mizer-package	mizer-package
.checkRateFunctionOutput	dot-checkRateFunctionOutput
addPlot	addPlot
addPlot.ArraySpeciesBySize	addPlot
addPlot.ArrayTimeBySpecies	addPlot
addSpecies	addSpecies
adjustSizeGrid	adjustSizeGrid
adjustSizeGrid.MizerParams	adjustSizeGrid
age_mat	age_mat
age_mat_vB	age_mat_vB
age_mat_vB.data.frame	age_mat_vB
age_mat_vB.default	age_mat_vB
age_mat_vB.MizerParams	age_mat_vB
animate	animate
animate.ArrayTimeBySpeciesBySize	animate
animate.MizerSim	animate
animateSpectra	animate
apply_wlim	apply_wlim
ArrayResourceBySize	ArrayResourceBySize
ArraySpeciesBySize	ArraySpeciesBySize
ArrayTimeByResourceBySize	ArrayTimeByResourceBySize
ArrayTimeBySpecies	ArrayTimeBySpecies
ArrayTimeBySpeciesBySize	ArrayTimeBySpeciesBySize
as.data.frame	as.data.frame
as.data.frame.ArraySpeciesBySize	as.data.frame
as.data.frame.ArrayTimeBySpecies	as.data.frame
as.data.frame.ArrayTimeBySpeciesBySize	as.data.frame
assertExtensionChain	assertExtensionChain
balance_resource_logistic	resource_logistic
balance_resource_semichemostat	resource_semichemostat
baseMizerClass	baseMizerClass
BevertonHoltRDD	BevertonHoltRDD
bin_average_summary_weight	bin_average_summary_weight
bin_average_weight	bin_average_weight
bin_midpoints	bin_midpoints
box_pred_kernel	box_pred_kernel
calculated_species_params	species_params
calc_selectivity	calc_selectivity
calibrateBiomass	calibrateBiomass
calibrateNumber	calibrateNumber
calibrateYield	calibrateYield
catchability	setFishing
catchability<-	setFishing
cdf_y_label	cdf_y_label
clearExtensionChain	clearExtensionChain
coerceToExtensionClass	coerceToExtensionClass
compareExtensionChains	compareExtensionChains
compareParams	compareParams
completeSpeciesParams	completeSpeciesParams
constantEggRDI	constantEggRDI
constantRDD	constantRDD
constant_other	constant_other
convert_plot_size_axis	convert_plot_size_axis
customFunction	customFunction
defaults_edition	defaults_edition
default_pred_kernel_params	default_pred_kernel_params
defineExtensionClasses	defineExtensionClasses
defineOrCheckClass	defineOrCheckClass
different	different
dispatchExtensions	dispatchExtensions
distanceMaxRelRDI	distanceMaxRelRDI
distanceSSLogN	distanceSSLogN
double_sigmoid_length	double_sigmoid_length
dw	w
dw_full	w
emptyParams	emptyParams
ensureExtensionNamespaces	ensureExtensionNamespaces
expandSizeGrid	expandSizeGrid
expandSizeGrid.MizerParams	expandSizeGrid
extensionRequirements	extensionRequirements
extensionVersion	extensionVersion
extensionVersions	extensionVersions
extension_needs_upgrading	extension_needs_upgrading
ext_diffusion	setExtDiffusion
ext_diffusion<-	setExtDiffusion
ext_encounter	setExtEncounter
ext_encounter<-	setExtEncounter
ext_mort	setExtMort
ext_mort<-	setExtMort
filter_plot_length_limits	filter_plot_length_limits
finalN	finalN
finalNOther	NOther
finalNResource	finalN
finalParams	finalParams
flux_from_rates	flux_from_rates
flux_units	flux_units
formatExtensionChain	formatExtensionChain
gear_params	gear_params
gear_params.data.frame	gear_params
gear_params.gear_params	gear_params
gear_params.MizerParams	gear_params
gear_params.MizerSim	gear_params
gear_params<-	gear_params
gear_params<-.MizerParams	gear_params
getBiomass	getBiomass
getCatchability	setFishing
getColours	setColours
getCommunitySlope	getCommunitySlope
getComponent	setComponent
getCriticalFeedingLevel	getCriticalFeedingLevel
getDiet	getDiet
getDiffusion	getDiffusion
getEffort	getEffort
