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gustavdelius

Improved documentation of resource parameters. Closes #303

Jan 27, 2025

ec71045 · Jan 27, 2025

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Name		Name	Last commit message	Last commit date
parent directory ..
figures		figures	Improving documentation	Oct 16, 2024
BevertonHoltRDD.Rd		BevertonHoltRDD.Rd	Updated man pages	Dec 15, 2022
MizerParams-class.Rd		MizerParams-class.Rd	Adding given_species_params slot	Dec 2, 2023
MizerParams.Rd		MizerParams.Rd	Ensure that all man pages state the return value, as required by CRAN.	Apr 25, 2023
MizerSim-class.Rd		MizerSim-class.Rd	Updates to documentation and website	Dec 22, 2022
MizerSim.Rd		MizerSim.Rd	Polishing	Mar 28, 2020
N.Rd		N.Rd	Improvements to examples on man pages.	Jul 27, 2021
NOther.Rd		NOther.Rd	Getting ready for release	Apr 2, 2020
NS_interaction.Rd		NS_interaction.Rd	Avoid use of \dontrun in examples wherever possible. Use \donttest on…	Apr 25, 2023
NS_params.Rd		NS_params.Rd	Avoid use of \dontrun in examples wherever possible. Use \donttest on…	Apr 25, 2023
NS_sim.Rd		NS_sim.Rd	Avoid use of \dontrun in examples wherever possible. Use \donttest on…	Apr 25, 2023
NS_species_params.Rd		NS_species_params.Rd	Update development web site	Aug 20, 2024
NS_species_params_gears.Rd		NS_species_params_gears.Rd	Update development web site	Aug 20, 2024
RickerRDD.Rd		RickerRDD.Rd	Graduating constantEggRDI() and customFunction() from mizerExperi…	Mar 6, 2021
SheperdRDD.Rd		SheperdRDD.Rd	Updated man pages	Dec 15, 2022
addSpecies.Rd		addSpecies.Rd	Improved error messages for addSpecies()	Mar 30, 2023
age_mat.Rd		age_mat.Rd	Updates to documentation and website	Dec 22, 2022
age_mat_vB.Rd		age_mat_vB.Rd	Updates to documentation and website	Dec 22, 2022
animateSpectra.Rd		animateSpectra.Rd	Improving documentation	Oct 16, 2024
box_pred_kernel.Rd		box_pred_kernel.Rd	Improving documentation	Oct 16, 2024
calc_selectivity.Rd		calc_selectivity.Rd	Improving documentation	Oct 16, 2024
calibrateBiomass.Rd		calibrateBiomass.Rd	Adds some 'experimental' badges	Sep 6, 2021
calibrateNumber.Rd		calibrateNumber.Rd	Updates to documentation and website	Dec 22, 2022
calibrateYield.Rd		calibrateYield.Rd	Make spelling checker happy	Oct 14, 2024
compareParams.Rd		compareParams.Rd	Ensure that all man pages state the return value, as required by CRAN.	Apr 25, 2023
completeSpeciesParams.Rd		completeSpeciesParams.Rd	validSpeciesParams() now also sets default for 'p' to be equal to 'n'.	Jan 6, 2025
constantEggRDI.Rd		constantEggRDI.Rd	Avoid use of \dontrun in examples wherever possible. Use \donttest on…	Apr 25, 2023
constantRDD.Rd		constantRDD.Rd	Graduating constantEggRDI() and customFunction() from mizerExperi…	Mar 6, 2021
constant_other.Rd		constant_other.Rd	Ensure that all man pages state the return value, as required by CRAN.	Apr 25, 2023
customFunction.Rd		customFunction.Rd	Ensure that all man pages state the return value, as required by CRAN.	Apr 25, 2023
