diff --git a/docs/404.html b/docs/404.html index 66f967a2..d0dc1084 100644 --- a/docs/404.html +++ b/docs/404.html @@ -79,13 +79,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/articles/flywire.html b/docs/articles/flywire.html index f7a8d5b8..853d1c13 100644 --- a/docs/articles/flywire.html +++ b/docs/articles/flywire.html @@ -38,12 +38,18 @@ hemibrainr - 0.2.0 + 0.3.0
#> Warning: top.nt may be taken on a per synapse, rather than per neuron, basis
#> Warning: top.nt may be taken on a per synapse, rather than per neuron, basis
#> Warning: top.nt may be taken on a per synapse, rather than per neuron, basis
#> Warning: top.nt may be taken on a per synapse, rather than per neuron, basis
#> Warning: top.nt may be taken on a per synapse, rather than per neuron, basis
+ # }
@@ -254,7 +260,7 @@

Contents

-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/hemibrain_connectivity_similarity.html b/docs/reference/hemibrain_connectivity_similarity.html index 6cb6941e..4045bb3c 100644 --- a/docs/reference/hemibrain_connectivity_similarity.html +++ b/docs/reference/hemibrain_connectivity_similarity.html @@ -80,13 +80,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/hemibrain_cut.html b/docs/reference/hemibrain_cut.html index b727e13e..d9d68f1a 100644 --- a/docs/reference/hemibrain_cut.html +++ b/docs/reference/hemibrain_cut.html @@ -80,13 +80,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/hemibrain_download_neurons.html b/docs/reference/hemibrain_download_neurons.html index 73bc34c4..6abfb64b 100644 --- a/docs/reference/hemibrain_download_neurons.html +++ b/docs/reference/hemibrain_download_neurons.html @@ -92,13 +92,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/hemibrain_extract_connections.html b/docs/reference/hemibrain_extract_connections.html index ee9300ee..cb49703b 100644 --- a/docs/reference/hemibrain_extract_connections.html +++ b/docs/reference/hemibrain_extract_connections.html @@ -85,13 +85,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/hemibrain_flow_centrality.html b/docs/reference/hemibrain_flow_centrality.html index 375809df..e98dae45 100644 --- a/docs/reference/hemibrain_flow_centrality.html +++ b/docs/reference/hemibrain_flow_centrality.html @@ -84,13 +84,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/hemibrain_get_meta.html b/docs/reference/hemibrain_get_meta.html index 920852aa..6027ef33 100644 --- a/docs/reference/hemibrain_get_meta.html +++ b/docs/reference/hemibrain_get_meta.html @@ -82,13 +82,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/hemibrain_matched.html b/docs/reference/hemibrain_matched.html index 80731f69..b031daa9 100644 --- a/docs/reference/hemibrain_matched.html +++ b/docs/reference/hemibrain_matched.html @@ -91,13 +91,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/hemibrain_matches.html b/docs/reference/hemibrain_matches.html index 3a8ee441..2ec0043b 100644 --- a/docs/reference/hemibrain_matches.html +++ b/docs/reference/hemibrain_matches.html @@ -86,13 +86,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/hemibrain_matching.html b/docs/reference/hemibrain_matching.html index 0e54fcd9..29ec0104 100644 --- a/docs/reference/hemibrain_matching.html +++ b/docs/reference/hemibrain_matching.html @@ -59,7 +59,7 @@ login details for this project recorded in your .Renviron for these functions to work. You are given neurons assigned to your initials on the matching google sheet (the User column) though you can look at other's assigned matches using superUser=TRUE. Your selection is further narrowed - by ommitting neurons whose matches have already been made, when using the default overwrite="TRUE". However, you + by omitting neurons whose matches have already been made, when using the default overwrite="TRUE". However, you can change this to overwrite matches, and to review made matches." /> @@ -93,13 +93,19 @@ hemibrainr - 0.2.0 + 0.3.0 @@ -325,7 +331,7 @@

Arg flywire.good -

logical, whether or not to only take 'well traced' flywire neurons, as annotated by the Drosophila Connectomics Group. This relies on the status column retreived +

logical, whether or not to only take 'well traced' flywire neurons, as annotated by the Drosophila Connectomics Group. This relies on the status column retrieved by flywire_meta.

