Package: LeMaRns 0.1.2

LeMaRns: Length-Based Multispecies Analysis by Numerical Simulation

Set up, run and explore the outputs of the Length-based Multi-species model (LeMans; Hall et al. 2006 <doi:10.1139/f06-039>), focused on the marine environment.

Authors:Michael A. Spence [aut, cre], Hayley J. Bannister [aut], Johnathan E. Ball [aut], Paul J. Dolder [aut], Robert B. Thorpe [aut], Christopher A. Griffiths [ctb]

LeMaRns_0.1.2.tar.gz
LeMaRns_0.1.2.zip(r-4.5)LeMaRns_0.1.2.zip(r-4.4)LeMaRns_0.1.2.zip(r-4.3)
LeMaRns_0.1.2.tgz(r-4.4-x86_64)LeMaRns_0.1.2.tgz(r-4.4-arm64)LeMaRns_0.1.2.tgz(r-4.3-x86_64)LeMaRns_0.1.2.tgz(r-4.3-arm64)
LeMaRns_0.1.2.tar.gz(r-4.5-noble)LeMaRns_0.1.2.tar.gz(r-4.4-noble)
LeMaRns_0.1.2.tgz(r-4.4-emscripten)LeMaRns_0.1.2.tgz(r-4.3-emscripten)
LeMaRns.pdf |LeMaRns.html✨
LeMaRns/json (API)

# Install 'LeMaRns' in R:
install.packages('LeMaRns', repos = c('https://michaelspence.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • NS_L50 - The length at 50% of the maximum catchability of the catchability curve
  • NS_eta - The steepness of the slope of the catchability curve
  • NS_mixed_fish - Gear selectivity data frame
  • NS_other - Other food for the North Sea
  • NS_par - North Sea data
  • NS_tau - North Sea interaction matrix

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

51 exports 0.36 score 3 dependencies 1 mentions 16 scripts 162 downloads

Last updated 5 years agofrom:1486684c4b. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 07 2024
R-4.5-win-x86_64OKSep 07 2024
R-4.5-linux-x86_64OKSep 07 2024
R-4.4-win-x86_64OKSep 07 2024
R-4.4-mac-x86_64OKSep 07 2024
R-4.4-mac-aarch64OKSep 07 2024
R-4.3-win-x86_64OKSep 07 2024
R-4.3-mac-x86_64OKSep 07 2024
R-4.3-mac-aarch64OKSep 07 2024

Exports:calc_biomasscalc_growthcalc_LFIcalc_LQcalc_M1calc_M1_constRNMcalc_M1_lincalc_M1_stdRNMcalc_M2calc_maturecalc_phicalc_prefscalc_Qcalc_ration_growthfaccalc_recruitscalc_SSBcalc_suit_vectcalc_TyLcomb_LeMans_runget_annual_catchget_biomassget_CPGget_CPUEget_indicatorsget_LFIget_LQget_M1get_MMLget_N0get_Qget_rec_funget_SSBget_TyLknife_edge_catchLeMansParamlog_gaussian_catchlogistic_catchmake_rec_funplot_biomassplot_indicatorsplot_LFIplot_LQplot_MMLplot_SSBplot_TyLrec_BHrec_constrec_hockeyrec_linearrec_Rickerrun_LeMans

Dependencies:abindRcppRcppArmadillo

LeMaRns

Michael A. Spence, Hayley J. Bannister, Johnathan E. Ball and Robert B. Thorpe

Rendered fromlemarns.Rmdusingknitr::rmarkdownon Sep 07 2024.

