From b6b4edc8042323b88bbe52bd6dd59e59141e63b9 Mon Sep 17 00:00:00 2001 From: dramanica Date: Tue, 19 Sep 2023 12:45:00 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20EvolEcol?= =?UTF-8?q?Group/pastclim@e1e2ddae31dcbdc005ea8dfe6245e237b189e2fb=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- dev/articles/a0_pastclim_overview.html | 32 +++++++++++++------------- dev/index.html | 12 ++-------- dev/pkgdown.yml | 2 +- dev/search.json | 2 +- 4 files changed, 20 insertions(+), 28 deletions(-) diff --git a/dev/articles/a0_pastclim_overview.html b/dev/articles/a0_pastclim_overview.html index f422f520..3c41ae8d 100644 --- a/dev/articles/a0_pastclim_overview.html +++ b/dev/articles/a0_pastclim_overview.html @@ -900,13 +900,13 @@

Random sampling of background) this_sample <- sample_region_slice(climate_20k, size = 100) head(this_sample) -#> cell x y bio01 bio10 -#> 1 41970 29.5 -26.5 10.958101 16.102800 -#> 2 13905 44.5 51.5 -3.361017 13.382350 -#> 3 35420 -40.5 -8.5 21.846605 22.572174 -#> 4 7875 134.5 68.5 -24.933590 8.104472 -#> 5 11538 -162.5 57.5 -7.650807 8.676710 -#> 6 36920 19.5 -12.5 16.683744 18.930542 +#> cell x y bio01 bio10 +#> 1 46552 -68.5 -39.5 9.860789 17.016119 +#> 2 13597 96.5 52.5 -11.601186 8.911233 +#> 3 20428 87.5 33.5 -11.007136 1.196979 +#> 4 21464 43.5 30.5 18.075909 27.193888 +#> 5 33074 133.5 -1.5 20.698126 21.044680 +#> 6 46547 -73.5 -39.5 8.727621 12.231992

If we have samples from multiple time steps, we need to sample the background proportionally to the number of points in each time step. So, for example, if we wanted 30 samples from 20k years ago and 50 samples @@ -920,15 +920,15 @@

Random sampling of background) sampled_climate <- sample_region_series(climate_ts, size = c(3,5)) sampled_climate -#> cell x y bio01 bio10 bio12 time_bp -#> -20000.1 3552 51.5 33.5 9.3066416 20.287823 197.7727 -20000 -#> -20000.2 3475 59.5 34.5 11.6466789 21.006063 203.7857 -20000 -#> -20000.3 2344 33.5 47.5 2.2621696 14.909022 355.6306 -20000 -#> -10000.1 2361 50.5 47.5 7.3322334 26.457670 188.1436 -10000 -#> -10000.2 2583 17.5 44.5 7.7263165 18.768158 1112.9365 -10000 -#> -10000.3 3290 44.5 36.5 13.6029644 29.856005 324.4944 -10000 -#> -10000.4 976 25.5 63.5 -0.3430011 5.919899 511.0482 -10000 -#> -10000.5 1777 61.5 54.5 0.9052616 21.623377 341.2618 -10000 +#> cell x y bio01 bio10 bio12 time_bp +#> -20000.1 3226 65.5 37.5 12.392502 23.0520477 143.3894 -20000 +#> -20000.2 679 68.5 67.5 -20.751783 4.5105953 168.2175 -20000 +#> -20000.3 1905 19.5 52.5 -7.694075 0.9745809 453.4263 -20000 +#> -10000.1 1660 29.5 55.5 3.574161 16.7066269 679.8518 -10000 +#> -10000.2 3542 41.5 33.5 18.795412 33.2396088 125.9552 -10000 +#> -10000.3 495 54.5 69.5 -6.267707 9.6924238 362.1932 -10000 +#> -10000.4 1454 -6.5 57.5 6.433328 11.4032202 1860.9585 -10000 +#> -10000.5 3071 -4.5 38.5 13.915345 26.0370026 587.0548 -10000

We could then use these data to build a PCA.

diff --git a/dev/index.html b/dev/index.html index 7eaf92fb..d1c56b69 100644 --- a/dev/index.html +++ b/dev/index.html @@ -116,17 +116,9 @@

Overview of functionality

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Current issues +

When something does not work

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If something does not work, check the issues on GitHub to see whether the problem has already been reported. If not, feel free to create an new issue. Please make sure you have updated to the latest version of pastclim on CRAN, as well as updating all other packages on your system, and provide a reproducible example for the developers to investigate the problem.

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Error in x$.self$finalize() -

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pastclim relies on terra to process rasters. There is a known bug in terra that leads to the occasional message:

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"Error in x$.self$finalize() : attempt to apply non-function"
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This is an error related to garbage collection, which does not affect the script being correctly executed, so it can be ignored. More discussion of this issue can be found on stackoverflow

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If something does not work, check the issues on GitHub to see whether the problem has already been reported. If not, feel free to create an new issue. Please make sure you have updated to the latest version of pastclim on CRAN, as well as updating all other packages on your system, and provide a reproducible example for the developers to investigate the problem.