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
#>  abind         1.4-5   2016-07-21 [1] CRAN (R 4.1.0)
#>  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
#> 
#> ──────────────────────────────────────────────────────────────────────────────