default_pred_kernel_params.Rd		default_pred_kernel_params.Rd	Updating website for development version.	Mar 6, 2021
defaults_edition.Rd		defaults_edition.Rd	Improved defaults can now be implemented while keeping backwards comp…	Jul 15, 2022
different.Rd		different.Rd	Rename w_inf to w_max. Closes #259	Dec 11, 2022
distanceMaxRelRDI.Rd		distanceMaxRelRDI.Rd	Updating website for development version.	Mar 6, 2021
distanceSSLogN.Rd		distanceSSLogN.Rd	Updating website for development version.	Mar 6, 2021
double_sigmoid_length.Rd		double_sigmoid_length.Rd	Updated man pages	Apr 12, 2024
emptyParams.Rd		emptyParams.Rd	Rename w_inf to w_max. Closes #259	Dec 11, 2022
finalN.Rd		finalN.Rd	Improving documentation	Oct 16, 2024
finalNOther.Rd		finalNOther.Rd	More work on and testing off extension mechanism. Updated docs.	Apr 1, 2020
gear_params.Rd		gear_params.Rd	Avoiding CRAN warnings	Oct 13, 2024
getBiomass.Rd		getBiomass.Rd	Updated tests/testthat/test-plotBiomassObservedVsModel.R, and correct…	Mar 27, 2024
getCommunitySlope.Rd		getCommunitySlope.Rd	Improvements to examples on man pages.	Jul 27, 2021
getComponent.Rd		getComponent.Rd	Update documentation and remove build errors and warnings.	Sep 6, 2021
getCriticalFeedingLevel.Rd		getCriticalFeedingLevel.Rd	Improving documentation	Oct 16, 2024
getDiet.Rd		getDiet.Rd	getDiet() now also includes the contribution of the external encoun…	Aug 19, 2024
getEGrowth.Rd		getEGrowth.Rd	Improving documentation	Oct 16, 2024
getERepro.Rd		getERepro.Rd	Improving documentation	Oct 16, 2024
getEReproAndGrowth.Rd		getEReproAndGrowth.Rd	Small clarification in help page	Dec 29, 2024
getESpawning.Rd		getESpawning.Rd	Improving documentation	Oct 16, 2024
getEffort.Rd		getEffort.Rd	Improvements to examples on man pages.	Jul 27, 2021
getEncounter.Rd		getEncounter.Rd	Updated tests/testthat/test-plotBiomassObservedVsModel.R, and correct…	Mar 27, 2024
getFMort.Rd		getFMort.Rd	Improving documentation	Oct 16, 2024
getFMortGear.Rd		getFMortGear.Rd	Improving documentation	Oct 16, 2024
getFeedingLevel.Rd		getFeedingLevel.Rd	Updated tests/testthat/test-plotBiomassObservedVsModel.R, and correct…	Mar 27, 2024
getGrowthCurves.Rd		getGrowthCurves.Rd	Updated tests/testthat/test-plotBiomassObservedVsModel.R, and correct…	Mar 27, 2024
getInteraction.Rd		getInteraction.Rd	Updates to documentation and website	Dec 22, 2022
getM2.Rd		getM2.Rd	Improving documentation	Oct 16, 2024
getM2Background.Rd		getM2Background.Rd	Updated tests/testthat/test-plotBiomassObservedVsModel.R, and correct…	Mar 27, 2024
getMeanMaxWeight.Rd		getMeanMaxWeight.Rd	Rename w_inf to w_max. Closes #259	Dec 11, 2022
getMeanWeight.Rd		getMeanWeight.Rd	Improvements to examples on man pages.	Jul 27, 2021
getMort.Rd		getMort.Rd	Improving documentation	Oct 16, 2024
getN.Rd		getN.Rd	Updated tests/testthat/test-plotBiomassObservedVsModel.R, and correct…	Mar 27, 2024
getParams.Rd		getParams.Rd	Improvements to examples on man pages.	Jul 27, 2021
getPhiPrey.Rd		getPhiPrey.Rd	Avoid use of \dontrun in examples wherever possible. Use \donttest on…	Apr 25, 2023
