Package: fishSim 0.0.0.9000

fishSim: Simulate Populations With Multiple Stocks, Movement, Mating, Mortality, and Parentage

Simulates population demography of an arbitrary number of stocks potentially connected by movement, with full parentage record-keeping. Includes functions for movement, mating, mortality, and aging, plus convenience functions to handle data archiving.

Authors:Shane Baylis [aut, cre]

fishSim_0.0.0.9000.tar.gz
fishSim_0.0.0.9000.zip(r-4.7-any)fishSim_0.0.0.9000.zip(r-4.6-any)fishSim_0.0.0.9000.zip(r-4.5-any)
fishSim_0.0.0.9000.tgz(r-4.6-any)fishSim_0.0.0.9000.tgz(r-4.5-any)
fishSim_0.0.0.9000.tar.gz(r-4.7-any)fishSim_0.0.0.9000.tar.gz(r-4.6-any)
fishSim_0.0.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
fishSim/json (API)

# Install 'fishSim' in R:

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

Bug tracker:https://github.com/smbaylis/fishsim/issues

On CRAN:

3.95 score 9 stars 5 scripts 28 exports 11 dependencies

Last updated from:3f0e181e9f. Checks:7 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel	ERROR	122
source / vignettes	OK	253
linux-release	ERROR	113
macos-release	ERROR	138
macos-oldrel	ERROR	137
windows-devel	ERROR	77
windows-release	ERROR	93
windows-oldrel	ERROR	77
wasm-release	OK	89

Exports:addmtDNA altMate archive_dead birthdays bondedMate capture check_growthrate findRelatives findRelativesPar grandparents great.grandparents great2.grandparents great3.grandparents great4.grandparents lookAtPair make_archive makeFounders mate mort move namedRelatives oldmove parents PoNG quickin remove_dead rTruncPoisson sexSwitch

Dependencies:askpass codetools doParallel fastmatch foreach ids iterators mvbutils openssl sys uuid

fishSim-vignette

Rendered fromfishSim-vignette.Rmdusingknitr::rmarkdown

Last update: 2024-10-15
Started: 2021-02-15

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
add mtDNA haplotypes to a completed simulation	addmtDNA
Breeding based on mature females	altMate
Take dead individuals and copy them to an archive	archive_dead
Add one to each individual's age	birthdays
mating between bonded pairs	bondedMate
Unique reals from ordered pairs of integers	both
Identify genetic captures/samples in population	capture
Estimate population growth under some 'mate()' and 'mort()' conditions	check_growthrate
convert an early 'makeFounders'-type matrix to 'data.frame'	dfify
Find shared ancestors between pairs of individuals	findRelatives
Partially-parallelized 'findRelatives()'	findRelativesPar
fishSim	fishSim-package fishSim
Look up the grandparents of one or more individuals	grandparents
look up the great-grandparents of one or more individuals	great.grandparents
Look up the great-great-grandparents of one or more individuals	great2.grandparents
Look up the great-great-great-grandparents of one or more individuals.	great3.grandparents
Look up the great-great-great-great-grandparents of one or more individuals	great4.grandparents
Show a readable relationship summary for a pair of relatives	lookAtPair
Set up an archive matrix for storing simulation outputs	make_archive
Make sim names, as a list	make_sim_names
Make a founding population	makeFounders
Find male-female pairs and breed until a quota is filled	mate
Kill some members of the population	mort
Age- and/or sex-specific Markovian movement between breeding stocks	move
Show numbers of pairs in named relationship classes	namedRelatives
Markovian movement between breeding stocks	oldmove
Look up the parents of one or more individuals	parents
Find a Point of No Growth (by tweaking first-year mortality)	PoNG
Quick lookup of CKMR-relevant relationships	quickin
Remove the dead from a population	remove_dead
Draw from a zero-truncated Poisson dist	rTruncPoisson
Induce sex-switching in a subset of the population	sexSwitch
Look up shared ancestors for 'quickin'-style kinship reporting	xpairs