Paleo habitat reconstruction

A collection of CMIP6 and PMIP4 ESM outputs used for ocean habitat reconstruction during the last glacial maximum

Reprex for loading data into R below:

# data available to download here
# https://doi.org/10.5281/zenodo.7016536
# substitute for own local path
stars::read_ncdf("~/Downloads/sos_Omon_MIROC-ES2L_lgm_r1i1p1f2_gn_320001-329912.nc", var = "sos")
#> Large netcdf source found, returning proxy object.
#> No projection information found in nc file.
#> Coordinate variable units found to be degrees,
#> assuming WGS84 Lat/Lon.
#> netcdf source stars proxy object from:
#> [1] "[...]/sos_Omon_MIROC-ES2L_lgm_r1i1p1f2_gn_320001-329912.nc"
#>
#> Available nc variables:
#> sos
#>
#> dimension(s):
#> from to offset delta refsys point
#> x 1 360 NA NA WGS 84 NA
#> y 1 256 NA NA WGS 84 FALSE
#> time 1 1200 NA NA POSIXct FALSE
#> values x/y
#> x [360] 0.5,...,359.5 [x]
#> y [256] -88,...,152.396 [y]
#> time 3200-01-16 12:00:00,...,3299-12-16 12:00:00
stars::read_stars("~/Downloads/sos_Omon_MIROC-ES2L_lgm_r1i1p1f2_gn_320001-329912.nc", var = "sos")
#> stars_proxy object with 1 attribute in 1 file(s):
#> $`Sea Surface Salinity`
#> [1] "[...]/sos_Omon_MIROC-ES2L_lgm_r1i1p1f2_gn_320001-329912.nc"
#>
#> dimension(s):
#> from to offset delta refsys point
#> x 1 360 0 1 NA NA
#> y 1 256 256 -1 NA NA
#> time 1 1200 NA NA POSIXct NA
#> values x/y
#> x NULL [x]
#> y NULL [y]
#> time 3200-01-16 12:00:00,...,3299-12-16 12:00:00
stars::read_ncdf("~/Downloads/sos_Omon_AWI-ESM-1-1-LR_lgm_r1i1p1f1_gn_390101-391012.nc", var = "sos")
#> Warning in FUN(X[[i]], ...): Non-canonical axis order found, attempting to
#> correct.
#> Will return stars object with 12531720 cells.
#> Warning: ignoring unrecognized unit: psu
#> Warning in .get_nc_projection(meta$attribute, rep_var, cv): No projection
#> information found in nc file.
#> stars object with 2 dimensions and 1 attribute
#> attribute(s), summary of first 1e+05 cells:
#> Min. 1st Qu. Median Mean 3rd Qu. Max.
#> sos 10.90844 34.23906 34.83165 34.70436 35.41966 44.15238
#> dimension(s):
#> from to offset delta refsys point
#> ncells 1 104431 NA NA NA NA
#> time 1 120 NA NA NA FALSE
#> values x/y
#> ncells [0.5,1.5),...,[104430.5,104431.5) [x]
#> time 3901-01-16 12:00:00,...,3910-12-16 12:00:00 [y]
stars::read_stars("~/Downloads/sos_Omon_AWI-ESM-1-1-LR_lgm_r1i1p1f1_gn_390101-391012.nc", var = "sos")
#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: dimension #1 (ncells) is not a
#> Longitude/X dimension.
#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: dimension #0 (time) is not a Latitude/Y
#> dimension.
#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: dimension #1 (ncells) is not a
#> Longitude/X dimension.
#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: dimension #0 (time) is not a Latitude/Y
#> dimension.
#> Warning: ignoring unrecognized unit: psu
#> stars object with 2 dimensions and 1 attribute
#> attribute(s), summary of first 1e+05 cells:
#> Min. 1st Qu. Median Mean 3rd Qu.
#> sos_Omon_AWI-ESM-1-1-LR_lgm_r1... 9.968027 34.31947 34.9049 34.73704 35.50075
#> Max.
#> sos_Omon_AWI-ESM-1-1-LR_lgm_r1... 43.24837
#> dimension(s):
#> from to offset delta refsys point values x/y
#> x 1 104431 0 1 NA NA NULL [x]
#> y 1 120 120 -1 NA NA NULL [y]