getEGrowth	getEGrowth
getEncounter	getEncounter
getERepro	getERepro
getEReproAndGrowth	getEReproAndGrowth
getESpawning	getESpawning
getExtEncounter	setExtEncounter
getExtMort	setExtMort
getFeedingLevel	getFeedingLevel
getFlux	getFlux
getFlux.MizerParams	getFlux
getFlux.MizerSim	getFlux
getFluxGradient	getFluxGradient
getFluxGradient.MizerParams	getFluxGradient
getFluxGradient.MizerSim	getFluxGradient
getFMort	getFMort
getFMortGear	getFMortGear
getGrowthCurves	getGrowthCurves
getInitialEffort	setFishing
getInteraction	getInteraction
getLinetypes	setColours
getM2	getM2
getM2Background	getM2Background
getMaturityProportion	setReproduction
getMaxIntakeRate	setMaxIntakeRate
getMeanMaxWeight	getMeanMaxWeight
getMeanWeight	getMeanWeight
getMetabolicRate	setMetabolicRate
getMetadata	setMetadata
getMort	getMort
getN	getN
getParams	getParams
getPhiPrey	getPhiPrey
getPredKernel	setPredKernel
getPredMort	getPredMort
getPredRate	getPredRate
getProportionOfLargeFish	getProportionOfLargeFish
getRateFunction	setRateFunction
getRates	getRates
getRDD	getRDD
getRDI	getRDI
getRegisteredExtensions	getRegisteredExtensions
getReproductionLevel	getReproductionLevel
getReproductionProportion	setReproduction
getRequiredRDD	getRequiredRDD
getResourceCapacity	getResourceDynamics
getResourceDynamics	getResourceDynamics
getResourceLevel	getResourceDynamics
getResourceMort	getResourceMort
getResourceRate	getResourceDynamics
getSearchVolume	setSearchVolume
getSelectivity	setFishing
getSimParams	getSimParams
getSSB	getSSB
getTimes	getTimes
getTrophicLevel	getTrophicLevel
getTrophicLevelBySpecies	getTrophicLevelBySpecies
getYield	getYield
getYieldGear	getYieldGear
getZ	getZ
get_ArrayResourceBySize_w	get_ArrayResourceBySize_w
get_ArraySpeciesBySize_w	get_ArraySpeciesBySize_w
get_ArrayTimeBySpeciesBySize_w	get_ArrayTimeBySpeciesBySize_w
get_f0_default	get_f0_default
get_gamma_default	get_gamma_default
get_h_default	get_h_default
get_initial_n	get_initial_n
get_ks_default	get_ks_default
get_phi	get_phi
get_sim_rate_slice	get_sim_rate_slice
get_sim_rate_time_elements	get_sim_rate_time_elements
get_size_range_array	get_size_range_array
get_species_size_rate_from_sim	get_species_size_rate_from_sim
get_species_time_rate_from_sim	get_species_time_rate_from_sim
get_steady_state_n	get_steady_state_n
get_time_elements	get_time_elements
given_species_params	species_params
given_species_params.data.frame	species_params
given_species_params.given_species_params	species_params
given_species_params.MizerParams	species_params
given_species_params.MizerSim	species_params
given_species_params<-	species_params
given_species_params<-.MizerParams	species_params
idxFinalT	finalN
indicator_functions	indicator_functions
initialN	initialN-set
initialN.MizerParams	initialN-set
initialN.MizerSim	initialN-set
initialN<-	initialN-set
initialNOther	initialNOther-set
initialNOther<-	initialNOther-set
initialNResource	initialNResource-set
initialNResource.MizerParams	initialNResource-set
initialNResource.MizerSim	initialNResource-set
initialNResource<-	initialNResource-set
initialParams	initialParams
initial_effort	initial_effort
initial_effort<-	initial_effort
intake_max	setMaxIntakeRate
intake_max<-	setMaxIntakeRate
inter	inter
interaction_matrix	setInteraction
interaction_matrix<-	setInteraction
is.ArrayResourceBySize	ArrayResourceBySize
is.ArraySpeciesBySize	ArraySpeciesBySize
