Load Biome Information
Pasqualina Vonlanthen & Jens Daniel Müller
29 April, 2022
Last updated: 2022-04-29
Checks: 7 0
Knit directory: bgc_argo_r_argodata/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | 2d44f8a | pasqualina-vonlanthendinenna | 2022-04-29 | Build site. |
| html | e61c08e | pasqualina-vonlanthendinenna | 2022-04-27 | Build site. |
| html | 10036ed | pasqualina-vonlanthendinenna | 2022-04-26 | Build site. |
| Rmd | 3e1ac14 | pasqualina-vonlanthendinenna | 2022-04-26 | separated loading data pages, added mayot biomes, switched to pH and temp flag A |
Task
Load in biome information and regional separations
RECCAP-2 Biome Separations
# load in the RECCAP biome separations
region_masks_all <-
stars::read_ncdf(paste(
path_basin_mask, "RECCAP2_region_masks_all_v20210412.nc", sep = "")) %>%
as_tibble() %>%
mutate(seamask = as.factor(seamask))Harmonise RECCAP biomes
# harmonise the latitude longitude bands of the biomes to the pH data (2x2 grid)
region_masks_all_seamask_2x2 <- region_masks_all %>%
select(lat, lon, seamask) %>%
mutate(lon = if_else(lon < 20, lon + 360, lon)) %>%
mutate(
lat = cut(lat, seq(-90, 90, 2), seq(-89, 89, 2)),
lat = as.numeric(as.character(lat)),
lon = cut(lon, seq(20, 380, 2), seq(21, 379, 2)),
lon = as.numeric(as.character(lon))
)
region_masks_all_seamask_1x1 <- region_masks_all %>%
select(lat, lon, seamask) %>%
mutate(lon = if_else(lon < 20, lon + 360, lon)) %>%
mutate(
lat = cut(lat, seq(-90, 90, 1), seq(-89.5, 89.5, 1)),
lat = as.numeric(as.character(lat)),
lon = cut(lon, seq(20, 380, 1), seq(20.5, 379.5, 1)),
lon = as.numeric(as.character(lon))
)
region_masks_all <- region_masks_all %>%
select(-seamask) %>%
pivot_longer(open_ocean:southern,
names_to = 'region',
values_to = 'value') %>%
mutate(value = as.factor(value))
# harmonise the lat/lon of the regional separations to our pH data
region_masks_all_1x1 <- region_masks_all %>%
mutate(lon = if_else(lon < 20, lon + 360, lon)) %>%
mutate(
lat = cut(lat, seq(-90, 90, 1), seq(-89.5, 89.5, 1)),
lat = as.numeric(as.character(lat)),
lon = cut(lon, seq(20, 380, 1), seq(20.5, 379.5, 1)),
lon = as.numeric(as.character(lon))
)
region_masks_all_2x2 <- region_masks_all %>%
mutate(lon = if_else(lon < 20, lon + 360, lon)) %>%
mutate(
lat = cut(lat, seq(-90, 90, 2), seq(-89, 89, 2)),
lat = as.numeric(as.character(lat)),
lon = cut(lon, seq(20, 380, 2), seq(21, 379, 2)),
lon = as.numeric(as.character(lon))
)
# add the region names to the surface pH dataframes
ph_surface_1x1 <- read_rds(file = paste0(path_argo_preprocessed, "/ph_surface_1x1.rds"))
ph_surface_2x2 <- read_rds(file = paste0(path_argo_preprocessed, "/ph_surface_2x2.rds"))
ph_surface_2x2 <- inner_join(ph_surface_2x2, region_masks_all_2x2)
ph_surface_1x1 <- inner_join(ph_surface_1x1, region_masks_all_1x1)Maps of Southern Ocean RECCAP biomes
map <-
read_rds(paste(path_emlr_utilities,
"map_landmask_WOA18.rds",
sep = ""))
# restrict base map to Southern Ocean
map <- map +
lims(y = c(-85, -30))
region_masks_all_1x1 <- region_masks_all_1x1 %>%
filter(region == 'southern',
value != 0) %>%
mutate(coast = as.character(coast))Coastal regions
map +
geom_tile(data = region_masks_all_1x1,
aes(x = lon,
y = lat,
fill = coast))+
scale_fill_brewer(palette = 'Dark2')
| Version | Author | Date |
|---|---|---|
| 10036ed | pasqualina-vonlanthendinenna | 2022-04-26 |
Biomes
map+
geom_tile(data = region_masks_all_1x1,
aes(x = lon,
y = lat,
fill = value))+
scale_fill_brewer(palette = 'Dark2')+
labs(title = 'RECCAP biomes')
| Version | Author | Date |
|---|---|---|
| 10036ed | pasqualina-vonlanthendinenna | 2022-04-26 |
basemap(limits = -30)+
geom_spatial_tile(data = region_masks_all_1x1,
aes(x = lon,
y = lat,
fill = value),
col = NA)+
scale_fill_brewer(palette = 'Dark2')+
labs(title = 'RECCAP biomes')
| Version | Author | Date |
|---|---|---|
| 10036ed | pasqualina-vonlanthendinenna | 2022-04-26 |
