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worksheet-13.R
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worksheet-13.R
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## Logistics
library(sf)
library(raster)
library(ggplot2)
out <- 'outputs_raster_ts'
dir.create(out, showWarnings = FALSE)
## Raster Stacks
ndvi_yrly <- ...('data/r_ndvi_*.tif')
ndvi <- ...
names(ndvi) <- c(
'Avg NDVI 2002',
'Avg NDVI 2009')
... <- '+init=epsg:3338'
## Wildfires in Alaska
scar <- ...(
'data/OVERLAY_ID_83_399_144_TEST_BURNT_83_144_399_reclassed',
crs = 3338)
plot(...)
plot(..., add = TRUE)
burn_bbox <- ...
ndvi <- ...(ndvi, burn_bbox)
## Pixel Change
diff_ndvi <- ...
names(diff_ndvi) <- 'Difference'
diff_ndvi_mean <-
...(diff_ndvi, 'mean')
diff_ndvi_sd <-
cellStats(diff_ndvi, 'sd')
diff_ndvi_stdz <-
... /
...
names(diff_ndvi_stdz) <- 'Std. Diff.'
## Raster Time Series
ndvi_16day <- Sys.glob(
'data/NDVI_alaska_2005/*.tif')
ndvi <- ...(ndvi_16day)
crs(ndvi) <- '+init=epsg:3338'
dates <- as.Date(
sub('alaska_NDVI_', '', names(ndvi)),
'%Y_%m_%d')
names(ndvi) <- format(dates, '%b %d %Y')
## Raster Bricks
ndvi <- crop(ndvi, ...,
... = file.path(out, 'crop_alaska_ndvi.grd'),
overwrite = TRUE)
## Pixel Time Series
idx <- match('Aug.13.2005', names(ndvi))
plot(ndvi[[idx]])
pixel <- c(2813, 3720, 2823, 4195, 9910)
scar_pixel <- data.frame(
Date = ...,
cell = rep(pixel, length(dates)),
Type = 'burn scar?',
NDVI = ...)
pixel <- c(1710, 4736, 7374, 1957, 750)
normal_pixel <- data.frame(
Date = rep(dates, each = length(pixel)),
cell = rep(pixel, length(dates)),
Type = 'normal',
NDVI = c(ndvi[pixel]))
pixel <- rbind(normal_pixel, scar_pixel)
ggplot(pixel,
aes(x = ..., y = ...,
group = ..., col = ...)) +
geom_line()
## Zonal Averages
scar_geom <-
as(st_geometry(scar), 'Spatial')
scar_zone <- rasterize(scar_geom, ndvi,
background = 0,
filename = 'outputs_raster_ts/scar.grd',
overwrite = TRUE)
crs(scar_zone) <- '+init=epsg:3338'
scar_zone <- crop(scar_zone, ndvi)
scar_ndvi <-
...(ndvi, scar_zone, ...)
zone <- factor(scar_ndvi[, 1])
scar_ndvi <- scar_ndvi[, -1]
scar_zone <- data.frame(
Date = rep(dates, each = nrow(scar_ndvi)),
Zone = rep(zone, length(dates)),
NDVI = c(scar_ndvi))
## Eliminating Time
ndvi_lS <- ...(
ndvi, ..., na.rm = TRUE)
ndvi_mean <- ndvi_lS[['mean']]
ndvi_cov <- ndvi_lS[['covariance']]
ndvi_cor <- cov2cor(ndvi_cov)
ndvi_std <- sqrt(diag(ndvi_cov))
ndvi_stdz <- ...(ndvi,
... ,
filename = file.path(out, 'ndvi_stdz.grd'),
overwrite = TRUE)
pca <- ...
plot(pca)
npc <- 4
loading <- data.frame(
Date = rep(dates, npc),
PC = factor(rep(1:npc, each = length(dates))),
Loading = ...
)
ggplot(loading,
aes(...,
...)) +
geom_line()
pca$center <- pca$scale * 0
ndvi_scores <- ...(
...
index = 1:npc,
filename = file.path(out, 'ndvi_scores.grd'),
overwrite = TRUE)
plot(ndvi_scores)
ndvi_dev <- ...(
...
fun = ... {
...
},
filename = file.path(out, 'ndvi_dev.grd'),
overwrite = TRUE)
names(ndvi_dev) <- names(ndvi)
plot(
ndvi_scores[[2]] < -2 |
ndvi_scores[[3]] < -2)
plot(st_geometry(scar), add = TRUE)