is.ArrayTimeByResourceBySize	ArrayTimeByResourceBySize
is.ArrayTimeBySpecies	ArrayTimeBySpecies
is.ArrayTimeBySpeciesBySize	ArrayTimeBySpeciesBySize
is.gear_params	gear_params
is.given_species_params	species_params
is.species_params	species_params
isSuffixChain	isSuffixChain
isVersionRequirement	isVersionRequirement
knife_edge	knife_edge
l2w	l2w
lognormal_pred_kernel	lognormal_pred_kernel
log_breaks	log_breaks
makeExtensions	makeExtensions
make_linesize	make_linesize
make_mizer_plot	make_mizer_plot
markBackground	markBackground
matchBiomasses	matchBiomasses
matchGrowth	matchGrowth
matchNumbers	matchNumbers
matchYields	matchYields
maturity	setReproduction
maturity<-	setReproduction
melt	reexports
metab	setMetabolicRate
metab<-	setMetabolicRate
mizer	mizer-package
mizerDiffusion	mizerDiffusion
mizerEGrowth	mizerEGrowth
mizerEncounter	mizerEncounter
mizerERepro	mizerERepro
mizerEReproAndGrowth	mizerEReproAndGrowth
mizerFeedingLevel	mizerFeedingLevel
mizerFMort	mizerFMort
mizerFMortGear	mizerFMortGear
mizerMort	mizerMort
MizerParams	MizerParams
MizerParams-class	MizerParams-class
mizerPredMort	mizerPredMort
mizerPredRate	mizerPredRate
mizerRates	mizerRates
mizerRDI	mizerRDI
mizerResourceMort	mizerResourceMort
MizerSim	MizerSim
MizerSim-class	MizerSim-class
mizer_needs_upgrading	mizer_needs_upgrading
mizer_rates_subset	mizer_rates_subset
mizer_tooltip_vars	mizer_tooltip_vars
N	N
needed_rates	needed_rates
needs_upgrading	needs_upgrading
newCommunityParams	newCommunityParams
newMultispeciesParams	newMultispeciesParams
newSingleSpeciesParams	newSingleSpeciesParams
newTraitParams	newTraitParams
noRDD	noRDD
NOther	NOther
NResource	N
NS_interaction	NS_interaction
NS_params	NS_params
NS_sim	NS_sim
NS_species_params	NS_species_params
NS_species_params_gears	NS_species_params_gears
objectExtensions	objectExtensions
other_params	setRateFunction
other_params<-	setRateFunction
parsePlotLog	parsePlotLog
parseTimePlotLog	parseTimePlotLog
plot	plot
plot.ArrayResourceBySize	plot.ArrayResourceBySize
plot.ArraySpeciesBySize	plot.ArraySpeciesBySize
plot.ArrayTimeByResourceBySize	plot.ArrayTimeByResourceBySize
plot.ArrayTimeBySpecies	plot.ArrayTimeBySpecies
plot.ArrayTimeBySpeciesBySize	plot.ArrayTimeBySpeciesBySize
plot.MizerParams	plotMizerParams
plot.MizerSim	plotMizerSim
plot2	plot2
plot2.ArraySpeciesBySize	plot2
plot2.ArrayTimeBySpecies	plot2
plot2.ArrayTimeBySpeciesBySize	plot2
plotBiomass	plotBiomass
plotBiomass.MizerSim	plotBiomass
plotBiomassObservedVsModel	plotBiomassObservedVsModel
plotCDF	plotCDF
plotCDF.MizerParams	plotCDF
plotCDF.MizerSim	plotCDF
plotCDF2	plotCDF2
plotComparisonDataFrame	plotComparisonDataFrame
plotDataFrame	plotDataFrame
plotDiet	plotDiet
plotDiet.MizerParams	plotDiet
plotDiet.MizerSim	plotDiet
plotFeedingLevel	plotFeedingLevel
plotFeedingLevel.MizerParams	plotFeedingLevel
plotFeedingLevel.MizerSim	plotFeedingLevel
plotFMort	plotFMort
plotFMort.MizerParams	plotFMort
plotFMort.MizerSim	plotFMort
plotGrowthCurves	plotGrowthCurves
plotGrowthCurves.MizerParams	plotGrowthCurves
plotGrowthCurves.MizerSim	plotGrowthCurves
plotHover	plotHover
plotHover.ArrayResourceBySize	plotHover
plotHover.ArraySpeciesBySize	plotHover
plotHover.ArrayTimeByResourceBySize	plotHover
plotHover.ArrayTimeBySpecies	plotHover
plotHover.ArrayTimeBySpeciesBySize	plotHover
plotHover.mizer_plot	plotHover
plotlyBiomass	plotBiomass
plotlyBiomassObservedVsModel	plotBiomassObservedVsModel
plotlyCDF	plotCDF
