diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 2511bbb..92cc378 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -55,8 +55,14 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: cache-version: 2 + # vignettes/import_hydrography_cmems dependencies extra-packages: | any::rcmdcheck + any::CopernicusMarine + any::CFtime + any::rnaturalearth + any::sf + any::units - name: Check env: @@ -65,6 +71,13 @@ jobs: run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--run-donttest"), error_on = "warning", check_dir = "check") shell: Rscript {0} + - name: Rebuild vignettes with CopernicusMarine + if: runner.os == 'Linux' + env: + COPERNICUSMARINE_SERVICE_USERNAME: ${{ secrets.COPERNICUSMARINE_SERVICE_USERNAME }} + COPERNICUSMARINE_SERVICE_PASSWORD: ${{ secrets.COPERNICUSMARINE_SERVICE_PASSWORD }} + run: make vignettes + - name: Upload check results if: ${{ !success() }} uses: actions/upload-artifact@main diff --git a/.gitignore b/.gitignore index 3c39047..b886768 100644 --- a/.gitignore +++ b/.gitignore @@ -3,5 +3,6 @@ /.Rprofile /*_*.tar.gz /example-datras-data +/data_provided/ /docs /vignettes/*.html diff --git a/vignettes/hydroVar.txt b/vignettes/hydroVar.txt deleted file mode 100644 index 7c15bc9..0000000 --- a/vignettes/hydroVar.txt +++ /dev/null @@ -1,709 +0,0 @@ -"rect" "month" "sob" "year" -"1" "38G7" 1 4.14668845628917 2018 -"2" "39G7" 1 5.95174610040806 2018 -"3" "40G7" 1 4.98104584437829 2018 -"4" "41G7" 1 5.04309182122902 2018 -"5" "42G7" 1 5.35343404699255 2018 -"6" "43G7" 1 5.27969861693487 2018 -"7" "44G7" 1 5.62229303033264 2018 -"8" "45G7" 1 5.31781619958462 2018 -"9" "46G7" 1 5.03313420878516 2018 -"10" "37G8" 1 5.7865211735601 2018 -"11" "38G8" 1 5.12739385873784 2018 -"12" "39G8" 1 5.97156739234924 2018 -"13" "40G8" 1 5.80561786139453 2018 -"14" "41G8" 1 5.6039805955357 2018 -"15" "42G8" 1 5.20416697289805 2018 -"16" "43G8" 1 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5.11745648574113 2018 -"696" "46H1" 12 5.31130821777113 2018 -"697" "43H2" 12 3.7998012474605 2018 -"698" "44H2" 12 3.80925124374466 2018 -"699" "45H2" 12 2.59131465077315 2018 -"700" "46H2" 12 4.13910487294197 2018 -"701" "42H3" 12 4.04840990116722 2018 -"702" "43H3" 12 4.81789046754686 2018 -"703" "44H3" 12 4.74448743030484 2018 -"704" "45H3" 12 3.24681270141922 2018 -"705" "46H3" 12 1.33311251964834 2018 -"706" "43H4" 12 4.75847155505623 2018 -"707" "44H4" 12 3.70584983253842 2018 -"708" "45H4" 12 1.03444656173392 2018 diff --git a/vignettes/ices.rect.sea.txt b/vignettes/ices.rect.sea.txt deleted file mode 100644 index c8f2ea8..0000000 --- a/vignettes/ices.rect.sea.txt +++ /dev/null @@ -1,60 +0,0 @@ -"rect" "areaSea_km2" -"1" "38G7" 1711.7282355114 -"2" "39G7" 3523.71698877352 -"3" "40G7" 3479.25494468894 -"4" "41G7" 3434.5280118031 -"5" "42G7" 3389.53960269141 -"6" "43G7" 3261.49250973656 -"7" "44G7" 3298.79204450941 -"8" "45G7" 3253.03981894911 -"9" "46G7" 2156.37563904363 -"10" "37G8" 374.260791124246 -"11" "38G8" 2366.38392344111 -"12" "39G8" 3523.71698877349 -"13" "40G8" 3479.25494468892 -"14" "41G8" 3434.5280118031 -"15" "42G8" 3314.24447745022 -"16" "43G8" 1859.84658900227 -"17" "44G8" 1939.16482530621 -"18" "45G8" 3253.03981894907 -"19" "46G8" 3159.64017056631 -"20" "37G9" 540.143799769937 -"21" "38G9" 3202.5755060268 -"22" "39G9" 3523.71698877351 -"23" "40G9" 3479.25494468894 -"24" "41G9" 3434.52801180311 -"25" "42G9" 3389.53960269134 -"26" "43G9" 3344.29312548706 -"27" "44G9" 3160.37720797677 -"28" "45G9" 3225.46513776867 -"29" "46G9" 3207.03993321144 -"30" "38H0" 391.066993848961 -"31" "39H0" 3400.83440836474 -"32" "40H0" 3479.2549478177 -"33" "41H0" 3398.72899458505 -"34" "42H0" 3388.79473220469 -"35" "43H0" 3344.29312849451 -"36" "44H0" 3298.7920474759 -"37" "45H0" 3253.03982187445 -"38" "46H0" 3207.03993609546 -"39" "38H1" 141.110212705233 -"40" "39H1" 754.496308868271 -"41" "40H1" 328.686704196703 -"42" "41H1" 80.7017025630464 -"43" "42H1" 338.645895839223 -"44" "43H1" 1545.89654688251 -"45" "44H1" 3111.26174596369 -"46" "45H1" 3120.8020111017 -"47" "46H1" 3197.6434433424 -"48" "43H2" 49.2293081892126 -"49" "44H2" 2398.3525938607 -"50" "45H2" 1423.36900933388 -"51" "46H2" 1749.73464527864 -"52" "42H3" 51.0917555180813 -"53" "43H3" 2691.63881720934 -"54" "44H3" 3288.30378157277 -"55" "45H3" 2780.06184145136 -"56" "46H3" 1429.4750970343 -"57" "43H4" 973.573654486459 -"58" "44H4" 1119.30685293973 -"59" "45H4" 986.147233420839 diff --git a/vignettes/import_hydrography_cmems.Rmd b/vignettes/import_hydrography_cmems.Rmd index 28b3633..a0c7174 100644 --- a/vignettes/import_hydrography_cmems.Rmd +++ b/vignettes/import_hydrography_cmems.Rmd @@ -38,14 +38,14 @@ CMEMS Baltic Sea Physical Reanalysis product provides a physical reanalysis for https://data.marine.copernicus.eu/?option=com_csw&view=details&product_id=BALTICSEA_REANALYSIS_PHY_003_011 As a demonstration we retrieve one year of already processed monthly means of bottom temperature (bottomT), but hydrographic products are also available for separate depth layers and at higher spatiotemporal resolution, and can be aggregated before import according to the needs. Note that an account has to be created to download data from Copernicus Marine Service using the script below. - -```{r eval=FALSE} +```{r eval=nchar(Sys.getenv("COPERNICUSMARINE_SERVICE_USERNAME")) > 0} stopifnot(requireNamespace("CFtime", quietly = TRUE)) # Needed to parse dates -options( - CopernicusMarine_uid = "...", - CopernicusMarine_pwd = "..." -) +# NB: Before running, set +# Sys.setenv( +# COPERNICUSMARINE_SERVICE_USERNAME="...", +# COPERNICUSMARINE_SERVICE_PASSWORD="...", +# ) y <- 2018 # year of interest dat <- CopernicusMarine::cms_download_subset( @@ -53,51 +53,29 @@ dat <- CopernicusMarine::cms_download_subset( layer = "cmems_mod_bal_phy_my_P1M-m", variable = "bottomT", region = c(17, 54, 30, 58.5), # c(lon_min, lat_min, lon_max, lat_max) - timerange = paste0(y, c("-01-01", "-12-31")), - verticalrange = c(0, 1) + timerange = paste0(y, c("-01-01", "-12-31")) ) ``` # Download ICES rectangles -```{r eval=FALSE} +```{r eval=nchar(Sys.getenv("COPERNICUSMARINE_SERVICE_USERNAME")) > 0} temp <- tempfile() download.file(url="https://gis.ices.dk/shapefiles/ICES_StatRec_mapto_ICES_Areas.zip", temp) unzip(temp, exdir="data_provided/ices_rect") unlink(temp) ``` -# Aggregate hydrographic data by ICES rectangles - -```{r eval=FALSE} -# load ICES rect -ices.rect <- sf::st_read("data_provided/ices_rect/StatRec_map_Areas_Full_20170124.dbf", quiet = T) - -# Aggregate bottomT by ICES rect -ar <- aggregate(dat, ices.rect$geometry, FUN = mean, na.rm = TRUE) |> dplyr::pull(bottomT) -dimnames(ar) <- list(ICESNAME = ices.rect$ICESNAME, month = 1:12) -hydroVar <- - as.data.frame.table(ar, responseName = "sob") |> - dplyr::filter(!is.na(sob)) |> - dplyr::mutate( - year = y, - month = as.numeric(month) - ) |> - dplyr::rename( - rect = ICESNAME, - ) - -write.table(hydroVar, file = 'hydroVar.txt') -``` - # Combine ICES rectangles with rnaturalearth::ne_countries() to get sea surface area -```{r eval=FALSE} +```{r eval=nchar(Sys.getenv("COPERNICUSMARINE_SERVICE_USERNAME")) > 0} ices.rect <- sf::st_read("data_provided/ices_rect/StatRec_map_Areas_Full_20170124.dbf", quiet = T) +## subset ICES rectangles based on hydrographic data extent +ices.rect <- sf::st_crop(ices.rect, dat) + ices.rect.sea <- ices.rect |> - dplyr::filter(ICESNAME %in% hydroVar$rect) |> sf::st_difference( rnaturalearth::ne_countries(returnclass = "sf", continent="Europe", scale="large") |> sf::st_union() @@ -110,25 +88,32 @@ ices.rect.sea <- areaSea_km2 = areaSea_km2 ) |> sf::st_drop_geometry() +``` + +# Aggregate hydrographic data by ICES rectangles -write.table(sf::st_drop_geometry(ices.rect.sea), file = 'ices.rect.sea.txt') +```{r eval=nchar(Sys.getenv("COPERNICUSMARINE_SERVICE_USERNAME")) > 0} +hydroVar <- aggregate(dat, ices.rect, FUN = mean, na.rm = TRUE) |> + sf::st_as_sf(long=T) |> + sf::st_intersection(ices.rect |> + dplyr::select(rect=ICESNAME)) |> + na.omit() |> + dplyr::left_join(ices.rect.sea) |> + dplyr::mutate(year = as.numeric(substring(time,1,4)), + month = as.numeric(substring(time,6,7))) ``` # Import bottom temperature into mfdb Import ICES rectangles and import the hydrographic data as a survey index. Then we can retrieve the hydrographic data as a weighted mean using ICES rectangle as a weighting variable: -```{r} +```{r, eval=nchar(Sys.getenv("COPERNICUSMARINE_SERVICE_USERNAME")) > 0} mdb <- mfdb(tempfile(fileext = '.duckdb')) -ices.rect.sea <- read.table('ices.rect.sea.txt') -hydroVar <- read.table('hydroVar.txt') |> - dplyr::inner_join(ices.rect.sea, by = "rect") - # import ICES rectangles mfdb_import_area(mdb, data.frame( name = as.character(ices.rect.sea$rect), - size = ices.rect.sea$areaSea_km2)) + size = as.numeric(ices.rect.sea$areaSea_km2))) # import area size as index for later use mfdb_import_cs_taxonomy(mdb, "index_type", data.frame(name=c("ices_rect", "bottom_temp"))) @@ -146,7 +131,7 @@ mfdb_import_survey_index(mdb, data.frame(year = hydroVar$year, month = hydroVar$month, areacell = as.character(hydroVar$rect), - value = hydroVar$sob, + value = as.numeric(hydroVar$bottomT), index_type = "bottom_temp", stringsAsFactors = TRUE)) @@ -164,10 +149,10 @@ dat <- dat[,c('year', 'step', 'area', 'mean')] dat ``` -```{r, echo=FALSE} +```{r, echo=FALSE, eval=nchar(Sys.getenv("COPERNICUSMARINE_SERVICE_USERNAME")) > 0} # NB: Calculated with: # raw <- hydroVar[hydroVar$year == 2018 & hydroVar$rect %in% c('44G7','44G8','44G9','45G7','45G8','45G9') & hydroVar$month %in% c(1,2,3),] -# sum(raw$sob * raw$areaSea_km2) / sum(raw$areaSea_km2) +# sum(raw$bottomT * raw$areaSea_km2) / sum(raw$areaSea_km2) ok(ut_cmp_equal(dat, read.table(blank.lines.skip = TRUE, header = TRUE, stringsAsFactors = FALSE, text = ' year step area mean 2018 1 a1 5.065878 @@ -181,7 +166,7 @@ year step area mean ', colClasses = c(NA, 'character', NA, NA)), tolerance = 1e-5), "extract mean bottom temperature by quarter and area") ``` -```{r} +```{r, eval=nchar(Sys.getenv("COPERNICUSMARINE_SERVICE_USERNAME")) > 0} mfdb_disconnect(mdb) options(unittest.output = NULL) ```