Skip to content

Commit

Permalink
Update slides
Browse files Browse the repository at this point in the history
  • Loading branch information
@mhesselbarth
mhesselbarth committed May 13, 2020
1 parent c967297 commit d8e3a20
Show file tree
Hide file tree
Showing 44 changed files with 61 additions and 79 deletions.
0 data/example_lndscp.tif → data/toy_landscape.tif
View file
File renamed without changes.
Binary file modified ialena-2020.zip
View file
Binary file not shown.
85 changes: 38 additions & 47 deletions index.Rmd
View file
Original file line number Diff line number Diff line change
Expand Up @@ -852,7 +852,8 @@ class: inverse, left, bottom, clear, nonum
# Break (30 minutes)

.large[
- You can ask us any questions related to spatial data analysis in R and the *landscapemetrics* package during the workshop using https://www.sli.do/
- You can ask us any questions related to spatial data analysis in R and the *landscapemetrics* package during the workshop using https://www.sli.do/IALENA

- The event code is `IALENA`
]

Expand All @@ -877,11 +878,12 @@ Maximilian H.K. Hesselbarth

Department of Ecosystem Modelling, University of Goettingen, Germany


---
# Introdution to landscape metrics

```{r load_data_part_2, echo=FALSE, purl=FALSE, purl=FALSE}
lc_data <- raster("data/example_lndscp.tif")
```{r load_data_part_2, echo = FALSE, purl = FALSE}
lc_data <- raster("data/toy_landscape.tif")
```

--
Expand All @@ -897,17 +899,17 @@ lc_data <- raster("data/example_lndscp.tif")

--
.pull-left[
```{r aerial_lsm, out.width = "75%", out.height = "75%", echo=FALSE, purl=FALSE, purl=FALSE}
```{r aerial_lsm, out.width = "75%", out.height = "75%", echo = FALSE, purl = FALSE}
knitr::include_graphics("figs/aerial_lsm.png")
```
]

.pull-right[
```{r example_lsm, out.width = "75%", out.height = "75%", echo=FALSE, purl=FALSE, purl=FALSE}
```{r example_lsm, out.width = "75%", out.height = "75%", echo = FALSE, purl = FALSE}
ras_df <- as.data.frame(lc_data, xy = TRUE)
ggplot(data = ras_df) +
geom_raster(aes(x = x, y = y, fill = as.factor(example_lndscp))) +
geom_raster(aes(x = x, y = y, fill = as.factor(toy_landscape))) +
scale_fill_manual(values = c("#98D2E1", "#EAB8BD", "#9B9555")) +
guides(fill = FALSE) +
coord_equal() +
Expand All @@ -918,32 +920,6 @@ ggplot(data = ras_df) +

</center>

<!-- --- -->
<!-- # Why a new R package was needed -->

<!-- -- -->
<!-- - *FRAGSTATS* <font size="3" color="grey"> (McGarigal et al., 2012) </font> -->

<!-- - <font color = "#63C03C"> Comprehensive collection of metrics </font> -->
<!-- - <font color = "#64AAC5"> Only on Windows, not open source </font> -->
<!-- - <font color = "#64AAC5"> Need to import/export data </font> -->
<!-- - <font color = "#64AAC5"> Hard to integrate into larger workflows </font> -->


<!-- -- -->
<!-- - *SDMTools* (R package) <font size="3" color="grey"> (VanDerWal et al., 2019) </font> -->

<!-- - <font color = "#63C03C"> Multiplatform, open source </font> -->
<!-- - <font color = "#64AAC5"> Only set of metrics, no metrics on landscape level </font> -->
<!-- - <font color = "#64AAC5"> Hard to integrate into larger workflows </font> -->
<!-- - <font color = "#64AAC5"> Not on CRAN anymore (archived on 12.01.2020) </font> -->


<!-- -- -->
<!-- - Several GIS add-ons (e.g. *r.li* <font size="3" color="grey"> (Porta et al., 2017) </font>)) -->

<!-- - <font color = "#63C03C"> Multiplatform, open source </font> -->
<!-- - <font color = "#64AAC5"> Need to use GIS software </font> -->