getPredMort.Rd		getPredMort.Rd	Improving documentation	Oct 16, 2024
getPredRate.Rd		getPredRate.Rd	Improving documentation	Oct 16, 2024
getProportionOfLargeFish.Rd		getProportionOfLargeFish.Rd	Improvements to examples on man pages.	Jul 27, 2021
getRDD.Rd		getRDD.Rd	Updated tests/testthat/test-plotBiomassObservedVsModel.R, and correct…	Mar 27, 2024
getRDI.Rd		getRDI.Rd	Updated tests/testthat/test-plotBiomassObservedVsModel.R, and correct…	Mar 27, 2024
getRates.Rd		getRates.Rd	Updated tests/testthat/test-plotBiomassObservedVsModel.R, and correct…	Mar 27, 2024
getReproductionLevel.Rd		getReproductionLevel.Rd	Integrating the improved setBevertonHolt() and new `getReproduction…	Aug 1, 2021
getResourceDynamics.Rd		getResourceDynamics.Rd	Ensure that all man pages state the return value, as required by CRAN.	Apr 25, 2023
getResourceMort.Rd		getResourceMort.Rd	Updated tests/testthat/test-plotBiomassObservedVsModel.R, and correct…	Mar 27, 2024
getSSB.Rd		getSSB.Rd	Updated tests/testthat/test-plotBiomassObservedVsModel.R, and correct…	Mar 27, 2024
getTimes.Rd		getTimes.Rd	Improvements to examples on man pages.	Jul 27, 2021
getYield.Rd		getYield.Rd	Now getSSB(), getBiomass(), getN(), getYieldGear() and `getYi…	Nov 9, 2021
getYieldGear.Rd		getYieldGear.Rd	Now getSSB(), getBiomass(), getN(), getYieldGear() and `getYi…	Nov 9, 2021
getZ.Rd		getZ.Rd	Improving documentation	Oct 16, 2024
get_f0_default.Rd		get_f0_default.Rd	doc pages missed from prevous commit	Apr 2, 2021
get_gamma_default.Rd		get_gamma_default.Rd	In defaults edition 2, get_gamma_default() ensures a feeding level …	Jul 15, 2022
get_h_default.Rd		get_h_default.Rd	Update a man page	Dec 1, 2023
get_initial_n.Rd		get_initial_n.Rd	Avoid use of \dontrun in examples wherever possible. Use \donttest on…	Apr 25, 2023
get_ks_default.Rd		get_ks_default.Rd	Implement gamma argument in newTraitParams(). Closes #188	Apr 2, 2021
get_phi.Rd		get_phi.Rd	Updating website for development version.	Mar 6, 2021
get_required_reproduction.Rd		get_required_reproduction.Rd	Updating website for development version.	Mar 6, 2021
get_size_range_array.Rd		get_size_range_array.Rd	Make it clearer that get_size_range_array() accepts vector argument…	Aug 19, 2021
get_time_elements.Rd		get_time_elements.Rd	Updating website for development version.	Mar 6, 2021
indicator_functions.Rd		indicator_functions.Rd	Changes to roxygen documentation	Jul 7, 2020
initialN-set.Rd		initialN-set.Rd	Adding some @Seealso	Apr 12, 2024
initialNOther-set.Rd		initialNOther-set.Rd	Adding some @Seealso	Apr 12, 2024
initialNResource-set.Rd		initialNResource-set.Rd	Adding some @Seealso	Apr 12, 2024
initial_effort.Rd		initial_effort.Rd	Improving documentation	Oct 16, 2024
inter.Rd		inter.Rd	Rename inter to NS_interaction.	Aug 21, 2021
knife_edge.Rd		knife_edge.Rd	Improvements to documentation of selectivity functions	Apr 12, 2024
l2w.Rd		l2w.Rd	Some documentation tweaks	Aug 28, 2024
log_breaks.Rd		log_breaks.Rd	Switch to using markdown in all documentation	Mar 28, 2020
