From 6c94f102dd91a538e5ea4a9e0ac12e0c29f14a3a Mon Sep 17 00:00:00 2001 From: Martin Petr Date: Wed, 21 Feb 2024 14:30:41 +0100 Subject: [PATCH] Update website --- NEWS.md | 8 +++--- docs/404.html | 2 +- docs/LICENSE-text.html | 2 +- docs/LICENSE.html | 2 +- docs/articles/index.html | 2 +- docs/articles/vignette-00-installation.html | 2 +- docs/articles/vignette-01-tutorial.html | 10 +++---- .../figure-html/plot_model-1.png | Bin 26066 -> 25258 bytes docs/articles/vignette-02-grid-model.html | 12 ++++----- .../figure-html/model_america-1.png | Bin 76087 -> 75951 bytes docs/articles/vignette-03-interactions.html | 2 +- .../vignette-04-nonspatial-models.html | 25 +++++++++++++++--- .../non-spatial-graph_sampling-1.png | Bin 0 -> 49838 bytes .../figure-html/non-spatial_graph-1.png | Bin 23013 -> 23044 bytes docs/articles/vignette-05-tree-sequences.html | 14 +++++----- .../figure-html/introgression_graph-1.png | Bin 27281 -> 27819 bytes docs/articles/vignette-06-locations.html | 2 +- .../figure-html/demographic_model-1.png | Bin 19722 -> 19842 bytes docs/articles/vignette-07-backends.html | 2 +- .../figure-html/unnamed-chunk-5-1.png | Bin 16826 -> 16916 bytes .../figure-html/unnamed-chunk-5-2.png | Bin 20604 -> 20790 bytes .../articles/vignette-08-nonslendr-tskit.html | 6 ++--- docs/articles/vignette-09-paper.html | 14 +++++----- .../figure-html/figure_ex1-1.png | Bin 60017 -> 60194 bytes .../figure-html/figure_ex3-1.png | Bin 73627 -> 73670 bytes docs/articles/vignette-10-tracts.html | 2 +- .../figure-html/introgression_model-1.png | Bin 21366 -> 21844 bytes docs/authors.html | 6 ++--- docs/index.html | 2 +- docs/news/index.html | 12 ++++----- docs/pkgdown.yml | 2 +- docs/reference/animate_model.html | 2 +- docs/reference/area.html | 2 +- docs/reference/as.phylo.slendr_phylo.html | 2 +- docs/reference/check_dependencies.html | 2 +- docs/reference/check_env.html | 8 +++--- docs/reference/clear_env.html | 2 +- docs/reference/compile_model.html | 2 +- docs/reference/distance.html | 2 +- docs/reference/expand_range.html | 2 +- docs/reference/explore_model.html | 2 +- docs/reference/gene_flow.html | 2 +- docs/reference/get_env.html | 2 +- docs/reference/index.html | 2 +- docs/reference/init_env.html | 2 +- docs/reference/join.html | 4 +-- docs/reference/move.html | 2 +- docs/reference/msprime.html | 2 +- docs/reference/overlap.html | 2 +- docs/reference/pipe.html | 2 +- docs/reference/plot_map.html | 2 +- docs/reference/plot_model.html | 2 +- docs/reference/population.html | 2 +- docs/reference/print.slendr_pop.html | 2 +- docs/reference/print.slendr_ts.html | 2 +- docs/reference/read_model-1.png | Bin 31283 -> 31200 bytes docs/reference/read_model.html | 2 +- docs/reference/region.html | 4 +-- docs/reference/reproject.html | 2 +- docs/reference/resize.html | 2 +- docs/reference/schedule_sampling.html | 2 +- docs/reference/set_dispersal.html | 2 +- docs/reference/set_range.html | 2 +- docs/reference/setup_env.html | 2 +- docs/reference/shrink_range.html | 2 +- docs/reference/slendr.html | 2 +- docs/reference/slim.html | 2 +- docs/reference/subtract.html | 2 +- docs/reference/summary.slendr_nodes.html | 2 +- docs/reference/ts_afs.html | 2 +- docs/reference/ts_ancestors.html | 2 +- docs/reference/ts_coalesced.html | 2 +- docs/reference/ts_descendants.html | 2 +- docs/reference/ts_divergence.html | 2 +- docs/reference/ts_diversity.html | 2 +- docs/reference/ts_draw.html | 2 +- docs/reference/ts_edges.html | 2 +- docs/reference/ts_eigenstrat.html | 2 +- docs/reference/ts_f4ratio.html | 2 +- docs/reference/ts_fst.html | 2 +- docs/reference/ts_genotypes.html | 2 +- docs/reference/ts_ibd.html | 2 +- docs/reference/ts_load.html | 2 +- docs/reference/ts_metadata.html | 2 +- docs/reference/ts_mutate.html | 2 +- docs/reference/ts_names.html | 2 +- docs/reference/ts_nodes.html | 2 +- docs/reference/ts_phylo.html | 2 +- docs/reference/ts_recapitate.html | 2 +- docs/reference/ts_samples.html | 2 +- docs/reference/ts_save.html | 2 +- docs/reference/ts_segregating.html | 2 +- docs/reference/ts_simplify.html | 2 +- docs/reference/ts_table.html | 2 +- docs/reference/ts_tajima.html | 2 +- docs/reference/ts_tree.html | 2 +- docs/reference/ts_vcf.html | 2 +- docs/reference/world.html | 4 +-- docs/search.json | 2 +- docs/sitemap.xml | 3 +++ 100 files changed, 150 insertions(+), 128 deletions(-) create mode 100644 docs/articles/vignette-04-nonspatial-models_files/figure-html/non-spatial-graph_sampling-1.png diff --git a/NEWS.md b/NEWS.md index bfa8e539b..7f411cc13 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,12 +1,12 @@ # slendr 0.9.1 -- A new helper function `get_env()` now returns the name of the built-in _slendr_ Python environment (without activating it). (#162ccc) +- A new helper function `get_env()` now returns the name of the built-in _slendr_ Python environment (without activating it). ([#162ccc](https://github.com/bodkan/slendr/commit/162ccc)) -- `clear_env()` now has a new argument `all = (TRUE|FALSE)` which allows deleting all _slendr_ Python environments. Previously, the function always removed only the recent environment, which lead to the accumulation of potentially large number of _slendr_ environments over time. (#8707b9) +- `clear_env()` now has a new argument `all = (TRUE|FALSE)` which allows deleting all _slendr_ Python environments. Previously, the function always removed only the recent environment, which lead to the accumulation of potentially large number of _slendr_ environments over time. ([#8707b9](https://github.com/bodkan/slendr/commit/8707b9)) -- `plot_model()` has a new optional argument `samples =` which will -- when set to a result of a sampling schedule created by `schedule_sampling()` -- visualize the counts of samples to be recorded at each given time-point. (#d72ac5) +- `plot_model()` has a new optional argument `samples =` which will -- when set to a result of a sampling schedule created by `schedule_sampling()` -- visualize the counts of samples to be recorded at each given time-point. ([#d72ac5](https://github.com/bodkan/slendr/commit/d72ac5)) -- The _msprime_ dependency of _slendr_ has been updated to version 1.3.1. As a result, `setup_env()` will have to be re-run to update the internal _slendr_ Python environment. (#dcb83d) +- The _msprime_ dependency of _slendr_ has been updated to version 1.3.1. As a result, `setup_env()` will have to be re-run to update the internal _slendr_ Python environment. ([#dcb83d](https://github.com/bodkan/slendr/commit/dcb83d)) # slendr 0.9.0 diff --git a/docs/404.html b/docs/404.html index 7454b8d65..c555382b0 100644 --- a/docs/404.html +++ b/docs/404.html @@ -31,7 +31,7 @@ slendr - 0.9.0 + 0.9.1