From 65c8f8062cf07fb1471c9f15f6f08757d00951df Mon Sep 17 00:00:00 2001
From: rafnuss <rafnuss@gmail.com>
Date: Mon, 11 Apr 2022 08:37:49 -0400
Subject: [PATCH] Move all data to `inst/extdata` to avoid having them loaded
 with the pacakge

---
 _pkgdown.yml                                  |  10 -
 inst/extdata/18LX.R                           | 232 ++++++++++++++++++
 data/grl.rda => inst/extdata/18LX_grl.rda     | Bin
 .../extdata/18LX_light_prob.rda               | Bin
 .../extdata/18LX_pressure_maps.rda            | Bin
 .../extdata/18LX_pressure_prob.rda            | Bin
 .../extdata/18LX_pressure_timeserie.rda       | Bin
 .../extdata/18LX_static_prob.rda              | Bin
 .../extdata/18LX_static_timeserie.rda         | Bin
 9 files changed, 232 insertions(+), 10 deletions(-)
 create mode 100644 inst/extdata/18LX.R
 rename data/grl.rda => inst/extdata/18LX_grl.rda (100%)
 rename data/light_prob.rda => inst/extdata/18LX_light_prob.rda (100%)
 rename data/pressure_maps.rda => inst/extdata/18LX_pressure_maps.rda (100%)
 rename data/pressure_prob.rda => inst/extdata/18LX_pressure_prob.rda (100%)
 rename data/pressure_timeserie.rda => inst/extdata/18LX_pressure_timeserie.rda (100%)
 rename data/static_prob.rda => inst/extdata/18LX_static_prob.rda (100%)
 rename data/static_timeserie.rda => inst/extdata/18LX_static_timeserie.rda (100%)

diff --git a/_pkgdown.yml b/_pkgdown.yml
index 05fd80f0..6025eed3 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -35,16 +35,6 @@ reference:
   desc: groundspeed or airspeed to probability
   contents:
   - starts_with("flight_")
-- title: Dataset
-  desc: Dataset used for vignettes
-  contents:
-  - "pressure_maps"
-  - "pressure_prob"
-  - "pressure_timeserie"
-  - "light_prob"
-  - "static_prob"
-  - "static_timeserie"
-  - "grl"
 
