Package: spreadrate 0.1.13
Facundo Muñoz
spreadrate: Estimate the spread-rate of epidemics
Estimate the local velocity of propagation of an epidemic event, given dates and locations of observed cases. The method estimates the surface of first date of invasion by interpolation of the earliest observations in a neighbourhood and derives the local spread rate as the inverse slope of the surface. Quantify the estimation uncertainty by a Monte Carlo approach. Visualise and simulate the spatio-temporal progress of epidemics.
Authors:
spreadrate_0.1.13.tar.gz
spreadrate_0.1.13.zip(r-4.5)spreadrate_0.1.13.zip(r-4.4)spreadrate_0.1.13.zip(r-4.3)
spreadrate_0.1.13.tgz(r-4.4-any)spreadrate_0.1.13.tgz(r-4.3-any)
spreadrate_0.1.13.tar.gz(r-4.5-noble)spreadrate_0.1.13.tar.gz(r-4.4-noble)
spreadrate_0.1.13.tgz(r-4.4-emscripten)spreadrate_0.1.13.tgz(r-4.3-emscripten)
spreadrate.pdf |spreadrate.html✨
spreadrate/json (API)
NEWS
| # Install 'spreadrate' in R: |
| install.packages('spreadrate', repos = c('https://cirad-astre.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://forgemia.inra.fr/umr-astre/spreadrate
Last updated 5 years agofrom:0fa071c495. Checks:OK: 1 ERROR: 6. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 05 2024 |
| R-4.5-win | ERROR | Oct 05 2024 |
| R-4.5-linux | ERROR | Oct 05 2024 |
| R-4.4-win | ERROR | Oct 05 2024 |
| R-4.4-mac | ERROR | Oct 05 2024 |
| R-4.3-win | ERROR | Oct 05 2024 |
| R-4.3-mac | ERROR | Oct 05 2024 |
Exports:dist2arcestimation_maskfilter_earliest_neighfit_surfaceget_lonlatvarsinvslopeneigh_tolrepresentative_pointssrsr_fdoisr_obssr_uq
Dependencies:classclassIntclicodetoolsDBIdigestdotCall64e1071fieldsfurrrfutureglobalsglueKernSmoothlatticelifecyclelistenvlwgeommagrittrmapsMASSparallellyproxypurrrrasterRcpprlangs2sfspspamterraunitsvctrsviridisLitewk
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Approximate angle for a distance | dist2arc |
| Raster termplate for estimation | estimation_mask |
| Earliest observations within a neighbourhood | filter_earliest_neigh |
| Fit a Thin-plate splines model to a set of observations | fit_surface |
| Identify variables with geographical coordinates | get_lonlatvars |
| Compute the inverse slope of the input surface | invslope |
| Monte Carlo samples from a dataset | mc_sample |
| Neighbourhood Tolerance Parameter | neigh_tol |
| Choose representative points | representative_points |
| Spread rate | sr |
| First-date of invasion | sr_fdoi |
| Define a observations dataset | sr_obs |
| Parameters for Uncertainty Quantification | sr_uq |
| Transform coordinates of a sr_obs object | st_transform.sr_obs |
| Jitter a vector of 1D values | time_jitter |
