FLCore-package: Core package of FLR, fisheries modelling in R.
In FLCore: Core package of FLR, fisheries modelling in R.
Description
Details
Author(s)
References
Description
FLCore contains the core classes and methods for FLR, a framework for fisheries modelling and management strategy simulation in R. Developed by a team of fisheries scientists in various countries. More information can be found at http://flr-project.org/, including a development mailing list.
Details
Package: FLCore
Version: 3.0
Date: 2009
Depends: methods, R(>= 2.8.1), graphics, stats, stats4, grid, lattice
License: GPL 2 or above
Collate: FLArray.R FLQuant.R FLQuantPoint.R FLAccesors.R FLComp.R FLlst-class.R FLStock.R FLCatch.R FLQuants-methods.R FLPar.R io.FLStock.R FLBiol.R FLCohort.R FLMetier.R FLFleet.R FLIndex.R FLlst-methods.R io.FLIndices.R FLModel.R FLSR.R SRmodels.R FLtest.R coerce.R zzz.R
LazyLoad: Yes
LazyData: Yes
Built: R 2.8.1; i686-pc-linux-gnu; 2009-01-22 12:08:46; unix
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FLArray Class FLArray
FLBiol Class FLBiol
FLBiols Class FLBiols
FLCatch Class FLCatch
FLCatches Class FLCatches
FLCohort Class FLCohort
FLCohorts Class FLCohorts
FLComp Class FLComp
FLFleet Class FLFleet
FLFleets Class FLFleets
FLIndex Class FLIndex
FLIndices Class FLIndices
FLMetier Class FLMetier
FLMetiers Class FLMetiers
FLModel Class FLModel for statistical models
FLPar Class FLPar
FLQuant FLQuant class for numerical data
FLQuantPoint Class FLQuantPoint
FLQuants Class FLQuants
FLSR Class FLSR
FLStoc Class FLStock
FLStocks Class FLStocks
FLlst Class FLlst
Methods:
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AIC Akaike information criterion (AIC) method
Arith Arithmetic methods for FLQuant objects
BIC Bayesian information criterion (BIC) method
E Method E
FLBiols-methods Method FLBiols
FLCatch-accesors Accesor and replacement methods for the FLCatch
class
FLCatch-methods Method FLCatch
FLCatches-methods Method FLCatches
FLCohort-methods Method FLCohort
FLCohorts-methods Method FLCohorts
FLCore-package FLCore package of the FLR system
FLFleet-methods Method FLFleet
FLFleets-methods Method FLFleets
FLIndex Create FLIndex objects
FLIndices-methods Method FLIndices
FLMetier-methods Method FLMetier
FLMetiers-methods Method FLMetiers
FLModel-methods Method FLModel
FLPar-methods Method FLPar
FLQuant-methods Create FLQuant objects
FLQuantPoint-accesors Method lowq
FLQuantPoint-methods Method FLQuantPoint
FLQuants-methods Method FLQuants
FLSR-methods Method FLSR
FLStock Create FLStock objects
FLStocks-methods Method FLStocks
FLlst-methods Method FLlst
FLtest FLtest functions for running simple units tests
SRModelName Convenience function to identify an SR model by
its formula
SRModels Stock-Recruitment models
[,FLArray,ANY,ANY-method
Extract or Replace Parts of an FLR Object
ac FLCore-internal
apply,ANY,missing,missing-method
Method apply
as.FLBiol Old S3 coercion methods
as.data.frame,ANY,ANY,ANY-method
Method as.data.frame
barchart,ANY,ANY-method
Method barchart
bkey Generate key for bubbles plot
bubbles Bubbles plot
catchNames Method catchNames
ccplot Catch-curves plot
coerce,FLlst,list-method
Method coerce
computeCatch Methods to compute total catch, landings,
discards and stock biomass
createFLAccesors Create accesor methods for a given class
cv Coefficient of Variation of FLR objects with
multiple iterations
dimnames<-,ANY,missing-method
Modify dimnames of an FLQuant
dims List with information on object dimensions
expand Trim FLR objects using named dimensions
fbar Calculates mean harvest rate or fishing
mortality
flc2flq Coerce FLCohort into FLQuant.
