From 8613a6ccbe3b255c9234a3451ae9897dc4c4629c Mon Sep 17 00:00:00 2001
From: Pleydell David <david.pleydell@inra.fr>
Date: Thu, 5 Mar 2020 11:30:09 +0100
Subject: [PATCH 1/7] Moved some code from Rmd to plan.
---
src/asf_challenge.Rmd | 68 ++++++++++++-------------------------------
src/plan.R | 38 ++++++++++++++++++++++--
2 files changed, 54 insertions(+), 52 deletions(-)
diff --git a/src/asf_challenge.Rmd b/src/asf_challenge.Rmd
index ea3d190..640b17c 100644
--- a/src/asf_challenge.Rmd
+++ b/src/asf_challenge.Rmd
@@ -48,7 +48,10 @@ loadd(
data_structure,
pig_sites,
outbreaks,
- animal_movements
+ animal_movements,
+ adminPigSiteMap,
+ proportionAgroCoverMap,
+ proportionForestCoverMap
)
```
@@ -97,21 +100,9 @@ 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 +130,15 @@ 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 +154,17 @@ 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)
-```
+<!-- ```{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) -->
+<!-- ``` -->
\clearpage
diff --git a/src/plan.R b/src/plan.R
index 10cbf68..ebadbae 100644
--- a/src/plan.R
+++ b/src/plan.R
@@ -62,8 +62,42 @@ plan <- drake_plan(
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),
+
+ ## 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")),
--
GitLab
From 4f302c3f0cafb381532b8f34b31eb74351767833 Mon Sep 17 00:00:00 2001
From: Pleydell David <david.pleydell@inra.fr>
Date: Thu, 5 Mar 2020 11:39:10 +0100
Subject: [PATCH 2/7] movementAnimation re-added to plan (with 'file_out's
removed).
---
src/plan.R | 25 ++++++++++++++++++++++++-
1 file changed, 24 insertions(+), 1 deletion(-)
diff --git a/src/plan.R b/src/plan.R
index ebadbae..82dc329 100644
--- a/src/plan.R
+++ b/src/plan.R
@@ -53,9 +53,13 @@ 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 ####
@@ -64,6 +68,25 @@ plan <- drake_plan(
## Distance matrix for pigs
distMatPigs = st_distance(pig_sites),
+ ## Some constants
+ nPigSites = nrow(pig_sites),
+
+ ## Animation
+ movementFileName = (here("animations/animal_moves_by_day.gif")), ## file_out
+
+ 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 = 3000), # loop=FALSE,
+
+
## Map of administrative areas with pigsites and first cases
adminPigSiteMap = tm_shape(admin) +
tm_graticules(col = "lightgrey") +
--
GitLab
From 48b6d56ba77d02a130ec29fd83fa8b94afc10819 Mon Sep 17 00:00:00 2001
From: Pleydell David <david.pleydell@inra.fr>
Date: Thu, 5 Mar 2020 12:01:20 +0100
Subject: [PATCH 3/7] Animation file path hardwired into Rmd file. Compiles.
---
src/asf_challenge.Rmd | 3 +++
src/plan.R | 2 +-
2 files changed, 4 insertions(+), 1 deletion(-)
diff --git a/src/asf_challenge.Rmd b/src/asf_challenge.Rmd
index 640b17c..332b63d 100644
--- a/src/asf_challenge.Rmd
+++ b/src/asf_challenge.Rmd
@@ -166,6 +166,9 @@ the official projection in France. Note, the units are in meters.
<!-- tm_lines(alpha = .3) -->
<!-- ``` -->
+{scale=30%}
+
+
\clearpage
diff --git a/src/plan.R b/src/plan.R
index 82dc329..2440bd5 100644
--- a/src/plan.R
+++ b/src/plan.R
@@ -84,7 +84,7 @@ plan <- drake_plan(
tm_facets(along = "day4display", free.coords=FALSE) +
tm_layout(bg.color = "lightblue"),
filename=(movementFileName), ## file_out
- width=2000, delay=100, restart.delay = 3000), # loop=FALSE,
+ width=2000, delay=100, restart.delay = 300), # loop=FALSE,
## Map of administrative areas with pigsites and first cases
--
GitLab
From e4717ba0fec1da9c7e60850f390ce274f5a8b9d2 Mon Sep 17 00:00:00 2001
From: Pleydell David <david.pleydell@inra.fr>
Date: Thu, 5 Mar 2020 12:39:15 +0100
Subject: [PATCH 4/7] Path taken from plan (movementFileName) used to display
animation. But no figure number.
