diff --git a/.gitignore b/.gitignore
index ecf3edb8b505acc92f08a8cf19451cb1bb4d27b3..9c15171ab5411096d3531c60ba538ff5733b6324 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,4 @@
.drake
.Rhistory
dave's_scratchpad.R
+plan_execute.R
diff --git a/src/asf_challenge.Rmd b/src/asf_challenge.Rmd
index ea3d19075d76dba2b092fc3603013017180a76d0..0dffe9d5b76237664c62447ed73beafe1f885293 100644
--- a/src/asf_challenge.Rmd
+++ b/src/asf_challenge.Rmd
@@ -48,7 +48,12 @@ loadd(
data_structure,
pig_sites,
outbreaks,
- animal_movements
+ animal_movements,
+ adminPigSiteMap,
+ proportionAgroCoverMap,
+ proportionForestCoverMap,
+ movementFileName,
+ movementAnimation
)
```
@@ -97,21 +102,9 @@ supposed to be an island.
```{r map-admin, fig.cap = cap}
cap <- "Administrative divisions of the dummy territory and pig sites. Observed cases are highlighted in dark red."
-tm_shape(admin) +
- tm_graticules(col = "lightgrey") +
- tm_polygons() +
- tm_compass(type = "8star", position = c("left", "top")) +
- tm_scale_bar(breaks = c(0, 100, 200), text.size = 1) +
- tm_layout(bg.color = "lightblue") +
- tm_shape(pig_sites) +
- tm_dots() +
- tm_shape(outbreaks) +
- tm_dots(size = .1, col = "darkred")
-
+adminPigSiteMap
```
-
-
### Land cover
Figure \@ref(fig:land-cover) shows a simplified version of the
@@ -139,38 +132,15 @@ Here land cover proportions of forest and agriculture are preressented on such a
```{r hex-land-cover-agri, message = FALSE, fig.cap = cap}
cap <- "Proportional cover of agriculture on hexagonal grid."
-
-tm_shape(admin) +
- tm_polygons() +
- tm_shape(hex) +
- tm_polygons(col = "pAgricultural")
-
+proportionAgroCoverMap
```
-
```{r hex-land-cover-forest, message = FALSE, fig.cap = cap}
cap <- "Proportional cover of forest on hexagonal grid, with detected cases among pig farms and wild boar."
-
-tm_shape(admin) +
- tm_polygons() +
- tm_graticules(col = "lightgrey") +
- tm_layout(bg.color = "lightblue") +
- tm_shape(hex) +
- tm_polygons(col = "pForest", lwd=0.2, border.col="grey", palette=get_brewer_pal("Greens", n = 10, plot=FALSE)) +
- tm_shape(pig_sites) +
- tm_dots() +
- tm_shape(outbreaks[outbreaks$HOST=="wild boar",]) +
- tm_dots(size = .2, col = "orange") +
- tm_shape(outbreaks[outbreaks$HOST=="pig herd",]) +
- tm_dots(size = .2, col = "red") +
- tm_add_legend(type="symbol", labels=c("pig herd","wild boar"), col=c("red", "orange"), border.col=c("red", "orange"), title="Cases") +
- tm_scale_bar(breaks = c(0, 50, 100, 150), text.size = 1, position = c("left", "top"))
-
+proportionForestCoverMap
```
-
-
#### Coordinate reference systems
The coordinate system used for shapefile Island_ADMIN.shp is
```{r map-admin-crs}
@@ -186,17 +156,9 @@ the official projection in France. Note, the units are in meters.