lognormal_pred_kernel.Rd		lognormal_pred_kernel.Rd	Improving documentation	Oct 16, 2024
matchBiomasses.Rd		matchBiomasses.Rd	Updates to documentation and website	Dec 22, 2022
matchGrowth.Rd		matchGrowth.Rd	matchGrowth() now also rescales the external encounter rate.	Aug 2, 2024
matchNumbers.Rd		matchNumbers.Rd	Updates to documentation and website	Dec 22, 2022
matchYields.Rd		matchYields.Rd	Make spelling checker happy	Oct 14, 2024
mizer-package.Rd		mizer-package.Rd	Updates to documentation and website	Dec 22, 2022
mizerEGrowth.Rd		mizerEGrowth.Rd	Updated tests/testthat/test-plotBiomassObservedVsModel.R, and correct…	Mar 27, 2024
mizerERepro.Rd		mizerERepro.Rd	Updated tests/testthat/test-plotBiomassObservedVsModel.R, and correct…	Mar 27, 2024
mizerEReproAndGrowth.Rd		mizerEReproAndGrowth.Rd	Small clarification in help page	Dec 29, 2024
mizerEncounter.Rd		mizerEncounter.Rd	Updated tests/testthat/test-plotBiomassObservedVsModel.R, and correct…	Mar 27, 2024
mizerFMort.Rd		mizerFMort.Rd	Updated tests/testthat/test-plotBiomassObservedVsModel.R, and correct…	Mar 27, 2024
mizerFMortGear.Rd		mizerFMortGear.Rd	Updated tests/testthat/test-plotBiomassObservedVsModel.R, and correct…	Mar 27, 2024
mizerFeedingLevel.Rd		mizerFeedingLevel.Rd	Updated tests/testthat/test-plotBiomassObservedVsModel.R, and correct…	Mar 27, 2024
mizerMort.Rd		mizerMort.Rd	Updated tests/testthat/test-plotBiomassObservedVsModel.R, and correct…	Mar 27, 2024
mizerPredMort.Rd		mizerPredMort.Rd	Updated tests/testthat/test-plotBiomassObservedVsModel.R, and correct…	Mar 27, 2024
mizerPredRate.Rd		mizerPredRate.Rd	Updated tests/testthat/test-plotBiomassObservedVsModel.R, and correct…	Mar 27, 2024
mizerRDI.Rd		mizerRDI.Rd	Updated tests/testthat/test-plotBiomassObservedVsModel.R, and correct…	Mar 27, 2024
mizerRates.Rd		mizerRates.Rd	Updated tests/testthat/test-plotBiomassObservedVsModel.R, and correct…	Mar 27, 2024
mizerResourceMort.Rd		mizerResourceMort.Rd	Updated tests/testthat/test-plotBiomassObservedVsModel.R, and correct…	Mar 27, 2024
needs_upgrading.Rd		needs_upgrading.Rd	Improving documentation	Oct 16, 2024
newCommunityParams.Rd		newCommunityParams.Rd	Updates to documentation and website	Dec 22, 2022
newMultispeciesParams.Rd		newMultispeciesParams.Rd	Improved documentation of resource parameters. Closes #303	Jan 27, 2025
newSingleSpeciesParams.Rd		newSingleSpeciesParams.Rd	Now using age_mat instead of von Bertalanffy parameters to calculat…	Dec 11, 2022
newTraitParams.Rd		newTraitParams.Rd	Updates to documentation and website	Dec 22, 2022
noRDD.Rd		noRDD.Rd	Graduating constantEggRDI() and customFunction() from mizerExperi…	Mar 6, 2021
plot-MizerParams-missing-method.Rd		plot-MizerParams-missing-method.Rd	Documentation fixes to avoid build warnings	Oct 16, 2024
plotBiomass.Rd		plotBiomass.Rd	Improving documentation	Oct 16, 2024
plotBiomassObservedVsModel.Rd		plotBiomassObservedVsModel.Rd	Improving documentation	Oct 16, 2024