Write RECCAP biomes to file
region_masks_all_seamask_1x1 %>%
write_rds(file = paste0(path_argo_preprocessed, "/region_masks_all_seamask_1x1.rds"))
region_masks_all_seamask_2x2 %>%
write_rds(file = paste0(path_argo_preprocessed, "/region_masks_all_seamask_2x2.rds"))
region_masks_all_1x1 %>%
write_rds(file = paste0(path_argo_preprocessed, "/region_masks_all_1x1.rds"))
region_masks_all_2x2 %>%
write_rds(file = paste0(path_argo_preprocessed, "/region_masks_all_2x2.rds"))
# joined RECCAP-biomes to surface pH data
ph_surface_1x1 %>%
write_rds(file = paste0(path_argo_preprocessed, "/ph_surface_1x1.rds"))
ph_surface_2x2 %>%
write_rds(file = paste0(path_argo_preprocessed, "/ph_surface_2x2.rds"))Mayot biomes
nm_biomes <- tidync::hyper_tibble(paste0(path_argo, "/SouthernOcean_mask_NM.nc"))
# 1 degree lon/lat grid
# table(nm_regions$LATITUDE) # 1 degree intervals
# table((nm_regions$LONGITUDE)) # 1 degree longitude intervalsHarmonise Mayot biomes
nm_biomes <- nm_biomes %>%
rename(lon = LONGITUDE,
lat = LATITUDE) %>%
mutate(lon = if_else(lon < 20, lon + 360, lon))
nm_biomes <- nm_biomes %>%
filter(ICE == 1 | STSS == 1 | SPSS == 1)
nm_biomes <- nm_biomes %>%
pivot_longer(cols = c(STSS, SPSS, ICE),
values_to = 'biome_mask',
names_to = 'biome_name')
nm_biomes <- nm_biomes %>%
filter(biome_mask==1,
lat <= -30)Maps of Southern Ocean Mayot biomes
map+
geom_tile(data = nm_biomes,
aes(x = lon,
y = lat,
fill = biome_name))+
scale_fill_brewer(palette = 'Dark2')+
labs(title = 'Mayot biomes')
| Version | Author | Date |
|---|---|---|
| 10036ed | pasqualina-vonlanthendinenna | 2022-04-26 |
basemap(limits = -30)+
geom_spatial_tile(data = nm_biomes,
aes(x = lon,
y = lat,
fill = biome_name),
col = NA)+
scale_fill_brewer(palette = 'Dark2')+
labs(title = 'Mayot biomes')
| Version | Author | Date |
|---|---|---|
| 10036ed | pasqualina-vonlanthendinenna | 2022-04-26 |
Write Mayot biomes to file
# write data to file
nm_biomes %>%
write_rds(file = paste0(path_argo_preprocessed, "/nm_biomes.rds"))
sessionInfo()R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: openSUSE Leap 15.3
Matrix products: default
BLAS: /usr/local/R-4.1.2/lib64/R/lib/libRblas.so
LAPACK: /usr/local/R-4.1.2/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] lubridate_1.8.0 ggOceanMaps_1.2.6 ggspatial_1.1.5 forcats_0.5.1
[5] stringr_1.4.0 dplyr_1.0.7 purrr_0.3.4 readr_2.1.1
[9] tidyr_1.1.4 tibble_3.1.6 ggplot2_3.3.5 tidyverse_1.3.1
[13] workflowr_1.7.0
loaded via a namespace (and not attached):
[1] fs_1.5.2 sf_1.0-5 RColorBrewer_1.1-2
[4] httr_1.4.2 rprojroot_2.0.2 tools_4.1.2
[7] backports_1.4.1 bslib_0.3.1 utf8_1.2.2
[10] rgdal_1.5-28 R6_2.5.1 KernSmooth_2.23-20
[13] rgeos_0.5-9 DBI_1.1.2 colorspace_2.0-2
[16] raster_3.5-11 withr_2.4.3 sp_1.4-6
[19] tidyselect_1.1.1 processx_3.5.2 compiler_4.1.2
[22] git2r_0.29.0 cli_3.1.1 rvest_1.0.2
[25] RNetCDF_2.5-2 xml2_1.3.3 labeling_0.4.2
[28] sass_0.4.0 scales_1.1.1 classInt_0.4-3
[31] ggOceanMapsData_1.0.1 callr_3.7.0 proxy_0.4-26
[34] digest_0.6.29 rmarkdown_2.11 pkgconfig_2.0.3
[37] htmltools_0.5.2 highr_0.9 dbplyr_2.1.1
[40] fastmap_1.1.0 tidync_0.2.4 rlang_1.0.2
[43] readxl_1.3.1 rstudioapi_0.13 farver_2.1.0
[46] jquerylib_0.1.4 generics_0.1.1 jsonlite_1.7.3
[49] magrittr_2.0.1 ncmeta_0.3.0 Rcpp_1.0.8
[52] munsell_0.5.0 fansi_1.0.2 abind_1.4-5
[55] lifecycle_1.0.1 terra_1.5-12 stringi_1.7.6
[58] whisker_0.4 yaml_2.2.1 grid_4.1.2
[61] parallel_4.1.2 promises_1.2.0.1 crayon_1.4.2
[64] lattice_0.20-45 haven_2.4.3 stars_0.5-5
[67] hms_1.1.1 knitr_1.37 ps_1.6.0
[70] pillar_1.6.4 codetools_0.2-18 reprex_2.0.1
[73] glue_1.6.0 evaluate_0.14 getPass_0.2-2
[76] modelr_0.1.8 vctrs_0.3.8 tzdb_0.2.0
[79] httpuv_1.6.5 cellranger_1.1.0 gtable_0.3.0
[82] assertthat_0.2.1 xfun_0.29 lwgeom_0.2-8
[85] broom_0.7.11 e1071_1.7-9 later_1.3.0
[88] ncdf4_1.19 class_7.3-20 units_0.7-2
[91] ellipsis_0.3.2