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Move all data to
inst/extdata
to avoid having them loaded with the …
…pacakge
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# This scripts combines all the codes from the vignettes of the packages. It generates all the | ||
# data needed to run the vignette. | ||
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# Load library | ||
library(GeoPressureR) | ||
library(raster) | ||
library(MASS) | ||
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# 1. PAM reading and labeling ---- | ||
# Read pam data | ||
pam_data <- pam_read( | ||
pathname = system.file("extdata", package = "GeoPressureR"), | ||
crop_start = "2017-06-20", crop_end = "2018-05-02" | ||
) | ||
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# Add labeling | ||
pam_data <- trainset_read(pam_data, pathname = system.file("extdata", package = "GeoPressureR")) | ||
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# Compute stationay period | ||
pam_data <- pam_sta(pam_data) | ||
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# 2. Pressure Map ---- | ||
# Compute pressure maps from GeoPressureAPI | ||
pressure_maps <- geopressure_map(pam_data$pressure, | ||
extent = c(50, -16, 0, 23), | ||
scale = 2, | ||
max_sample = 250, | ||
margin = 30) | ||
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# Convert to probability map | ||
pressure_prob <- geopressure_prob_map(pressure_maps, | ||
s = 1, | ||
thr = 0.9) | ||
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# Compute the most likely path | ||
path <- geopressure_map2path(pressure_prob) | ||
path$lat[5] <- path$lat[5] + .25 | ||
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# Query the pressure timeserie at each path | ||
pressure_timeserie <- geopressure_ts_path(path, pam_data$pressure) | ||
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saveRDS(pressure_maps, "inst/extdata/18LX_pressure_maps.rda") | ||
saveRDS(pressure_prob, "inst/extdata/18LX_pressure_prob.rda") | ||
saveRDS(pressure_timeserie, "inst/extdata/18LX_pressure_timeserie.rda") | ||
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# 3. Light Map ---- | ||
# Define calibration information | ||
lon_calib <- 17.05 | ||
lat_calib <- 48.9 | ||
tm_calib_1 <- c(pam_data$sta$start[1], pam_data$sta$end[1]) | ||
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# Compute twilight and read labeling file | ||
twl <- find_twilights(pam_data$light) | ||
csv <- read.csv(paste0(system.file("extdata", package = "GeoPressureR"), "/18LX_light-labeled.csv")) | ||
twl$deleted <- !csv$label == "" | ||
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# Extract twilight at calibration | ||
twl_calib <- subset(twl, !deleted & twilight >= tm_calib_1[1] & twilight <= tm_calib_1[2]) | ||
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# Compute zenith angle and fit distribution | ||
sun <- solar(twl_calib$twilight) | ||
z <- refracted(zenith(sun, lon_calib, lat_calib)) | ||
fit_e <- fitdistr(z, "gamma") | ||
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# Add stationay period information on the twilight | ||
twilight_sta_id <- sapply(twl$twilight, function(x) which(pam_data$sta$start < x & x < pam_data$sta$end)) | ||
twilight_sta_id[sapply(twilight_sta_id, function(x) length(x) == 0)] <- 0 | ||
twl$sta_id <- unlist(twilight_sta_id) | ||
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# Find grid information from pressure map | ||
g <- as.data.frame(pressure_prob[[1]], xy = TRUE) | ||
g$layer <- NA | ||
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# Compute zenith angle and corresponding probability on twilight | ||
twl_clean <- subset(twl, !deleted) | ||
sun <- solar(twl_clean$twilight) | ||
pgz <- apply(g, 1, function(x) { | ||
z <- refracted(zenith(sun, x[1], x[2])) | ||
dgamma(z, fit_e$estimate["shape"], fit_e$estimate["rate"]) | ||
}) | ||
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# Define Log-linear Pooling | ||
w <- 0.05 | ||
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# Produce proabibility map from light data | ||
light_prob <- c() | ||
for (i_s in seq_len(nrow(pam_data$sta))) { | ||
id <- twl_clean$sta_id == pam_data$sta$sta_id[i_s] | ||
if (sum(id) > 1) { | ||
g$layer <- exp(colSums(w * log(pgz[id, ]))) # Log-linear equation express in log | ||
} else if (sum(id) == 1) { | ||
g$layer <- pgz[id, ] | ||
} else { | ||
g$layer <- 1 | ||
} | ||
gr <- rasterFromXYZ(g) | ||
crs(gr) <- "+proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0" | ||
metadata(gr) <- list( | ||
sta_id = pam_data$sta$sta_id[i_s], | ||
nb_sample = sum(id) | ||