---
layout: false
Expand All @@ -970,7 +946,7 @@ background-size: 15%
<center>

--
```{r levels_lsm, fig.hold = "hold", fig.align = "default", out.width="30%", echo=FALSE, purl=FALSE, purl=FALSE}
```{r levels_lsm, fig.hold = "hold", fig.align = "default", out.width = "30%", echo = FALSE, purl = FALSE}
lsm_patch <- get_patches(lc_data, class = 1)[[1]] %>%
as.data.frame(xy = TRUE) %>%
mutate(level = "patch") %>%
Expand All @@ -988,10 +964,10 @@ lsm_patch <- get_patches(lc_data, class = 1)[[1]] %>%
text = element_text(family = "Metropolis"))
lsm_class <- ras_df %>%
mutate(example_lndscp = case_when(example_lndscp == 1 ~ 1),
mutate(toy_landscape = case_when(toy_landscape == 1 ~ 1),
level = "class") %>%
ggplot() +
geom_raster(aes(x = x, y = y, fill = as.factor(example_lndscp))) +
geom_raster(aes(x = x, y = y, fill = as.factor(toy_landscape))) +
scale_fill_manual(values = "#98D2E1", na.value = "grey75") +
guides(fill = FALSE) +
labs(title = "Class level") +
Expand All @@ -1003,7 +979,7 @@ lsm_class <- ras_df %>%
lsm_landscape <- ras_df %>%
mutate(level = "landscape") %>%
ggplot() +
geom_raster(aes(x = x, y = y, fill = as.factor(example_lndscp))) +
geom_raster(aes(x = x, y = y, fill = as.factor(toy_landscape))) +
scale_fill_manual(values = c("#98D2E1", "#EAB8BD", "#9B9555")) +
guides(fill = FALSE) +
labs(title = "Landscape level") +
Expand All @@ -1019,6 +995,7 @@ lsm_landscape

</center>


---
# Getting ready to use *landscapemetrics*

Expand All @@ -1029,7 +1006,7 @@ Import and check data
# install.packages("landscapemetrics")
library(landscapemetrics)
library(dplyr)
lc_data <- raster("data/example_lndscp.tif")
lc_data <- raster("data/toy_landscape.tif")
check_landscape(lc_data)
```

Expand All @@ -1040,6 +1017,7 @@ List available metrics
list_lsm()
```


---
# How to calculate landscape metrics

Expand All @@ -1066,6 +1044,7 @@ bind_rows(class_mean, lsm_total)
```
]


---
# Easy integration into larger workflows

Expand All @@ -1085,6 +1064,7 @@ sample(x = c(1, 2, 3), prob = c(0.5, 0.25, 0.25), size = 2500, replace = TRUE) %
arrange(-n)
```


---
# Calculation of multiple metrics

Expand All @@ -1097,6 +1077,7 @@ calculate_lsm(landscape = lc_data,
classes_max = 5)
```


---
class: left, middle, clear, nonum

Expand All @@ -1107,7 +1088,7 @@ The exercise will teach you how to calculate single and multiple landscape metri

During the exercise there are part where you are supposed to type your own solution indicated by the following structure:

```{r exercise_code_1, eval = FALSE, purl=FALSE}
```{r exercise_code_1, eval = FALSE, purl = FALSE}
# /Start Code/ #
print("Hello World") # This would be your code contribution
Expand All @@ -1119,6 +1100,7 @@ In case you run into problems or have any questions, please contact us at any ti

For a general overview of *landscapemetrics*, please see <https://r-spatialecology.github.io/landscapemetrics>.


---
# Visualize patches

Expand All @@ -1129,6 +1111,7 @@ Easily visualize patches of several classes or the whole landscape
show_patches(augusta_nlcd, labels = FALSE, class = 42)
```


---
# Further visualization

Expand All @@ -1142,7 +1125,7 @@ show_cores(augusta_nlcd,
labels = FALSE, class = 42)
```

```{r, show_cores, echo=FALSE, purl=FALSE}
```{r, show_cores, echo = FALSE, cache = TRUE, purl = FALSE}
show_cores(augusta_nlcd,
labels = FALSE, class = 42, edge_depth = 5)
```
Expand All @@ -1158,13 +1141,14 @@ show_lsm(augusta_nlcd, labels = FALSE,
class = 42, what = "lsm_p_area")
```

```{r, show_lsm, echo=FALSE, purl=FALSE, cache=TRUE}
```{r, show_lsm, echo = FALSE, cache = TRUE, purl = FALSE}
show_lsm(augusta_nlcd, labels = FALSE,
class = 42, what = "lsm_p_area") +
theme(legend.position = "none")
```
]


---
# Sample metrics in buffer areas

Expand All @@ -1178,7 +1162,7 @@ show_lsm(augusta_nlcd, labels = FALSE,
- Metrics can be specified identical to `list_lsm()` and `calculate_lsm()`