plotDataFrame.Rd		plotDataFrame.Rd	Ensure that all man pages state the return value, as required by CRAN.	Apr 25, 2023
plotDiet.Rd		plotDiet.Rd	Improving documentation	Oct 16, 2024
plotFMort.Rd		plotFMort.Rd	Improving documentation	Oct 16, 2024
plotFeedingLevel.Rd		plotFeedingLevel.Rd	Improving documentation	Oct 16, 2024
plotGrowthCurves.Rd		plotGrowthCurves.Rd	Improving documentation	Oct 16, 2024
plotM2.Rd		plotM2.Rd	Improving documentation	Oct 16, 2024
plotMizerSim.Rd		plotMizerSim.Rd	Improving documentation	Oct 16, 2024
plotPredMort.Rd		plotPredMort.Rd	Improving documentation	Oct 16, 2024
plotSpectra.Rd		plotSpectra.Rd	Improving documentation	Oct 16, 2024
plotYield.Rd		plotYield.Rd	Improving documentation	Oct 16, 2024
plotYieldGear.Rd		plotYieldGear.Rd	Improving documentation	Oct 16, 2024
plotYieldObservedVsModel.Rd		plotYieldObservedVsModel.Rd	Updates to documentation and website	Dec 22, 2022
plotting_functions.Rd		plotting_functions.Rd	Improving documentation	Oct 16, 2024
power_law_pred_kernel.Rd		power_law_pred_kernel.Rd	Improving documentation	Oct 16, 2024
project.Rd		project.Rd	Improving documentation of effort argument in project().	May 4, 2023
projectToSteady.Rd		projectToSteady.Rd	Improve documentation of return_sim argument.	Mar 5, 2024
project_simple.Rd		project_simple.Rd	Updating documentation of development version	Jun 13, 2022
reexports.Rd		reexports.Rd	Changes to roxygen documentation	Jul 7, 2020
removeSpecies.Rd		removeSpecies.Rd	Updated man pages	Dec 15, 2022
renameSpecies.Rd		renameSpecies.Rd	Update time_modified slot in all functions that modify a MizerParam…	Aug 31, 2021
resource_constant.Rd		resource_constant.Rd	Improved documentation of resource parameters. Closes #303	Jan 27, 2025
resource_logistic.Rd		resource_logistic.Rd	Improved documentation of resource parameters. Closes #303	Jan 27, 2025
resource_params.Rd		resource_params.Rd	Improved documentation of resource parameters. Closes #303	Jan 27, 2025
resource_semichemostat.Rd		resource_semichemostat.Rd	Improved documentation of resource parameters. Closes #303	Jan 27, 2025
saveParams.Rd		saveParams.Rd	Ensure that all man pages state the return value, as required by CRAN.	Apr 25, 2023
scaleModel.Rd		scaleModel.Rd	Updates to documentation and website	Dec 22, 2022
setBevertonHolt.Rd		setBevertonHolt.Rd	Updated man pages	Dec 15, 2022
setColours.Rd		setColours.Rd	Updates to documentation and website	Dec 22, 2022
setComponent.Rd		setComponent.Rd	Don't require component parameters to be given in the form of a named…	Mar 26, 2021
setExtEncounter.Rd		setExtEncounter.Rd	setExtEncounter() no longer resets the external encounter rate to z…	Aug 2, 2024
setExtMort.Rd		setExtMort.Rd	Introduce external encounter rate	Dec 1, 2023
setFishing.Rd		setFishing.Rd	Updated man pages	Apr 12, 2024
setInitialValues.Rd		setInitialValues.Rd	Introduce external encounter rate	Dec 1, 2023
setInteraction.Rd		setInteraction.Rd	Introduce external encounter rate	Dec 1, 2023
setMaxIntakeRate.Rd		setMaxIntakeRate.Rd	Introduce external encounter rate	Dec 1, 2023
