Package: SimSurvey 0.1.8

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]

SimSurvey_0.1.8.tar.gz
SimSurvey_0.1.8.zip(r-4.7)SimSurvey_0.1.8.zip(r-4.6)SimSurvey_0.1.8.zip(r-4.5)
SimSurvey_0.1.8.tgz(r-4.6-any)SimSurvey_0.1.8.tgz(r-4.5-any)
SimSurvey_0.1.8.tar.gz(r-4.7-any)SimSurvey_0.1.8.tar.gz(r-4.6-any)
SimSurvey_0.1.8.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SimSurvey/json (API)

# Install 'SimSurvey' in R:

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

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

Pkgdown/docs site:https://paulregular.github.io

Datasets:

bathy - Southern Newfoundland bathymetry
land - Southern Newfoundland coastline
survey_grid - Sample survey simulation grid
survey_lite_mesh - Lite sample survey mesh and related items
survey_mesh - Sample survey meshes and related items

On CRAN:

analysis fisheries-research simulation-testing survey-design

6.93 score 13 stars 144 scripts 642 downloads 1 mentions 41 exports 87 dependencies

Last updated from:fa96bf5ebd. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	216
source / vignettes	OK	219
linux-release-x86_64	OK	254
macos-release-arm64	OK	183
macos-oldrel-arm64	OK	175
windows-devel	OK	184
windows-release	OK	148
windows-oldrel	OK	179
wasm-release	OK	153

Exports:convert_N error_stats expand_surveys fibonacci group_lengths icc make_grid make_mesh object_size plot_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 resume_test round_sim run_strat sim_abundance sim_ays_covar sim_ays_covar_spde sim_distribution sim_logistic sim_N0 sim_nlf sim_parabola sim_R sim_sets sim_survey sim_survey_parallel sim_vonB sim_Z strat_data strat_error strat_means test_surveys vis_sim

Dependencies:abind askpass base64enc bslib cachem class classInt cli codetools cpp11 crayon crosstalk curl data.table DBI digest doParallel dplyr e1071 evaluate farver fastmap fontawesome foreach fs generics ggplot2 glue gtable highr hms htmltools htmlwidgets httr isoband iterators jquerylib jsonlite KernSmooth knitr labeling later lattice lazyeval lifecycle magrittr MASS Matrix memoise mime openssl otel pillar pkgconfig plotly prettyunits progress promises proxy purrr R6 rappdirs RColorBrewer Rcpp rlang rmarkdown s2 S7 sass scales sf stars stringi stringr sys tibble tidyr tidyselect tinytex units utf8 vctrs viridisLite withr wk xfun yaml

Custom closures

Built-in closures | References

Rendered fromcustom_closures.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Southern Newfoundland bathymetry	bathy
Convert abundance-at-age matrix to abundance-at-length	convert_N
Calculate common error statistics	error_stats
Set up a series of surveys from all combinations of settings supplied	expand_surveys
Generate Fibonacci sequence	fibonacci
Convert length to length group	group_lengths
Calculate intraclass correlation	icc
Southern Newfoundland coastline	land
Make a depth-stratified survey grid	make_grid
Make an R-INLA mesh based on a grid	make_mesh
Print object size	object_size
Simple plotting functions	plot_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 population	round_sim
Run stratified analysis on simulated data	run_strat
Simulate basic population dynamics model	sim_abundance
Simulate age-year-space covariance	sim_ays_covar
Simulate age-year-space covariance using SPDE approach	sim_ays_covar_spde
Simulate spatial and temporal distribution	sim_distribution
Closure for simulating logistic curve	sim_logistic
Define a non-linear relationship	sim_nlf
Define a parabolic relationship	sim_parabola
Simulate starting abundance, random recruitment, and total mortality	sim_N0 sim_R sim_Z
Simulate survey sets	sim_sets
Simulate stratified-random survey	sim_survey
Simulate stratified random surveys using parallel computation	sim_survey_parallel
Closure for simulating length given age using von Bertalanffy notation	sim_vonB
Prepare simulated data for stratified analysis	strat_data
Calculate error of stratified estimates	strat_error
Calculate stratified means, variances, and confidence intervals across groups	strat_means
Sample survey simulation grid	survey_grid
Lite sample survey mesh and related items	survey_lite_mesh
Sample survey meshes and related items	survey_mesh
Test sampling design of multiple surveys using a stratified analysis	resume_test test_surveys
Make a flexdashboard for visualizing the simulation	vis_sim