library(extractr) # devtools::install_local(force = T) # devtools::load_all()
#> The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
#> which was just loaded, will retire in October 2023.
#> Please refer to R-spatial evolution reports for details, especially
#> https://r-spatial.org/r/2023/05/15/evolution4.html.
#> It may be desirable to make the sf package available;
#> package maintainers should consider adding sf to Suggests:.
#> The sp package is now running under evolution status 2
#> (status 2 uses the sf package in place of rgdal)
Get regions of interests
if (!require("librarian"))
install.packages("librarian")
#> Loading required package: librarian
librarian::shelf(
dplyr, here, mapview, sf)
fk_roi_geo <- "https://github.com/marinebon/extract-app/raw/main/data/fk_roi.geojson"
fk_sta_geo <- "https://github.com/marinebon/extract-app/raw/main/data/fk_sta.geojson"
fk_roi_sf <- read_sf(fk_roi_geo)
fk_sta_sf <- read_sf(fk_sta_geo)
fk_sf <- bind_rows(fk_roi_sf, fk_sta_sf)
mapview(fk_sf)
ed_info <- get_ed_info("https://coastwatch.pfeg.noaa.gov/erddap/griddap/jplMURSST41mday.html")
ed_info
#> <ERDDAP info> jplMURSST41mday
#> Base URL: https://coastwatch.pfeg.noaa.gov/erddap
#> Dataset Type: griddap
#> Dimensions (range):
#> time: (2002-06-16T00:00:00Z, 2023-08-16T00:00:00Z)
#> latitude: (-89.99, 89.99)
#> longitude: (-179.99, 180.0)
#> Variables:
#> mask:
#> nobs:
#> sst:
#> Units: degree_C
dir_tif <- here::here("data_tmp")
grds <- get_ed_grds(
ed_info, ed_var="sst", ply=fk_sf, dir_tif=dir_tif, date_beg = "2021-10-01")
#> Found 22 dates between 2021-10-01 and 2023-08-16.
#> Found 22 matching tifs of 22 dates.
#> Reading existing grids ([dir_tif]/grd_sst_[date].tif) vs fetching fresh data via ERDDAP.
# Found 17 dates between 2021-10-01 and 2023-03-16
Summarize
ts_csv <- here::here("data_tmp/ts.csv")
ts <- grds_to_ts(
grds, fxns = c("mean", "sd"), ts_csv, verbose = T)
#> Reading ts_csv
#> All grds_dates found in ts_csv$date, so returning vs recalculating.
head(ts)
#> # A tibble: 6 × 4
#> lyr date mean sd
#> <chr> <date> <dbl> <dbl>
#> 1 sst_2021.10.16 2021-10-16 29.0 0.116
#> 2 sst_2021.11.16 2021-11-16 27.2 0.945
#> 3 sst_2021.12.16 2021-12-16 26.6 1.12
#> 4 sst_2022.01.16 2022-01-16 25.7 1.25
#> 5 sst_2022.02.16 2022-02-16 25.0 1.64
#> 6 sst_2022.03.16 2022-03-16 26.1 0.948