plotlyCDF2	plotCDF2
plotlyDiet	plotDiet
plotlyFeedingLevel	plotFeedingLevel
plotlyFMort	plotFMort
plotlyGrowthCurves	plotGrowthCurves
plotlyPredMort	plotPredMort
plotlySpectra	plotSpectra
plotlySpectra2	plotSpectra2
plotlySpectraRelative	plotSpectraRelative
plotlyYield	plotYield
plotlyYieldGear	plotYieldGear
plotlyYieldObservedVsModel	plotYieldObservedVsModel
plotM2	plotM2
plotMizerParams	plotMizerParams
plotMizerSim	plotMizerSim
plotPredMort	plotPredMort
plotPredMort.MizerParams	plotPredMort
plotPredMort.MizerSim	plotPredMort
plotRelative	plotRelative
plotRelative.ArraySpeciesBySize	plotRelative
plotRelative.ArrayTimeBySpecies	plotRelative
plotRelative.ArrayTimeBySpeciesBySize	plotRelative
plotRelativeDataFrame	plotRelativeDataFrame
plotSpectra	plotSpectra
plotSpectra.MizerParams	plotSpectra
plotSpectra.MizerSim	plotSpectra
plotSpectra2	plotSpectra2
plotSpectraRelative	plotSpectraRelative
plotting_functions	plotting_functions
plotYield	plotYield
plotYield.MizerSim	plotYield
plotYieldGear	plotYieldGear
plotYieldGear.MizerSim	plotYieldGear
plotYieldObservedVsModel	plotYieldObservedVsModel
plot_cdf	plot_cdf
plot_diet	plot_diet
plot_feeding_level	plot_feeding_level
plot_growth_curves	plot_growth_curves
plot_size_axis	plot_size_axis
plot_size_tooltip	plot_size_tooltip
plot_size_xlab	plot_size_xlab
plot_size_xlim	plot_size_xlim
plot_size_x_var	plot_size_x_var
plot_spectra	plot_spectra
power_law_bin_average	power_law_bin_average
power_law_pred_kernel	power_law_pred_kernel
pred_kernel	setPredKernel
pred_kernel<-	setPredKernel
prepare_spectra_cdf_data	prepare_spectra_cdf_data
print	print
print.ArraySpeciesBySize	print
print.ArrayTimeBySpecies	print
print.ArrayTimeBySpeciesBySize	print
print.mizer_plot	print.mizer_plot
print.summary.ArraySpeciesBySize	print
print.summary.ArrayTimeBySpecies	print
print.summary.ArrayTimeBySpeciesBySize	print
project	project
project.MizerParams	project
project.MizerSim	project
projectDiffusion	mizerDiffusion
projectDiffusion.MizerParams	mizerDiffusion
projectEGrowth	mizerEGrowth
projectEGrowth.MizerParams	mizerEGrowth
projectEncounter	mizerEncounter
projectEncounter.MizerParams	mizerEncounter
projectERepro	mizerERepro
projectERepro.MizerParams	mizerERepro
projectEReproAndGrowth	mizerEReproAndGrowth
projectEReproAndGrowth.MizerParams	mizerEReproAndGrowth
projectFeedingLevel	mizerFeedingLevel
projectFeedingLevel.MizerParams	mizerFeedingLevel
projectFMort	mizerFMort
projectFMort.MizerParams	mizerFMort
projectMort	mizerMort
projectMort.MizerParams	mizerMort
projectPredMort	mizerPredMort
projectPredMort.MizerParams	mizerPredMort
projectPredRate	mizerPredRate
projectPredRate.MizerParams	mizerPredRate
projectRates	mizerRates
projectRDD	projectRDD
projectRDD.MizerParams	projectRDD
projectRDI	mizerRDI
projectRDI.MizerParams	mizerRDI
projectResourceMort	mizerResourceMort
projectResourceMort.MizerParams	mizerResourceMort
projectToSteady	projectToSteady
project_n	project_n
project_n_2	project_n_2
project_n_no_diffusion	project_n
project_n_tr_bdf2	project_n_tr_bdf2
project_simple	project_simple
providesDispatchMethods	providesDispatchMethods
psi	setReproduction
readParams	saveParams
readSim	saveParams
recordExtension	recordExtension
record_given_species_params	record_given_species_params
reexports	reexports
registerExtension	registerExtension
registerExtensions	registerExtensions
relative_difference	relative_difference
