mbar(FLStock) returns the mean natural mortality, M, over the fully selected age range.
window(FLlst) will lapply window over all elements.
computeQ(FLindices, FLStock, FLQuants) computes index.q from indices and fit.
comine() method now available for all (or most) classes.
New SRR model, bevholtisg, implements a sigmoidal Beverton-Holt model.
Class FLStockR contains slots for reference points (@refpts, FLPar) and stock recruitment relationship (@sr, predictModel).
BUG FIXES
simplify(FLStock) recoded in a simpler way supported by noseason/unit/area functions.
Ensure harvest(FLQuant) returns 0 when catch or n are 0.
Further improvements to simplify. nounit, noseason and noarea do nmot call harvest().
qapply now works properly in noseason.
fwdWindow(FLBiol) did not respect residuals FLQuant sometimes.
USER-VISIBLE CHANGES
FLStock() constructor defaults to ‘age’ as quant.
append(FLQuant, FLQuant) will propagate the first object if required.
noseason() can either use weighted or unweighted wt means.
Accessor and replacement methods sr and sr<- operate directly on the predictModel in FLBiol@rec. rec() returns the observation, from @n[1,], and rec.hat the prediction from the model params.
FLCore 2.6.18
BUG FIXES
survey(FLStock, FLIndex) returns full FLIndex object.
rbind(FLPar, FLPar) will keep dimnames names to those of first element, e.g. ‘refpts’
FLCore 2.6.17
BUG FIXES
qname in data.frame from FLPars is now a factor to not brake geom_flpar.
sel as argument in survey(FLStock, FLIndex).
vb(FLStock) now uses directly catch.sel().
segreg simplified to play better with plots.
USER-VISIBLE CHANGES
Added g (gram) as recognized uom
Added uoms operations for g (gram).
New fwd(FLStock) method projects from first year N for F and M.
Renamed fwd(FLStock) as adjust.
Reformulated survey() methods, now works for both FLIndex and FLIndexBiomass.
oem(biomass=TRUE) returns an aggregated index ib biomass.
FLCore 2.6.16
BUG FIXES
uom() does not strip spaces inside the string, makes ‘1000 t’ work.
Products of t and multiples of 10 return correct units #62
getPlural ignored derived classes, like FLIndexBiomass, now dispatches on FLI and FLS.
harvest(FLQ) now runs optimize for one year objects, handles well iters.
computeCatch(FLStock) propagates slots if not matching. Logical subsetting fails otherwise.
runstest made safer.
vb(FLStock) now uses directly catch.sel().
USER-VISIBLE CHANGES
uom() is not called anymore on FLQuant - numeric operations.
NEW FEATURES
survivors(FLStock) function calculates the population survivors and returns them as an FLQuant.
Methods have been defined for aithmetic operations element by element between two FLQuants objects, and for dividing each of an FLQuants by each of an FLPars of the same length.
fwdWindow(FLStock) method to extend with same syntax as for other classes.
fwd(FLStock) method projects forward from iniial timestep to reconstruct abundances from F and M.
FLCore 2.6.15
USER-VISIBLE CHANGES
FLCore now imports ggplot2 to avoid the clash over the %+% operator veings defined in both packages. FLCore now uses ggplot::%+% as basis for the method generic. Only this function is imported, as FLCore does not use any other ggplot2 method.
qapply() now has a simplify argument to call unlist() on the output and return a vector. Deafults to simplify=FALSE
windows accepts a negative value for end and will substract that number of years from the object.
metrics() can now handle formulas combining object functions and vector or FLPar elements, e.g. metrics(ple4, ~ssb/Blim, FLPar(Blim=300000))
NEW FEATURES
mohnMatrix to construct a table of metrics to compute Mohn’s rho from an FLStocks object obtained from a restrospective analysis.
readVPAInterCatch creates an FLQuant from a VPA file in the format exported by ICES Intercatch system.
fwd(FLQuant) to move one year forward a population vector.
fwd(FLStock) calculates survivors and places them one year one age ahead.
qapply can simplify output, calling unlist.
divide() separates object along iters into list.
cv(FLQuantPoint) returns std/mean.
New as.data.frame method for FLQuantPoint.
‘1000 t’ is now accepted by uom().
BUG FIXES
iter<- method for FLBiol and predictModel.
logrstandard can now deal with NaN
FLCore 2.6.14
NEW FEATURES
intersect method called on two FLQuants returns them subset to only the common dimension names.
standardUnits provides a possible set of standard units of measurement in complex object. Set now for FLS/FLStock, using 1000, kg, t, m, and f, as in data(ple4).
append method for FLQuant and FLStock adss an object to another by year dimnames or ar year specified by ‘after’.
