inst/doc/a0_pastclim_overview.R

In pastclim: Manipulate Time Series of Climate Reconstructions

## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----install_cran, eval=FALSE-------------------------------------------------
# install.packages("pastclim")

## ----install_dev, eval=FALSE--------------------------------------------------
# install.packages("terra", repos = "https://rspatial.r-universe.dev")
# devtools::install_github("EvolEcolGroup/pastclim", ref = "dev")

## ----install_vignette, eval=FALSE---------------------------------------------
# devtools::install_github("EvolEcolGroup/pastclim",
#   ref = "dev",
#   build_vignettes = TRUE
# )

## ----vignette, eval=FALSE-----------------------------------------------------
# vignette("pastclim_overview", package = "pastclim")

## -----------------------------------------------------------------------------
library(pastclim)
get_available_datasets()

## -----------------------------------------------------------------------------
citation("pastclim")

## ----eval=FALSE---------------------------------------------------------------
# help("Beyer2020")

## ----echo=FALSE---------------------------------------------------------------
pastclim:::get_dataset_info(dataset = "Beyer2020")

## ----eval=FALSE---------------------------------------------------------------
# library(pastclim)
# set_data_path()

## ----echo=FALSE, results='hide'-----------------------------------------------
library(pastclim)
set_data_path(on_CRAN = TRUE)

## ----eval=FALSE---------------------------------------------------------------
# set_data_path(path_to_nc = "~/my_reconstructions")

## -----------------------------------------------------------------------------
get_vars_for_dataset(dataset = "Example")

## -----------------------------------------------------------------------------
get_time_bp_steps(dataset = "Example")

## -----------------------------------------------------------------------------
get_resolution(dataset = "Example")

## -----------------------------------------------------------------------------
get_vars_for_dataset(dataset = "Beyer2020")

## -----------------------------------------------------------------------------
get_vars_for_dataset(dataset = "Krapp2021")

## -----------------------------------------------------------------------------
get_vars_for_dataset(dataset = "Beyer2020", annual = FALSE, monthly = TRUE)

## -----------------------------------------------------------------------------
get_vars_for_dataset(dataset = "Example", details = TRUE)

## -----------------------------------------------------------------------------
get_downloaded_datasets()

## ----eval=FALSE---------------------------------------------------------------
# download_dataset(dataset = "Beyer2020", bio_variables = c("bio01", "bio05"))

## -----------------------------------------------------------------------------
locations <- data.frame(
  name = c("Iho Eleru", "La Riera", "Chalki", "Oronsay", "Atlantis"),
  longitude = c(5, -4, 27, -6, -24), latitude = c(7, 44, 36, 56, 31),
  time_bp = c(-11200, -18738, -10227, -10200, -11600)
)
locations

## -----------------------------------------------------------------------------
location_slice(
  x = locations, bio_variables = c("bio01", "bio12"),
  dataset = "Example", nn_interpol = FALSE
)

## -----------------------------------------------------------------------------
location_slice(
  x = locations, bio_variables = c("bio01", "bio12"),
  dataset = "Example", nn_interpol = TRUE
)

## -----------------------------------------------------------------------------
locations_ts <- location_series(
  x = locations,
  bio_variables = c("bio01", "bio12"),
  dataset = "Example"
)

## -----------------------------------------------------------------------------
subset(locations_ts, name == "Iho Eleru")

## -----------------------------------------------------------------------------
subset(locations_ts, name == "Oronsay")

## ----warning=TRUE, fig.width=4, fig.height=3----------------------------------
library(ggplot2)
ggplot(data = locations_ts, aes(x = time_bp, y = bio01, group = name)) +
  geom_line(aes(col = name)) +
  geom_point(aes(col = name))

## ----warning=TRUE, fig.width=4, fig.height=3----------------------------------
library(ggplot2)
ggplot(data = locations_ts, aes(x = time_bp, y = bio01, group = name)) +
  geom_line(aes(col = name)) +
  geom_point(aes(col = name)) +
  labs(
    y = var_labels("bio01", dataset = "Example", abbreviated = TRUE),
    x = "time BP (yr)"
  )