removeBackgroundSpecies	removeBackgroundSpecies
removeComponent	setComponent
removeSpecies	removeSpecies
renameGear	renameGear
renameSpecies	renameSpecies
repro_prop	setReproduction
repro_prop<-	setReproduction
resolve_second_order_w	resolve_second_order_w
resource_capacity	setResource
resource_capacity<-	setResource
resource_constant	resource_constant
resource_dynamics	setResource
resource_dynamics<-	setResource
resource_level	setResource
resource_level<-	setResource
resource_logistic	resource_logistic
resource_params	resource_params
resource_params<-	resource_params
resource_power_law	resource_power_law
resource_rate	setResource
resource_rate<-	setResource
resource_semichemostat	resource_semichemostat
RickerRDD	RickerRDD
runExtensionUpgrades	runExtensionUpgrades
saveParams	saveParams
saveSim	saveParams
scaleModel	scaleModel
scaleRates	scaleRates
search_vol	setSearchVolume
search_vol<-	setSearchVolume
second_order_w	second_order_w
second_order_w<-	second_order_w
selectivity	setFishing
selectivity<-	setFishing
setBevertonHolt	setBevertonHolt
setColours	setColours
setComponent	setComponent
setExtDiffusion	setExtDiffusion
setExtDiffusion.MizerParams	setExtDiffusion
setExtEncounter	setExtEncounter
setExtMort	setExtMort
setFishing	setFishing
setInitialValues	setInitialValues
setInteraction	setInteraction
setLinetypes	setColours
setMaxIntakeRate	setMaxIntakeRate
setMetabolicRate	setMetabolicRate
setMetadata	setMetadata
setParams	setParams
setPredKernel	setPredKernel
setRateFunction	setRateFunction
setReproduction	setReproduction
setResource	setResource
setRmax	setRmax
setSearchVolume	setSearchVolume
set_community_model	set_community_model
set_multispecies_model	set_multispecies_model
set_species_param_default	set_species_param_default
set_trait_model	set_trait_model
SheperdRDD	SheperdRDD
sigmoid_length	sigmoid_length
sigmoid_weight	sigmoid_weight
simExtensionClass	simExtensionClass
sim_size_rate	sim_size_rate
sim_species_rate	sim_species_rate
species_params	species_params
species_params.data.frame	species_params
species_params.MizerParams	species_params
species_params.MizerSim	species_params
species_params.species_params	species_params
species_params<-	species_params
species_params<-.MizerParams	species_params
spectra_bin_width	spectra_bin_width
spectra_y_label	spectra_y_label
steady	steady
steadySingleSpecies	steadySingleSpecies
str	str
str.ArraySpeciesBySize	str
str.ArrayTimeBySpecies	str
str.ArrayTimeBySpeciesBySize	str
str.MizerParams	str
str.MizerSim	str
summary	summary
summary.ArraySpeciesBySize	summary
summary.ArrayTimeBySpecies	summary
summary.ArrayTimeBySpeciesBySize	summary
summary.MizerParams	summary
summary.MizerSim	summary
summary_functions	summary_functions
truncated_lognormal_pred_kernel	truncated_lognormal_pred_kernel
upgrade.MizerParams	upgrade.MizerParams
upgrade.MizerSim	upgrade.MizerSim
upgradeParams	upgradeParams
upgradeSim	upgradeSim
usesExtensionDispatch	usesExtensionDispatch
use_predation_diffusion	use_predation_diffusion
use_predation_diffusion<-	use_predation_diffusion
validateExtensionsVector	validateExtensionsVector
validate_second_order_w	validate_second_order_w
validEffortVector	validEffortVector
validGearParams	validGearParams
validGivenSpeciesParams	validSpeciesParams
validParams	validParams
validSim	validSim
validSpeciesParams	validSpeciesParams
valid_gears_arg	valid_gears_arg
valid_species_arg	valid_species_arg
w	w
w2l	l2w
w_full	w