 navbar:
   left:
diff --git a/inst/extdata/18LX.R b/inst/extdata/18LX.R
new file mode 100644
index 00000000..75dee294
--- /dev/null
+++ b/inst/extdata/18LX.R
@@ -0,0 +1,232 @@
+# This scripts combines all the codes from the vignettes of the packages. It generates all the
+# data needed to run the vignette.
+
+# Load library
+library(GeoPressureR)
+library(raster)
+library(MASS)
+
+# 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"
+)
+
+# Add labeling
+pam_data <- trainset_read(pam_data, pathname = system.file("extdata", package = "GeoPressureR"))
+
+# Compute stationay period
+pam_data <- pam_sta(pam_data)
+
+
+
+
+
+
+
+
+
+
+# 2. Pressure Map ----
+# Compute pressure maps from GeoPressureAPI
+pressure_maps <- geopressure_map(pam_data$pressure,
+                                 extent = c(50, -16, 0, 23),
+                                 scale = 2,
+                                 max_sample = 250,
+                                 margin = 30)
+
+# Convert to probability map
+pressure_prob <- geopressure_prob_map(pressure_maps,
+                                      s = 1,
+                                      thr = 0.9)
+
+# Compute the most likely path
+path <- geopressure_map2path(pressure_prob)
+path$lat[5] <- path$lat[5] + .25
+
+# Query the pressure timeserie at each path
+pressure_timeserie <- geopressure_ts_path(path, pam_data$pressure)
+
+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")
+
+
+
+
+
+
+# 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])
+
+# 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$label == ""
+
+# Extract twilight at calibration
+twl_calib <- subset(twl, !deleted & twilight >= tm_calib_1[1] & twilight <= tm_calib_1[2])
+
+# Compute zenith angle and fit distribution
+sun <- solar(twl_calib$twilight)
+z <- refracted(zenith(sun, lon_calib, lat_calib))
+fit_e <- fitdistr(z, "gamma")
+
+# 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)
+
+# Find grid information from pressure map
+g <- as.data.frame(pressure_prob[[1]], xy = TRUE)
+g$layer <- NA
+
+# Compute zenith angle and corresponding probability on twilight
+twl_clean <- subset(twl, !deleted)
+sun <- solar(twl_clean$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"])
+})
+
+# Define Log-linear Pooling
+w <- 0.05
+
+# 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$sta_id[i_s],
+    nb_sample = sum(id)
+  )
+  light_prob[[i_s]] <- gr
+}
+
+saveRDS(light_prob, "inst/extdata/light_prob.rda")
+
+
+
+
+
+
+
+
+
+
+
+
+
+# 4. Preparing Data  ----
+
+# Combine light and pressure map
+thr_sta_dur = 0 # in hours
+sta_pres <- unlist(lapply(pressure_prob, function(x) raster::metadata(x)$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$start, units = "hours") > thr_sta_dur]
+# Get the sta_id present on all three data sources
+sta_id_keep = intersect(intersect(sta_pres,sta_light),sta_thres)
+# Filter pressure and light map
+pressure_prob <- pressure_prob[sta_pres %in% sta_id_keep]
+light_prob <- light_prob[sta_light %in% sta_id_keep]
+
+# Compute flight information
+flight = list()
+for (i_f in seq_len(length(sta_id_keep)-1)){
+  from_sta_id <- sta_id_keep[i_f]
+  to_sta_id <- sta_id_keep[i_f+1]
+  flight[[i_f]] <- list(
+    start = pam_data$sta$end[seq(from_sta_id,to_sta_id-1)],
+    end = pam_data$sta$start[seq(from_sta_id+1,to_sta_id)],
+    sta_id = seq(from_sta_id,to_sta_id-1)
+  )
+}
+flight[[i_f+1]]=list()
+
+# Compute static prob
+static_prob <- mapply(function(light, pressure, flight) {
+  # define static prob as the product of light and pressure prob
+  static_prob <- light * pressure
+
+  # replace na by zero
+  # tmp <- values(static_prob)
+  # tmp[is.na(tmp)] <- 0
+  # values(static_prob) <- tmp
+
+  # define metadata
+  metadata(static_prob) <- metadata(pressure)
+  metadata(static_prob)$flight <- flight
+
+  # return
+  static_prob
+}, light_prob, pressure_prob, flight)
+
+# 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
+
+lon_calib_id <- which.min(abs(lon_calib - lon))
+lat_calib_id <- which.min(abs(lat_calib - lat))
+
+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
+
+# 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$pressure)
+
+# Downscale map
+# static_prob <- lapply(static_prob, function(raster) {
+#   raster_ds <- aggregate(raster, fact = 1, fun = max, na.rm = T, expand = T)
+#   # keep metadata
+#   metadata(raster_ds) <- metadata(raster)
+#   return(raster_ds)
+# })
+
+saveRDS(static_prob, "inst/extdata/static_prob.rda")
+saveRDS(static_timeserie, "inst/extdata/static_timeserie.rda")
+
+
+
+
+
+
+
+
+# 4-5. Basic and wind Graph ----
+
+# Location of wind data
+dir.save <- '~'
+
+# create graph
+grl <- graph_create(static_prob, thr_prob_percentile = .99, thr_gs = 150)
+
+# Add wind data
+filename = paste0(dir.save,"/","18IC_")
+grl <- graph_add_wind(grl, pressure=pam_data$pressure, filename, thr_as = 100)
+
+saveRDS(grl, "inst/extdata/grl.rda")
diff --git a/data/grl.rda b/inst/extdata/18LX_grl.rda
similarity index 100%
rename from data/grl.rda
rename to inst/extdata/18LX_grl.rda
diff --git a/data/light_prob.rda b/inst/extdata/18LX_light_prob.rda
similarity index 100%
rename from data/light_prob.rda
rename to inst/extdata/18LX_light_prob.rda
diff --git a/data/pressure_maps.rda b/inst/extdata/18LX_pressure_maps.rda
similarity index 100%
rename from data/pressure_maps.rda
rename to inst/extdata/18LX_pressure_maps.rda
diff --git a/data/pressure_prob.rda b/inst/extdata/18LX_pressure_prob.rda
similarity index 100%
rename from data/pressure_prob.rda
rename to inst/extdata/18LX_pressure_prob.rda
diff --git a/data/pressure_timeserie.rda b/inst/extdata/18LX_pressure_timeserie.rda
similarity index 100%
rename from data/pressure_timeserie.rda
rename to inst/extdata/18LX_pressure_timeserie.rda
diff --git a/data/static_prob.rda b/inst/extdata/18LX_static_prob.rda
similarity index 100%
rename from data/static_prob.rda
rename to inst/extdata/18LX_static_prob.rda
diff --git a/data/static_timeserie.rda b/inst/extdata/18LX_static_timeserie.rda
similarity index 100%
rename from data/static_timeserie.rda
rename to inst/extdata/18LX_static_timeserie.rda