## -----------------------------------------------------------------------------
climate_20k <- region_slice(
  time_bp = -20000,
  bio_variables = c("bio01", "bio10", "bio12"),
  dataset = "Example"
)

## -----------------------------------------------------------------------------
climate_20k

## ----fig.width=6, fig.height=5------------------------------------------------
terra::plot(climate_20k)

## ----fig.width=6, fig.height=5------------------------------------------------
terra::plot(climate_20k,
  main = var_labels(climate_20k, dataset = "Example", abbreviated = TRUE)
)

## -----------------------------------------------------------------------------
climate_region <- region_series(
  time_bp = list(min = -15000, max = 0),
  bio_variables = c("bio01", "bio10", "bio12"),
  dataset = "Example"
)
climate_region

## -----------------------------------------------------------------------------
climate_region$bio01

## -----------------------------------------------------------------------------
time_bp(climate_region)

## ----fig.width=6, fig.height=5------------------------------------------------
terra::plot(climate_region$bio01, main = time_bp(climate_region))

## ----fig.width=6, fig.height=5------------------------------------------------
slice_10k <- slice_region_series(climate_region, time_bp = -10000)
terra::plot(slice_10k)

## -----------------------------------------------------------------------------
mis1_steps <- get_mis_time_steps(mis = 1, dataset = "Example")
mis1_steps

## -----------------------------------------------------------------------------
climate_mis1 <- region_series(
  time_bp = mis1_steps,
  bio_variables = c("bio01", "bio10", "bio12"),
  dataset = "Example"
)
climate_mis1

## -----------------------------------------------------------------------------
names(region_extent)

## -----------------------------------------------------------------------------
region_extent$Europe

## ----fig.width=6, fig.height=5------------------------------------------------
europe_climate_20k <- region_slice(
  time_bp = -20000,
  bio_variables = c("bio01", "bio10", "bio12"),
  dataset = "Example",
  ext = region_extent$Europe
)
terra::plot(europe_climate_20k)

## -----------------------------------------------------------------------------
names(region_outline)

## ----fig.width=6, fig.height=5------------------------------------------------
europe_climate_20k <- region_slice(
  time_bp = -20000,
  bio_variables = c("bio01", "bio10", "bio12"),
  dataset = "Example",
  crop = region_outline$Europe
)
terra::plot(europe_climate_20k)

## ----fig.width=6, fig.height=5------------------------------------------------
library(sf)
afr_eurasia <- sf::st_union(region_outline$Africa, region_outline$Eurasia)
climate_20k_afr_eurasia <- region_slice(
  time_bp = -20000,
  bio_variables = c("bio01", "bio10", "bio12"),
  dataset = "Example",
  crop = afr_eurasia
)
terra::plot(climate_20k_afr_eurasia)

## ----fig.width=6, fig.height=5------------------------------------------------
custom_vec <- terra::vect("POLYGON ((0 70, 25 70, 50 80, 170 80, 170 10,
                              119 2.4, 119 0.8, 116 -7.6, 114 -12, 100 -40,
                              -25 -40, -25 64, 0 70))")
climate_20k_custom <- region_slice(
  time_bp = -20000,
  bio_variables = c("bio01", "bio10", "bio12"),
  dataset = "Example",
  crop = custom_vec
)
terra::plot(climate_20k_custom)

## -----------------------------------------------------------------------------
get_biome_classes("Example")

## ----fig.width=8, fig.height=6------------------------------------------------
biome_20k <- region_slice(
  time_bp = -20000,
  bio_variables = c("biome"),
  dataset = "Example"
)
plot(biome_20k)

## ----fig.width=6, fig.height=2.5----------------------------------------------
biome_20k$desert <- biome_20k$biome
biome_20k$desert[biome_20k$desert != 21] <- NA
terra::plot(biome_20k$desert)

## ----fig.width=6, fig.height=2.5----------------------------------------------
ice_mask <- get_ice_mask(-20000, dataset = "Example")
land_mask <- get_land_mask(-20000, dataset = "Example")
terra::plot(c(ice_mask, land_mask))

## -----------------------------------------------------------------------------
ice_mask_vect <- as.polygons(ice_mask)

## ----fig.width=6, fig.height=5------------------------------------------------
plot(climate_20k,
  fun = function() polys(ice_mask_vect, col = "gray", lwd = 0.5)
)