---
src/asf_challenge.Rmd | 18 ++++--------------
src/plan.R | 2 +-
2 files changed, 5 insertions(+), 15 deletions(-)
diff --git a/src/asf_challenge.Rmd b/src/asf_challenge.Rmd
index 332b63d..1766948 100644
--- a/src/asf_challenge.Rmd
+++ b/src/asf_challenge.Rmd
@@ -51,7 +51,8 @@ loadd(
animal_movements,
adminPigSiteMap,
proportionAgroCoverMap,
- proportionForestCoverMap
+ proportionForestCoverMap,
+ movementFileName
)
```
@@ -154,19 +155,8 @@ 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) -->
-<!-- ``` -->
-
-{scale=30%}
+{ scale=10% }
+
diff --git a/src/plan.R b/src/plan.R
index 2440bd5..5ebd053 100644
--- a/src/plan.R
+++ b/src/plan.R
@@ -72,7 +72,7 @@ plan <- drake_plan(
nPigSites = nrow(pig_sites),
## Animation
- movementFileName = (here("animations/animal_moves_by_day.gif")), ## file_out
+ movementFileName = file_out(here("animations/animal_moves_by_day.gif")),
movementAnimation = tmap_animation(tm_shape(admin) +
tm_graticules(col = "lightgrey") +
--
GitLab
From 454835c87e9d2732e4fe5601ed2d3e3b8780572d Mon Sep 17 00:00:00 2001
From: Pleydell David <david.pleydell@inra.fr>
Date: Thu, 5 Mar 2020 12:56:25 +0100
Subject: [PATCH 5/7] Bug fix (scale -> width) for displaying animation.
---
src/asf_challenge.Rmd | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/src/asf_challenge.Rmd b/src/asf_challenge.Rmd
index 1766948..0dffe9d 100644
--- a/src/asf_challenge.Rmd
+++ b/src/asf_challenge.Rmd
@@ -52,7 +52,8 @@ loadd(
adminPigSiteMap,
proportionAgroCoverMap,
proportionForestCoverMap,
- movementFileName
+ movementFileName,
+ movementAnimation
)
```
@@ -155,7 +156,7 @@ the official projection in France. Note, the units are in meters.
### Animal movements
-{ scale=10% }
+{ width=60% }
--
GitLab
From a034401211f53924c8939e6a0a992293c76c885b Mon Sep 17 00:00:00 2001
From: Pleydell David <david.pleydell@inra.fr>
Date: Thu, 5 Mar 2020 13:02:04 +0100
Subject: [PATCH 6/7] Returned animal_movements to full size (filter on date
commented).
---
src/plan.R | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/src/plan.R b/src/plan.R
index 5ebd053..59d5767 100644
--- a/src/plan.R
+++ b/src/plan.R
@@ -57,9 +57,10 @@ plan <- drake_plan(
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),
+ ## filter(date < 10),
zones = pig_sites),
#### PRE-COMPUTE COMPLICATED FIGURES ####
--
GitLab
From 037dde5f37bd4f1286aa3864c7afcf3ba5847209 Mon Sep 17 00:00:00 2001
From: Pleydell David <david.pleydell@inra.fr>
Date: Thu, 5 Mar 2020 13:07:22 +0100
Subject: [PATCH 7/7] Update in .gitignore.
---
.gitignore | 1 +
1 file changed, 1 insertion(+)
diff --git a/.gitignore b/.gitignore
index ecf3edb..9c15171 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,4 @@
.drake
.Rhistory
dave's_scratchpad.R
+plan_execute.R
--
GitLab