, added legend, better spacingmohns_rho
now works for the predicted index Ipred
Bug fixes:
New features:
inp$maninterval
and inp$maneval
. The first is comprised of two numeric
values which define the start and end of the management period, i.e. the period
to which fishing mortality or catch restrictions are applied to and for which
the catch (or TAC) is predicted for. inp$maneval
defines the management
evaluation time, i.e. the time point at which model states should be predicted
for (corresponds to the 'p' quantities in the model, e.g. logBpBmsy
). Thus, these
variables replace the deprecated variables 'timepredc', 'dtpredc', and
'manstart'. The new variables have a higher priority than the older ones, but
old variables can still be used.logBp
.manage()
functionadd.man.scenario()
to add customised scenarios to rep$man
get.TAC()
to estimate TAC of a specified scenarioman.tac()
to estimate TAC of all scenarios in rep$man
man.timeline()
to visualise management times in form of a timelinesumspict.manage()
to print a summary of all management scenarioscheck.man.time()
to check and correct model times in respect to management timesman.select()
to select certain scenarios from rep$man
plot2()
allowing to plot a selection of 4 plots: biomass
relative to Bmsy, Fishing mortality relative to Fmsy, catches, and the Kobe
plot.fit.spict()
and
check.inp()
which allows to turn off console printing. This may be relevant
for automatic reports and parallel scripts. By default verbose = TRUE
and
informative text messages and warnings are printed to the console.0
) which reports all quantities, a
minimal selection of quantities relevant for management (1
), and the option
to only report the predicted catch (logCp
with inp$reportmode == 2
) are
implemented.logFmFmsy
, correspond to the start of the management period.mohns_rho
that calculates Mohn's rho from the retrospective analysis
of user selected quantitiesMinor changes:
manage()
function overwrites all scenarios in rep$man
.Bug fixes:
inp$indlastobs
which is used to estimate all 'l' quantities,
e.g. logFlFmsy
, did not consider the length of the catch (or effort)
interval. Fixing this bug might lead to different values for some quantities
(e.g. 'States' in the summary output of a SPiCT assessment), because they
affect the 'l' states in the model, e.g. logBl
.shorten.inp()
did not account for the
length of the catch (or effort) interval. Thus, a catch observation for the
interval 1990-1991 was included although maxtime = 1990
. After this bug fix,
this observation is not included anymore as it ranges beyond 'maxtime'.New features:
calc.bmsyk
that returns the Bmsy / K ratio of a fitted
objectcalc.om
that return a matrix with the order of
magnitude of the confidence interval range of F/Fmsy and B/Bmsyshorten.inp
that cuts the input time series to the
specified rangen
) curve on the log scaleBrel
and Frel
, respectivelyMinor changes:
manage
that sets the standard deviation factor keep
current catch scenarionlminb
optimiserBug fixes:
manage
take.c
New features:
Minor changes: