Package: SimSurvey 0.1.6

SimSurvey: Test Surveys by Simulating Spatially-Correlated Populations

Simulate age-structured populations that vary in space and time and explore the efficacy of a range of built-in or user-defined sampling protocols to reproduce the population parameters of the known population. (See Regular et al. (2020) <doi:10.1371/journal.pone.0232822> for more details).

Authors:Paul Regular [aut, cre], Jonathan Babyn [ctb], Greg Robertson [ctb]

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SimSurvey.pdf |SimSurvey.html✨
SimSurvey/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/paulregular/simsurvey/issues

Datasets:

On CRAN:

analysisfisheries-researchsimulation-testingsurvey-design

42 exports 10 stars 1.92 score 90 dependencies 1 mentions 103 scripts 315 downloads

Last updated 1 years agofrom:d2f1de207d. Checks:OK: 4 NOTE: 3. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 12 2024
R-4.5-winNOTESep 12 2024
R-4.5-linuxNOTESep 12 2024
R-4.4-winOKSep 12 2024
R-4.4-macOKSep 12 2024
R-4.3-winNOTESep 12 2024
R-4.3-macOKSep 12 2024

Exports:%>%convert_Nerror_statsexpand_surveysfibonaccigroup_lengthsiccmake_gridmake_meshobject_sizeplot_age_strat_fanplot_distributionplot_error_surfaceplot_gridplot_length_strat_fanplot_surfaceplot_surveyplot_survey_rankplot_total_strat_fanplot_trendresume_testround_simrun_stratsim_abundancesim_ays_covarsim_ays_covar_spdesim_distributionsim_logisticsim_N0sim_nlfsim_parabolasim_Rsim_setssim_surveysim_survey_parallelsim_vonBsim_Zstrat_datastrat_errorstrat_meanstest_surveysvis_sim

Dependencies:abindaskpassbase64encbslibcachemclassclassIntclicodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIdigestdoParalleldplyre1071evaluatefansifarverfastmapfontawesomeforeachfsgenericsggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttrisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplotlyprettyunitsprogresspromisesproxypurrrR6rappdirsRColorBrewerRcpprlangrmarkdowns2sassscalessfstarsstringistringrsystibbletidyrtidyselecttinytexunitsutf8vctrsviridisLitewithrwkxfunyaml

Custom closures

Rendered fromcustom_closures.Rmdusingknitr::rmarkdownon Sep 12 2024.

Last update: 2020-07-30
Started: 2020-04-09

Readme and manuals

Help Manual

Help pageTopics
Southern Newfoundland bathymetrybathy
Convert abundance-at-age matrix to abundance-at-lengthconvert_N
Calculate common error statisticserror_stats
Set-up a series of surveys from all combinations of settings suppliedexpand_surveys
Generate Fibonacci sequencefibonacci
Convert length to length groupgroup_lengths
Calculate intraclass correlationicc
Southern Newfoundland coastlineland
Make a depth stratified survey gridmake_grid
Make an R-INLA mesh based off a gridmake_mesh
Print object sizeobject_size
Simple plotting functionsplot_age_strat_fan plot_distribution plot_error_surface plot_grid plot_length_strat_fan plot_surface plot_survey plot_survey_rank plot_total_strat_fan plot_trend
Round simulated populationround_sim
Run stratified analysis on simulated datarun_strat
Simulate basic population dynamics modelsim_abundance
Simulate age-year-space covariancesim_ays_covar
Simulate age-year-space covariance using SPDE approachsim_ays_covar_spde
Simulate spatial and temporal distributionsim_distribution
Closure for simulating logistic curvesim_logistic
Define a non-linear relationshipsim_nlf
Define a parabolic relationshipsim_parabola
Simulate starting abundance, random recruitment and total mortalitysim_N0 sim_R sim_Z
Simulate survey setssim_sets
Simulate stratified-random surveysim_survey
Simulate stratified random surveys using parallel computationsim_survey_parallel
Closure for simulating length given age using von Bertalanffy notationsim_vonB
Prepare simulated data for stratified analysisstrat_data
Calculate error of stratified estimatesstrat_error
Calculate stratified means, variances and confidence intervals across groupsstrat_means
Sample survey simulation grid.survey_grid
Lite sample survey mesh and related itemssurvey_lite_mesh
Sample survey meshes and related itemssurvey_mesh
Test sampling design of multiple surveys using a stratified analysisresume_test test_surveys
Make a flexdashboard for visualizing the simulationvis_sim