--
```{r, plot_sample_points, echo=FALSE, purl=FALSE}
```{r, plot_sample_points, echo = FALSE, cache = TRUE, purl = FALSE}
sample_points <- matrix(c(1253709, 1249455,
1261857, 1256055,
1252009, 1257055), ncol = 2, byrow = TRUE)
Expand Down Expand Up @@ -1213,6 +1197,7 @@ ggplot(data = raster::as.data.frame(augusta_nlcd, xy = TRUE)) +
theme_void()
```


---
# Sample metrics in buffer areas

Expand All @@ -1228,6 +1213,7 @@ sample_lsm(landscape = augusta_nlcd, y = sample_points,
size = 1000, what = "lsm_l_np")
```


---
# Moving window

Expand All @@ -1238,7 +1224,7 @@ sample_lsm(landscape = augusta_nlcd, y = sample_points,
- Use matrix to specify moving window and focal cell

--
```{r moving_window_plot, echo=FALSE, cache=TRUE, purl=FALSE}
```{r moving_window_plot, echo = FALSE, cache = TRUE, purl = FALSE}
focal_i <- cbind(ras_df[ ,c(1, 2)], id = 1:nrow(ras_df))
focal_poly <- purrr::map_dfr(1:nrow(focal_i), function(i) {
Expand All @@ -1259,7 +1245,7 @@ focal_i <- focal_i[1:250, ]
focal_poly <- focal_poly[focal_poly$id %in% 1:250, ]
gg_window <- ggplot(data = ras_df) +
geom_raster(aes(x = x, y = y, fill = as.factor(example_lndscp))) +
geom_raster(aes(x = x, y = y, fill = as.factor(toy_landscape))) +
geom_point(data = focal_i, aes(x = x, y = y), pch = 1) +
geom_polygon(data = focal_poly, aes(x = x, y = y),
fill = NA, col = "black") +
Expand All @@ -1274,17 +1260,18 @@ gg_window <- ggplot(data = ras_df) +
gganimate::animate(gg_window, nframes = 250, fps = 5, duration = 50)
```


---
# Moving window

Results in list with *raster* objects

```{r moving_window, cache=TRUE}
```{r moving_window, cache = TRUE}
window <- matrix(1, nrow = 5, ncol = 5)
window_result <- window_lsm(lc_data, window = window, what = "lsm_l_np")
```

```{r moving_window_result, echo=FALSE, purl=FALSE, out.width = "40%", cache=TRUE}
```{r moving_window_result, echo = FALSE, out.width = "40%", cache = TRUE, purl=FALSE}
ggplot(data = raster::as.data.frame(window_result[[1]]$lsm_l_np, xy = TRUE)) +
geom_raster(aes(x = x, y = y, fill = factor(layer))) +
scale_fill_viridis_d(option = "A") +
Expand All @@ -1294,6 +1281,7 @@ ggplot(data = raster::as.data.frame(window_result[[1]]$lsm_l_np, xy = TRUE)) +
```


---
# Building blocks

Expand Down Expand Up @@ -1323,14 +1311,15 @@ get_adjacencies(lc_data)
]

--
```{r bench, eval = FALSE, purl=FALSE}
```{r bench, eval = FALSE, purl = FALSE}
# A tibble: 2 x 3
expression mean mem_alloc
<chr> <bch:tm> <bch:byt>
1 adj_raster(landscape) 8900 μs 1470 KB
2 get_adjacencies(landscape) 562 μs 6 KB
```


---
## Second practical part

Expand All @@ -1339,7 +1328,7 @@ The exercise will teach you how to use all utility functions of the *landscapeme

During the exercise there are parts where you are supposed to code your own solution indicated by the following structure:

```{r exercise_code_2, eval = FALSE, purl=FALSE}
```{r exercise_code_2, eval = FALSE, purl = FALSE}
# /Start Code/ #
print("Hello World") # This would be your code contribution
Expand All @@ -1351,6 +1340,7 @@ In case you run into problems or have any questions, please contact us at any ti

For a general overview of *landscapemetrics*, please see <https://r-spatialecology.github.io/landscapemetrics>.


---
# Citation

Expand All @@ -1361,6 +1351,7 @@ For a general overview of *landscapemetrics*, please see <https://r-spatialecolo
citation("landscapemetrics")
```


---
class: left, top, clear

Expand Down
Loading

0 comments on commit d8e3a20

Please sign in to comment.