Last update: 2019-10-08
Started: 2019-06-03

Readme and manuals

Help Manual

Help pageTopics
Calculate growthcalc_growth
Calculate community indicatorscalc_LFI calc_LQ calc_TyL
Calculate background mortalitycalc_M1 calc_M1_constRNM calc_M1_lin calc_M1_stdRNM get_M1
Calculate predation mortalitycalc_M2
Calculate the proportion of mature individualscalc_mature
Calculate the proportion of individuals that leave each length class for each species each length class each time step.calc_phi
Calculate predator-prey size preferencescalc_prefs
Calculate gear catchabilitycalc_Q get_Q knife_edge_catch logistic_catch log_gaussian_catch
Calculate growth incrementscalc_ration_growthfac
Calculate the number of recruitscalc_recruits
Calculate Spawning Stock Biomass (SSB) or total biomasscalc_biomass calc_SSB
Combines prey preference and prey suitabilitycalc_suit_vect
Combine two 'LeMans_outputs' objectscomb_LeMans_run
Get annual catch for each species, catch per unit effort or catch per gearget_annual_catch get_annual_catch,LeMans_param,LeMans_outputs-method get_annual_catch,LeMans_param,missing-method get_annual_catch,missing,LeMans_outputs-method get_annual_catch,missing,missing-method get_CPG get_CPG,LeMans_param,LeMans_outputs-method get_CPG,LeMans_param,missing-method get_CPG,missing,LeMans_outputs-method get_CPG,missing,missing-method get_CPUE get_CPUE,LeMans_param,LeMans_outputs-method get_CPUE,LeMans_param,missing-method get_CPUE,missing,LeMans_outputs-method get_CPUE,missing,missing-method
Calculate indicatorsget_indicators get_indicators,LeMans_param,LeMans_outputs-method get_indicators,LeMans_param,missing-method get_indicators,missing,LeMans_outputs-method get_indicators,missing,missing-method get_LFI get_LFI,LeMans_param,LeMans_outputs-method get_LFI,LeMans_param,missing-method get_LFI,missing,LeMans_outputs-method get_LFI,missing,missing-method get_LQ get_LQ,LeMans_param,LeMans_outputs-method get_LQ,LeMans_param,missing-method get_LQ,missing,LeMans_outputs-method get_LQ,missing,missing-method get_MML get_MML,LeMans_param,LeMans_outputs-method get_MML,LeMans_param,missing-method get_MML,missing,LeMans_outputs-method get_MML,missing,missing-method get_TyL get_TyL,LeMans_param,LeMans_outputs-method get_TyL,LeMans_param,missing-method get_TyL,missing,LeMans_outputs-method get_TyL,missing,missing-method
Generate a starting value for Nget_N0
Collate the stock recruitment functionsget_rec_fun
Calculate Spawning Stock Biomass (SSB) or total biomassget_biomass get_biomass,LeMans_param,LeMans_outputs-method get_biomass,LeMans_param,missing-method get_biomass,missing,LeMans_outputs-method get_biomass,missing,missing-method get_SSB get_SSB,LeMans_param,LeMans_outputs-method get_SSB,LeMans_param,missing-method get_SSB,missing,LeMans_outputs-method get_SSB,missing,missing-method
An S4 class representing the outputs of the LeMans modelLeMans_outputs-class
An S4 class representing the inputs of the LeMans modelLeMans_param-class
A constructor for the 'LeMansParam' classLeMansParam LeMansParam,ANY,ANY-method LeMansParam,missing,ANY-method LeMansParam,missing,missing-method
Generate the stock recruitment functionsmake_rec_fun
The steepness of the slope of the catchability curveNS_eta
The length at 50% of the maximum catchability of the catchability curveNS_L50
Gear selectivity data frameNS_mixed_fish
Other food for the North SeaNS_other
North Sea dataNS_par
North Sea interaction matrixNS_tau
Plot indicatorsplot_indicators plot_indicators,LeMans_param,LeMans_outputs-method plot_indicators,LeMans_param,missing-method plot_indicators,missing,LeMans_outputs-method plot_indicators,missing,missing-method plot_LFI plot_LFI,LeMans_param,LeMans_outputs-method plot_LFI,LeMans_param,missing-method plot_LFI,missing,LeMans_outputs-method plot_LFI,missing,missing-method plot_LQ plot_LQ,LeMans_param,LeMans_outputs-method plot_LQ,LeMans_param,missing-method plot_LQ,missing,LeMans_outputs-method plot_LQ,missing,missing-method plot_MML plot_MML,LeMans_param,LeMans_outputs-method plot_MML,LeMans_param,missing-method plot_MML,missing,LeMans_outputs-method plot_MML,missing,missing-method plot_TyL plot_TyL,LeMans_param,LeMans_outputs-method plot_TyL,LeMans_param,missing-method plot_TyL,missing,LeMans_outputs-method plot_TyL,missing,missing-method
Plot Spawning Stock Biomass (SSB)plot_biomass plot_biomass,LeMans_param,LeMans_outputs-method plot_biomass,LeMans_param,missing-method plot_biomass,missing,LeMans_outputs-method plot_biomass,missing,missing-method plot_SSB plot_SSB,LeMans_param,LeMans_outputs-method plot_SSB,LeMans_param,missing-method plot_SSB,missing,LeMans_outputs-method plot_SSB,missing,missing-method
The Beverton-Holt stock recruitment functionrec_BH
The constant stock recruitment functionrec_const
The hockey-stick stock recruitment functionrec_hockey
The density-independent stock recruitment functionrec_linear
The Ricker stock recruitment functionrec_Ricker
Project the LeMans modelrun_LeMans run_LeMans,LeMans_param-method run_LeMans,missing-method