FLCore 2.6.12
DEPRECATED & DEFUNCT
flc2flq has been deprecated. Use as(object, ‘FLQuant’) instead.
BUG FIXES
Fix to iter(vector) after addition of iterators dependency.
FLCore 2.6.11
NEW FEATURES
dimnames(FLComp) method defined, returns dimnames corresponding to maximum length per dimension.
USER-VISIBLE CHANGES
combine(FLQuant) and combine (FLComp) can now accept multiple objects, useful for using with foreach’s .multicombine.
Replacement method for FLlst elements ([[<-) now allows extending it.
Dependency added on iterators package. iter() method was overwritten when iterators was loaded.
window(FLQuantDistr) method added to deal with @var slot
Method %*% for FLQuants,FLPar added
Better handling of currency units, so far for EUR and USD. Symbols are accepted
show() for FLComp-derived classes will call summary instead of printDefault. print() will still show the full object
BUG FIXES
propagate(FLPar) placed the original object in the matching dimname$iter, instead of iter=1
Methods for %^% and ^ did not deal properly with units. Exponentation now returns the units of the base
FLCore 2.6.9
NEW FEATURES
survSRR implements Taylor et al (2013, doi: 10.1016/j.fishres.2012.04.018) model for low fecundity species.
ssf(FLStock) method returns the Spawning Stock Fecundity, as stock.n times mat, where mat holds fecundity by individual
spread() function to make available inside a function a list of parameters
USER-VISIBLE CHANGES
Added calcF=TRUE to simplify(), to speed it up when harvest is not needed
FLCore 2.6.7
NEW FEATURES
Added iterProb(FLQuant) method
USER-VISIBLE CHANGES
writeADMB now accepts append=TRUE/FALSE
Added generics from mpb and FLRP
Improved simplify(FLStock)
predict(predictModel) now accepts numeric vectors and FLPar objects in …
BUG FIXES
Corrected simplify(FLStock) to use unweighted means for wts
Added … to msy et al generics
Added numeric code 23 for bevholtss3
BUG in ‘[’, wrong pgroup if i=-1
Corrected simplify(FLStock) to use unweighted means for wt
Bug in uom for FLQ,numeric when numeric was of length > 1
Bug when dims was only one of unit or area
Convert numeric to uom in Arith only if length==1
FLCore 2.6.6
NEW FEATURES
window(FLStocks) method to apply same window call across all elements.
combine(FLStocks) method collapses all elements into a single FLStock object. with as many iters as elements in the list, must all have 1 iter.
combine(FLQuants, FLQuants) merges them one element at a time.
drop(FLQuant) returns the result of a call to base::drop on @.Data.
New verify() method for complex classes evaluates object against a set of rules. Checks content rather than structure, as validity functions do.
New ruleset method to return standard verify rules per class.
window() and expand() methods for FLPar.
iter() method for FLlst, lapplies it along the list
USER-VISIBLE CHANGES
propagate(FLPar) to return object if iter == iters #45.
Ratios of numbers written in alternative ways now also return an empty character.
BUG FIXES
dimnames<- for FLStock with no ages failed when changing age name #42.
uom can now handle better products with units containing divisions.
coerce(FLBiol, FLBiolcpp) will now extend srparam to have as many years as the object, to allow params per time period to be passed and used.
coerce(FLBiol, FLBiolcpp) now windows FLPar if year is given.
trim(FLBiol) is able to handle predictModel slots.
[[<- and $<- FLlst now work on extended classes, like predictModel.
predict(predictModel) now handles correctly iters and extra FLPar dimensions.
DEPRECATED & DEFUNCT
catchSel is to be substituted by catch.sel, use the later instead
wt<-(FLStock) is to be deprecated, use the individual accessor methods instead
FLCore 2.6.5
NEW FEATURES
New harvest method for stock.n, catch.n and m, by minimizing diff in catch.
survey and cpue methods to generate observations from an operating model
knit_print.FLQuant method for the printr package, better printing of FLQuant objects in knitr documents
USER-VISIBLE CHANGES
FLStock creator uses empty object for sizing, keeps iters but drops them if object(s) are named.
BUG FIXES
Add tiny value to landings and discards to ensure no division by zero in computeCatch.
