Introduction | Setting up the model | Dataset for the North Sea | Setting the species-independent parameters | Setting the species-specific parameters | Size, growth and maturity | Recruitment | Mortality | LeMans_param objects | Running the model | Initialising the model | The model run | Growth | run_LeMans function | Exploring the outputs | Biomass | Spawning Stock Biomass (SSB) | Indicators | Catch | Case Study | Fishing fleets | Dynamic fishing | Nash equilibrium | References
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:
LeMaRns_0.1.2.tar.gz
LeMaRns_0.1.2.zip(r-4.7-x86_64)LeMaRns_0.1.2.zip(r-4.7-arm64)LeMaRns_0.1.2.zip(r-4.6-x86_64)LeMaRns_0.1.2.zip(r-4.6-arm64)LeMaRns_0.1.2.zip(r-4.5-x86_64)
LeMaRns_0.1.2.tgz(r-4.6-x86_64)LeMaRns_0.1.2.tgz(r-4.6-arm64)LeMaRns_0.1.2.tgz(r-4.5-x86_64)LeMaRns_0.1.2.tgz(r-4.5-arm64)
LeMaRns_0.1.2.tar.gz(r-4.7-arm64)LeMaRns_0.1.2.tar.gz(r-4.7-x86_64)LeMaRns_0.1.2.tar.gz(r-4.6-arm64)LeMaRns_0.1.2.tar.gz(r-4.6-x86_64)
LeMaRns_0.1.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
LeMaRns/json (API)
| # Install 'LeMaRns' in R: |
| install.packages('LeMaRns', repos = c('https://michaelspence.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:1486684c4b. Checks:15 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 104 | ||
| linux-devel-x86_64 | OK | 116 | ||
| source / vignettes | OK | 170 | ||
| linux-release-arm64 | OK | 127 | ||
| linux-release-x86_64 | OK | 117 | ||
| macos-release-arm64 | OK | 157 | ||
| macos-release-x86_64 | OK | 296 | ||
| macos-oldrel-arm64 | OK | 202 | ||
| macos-oldrel-x86_64 | OK | 370 | ||
| windows-devel-arm64 | OK | 330 | ||
| windows-devel-x86_64 | OK | 173 | ||
| windows-release-arm64 | OK | 338 | ||
| windows-release-x86_64 | OK | 119 | ||
| windows-oldrel-x86_64 | OK | 138 | ||
| wasm-release | OK | 89 |
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
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calculate growth | calc_growth |
| Calculate community indicators | calc_LFI calc_LQ calc_TyL |
| Calculate background mortality | calc_M1 calc_M1_constRNM calc_M1_lin calc_M1_stdRNM get_M1 |
| Calculate predation mortality | calc_M2 |
| Calculate the proportion of mature individuals | calc_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 preferences | calc_prefs |
| Calculate gear catchability | calc_Q get_Q knife_edge_catch logistic_catch log_gaussian_catch |
| Calculate growth increments | calc_ration_growthfac |
| Calculate the number of recruits | calc_recruits |
| Calculate Spawning Stock Biomass (SSB) or total biomass | calc_biomass calc_SSB |
| Combines prey preference and prey suitability | calc_suit_vect |
| Combine two 'LeMans_outputs' objects | comb_LeMans_run |
| Get annual catch for each species, catch per unit effort or catch per gear | get_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 indicators | get_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 N | get_N0 |
| Collate the stock recruitment functions | get_rec_fun |
| Calculate Spawning Stock Biomass (SSB) or total biomass | get_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 model | LeMans_outputs-class |
| An S4 class representing the inputs of the LeMans model | LeMans_param-class |
| A constructor for the 'LeMansParam' class | LeMansParam LeMansParam,ANY,ANY-method LeMansParam,missing,ANY-method LeMansParam,missing,missing-method |
| Generate the stock recruitment functions | make_rec_fun |
| The steepness of the slope of the catchability curve | NS_eta |
| The length at 50% of the maximum catchability of the catchability curve | NS_L50 |
| Gear selectivity data frame | NS_mixed_fish |
| Other food for the North Sea | NS_other |
| North Sea data | NS_par |
| North Sea interaction matrix | NS_tau |
| Plot indicators | plot_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 function | rec_BH |
| The constant stock recruitment function | rec_const |
| The hockey-stick stock recruitment function | rec_hockey |
| The density-independent stock recruitment function | rec_linear |
| The Ricker stock recruitment function | rec_Ricker |
| Project the LeMans model | run_LeMans run_LeMans,LeMans_param-method run_LeMans,missing-method |