) | ||
light_prob[[i_s]] <- gr | ||
} | ||
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saveRDS(light_prob, "inst/extdata/light_prob.rda") | ||
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# 4. Preparing Data ---- | ||
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# Combine light and pressure map | ||
thr_sta_dur = 0 # in hours | ||
sta_pres <- unlist(lapply(pressure_prob, function(x) raster::metadata(x)$sta_id)) | ||
sta_light <- unlist(lapply(light_prob, function(x) raster::metadata(x)$sta_id)) | ||
sta_thres <- pam_data$sta$sta_id[difftime(pam_data$sta$end, pam_data$sta$start, units = "hours") > thr_sta_dur] | ||
# Get the sta_id present on all three data sources | ||
sta_id_keep = intersect(intersect(sta_pres,sta_light),sta_thres) | ||
# Filter pressure and light map | ||
pressure_prob <- pressure_prob[sta_pres %in% sta_id_keep] | ||
light_prob <- light_prob[sta_light %in% sta_id_keep] | ||
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# Compute flight information | ||
flight = list() | ||
for (i_f in seq_len(length(sta_id_keep)-1)){ | ||
from_sta_id <- sta_id_keep[i_f] | ||
to_sta_id <- sta_id_keep[i_f+1] | ||
flight[[i_f]] <- list( | ||
start = pam_data$sta$end[seq(from_sta_id,to_sta_id-1)], | ||
end = pam_data$sta$start[seq(from_sta_id+1,to_sta_id)], | ||
sta_id = seq(from_sta_id,to_sta_id-1) | ||
) | ||
} | ||
flight[[i_f+1]]=list() | ||
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# Compute static prob | ||
static_prob <- mapply(function(light, pressure, flight) { | ||
# define static prob as the product of light and pressure prob | ||
static_prob <- light * pressure | ||
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# replace na by zero | ||
# tmp <- values(static_prob) | ||
# tmp[is.na(tmp)] <- 0 | ||
# values(static_prob) <- tmp | ||
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# define metadata | ||
metadata(static_prob) <- metadata(pressure) | ||
metadata(static_prob)$flight <- flight | ||
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# return | ||
static_prob | ||
}, light_prob, pressure_prob, flight) | ||
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# Add known position | ||
lat <- seq(raster::ymax(static_prob[[1]]), raster::ymin(static_prob[[1]]), length.out = nrow(static_prob[[1]]) + 1) | ||
lat <- lat[seq_len(length(lat) - 1)] + diff(lat[1:2]) / 2 | ||
lon <- seq(raster::xmin(static_prob[[1]]), raster::xmax(static_prob[[1]]), length.out = ncol(static_prob[[1]]) + 1) | ||
lon <- lon[seq_len(length(lon) - 1)] + diff(lon[1:2]) / 2 | ||
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lon_calib_id <- which.min(abs(lon_calib - lon)) | ||
lat_calib_id <- which.min(abs(lat_calib - lat)) | ||
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tmp <- as.matrix(static_prob[[1]]) | ||
tmp[!is.na(tmp)] <- 0 | ||
tmp[lat_calib_id, lon_calib_id] <- 1 | ||
values(static_prob[[1]]) <- tmp | ||
tmp <- as.matrix(static_prob[[length(static_prob)]]) | ||
tmp[!is.na(tmp)] <- 0 | ||
tmp[lat_calib_id, lon_calib_id] <- 1 | ||
values(static_prob[[length(static_prob)]]) <- tmp | ||
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# Compute the most likely path | ||
path <- geopressure_map2path(static_prob) | ||
path$lat[3] <- path$lat[3] + .25 | ||
path$lat[5] <- path$lat[5] + .25 | ||
path$lat[13] <- path$lat[13] - .25 | ||
static_timeserie <- geopressure_ts_path(path, pam_data$pressure) | ||
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# Downscale map | ||
# static_prob <- lapply(static_prob, function(raster) { | ||
# raster_ds <- aggregate(raster, fact = 1, fun = max, na.rm = T, expand = T) | ||
# # keep metadata | ||
# metadata(raster_ds) <- metadata(raster) | ||
# return(raster_ds) | ||
# }) | ||
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saveRDS(static_prob, "inst/extdata/static_prob.rda") | ||
saveRDS(static_timeserie, "inst/extdata/static_timeserie.rda") | ||
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# 4-5. Basic and wind Graph ---- | ||
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# Location of wind data | ||
dir.save <- '~' | ||
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# create graph | ||
grl <- graph_create(static_prob, thr_prob_percentile = .99, thr_gs = 150) | ||
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# Add wind data | ||
filename = paste0(dir.save,"/","18IC_") | ||
grl <- graph_add_wind(grl, pressure=pam_data$pressure, filename, thr_as = 100) | ||
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saveRDS(grl, "inst/extdata/grl.rda") |
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