fmle Method fmle
harvest,FLBiol-method Harvest calculations for FLBiol
is.FLBiol Methods to determine the class of a given
object
iter Select or modify iterations of an FLR object
iters Method iters
jacknife Jacknife resampling
lapply,ANY,missing-method
Method lapply
leslie Method for calculating Leslie matrix dynamics
of an FLBiol object
lowess,FLSR,missing-method
Method lowess
mcf Method mcf
mean,ANY-method Method mean
mean.lifespan Method for calculating mean lifespan, given the
natural mortality
median,ANY,missing-method
Method median
mergeFLStock Merging FLStock objects
metier Method metier
model.frame,ANY-method
Method model.frame
name Accesor and replacement methods for complex S4
classes
names,ANY-method Method names
nls,ANY,ANY,missing,missing,missing,missing,missing,missing,missing,missing,missing,missing-method
Method nls
ple4 FLCore datasets
plot,ANY,ANY-method Method plot
predict,ANY-method Method predict
print,ANY-method Method print
propagate Extend an FLQuant along the iter dimension
pv Population variability
qapply Method qapply
quant Method quant
quantSums Methods to compute sums, means and vars of
FLQuant objects
quantTotals Method quantTotals
quantile,ANY-method Method quantile
r Method for calculating intrinsic rate of
increase from an FLBiol object
range-methods Method range
readVPAFile Input/Output of FLR objects
revenue Method revenue
rgamma,ANY,ANY,ANY,ANY-method
Method rgamma
rlnorm,ANY,ANY,ANY-method
Method rlnorm
rnorm,ANY,ANY,ANY-method
Method rnorm
rpois,ANY,ANY,ANY-method
Method rpois
sd,FLModel,missing-method
Standard deviation of an FLModel object
setPlusGroup Method setPlusGroup
show,ANY-method Method show
sop Calculates the sum of products correction
splom,ANY,ANY-method Method splom
spr0 Method spr0
sr Stock-recruitment model function
ssb Method ssb
ssbpurec Method ssbpurec
ssn Method ssn
stripplot,ANY,ANY-method
Method stripplot
summary,ANY-method Method summary
survprob Method for calculating survival probabilties
given mortaloty in the FLBiol object
sweep-methods Sweep out FLQuant Summaries
transform,ANY-method Transform elements of a complex FLR object
trim Trim FLR objects using named dimensions
units,ANY-method units attribute for FLQuant objects
update,FLModel-method Method update
upper Methods upper and lower
var,ANY,missing,missing,missing-method
Variance of an FLPar
window,ANY-method Extract time (year) windows of an FLR object
Author(s)
FLR Team and various contributors. Initial design by Laurence T. Kell & Philippe Grosjean.
Maintainer: FLR Team <flr-team@flr-project.org>
References
Website at http://flr-project.org/
Kell L.T., Mosqueira I., Grosjean P., Fromentin J-M., Garcia D.,
Hillary R., Jardim E., Pastoors M., Poos J.J., Scott F. & Scott R.D. 2007.
FLR: an open-source framework for the evaluation and development of management
strategies. ICES J. of Mar. Sci. 20: 289-290.
FLCore documentation built on May 2, 2019, 5:46 p.m.
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Description Details Author(s) References
Description
FLCore contains the core classes and methods for FLR, a framework for fisheries modelling and management strategy simulation in R. Developed by a team of fisheries scientists in various countries. More information can be found at http://flr-project.org/, including a development mailing list.
Details
| Package: | FLCore |
| Version: | 3.0 |
| Date: | 2009 |
| Depends: | methods, R(>= 2.8.1), graphics, stats, stats4, grid, lattice |
| License: | GPL 2 or above |
| Collate: | FLArray.R FLQuant.R FLQuantPoint.R FLAccesors.R FLComp.R FLlst-class.R FLStock.R FLCatch.R FLQuants-methods.R FLPar.R io.FLStock.R FLBiol.R FLCohort.R FLMetier.R FLFleet.R FLIndex.R FLlst-methods.R io.FLIndices.R FLModel.R FLSR.R SRmodels.R FLtest.R coerce.R zzz.R |
| LazyLoad: | Yes |
| LazyData: | Yes |
| Built: | R 2.8.1; i686-pc-linux-gnu; 2009-01-22 12:08:46; unix |
Classes:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | FLArray Class FLArray
FLBiol Class FLBiol
FLBiols Class FLBiols
FLCatch Class FLCatch
FLCatches Class FLCatches
FLCohort Class FLCohort
FLCohorts Class FLCohorts
FLComp Class FLComp
FLFleet Class FLFleet
FLFleets Class FLFleets
FLIndex Class FLIndex
FLIndices Class FLIndices
FLMetier Class FLMetier
FLMetiers Class FLMetiers
FLModel Class FLModel for statistical models
FLPar Class FLPar
FLQuant FLQuant class for numerical data
FLQuantPoint Class FLQuantPoint
FLQuants Class FLQuants
FLSR Class FLSR
FLStoc Class FLStock
FLStocks Class FLStocks
FLlst Class FLlst
|
Methods:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 | AIC Akaike information criterion (AIC) method
Arith Arithmetic methods for FLQuant objects
BIC Bayesian information criterion (BIC) method
E Method E
