| Type: | Package |
| Title: | Spatio-Dynamic Wetland Plant Communities Model |
| Description: | A spatio-dynamic modelling package that focuses on three characteristic wetland plant communities in a semiarid Mediterranean wetland in response to hydrological pressures from the catchment. The package includes the data on watershed hydrological pressure and the initial raster maps of plant communities but also allows for random initial distribution of plant communities. For more detailed info see: Martinez-Lopez et al. (2015) <doi:10.1016/j.ecolmodel.2014.11.024>. |
| Version: | 1.1.6 |
| Date: | 2022-01-04 |
| Author: | Javier Martinez-Lopez <javi.martinez.lopez@gmail.com>, Babak Naimi <naimi.b@gmail.com>, Julia Martinez-Fernandez <juliamf@um.es> |
| Maintainer: | Javier Martinez-Lopez <javi.martinez.lopez@gmail.com> |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| URL: | https://github.com/javimarlop/spdynmod |
| BugReports: | https://github.com/javimarlop/spdynmod/issues |
| LazyLoad: | yes |
| VignetteBuilder: | knitr |
| Imports: | deSolve, animation |
| Depends: | raster, sp |
| Suggests: | knitr, roxygen2, igraph, testthat |
| NeedsCompilation: | no |
| Packaged: | 2022-02-04 22:01:18 UTC; javier |
| Repository: | CRAN |
| Date/Publication: | 2022-02-04 22:20:02 UTC |
spdynmod model
Description
spdynmod model
The wetland model function.
Usage
spdynmod(t, init, parameters, nr, nc)
Arguments
t |
time |
init |
init |
parameters |
model parameters |
nr |
number of raster map rows |
nc |
number of raster map columns |
Value
Model solver
Examples
## Not run spdynmod()
Make an animation of the model output in relation to bare soil.
Description
It requires ImageMagick installed in the system to work.
Usage
animate_bs()
Value
a GIF animated file
Examples
## Not run animate_bs()
Make an animation of the model output containing all state variables.
Description
It requires ImageMagick installed in the system to work.
Usage
animate_model()
Value
a GIF animated file
Examples
## Not run animate_model()
Make an animation of the model output in relation to reed beds.
Description
It requires ImageMagick installed in the system to work.
Usage
animate_rb()
Value
a GIF animated file
Examples
## Not run animate_rb()
Make an animation of the model output in relation to the salt marsh community.
Description
It requires ImageMagick installed in the system to work.
Usage
animate_sm()
Value
a GIF animated file
Examples
## Not run animate_sm()
Make an animation of the model output in relation to the salt steppe community.
Description
It requires ImageMagick installed in the system to work.
Usage
animate_ss()
Value
a GIF animated file
Examples
## Not run animate_ss()
A function to perform Multiple Resolution Goodness of Fit.
Description
Returns the results of a Multiple Resolution Goodness of Fit after the modified method of Kuhnert et al. 2005, originally by Costanza 1989. This function is computationally intensive and consumes a lot of RAM memory.
Usage
mrgf(year = "1992", w1 = 1, w2 = 27, k = 0)
Arguments
year |
year validation year (by default 1992) |
w1 |
w1 initial window size (by default 1) |
w2 |
w2 final window size (by default 27; max. 113) |
k |
k parameter for weighting Ft with lower/larger windows resolutions |
Value
Fw vector of fits for each window size
Ft weighted overall fit
Examples
## Not run mrgf(year='1992',w1=1,w2=113,k=0)
A function to identify neighboring cells.
Description
Returns cell numbers of neighboring pixels to a reference cell
Usage
neigh_cell(cell)
Arguments
cell |
cell number from which to compute neighbor cells |
Value
returns cell numbers of neighboring pixels to the reference one
Examples
## Not run neigh_cell(n)
Plot abundance maps of plant communities.
Description
Plot abundance maps of plant communities in a given year.
Usage
plot_maps(year = 2008)
Arguments
year |
year to plot (from 1984 to 2008) |
Value
by default plots the final plant communities map (year = 2008).
Examples
## Not run plot_maps()
Run the model.
Description
Model solving function using ode.2D from the 'deSolve' package.
Usage
run_model(pgr_rb = 0.005, pgr_sm = 0.2, rnd = FALSE, method = "euler",
TS = 0.25)
Arguments
pgr_rb |
potential growth rate of reed beds |
pgr_sm |
potential growth rate of salt marsh |
rnd |
create random initial state variables map. It is calculated based on a script adapted from Murray Efford (University of Auckland, New Zealand) and Santiago Saura (Universidad Politecnica de Madrid, Spain). This option requires that the igraph package is available. |
method |
integration method: "lsodes", "euler", "rk4", "ode23", "ode45", "adams", "iteration" |
TS |
time step |
Value
the function outputs a matrix named "out" which contains the model simulated values for every pixel, time step and state variable.
Examples
## Not run run_model()