setMetabolicRate.Rd		setMetabolicRate.Rd	Introduce external encounter rate	Dec 1, 2023
setMetadata.Rd		setMetadata.Rd	Tiny change in man page	Oct 3, 2024
setParams.Rd		setParams.Rd	Improved documentation of resource parameters. Closes #303	Jan 27, 2025
setPredKernel.Rd		setPredKernel.Rd	Introduce external encounter rate	Dec 1, 2023
setRateFunction.Rd		setRateFunction.Rd	Updating documentation of development version	Jun 13, 2022
setReproduction.Rd		setReproduction.Rd	Improved documentation of resource parameters. Closes #303	Jan 27, 2025
setResource.Rd		setResource.Rd	Improved documentation of resource parameters. Closes #303	Jan 27, 2025
setRmax.Rd		setRmax.Rd	Rename w_inf to w_max. Closes #259	Dec 11, 2022
setSearchVolume.Rd		setSearchVolume.Rd	Introduce external encounter rate	Dec 1, 2023
set_community_model.Rd		set_community_model.Rd	Avoid use of \dontrun in examples wherever possible. Use \donttest on…	Apr 25, 2023
set_multispecies_model.Rd		set_multispecies_model.Rd	Ensure that all man pages state the return value, as required by CRAN.	Apr 25, 2023
set_species_param_default.Rd		set_species_param_default.Rd	Updating website for development version.	Mar 6, 2021
set_trait_model.Rd		set_trait_model.Rd	Rename w_inf to w_max. Closes #259	Dec 11, 2022
sigmoid_length.Rd		sigmoid_length.Rd	Improvements to documentation of selectivity functions	Apr 12, 2024
sigmoid_weight.Rd		sigmoid_weight.Rd	Avoiding CRAN warnings	Oct 13, 2024
species_params.Rd		species_params.Rd	Now validGivenSpeciesParams() validates the given species parameter…	Oct 13, 2024
steady.Rd		steady.Rd	Improve documentation of return_sim argument.	Mar 5, 2024
steadySingleSpecies.Rd		steadySingleSpecies.Rd	Updates to documentation and website	Dec 22, 2022
summary-MizerParams-method.Rd		summary-MizerParams-method.Rd	Updating website	Apr 25, 2023
summary-MizerSim-method.Rd		summary-MizerSim-method.Rd	Updating website	Apr 25, 2023
summary_functions.Rd		summary_functions.Rd	Changes to roxygen documentation	Jul 7, 2020
truncated_lognormal_pred_kernel.Rd		truncated_lognormal_pred_kernel.Rd	Improving documentation	Oct 16, 2024
upgradeParams.Rd		upgradeParams.Rd	Improving documentation	Oct 16, 2024
upgradeSim.Rd		upgradeSim.Rd	Improving documentation	Oct 16, 2024
validGearParams.Rd		validGearParams.Rd	Updating development documentation	Jul 15, 2022
validParams.Rd		validParams.Rd	validParams() checks that w_min is valid for all species and incr…	Oct 19, 2024
validSim.Rd		validSim.Rd	Improving documentation	Oct 16, 2024
validSpeciesParams.Rd		validSpeciesParams.Rd	validSpeciesParams() now also sets default for 'p' to be equal to 'n'.	Jan 6, 2025
valid_gears_arg.Rd		valid_gears_arg.Rd	In plotYieldGear() one can select a subset of gears with new `gears…	Aug 20, 2024
valid_species_arg.Rd		valid_species_arg.Rd	Avoid cryptic errors if functions are called with no valid species se…	Nov 3, 2022
w.Rd		w.Rd	Updates to documentation and website	Dec 22, 2022
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