index.utf8.md

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# LAB: {STManaged} R package

### Willian Vieira

[WillVieira/talk_biodiversityModeling2019](https://github.com/willvieira/talk_biodiversityModeling2019)

[https://willvieira.github.io/STManaged/](https://willvieira.github.io/STManaged/)

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# LAB

## {STManaged} R package

---

## LAB steps

1. Install package
2. Functions of the package
3. Understanding the package output

---
## STManaged R package: install

[WillVieira/talk_biodiversityModeling2019](https://github.com/willvieira/talk_biodiversityModeling2019)

```r
devtools::install_github("willvieira/STManaged")
```

For Linux users, install `ImageMagick++` library before

---
## STManaged R package: main functions

- Create the initial landscape
```r
create_virtual_landscape()
```

- run the model
```r
run_model()
```

---
## STManaged R package: initial landscape

```r
initLand <- create_virtual_landscape(climRange = c(-2.61, 5.07),
 cellSize = 1)
```

plot `initLand`:

```r
plot_landscape(initLand, xaxis = TRUE)
```

---
## STManaged R package: run the model

```r
lands <- run_model(steps = 20,
 initLand,
 managInt = c(0, 0, 0, 0),
 RCP = 8.5)
```

```r
names(lands)
#  [1] "land_T0"  "land_T1"  "land_T2"  "land_T3"  "land_T4"  "land_T5" 
#  [7] "land_T6"  "land_T7"  "land_T8"  "land_T9"  "land_T10" "land_T11"
# [13] "land_T12" "land_T13" "land_T14" "land_T15" "land_T16" "land_T17"
# [19] "land_T18" "land_T19" "land_T20" "env1"     "steps"    "manag"   
# [25] "RCP"      "nCol"     "nRow"
```

---
## STManaged R package: output

- landscape occupancy

```r
par(mfrow = c(1, 2))
plot_occupancy(lands, step = 0, spar = 0.4)
plot_occupancy(lands, step = 20, spar = 0.4)
```

---
## STManaged R package: output

- animate temporal dynamic

```r
animate(lands, fps = 2)
```

![](images/RCP8.5_virtual.gif)

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# Using real landscape

---
## STManaged R package: initial landscape

```r
initLand <- create_real_landscape()
```

plot `initLand`:

```r
plot_landscape(initLand)
```

---
## STManaged R package: run the model

```r
lands <- run_model(steps = 20,
 initLand,
 managInt = c(0, 0, 0, 0))
```

Note: the only `RCP` scenario is `8.5`

```r
names(lands)
# [1] "lands" "steps" "manag" "RCP"   "nCol"  "nRow"
class(lands[['lands']])
# [1] "RasterStack"
# attr(,"package")
# [1] "raster"
names(lands[['lands']])
#  [1] "land_T0"  "tp"       "pp"       "land_T1"  "land_T2"  "land_T3" 
#  [7] "land_T4"  "land_T5"  "land_T6"  "land_T7"  "land_T8"  "land_T9" 
# [13] "land_T10" "land_T11" "land_T12" "land_T13" "land_T14" "land_T15"
# [19] "land_T16" "land_T17" "land_T18" "land_T19" "land_T20"
```

---
## STManaged R package: output

- animate temporal dynamic

```r
animate(lands, fps = 2)
```

--
.center[
  ![:scale 85%](images/RCP8.5_real.gif)
]