Package: openMSE 1.1.1
Adrian Hordyk
openMSE: Easily Install and Load the 'openMSE' Packages
The 'openMSE' package is designed for building operating models, doing simulation modelling and management strategy evaluation for fisheries. 'openMSE' is an umbrella package for the 'MSEtool' (Management Strategy Evaluation toolkit), 'DLMtool' (Data-Limited Methods toolkit), and SAMtool (Stock Assessment Methods toolkit) packages. By loading and installing 'openMSE', users have access to the full functionality contained within these packages. Learn more about 'openMSE' at <https://openmse.com/>.
Authors:
openMSE_1.1.1.tar.gz
openMSE_1.1.1.zip(r-4.5)openMSE_1.1.1.zip(r-4.4)openMSE_1.1.1.zip(r-4.3)
openMSE_1.1.1.tgz(r-4.4-any)openMSE_1.1.1.tgz(r-4.3-any)
openMSE_1.1.1.tar.gz(r-4.5-noble)openMSE_1.1.1.tar.gz(r-4.4-noble)
openMSE_1.1.1.tgz(r-4.4-emscripten)openMSE_1.1.1.tgz(r-4.3-emscripten)
openMSE.pdf |openMSE.html✨
openMSE/json (API)
NEWS
| # Install 'openMSE' in R: |
| install.packages('openMSE', repos = c('https://blue-matter.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/blue-matter/openmse/issues
- At_Age_TS_Variables - At-Age Time Series Variables
- TS_Variables - Time Series Variables
Last updated 3 months agofrom:73730d604e. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 12 2024 |
| R-4.5-win | OK | Sep 12 2024 |
| R-4.5-linux | OK | Sep 12 2024 |
| R-4.4-win | OK | Sep 12 2024 |
| R-4.4-mac | OK | Sep 12 2024 |
| R-4.3-win | OK | Sep 12 2024 |
| R-4.3-mac | OK | Sep 12 2024 |
Exports:cm2inchdemodivide_10divide_100divide_1000get_Assess_Estimatesget_at_Ageget_at_age_tsget_at_Lengthget_Biomassget_Biomass_at_Ageget_Fget_Landingsget_LifeHistoryget_Metadataget_Number_at_Ageget_Recruitsget_Removalsget_SB_SBMSYget_SSBget_SSB_at_Ageget_tsget_Yearsinch2cminch2mmkg2_1000lbkg2lbkg2mtlb2kglb2mtmm2inchmultiply_10multiply_100multiply_1000plot_at_Ageplot_Biomassplot_Fplot_Landingsplot_Lengthplot_LifeHistoryplot_Maturityplot_N.Mortalityplot_Recruitsplot_Removalsplot_Retentionplot_Selectplot_Select_Maturityplot_SSBplot_TSplot_Weighttheme_defaultuserguidevalid_at_age_ts_variablesvalid_ts_variables
Dependencies:abindbase64encbitopsbslibcachemcaToolsclicolorspacecpp11crayondigestDLMtooldplyrevaluatefansifarverfastmapfontawesomefsgenericsggplot2ggrepelgluegplotsgridExtragtablegtoolshighrhtmltoolsisobandjquerylibjsonliteKernSmoothknitrlabelinglatticelifecyclelmtestmagrittrMASSMatrixmemoisemgcvmimeMSEtoolmunsellnlmepbapplypillarpkgconfigpurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenrlangrmarkdownSAMtoolsandwichsassscalessnowsnowfallstringistringrstrucchangetibbletidyrtidyselecttinytexTMBurcautf8varsvctrsviridisLitewithrxfunyamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| At-Age Time Series Variables | At_Age_TS_Variables |
| Run an example MSE | demo |
| Create a data.frame with estimated values from a 'SAMtool' assessment method used in an MSE | get_Assess_Estimates get_Assess_Estimates.list get_Assess_Estimates.MMSE get_Assess_Estimates.MSE |
| Create a data.frame with at-age schedules by simulation and year | get_at_Age get_at_Age.Hist get_at_Age.list get_at_Age.MMSE get_at_Age.MSE get_at_Age.multiHist |
| Create a data.frame with time-series information by simulation and year | get_at_age_ts |
| Create a data.frame with at-length selectivity and retention schedules by simulation and year | get_at_Length get_at_Length.multiHist |
| Get Life History Parameters | get_LifeHistory get_LifeHistory.Hist get_LifeHistory.list get_LifeHistory.MMSE get_LifeHistory.MSE |
| Extract the meta-data from a 'Hist' or 'MSE' object | get_Metadata get_Metadata.Hist get_Metadata.list get_Metadata.MMSE get_Metadata.MSE |
| Create a data.frame with time-series information by simulation and year | get_Biomass get_Biomass_at_Age get_F get_Landings get_Number_at_Age get_Recruits get_Removals get_SB_SBMSY get_SSB get_SSB_at_Age get_ts get_ts.Hist get_ts.list get_ts.MMSE get_ts.MSE get_ts.multiHist valid_at_age_ts_variables valid_ts_variables |
| Create a data.frame with Historical and Projection years | get_Years get_Years.Hist get_Years.MMSE get_Years.MSE get_Years.multiHist |
| Convert numeric values to a different scale | cm2inch divide_10 divide_100 divide_1000 inch2cm inch2mm kg2lb kg2mt kg2_1000lb lb2kg lb2mt mm2inch multiply_10 multiply_100 multiply_1000 |
| Plot at-Age schedules | plot_at_Age plot_Length plot_Maturity plot_N.Mortality plot_Retention plot_Select plot_Select_Maturity plot_Weight |
| Plots the median and quantiles of a time-series | plot_Biomass plot_F plot_Landings plot_LifeHistory plot_Recruits plot_Removals plot_SSB plot_TS |
| A ggplot2 theme | theme_default |
| Time Series Variables | TS_Variables |
| Open the openMSE Documentation website | userguide |