FLBiols-methods Method FLBiols
FLCatch-accesors Accesor and replacement methods for the FLCatch
class
FLCatch-methods Method FLCatch
FLCatches-methods Method FLCatches
FLCohort-methods Method FLCohort
FLCohorts-methods Method FLCohorts
FLCore-package FLCore package of the FLR system
FLFleet-methods Method FLFleet
FLFleets-methods Method FLFleets
FLIndex Create FLIndex objects
FLIndices-methods Method FLIndices
FLMetier-methods Method FLMetier
FLMetiers-methods Method FLMetiers
FLModel-methods Method FLModel
FLPar-methods Method FLPar
FLQuant-methods Create FLQuant objects
FLQuantPoint-accesors Method lowq
FLQuantPoint-methods Method FLQuantPoint
FLQuants-methods Method FLQuants
FLSR-methods Method FLSR
FLStock Create FLStock objects
FLStocks-methods Method FLStocks
FLlst-methods Method FLlst
FLtest FLtest functions for running simple units tests
SRModelName Convenience function to identify an SR model by
its formula
SRModels Stock-Recruitment models
[,FLArray,ANY,ANY-method
Extract or Replace Parts of an FLR Object
ac FLCore-internal
apply,ANY,missing,missing-method
Method apply
as.FLBiol Old S3 coercion methods
as.data.frame,ANY,ANY,ANY-method
Method as.data.frame
barchart,ANY,ANY-method
Method barchart
bkey Generate key for bubbles plot
bubbles Bubbles plot
catchNames Method catchNames
ccplot Catch-curves plot
coerce,FLlst,list-method
Method coerce
computeCatch Methods to compute total catch, landings,
discards and stock biomass
createFLAccesors Create accesor methods for a given class
cv Coefficient of Variation of FLR objects with
multiple iterations
dimnames<-,ANY,missing-method
Modify dimnames of an FLQuant
dims List with information on object dimensions
expand Trim FLR objects using named dimensions
fbar Calculates mean harvest rate or fishing
mortality
flc2flq Coerce FLCohort into FLQuant.
fmle Method fmle
harvest,FLBiol-method Harvest calculations for FLBiol
is.FLBiol Methods to determine the class of a given
object
iter Select or modify iterations of an FLR object
iters Method iters
jacknife Jacknife resampling
lapply,ANY,missing-method
Method lapply
leslie Method for calculating Leslie matrix dynamics
of an FLBiol object
lowess,FLSR,missing-method
Method lowess
mcf Method mcf
mean,ANY-method Method mean
mean.lifespan Method for calculating mean lifespan, given the
natural mortality
median,ANY,missing-method
Method median
mergeFLStock Merging FLStock objects
metier Method metier
model.frame,ANY-method
Method model.frame
name Accesor and replacement methods for complex S4
classes
names,ANY-method Method names
nls,ANY,ANY,missing,missing,missing,missing,missing,missing,missing,missing,missing,missing-method
Method nls
ple4 FLCore datasets
plot,ANY,ANY-method Method plot
predict,ANY-method Method predict
print,ANY-method Method print
propagate Extend an FLQuant along the iter dimension
pv Population variability
qapply Method qapply
quant Method quant
quantSums Methods to compute sums, means and vars of
FLQuant objects
quantTotals Method quantTotals
quantile,ANY-method Method quantile
r Method for calculating intrinsic rate of
increase from an FLBiol object
range-methods Method range
readVPAFile Input/Output of FLR objects
revenue Method revenue
rgamma,ANY,ANY,ANY,ANY-method
Method rgamma
rlnorm,ANY,ANY,ANY-method
Method rlnorm
rnorm,ANY,ANY,ANY-method
Method rnorm
rpois,ANY,ANY,ANY-method
Method rpois
sd,FLModel,missing-method
Standard deviation of an FLModel object
setPlusGroup Method setPlusGroup
show,ANY-method Method show
sop Calculates the sum of products correction
splom,ANY,ANY-method Method splom
spr0 Method spr0
sr Stock-recruitment model function
ssb Method ssb
ssbpurec Method ssbpurec
ssn Method ssn
stripplot,ANY,ANY-method
Method stripplot
summary,ANY-method Method summary
survprob Method for calculating survival probabilties
given mortaloty in the FLBiol object
sweep-methods Sweep out FLQuant Summaries
transform,ANY-method Transform elements of a complex FLR object
trim Trim FLR objects using named dimensions
units,ANY-method units attribute for FLQuant objects
update,FLModel-method Method update
upper Methods upper and lower
var,ANY,missing,missing,missing-method
Variance of an FLPar
window,ANY-method Extract time (year) windows of an FLR object
|
Author(s)
FLR Team and various contributors. Initial design by Laurence T. Kell & Philippe Grosjean.
Maintainer: FLR Team <flr-team@flr-project.org>
References
Website at http://flr-project.org/
Kell L.T., Mosqueira I., Grosjean P., Fromentin J-M., Garcia D., Hillary R., Jardim E., Pastoors M., Poos J.J., Scott F. & Scott R.D. 2007. FLR: an open-source framework for the evaluation and development of management strategies. ICES J. of Mar. Sci. 20: 289-290.
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