FLCore 2.6.17 Unreleased

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’s 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 Unreleased

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.
  • sr(FLBiol) to access full @rec slot.
  • 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 Unreleased

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 Unreleased

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 Unreleased

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 Unreleased

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.

BUG FIXES

FLCore 2.6.10 Unreleased

NEW FEATURES

  • 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 Unreleased

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 Unreleased

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 Unreleased

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 Unreleased

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 Unreleased

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
  • propagate(FLQuant) now accepts iter == dim[6]
  • Faulty comparison in expand(FLArray) fixed #7
  • Wrong test in validity for FLModelSim
  • Fixed bug in FLPar %% FLPar when objects were actually equal in dims, always returned product
  • quantile(FLQuant) returned oject with wrong dimensions
  • FLPar(missing) now creates objects with right number of iters, works when used with call()
  • lapply(FLst) works on zero length object, does nothing
  • square operators for FLlst return the right names, desc and lock
  • Attributes of FLPar maintained by [ and [<-
  • as(data.frame, ‘FLPar’) transposed objects without need
  • [<- FLlst now respects names when list elements are added
  • rbind(FLPar) should work better now
  • slot now has by default an emptyenv()
  • uom is now safer to non-strings by using sprintf() for conversion
  • Quick fix for readIndicesAdapt dimensions
  • apply(FLArray) did not return an FLQuant if function did not change the dimensions of the object

DOCUMENTATION

  • All of the documentation has been converted to roxygen2.

DEPRECATED & DEFUNCT

  • FLFleet, FLMetier and FLCatch classes (plus their plurals) and methods have been moved to the FLFleet package