### Animal movements
-```{r eval = FALSE}
-## This is useless
-tm_shape(admin) +
- tm_graticules(col = "lightgrey") +
- tm_polygons() +
- tm_layout(bg.color = "lightblue") +
- tm_shape(pig_sites) +
- tm_dots() +
- tm_shape(animal_movements) +
- tm_lines(alpha = .3)
-```
+{ width=60% }
+
+
\clearpage
diff --git a/src/plan.R b/src/plan.R
index 10cbf687d8a973aabf67d5f723545d4828028922..59d5767c69af0e6caa49e9803830f49777fbd153 100644
--- a/src/plan.R
+++ b/src/plan.R
@@ -53,17 +53,75 @@ plan <- drake_plan(
## (NE sites, see doc (?))
## 18794 lines removed. Produced invalid lines.
filter(source != dest) %>%
+ ## Add a column to provide title when using tmap_animation
+ mutate(day4display=paste("Day", stringr::str_pad(date, nchar(max(date)), pad="0"))) %>%
## Put source and dest as the first two cols.
## Necessary to match with ID in pig_sites
- select(source, dest, everything()),
+ select(source, dest, everything()),
+ ## %>%
+ ## FOR RAPID COMPILATION WHILE DEBUGGING - REMOVE WHEN DEBUGGED
+ ## filter(date < 10),
zones = pig_sites),
#### PRE-COMPUTE COMPLICATED FIGURES ####
data_structure = plot_data_structure(fname = here("src/data_structure.yml")),
## Distance matrix for pigs
- distMatPigs = st_distance(pig_sites),
-
+ distMatPigs = st_distance(pig_sites),
+
+ ## Some constants
+ nPigSites = nrow(pig_sites),
+
+ ## Animation
+ movementFileName = file_out(here("animations/animal_moves_by_day.gif")),
+
+ movementAnimation = tmap_animation(tm_shape(admin) +
+ tm_graticules(col = "lightgrey") +
+ tm_polygons() +
+ tm_shape(pig_sites) +
+ tm_dots(alpha = .3) + # tm_shape(littleAM) + ##
+ tm_shape(animal_movements) +
+ tm_lines(alpha=0.5) +
+ tm_facets(along = "day4display", free.coords=FALSE) +
+ tm_layout(bg.color = "lightblue"),
+ filename=(movementFileName), ## file_out
+ width=2000, delay=100, restart.delay = 300), # loop=FALSE,
+
+
+ ## Map of administrative areas with pigsites and first cases
+ adminPigSiteMap = tm_shape(admin) +
+ tm_graticules(col = "lightgrey") +
+ tm_polygons() +
+ tm_compass(type = "8star", position = c("left", "top")) +
+ tm_scale_bar(breaks = c(0, 100, 200), text.size = 1) +
+ tm_layout(bg.color = "lightblue") +
+ tm_shape(pig_sites) +
+ tm_dots() +
+ tm_shape(outbreaks) +
+ tm_dots(size = .1, col = "darkred"),
+
+ ## Map of proportional agriculture cover
+ proportionAgroCoverMap = tm_shape(admin) +
+ tm_polygons() +
+ tm_shape(hex) +
+ tm_polygons(col = "pAgricultural"),
+
+ ## Map of proportional forest cover
+ proportionForestCoverMap = tm_shape(admin) +
+ tm_polygons() +
+ tm_graticules(col = "lightgrey") +
+ tm_layout(bg.color = "lightblue") +
+ tm_shape(hex) +
+ tm_polygons(col = "pForest", lwd=0.2, border.col="grey", palette=get_brewer_pal("Greens", n = 10, plot=FALSE)) +
+ tm_shape(pig_sites) +
+ tm_dots() +
+ tm_shape(outbreaks[outbreaks$HOST=="wild boar",]) +
+ tm_dots(size = .2, col = "orange") +
+ tm_shape(outbreaks[outbreaks$HOST=="pig herd",]) +
+ tm_dots(size = .2, col = "red") +
+ tm_add_legend(type="symbol", labels=c("pig herd","wild boar"), col=c("red", "orange"), border.col=c("red", "orange"), title="Cases") +
+ tm_scale_bar(breaks = c(0, 50, 100, 150), text.size = 1, position = c("left", "top")),
+
#### REPORTS ####
report = rmarkdown::render(
knitr_in(here("src/asf_challenge.Rmd")),