Created on 2022-08-23 by the reprex package (v2.0.1)

Session info

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.1.2 (2021-11-01)
#> os macOS Big Sur 10.16
#> system x86_64, darwin17.0
#> ui X11
#> language (EN)
#> collate en_GB.UTF-8
#> ctype en_GB.UTF-8
#> tz Europe/London
#> date 2022-08-23
#> pandoc 2.17.1.1 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
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#> assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.0)
#> class 7.3-20 2022-01-13 [1] CRAN (R 4.1.2)
#> classInt 0.4-7 2022-06-10 [1] CRAN (R 4.1.2)
#> cli 3.3.0 2022-04-25 [1] CRAN (R 4.1.2)
#> crayon 1.5.1 2022-03-26 [1] CRAN (R 4.1.2)
#> DBI 1.1.3 2022-06-18 [1] CRAN (R 4.1.2)
#> digest 0.6.29 2021-12-01 [1] CRAN (R 4.1.0)
#> dplyr 1.0.9 2022-04-28 [1] CRAN (R 4.1.2)
#> e1071 1.7-11 2022-06-07 [1] CRAN (R 4.1.2)
#> ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.0)
#> evaluate 0.16 2022-08-09 [1] CRAN (R 4.1.2)
#> fansi 1.0.3 2022-03-24 [1] CRAN (R 4.1.2)
#> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.0)
#> fs 1.5.2 2021-12-08 [1] CRAN (R 4.1.0)
#> generics 0.1.3 2022-07-05 [1] CRAN (R 4.1.2)
#> glue 1.6.2 2022-02-24 [1] CRAN (R 4.1.2)
#> highr 0.9 2021-04-16 [1] CRAN (R 4.1.0)
#> htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.1.2)
#> KernSmooth 2.23-20 2021-05-03 [1] CRAN (R 4.1.2)
#> knitr 1.39 2022-04-26 [1] CRAN (R 4.1.2)
#> lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.1.0)
#> lwgeom 0.2-8 2021-10-06 [1] CRAN (R 4.1.0)
#> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.1.2)
#> ncmeta 0.3.0 2020-08-27 [1] CRAN (R 4.1.0)
#> pillar 1.8.1 2022-08-19 [1] CRAN (R 4.1.2)
#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0)
#> proxy 0.4-27 2022-06-09 [1] CRAN (R 4.1.2)
#> purrr 0.3.4 2020-04-17 [1] CRAN (R 4.1.0)
#> R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.0)
#> Rcpp 1.0.9 2022-07-08 [1] CRAN (R 4.1.2)
#> reprex 2.0.1 2021-08-05 [1] CRAN (R 4.1.0)
#> rlang 1.0.4 2022-07-12 [1] CRAN (R 4.1.2)
#> rmarkdown 2.14 2022-04-25 [1] CRAN (R 4.1.2)
#> RNetCDF 2.6-1 2022-06-27 [1] CRAN (R 4.1.2)
#> rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.1.0)
#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.1.0)
#> sf 1.0-8 2022-07-14 [1] CRAN (R 4.1.2)
#> stars 0.5-6 2022-07-21 [1] CRAN (R 4.1.2)
#> stringi 1.7.8 2022-07-11 [1] CRAN (R 4.1.2)
#> stringr 1.4.1 2022-08-20 [1] CRAN (R 4.1.2)
#> tibble 3.1.8 2022-07-22 [1] CRAN (R 4.1.2)
#> tidyr 1.2.0 2022-02-01 [1] CRAN (R 4.1.2)
#> tidyselect 1.1.2 2022-02-21 [1] CRAN (R 4.1.2)
#> units 0.8-0 2022-02-05 [1] CRAN (R 4.1.2)
#> utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.0)
#> vctrs 0.4.1 2022-04-13 [1] CRAN (R 4.1.2)
#> withr 2.5.0 2022-03-03 [1] CRAN (R 4.1.2)
#> xfun 0.32 2022-08-10 [1] CRAN (R 4.1.2)
#> yaml 2.3.5 2022-02-21 [1] CRAN (R 4.1.2)
#>
#> [1] /Library/Frameworks/R.framework/Versions/4.1/Resources/library
#>
#> ──────────────────────────────────────────────────────────────────────────────