Added reduced version to print(FLPar, reduced=TRUE) to reuse in summary methods
FLCore 2.6.4
NEW FEATURES
%=% operator to modify on thed fly the content of an FLQuant/FLArray. Object structure can be reused with contents being changed, e.g. FLQuant(2, dim=c(3,10)) %=% 0 will return the object with zeros.
FLModelSim and FLModelSims new classes
[<- FLArray now accepts an input FLQuant and keeps the structure, still recyling as appropriate.
New FLStockLen class for length-based stock data and results.
New tS and tS<- method to extract and replace individual time steps in an object with years and seasons
tsp method for FLQuant returns ‘tsp’ attribute: start, end and frequency (seasons)
Arith method for FLQuant is now unit-aware, see ?units
wireframe method from lattice now available for FLQuant
[ method for FLQuantDistr
FLIndexBiomass class for biomass-based indices of abundance.
Class FLBiolcpp for interfacing with CPP
New catch.sel method for FLStock, computed as proportion across ages of harvest
predictMosdel class for use in FLBiol
A set of aliases for the class creators is now available. Should be used only when working interactively.
Added dim method to FLQuant and FLStock, ensures an unnamed vector is returned
Added $ method for FLQuant, operates along ‘quant’ dimension
New method metrics to compute from list or function
Added vb method for vulnerable biomass
USER-VISIBLE CHANGES
model.frame(FLComp) now has an mcf=TRUE argument to correct slots of different dim
computeLogLik method added to FLModel. Will return a logLik object calculated with the data and params in the object
New iterMedians(FLQuant) method to applky median along iter dim
coerce method for data.frame to FLPar now assumes a 2D structure with iters as rows and params as columns
rlnorm(FLPar, …) and rnorm(FLPar, …) now available
mvrnorm(numeric, FLQuant) and mvrnorm(numeric, FLQuant, matrix) now available
propagate(FLComp) now propagates FLPar slots as well
FLFleet, FLMetier and FLCatch classes (plus their plurals) and methods have been moved to the FLFleet package
ifelse has now been definedx for test=“FLQuant”
as.data.frame for FLQuant(s) and FLComp now has an option cohort=FALSE to return a column named cohort, calculated as year-age. Ony for age-quanted objects
getPlural is now an S4 method dispatching on singular classes and returning the name of the corresponding FLlst-based class
as.data.frame(FLQuants) returns qname as factor with levels in the order of the input object
modified quantile(FLQuant) so dimnames in iter follow quantile(array), e.g. 50%
tail method for FLQuant, operates by default along the year dimension.
deprecated sr function is now a method to return aligned stock/recruits FLQuants from an FLStock
propagate(FLComp) accepts extending an object to existing nu mber of iters for all other slots of length 1.
trim(FLS) u[pdates min/maxfbar if needed
transform(FLComp) now accepts a named FLQuants object as substitution argument (…)
FLQuants() now accepts an FLCOMP object and a list of names/functions to be used to extract individual FLQuant(s)
FLPar validity now checks that content is numeric. Default frist dimname is now ‘params’
FLIndices class can take both FLIndex and FLIndexBiomass objects
mean.lifespan renamed as meanLifespan to avoid S3 conflict
uom() returns kg for 1 * kg
expand() now stops if new dimnames do not contain old ones and these were of length greater than 1
seasonSums is now based on colSums and aperm, 75 times faster
new lattice-based plot(FLStocks)
Added dimensions line to summary(FLComp)
Defining fwd generic here so it can be used by mpb and Flash(er)
Validity for FLlst is now more flexible to accomodate children classes like FLIndexBiomass
Dropped redundant Sums and Products methods for FLQuants, use Reduce(“+”, …) instead
BUG FIXES
coerce of data.frame to FLPar deals rightly with multiple params and no iters in wide format.
iterMeans(FLQuant) was not operating along the 6th dim
coerce from FLPar to data.frame now works as expected
Added check for range names to FLComp class validity. Elements must be named with non-empty strings and contain, at least, min, max, minyear and maxyear
coerce from data.frame to FLPar now handles correctly iters
apply(FLArray) did not keep the object units
rnorm, rlnorm and rpois did not keep tje object units
code2name for FLSR did not reocngize properly bevholtSV
fmle() can now use method=“Brent” for one parameter problems
New ple4.biol with data up to 2008. No integer value
prototype object for FLComp VIRTUAl class has name as character(1)
as.FLQuant(df) failed on objects with no ‘year’ column