The oshinys R-package contains shinyApps of a variety of ecological and epidemiological models.
The package REQUIRES shiny, scatterplot3d, deSolve, phaseR and polspline R-packages from CRAN to run.
The source of the Apps are in /source/R/
Easisest way to install is from within R do:
install.packages(c("shiny", "deSolve", "scatterplot3d", "polspline", devtools))
require('devtools')
devtools::install_github('objornstad/oshinys/source/')
THEN launch any app from within R, for example:
require('oshinys')
runApp(rosenzweigmacarthur.app)
IF you can't install devtools; see HOWTO for "manual" installation
The current models are:
lpatribolium.app - LPA Tribolium model with a 2D and 3D phase plane
lotkavolterracompetition.app - Lotka-Volterra competion model with phase plane and isoclines
lotkavolterrapredation.app - Lotka-Volterra predation model with phase plane and isoclines
negbinparasitoid.app - May's Negative-Binomial parasitoid-host model
nicholsonbailey.app - Nicholson-Bailey Host-Parasitoid model
ricker.app - The Ricker ("discrete logistic") model
rosenzweigmacarthur.app - Rosenzweig-MacArthur Predator-Prey model with phase plane and isoclines
rossmacdonald.App - A simple Ross-Macdonald type malaria model
seir.app - the seasonally forced SEIR model in time and in the phase plane
seirs.app - the unforced SEIRS model in time and in the phase plane with ressonant periodicity calculations
sir.app - the unforced SIR model in time and in the phase plane with R0 calculations
tsir.app - the unforced TSIR model with demographic an environmental stochasticity in time and in the phase plane and with simulated and transfer function derived periodograms
NEW! I'm working to embed the Apps in standalone Rmarkdown documents. See
https://github.com/objornstad/ecomodelmarkdowns
All these can be launced without compilation after downloading from Rstudio with "> Run Document".
All code was written by Ottar N. Bjornstad ([email protected]) and is licensed under the CC-BY-NC Creative Commons attribution-noncommercial license (http://creativecommons.org/licenses/by-nc/3.0/). Please share & remix non-commercially, mentioning its origin.
When change, modify and improve any of the apps, please update me with any improvements (as per the CC-BY-NC lisence).