## ----fig.width=6, fig.height=5------------------------------------------------
europe_climate <- region_series(
  time_bp = c(-20000, -15000, -10000, 0),
  bio_variables = c("bio01"),
  dataset = "Example",
  ext = region_extent$Europe
)
ice_masks <- get_ice_mask(c(-20000, -15000, -10000, 0),
  dataset = "Example"
)
ice_poly_list <- lapply(ice_masks, as.polygons)
plot(europe_climate$bio01,
  main = time_bp(europe_climate),
  fun = function(i) {
    polys(ice_poly_list[[i]],
      col = "gray",
      lwd = 0.5
    )
  }
)

## ----fig.width=6, fig.height=2.5----------------------------------------------
distances_sea <- distance_from_sea(time_bp = c(-20000, 0), dataset = "Example")
distances_sea_australia <- crop(distances_sea, terra::ext(100, 170, -60, 20))
plot(distances_sea_australia, main = time_bp(distances_sea_australia))

## -----------------------------------------------------------------------------
locations_vect <- vect(locations, geom = c("longitude", "latitude"))
locations_vect

## ----fig.width=6, fig.height=5------------------------------------------------
plot(europe_climate_20k,
  fun = function() points(locations_vect, col = "red", cex = 2)
)

## ----fig.width=6, fig.height=5------------------------------------------------
plot(europe_climate_20k,
  fun = function() {
    polys(ice_mask_vect, col = "gray", lwd = 0.5)
    points(locations_vect, col = "red", cex = 2)
  }
)

## ----fig.width=4, fig.height=4------------------------------------------------
bio_vars <- c("bio01", "bio10", "bio12")
climate_10k <- region_slice(-10000,
  bio_variables = bio_vars,
  dataset = "Example"
)
climate_values_10k <- df_from_region_slice(climate_10k)
climate_10k_pca <- prcomp(climate_values_10k[, bio_vars],
  scale = TRUE, center = TRUE
)
plot(climate_10k_pca$x[, 2] ~ climate_10k_pca$x[, 1],
  pch = 20, col = "lightgray",
  xlab = "PC1", ylab = "PC2"
)

## -----------------------------------------------------------------------------
locations_10k <- data.frame(
  longitude = c(0, 90, 20, 5), latitude = c(20, 45, 50, 47),
  time_bp = c(-9932, -9753, -10084, -10249)
)
climate_loc_10k <- location_slice(
  x = locations_10k[, c("longitude", "latitude")],
  time_bp = locations_10k$time_bp, bio_variables = bio_vars,
  dataset = "Example"
)
locations_10k_pca_scores <- predict(climate_10k_pca,
  newdata = climate_loc_10k[, bio_vars]
)

## ----fig.width=4, fig.height=4------------------------------------------------
plot(climate_10k_pca$x[, 2] ~ climate_10k_pca$x[, 1],
  pch = 20, col = "lightgray",
  xlab = "PC1", ylab = "PC2"
)
points(locations_10k_pca_scores, pch = 20, col = "red")

## -----------------------------------------------------------------------------
climate_20k <- region_slice(
  time_bp = -20000,
  bio_variables = c("bio01", "bio10"),
  dataset = "Example"
)
this_sample <- sample_region_slice(climate_20k, size = 100)
head(this_sample)

## -----------------------------------------------------------------------------
climate_ts <- region_series(
  time_bp = c(-20000, -10000),
  bio_variables = c("bio01", "bio10", "bio12"),
  dataset = "Example",
  ext = terra::ext(region_extent$Europe)
)
sampled_climate <- sample_region_series(climate_ts, size = c(3, 5))
sampled_climate

## ----fig.width=6, fig.height=4------------------------------------------------
europe_10k <- region_slice(
  dataset = "Example",
  bio_variables = c("bio01"),
  time_bp = -10000, ext = region_extent$Europe
)
terra::plot(europe_10k)

## ----fig.width=6, fig.height=4------------------------------------------------
europe_ds <- terra::disagg(europe_10k, fact = 25, method = "bilinear")
terra::plot(europe_ds)