@@ -405,7 +411,7 @@

Contents

-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/hemibrain_metrics-1.png b/docs/reference/hemibrain_metrics-1.png index ace8e77d..ae2fa6e1 100644 Binary files a/docs/reference/hemibrain_metrics-1.png and b/docs/reference/hemibrain_metrics-1.png differ diff --git a/docs/reference/hemibrain_metrics.html b/docs/reference/hemibrain_metrics.html index 9c613b92..331be062 100644 --- a/docs/reference/hemibrain_metrics.html +++ b/docs/reference/hemibrain_metrics.html @@ -87,13 +87,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/hemibrain_nblast.html b/docs/reference/hemibrain_nblast.html index b4188b4a..a1d1b8ee 100644 --- a/docs/reference/hemibrain_nblast.html +++ b/docs/reference/hemibrain_nblast.html @@ -87,13 +87,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/hemibrain_neuron_meshes.html b/docs/reference/hemibrain_neuron_meshes.html index d54a955f..92e774c4 100644 --- a/docs/reference/hemibrain_neuron_meshes.html +++ b/docs/reference/hemibrain_neuron_meshes.html @@ -81,13 +81,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/hemibrain_precomputed_splitpoints.html b/docs/reference/hemibrain_precomputed_splitpoints.html index c444de88..e1d2ab8b 100644 --- a/docs/reference/hemibrain_precomputed_splitpoints.html +++ b/docs/reference/hemibrain_precomputed_splitpoints.html @@ -86,13 +86,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/hemibrain_read_neurons.html b/docs/reference/hemibrain_read_neurons.html index 328386bf..c04f8b1b 100644 --- a/docs/reference/hemibrain_read_neurons.html +++ b/docs/reference/hemibrain_read_neurons.html @@ -84,13 +84,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/hemibrain_remove_bad_synapses.html b/docs/reference/hemibrain_remove_bad_synapses.html index 9e4ff2ac..4ca4a6db 100644 --- a/docs/reference/hemibrain_remove_bad_synapses.html +++ b/docs/reference/hemibrain_remove_bad_synapses.html @@ -86,13 +86,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/hemibrain_reroot.html b/docs/reference/hemibrain_reroot.html index ac47b1e1..cef8f2f7 100644 --- a/docs/reference/hemibrain_reroot.html +++ b/docs/reference/hemibrain_reroot.html @@ -86,13 +86,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/hemibrain_roi_meshes.html b/docs/reference/hemibrain_roi_meshes.html index 1b24d097..c49d0295 100644 --- a/docs/reference/hemibrain_roi_meshes.html +++ b/docs/reference/hemibrain_roi_meshes.html @@ -84,13 +84,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/hemibrain_skeleton_check.html b/docs/reference/hemibrain_skeleton_check.html index ca47e61b..e4118aab 100644 --- a/docs/reference/hemibrain_skeleton_check.html +++ b/docs/reference/hemibrain_skeleton_check.html @@ -84,13 +84,19 @@ hemibrainr - 0.2.0 + 0.3.0
#> Re-rooting 1 neurons without a soma
#> Removing synapses outside the hemibrain neuropil volume for 3 neurons
#> Warning: invalid factor level, NA generated
#> Warning: invalid factor level, NA generated
#> Warning: invalid factor level, NA generated
#> Warning: invalid factor level, NA generated
+
#> Re-rooting 1 neurons without a soma
#> Removing synapses outside the hemibrain neuropil volume for 3 neurons
if (FALSE) { # Let's check that this worked nat::nopen3d() @@ -281,7 +287,7 @@

Contents

-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/hemibrain_somas.html b/docs/reference/hemibrain_somas.html index 3e7a9d44..94272a24 100644 --- a/docs/reference/hemibrain_somas.html +++ b/docs/reference/hemibrain_somas.html @@ -85,13 +85,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/hemibrain_splitpoints.html b/docs/reference/hemibrain_splitpoints.html index fc6a96de..e6445ab9 100644 --- a/docs/reference/hemibrain_splitpoints.html +++ b/docs/reference/hemibrain_splitpoints.html @@ -81,13 +81,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/hemibrain_tags.html b/docs/reference/hemibrain_tags.html index 78ba5200..a586b831 100644 --- a/docs/reference/hemibrain_tags.html +++ b/docs/reference/hemibrain_tags.html @@ -80,13 +80,19 @@ hemibrainr - 0.2.0 + 0.3.0
#> Reading from Google Team Drive: hemibrainr
#> Warning: 1 neurons cropped, split likely to be inaccurate for: 2068966051
#> Warning: 1 neurons have no soma tagged, split could be inaccurate for: 2068966051
#> Warning: No meta data could be retieved, returning NULL
#> Error in neurons.flow[, ] <- hemibrain_get_meta(names(neurons.flow)): incorrect number of subscripts on matrix
+
#> Reading from Google Team Drive: hemibrainr
#> Warning: 1 neurons cropped, split likely to be inaccurate for: 2068966051
#> Warning: 1 neurons have no soma tagged, split could be inaccurate for: 2068966051
#> Warning: No meta data could be retieved, returning NULL
#> Error in neurons.flow[, ] = hemibrain_get_meta(names(neurons.flow)): incorrect number of subscripts on matrix
# Tag neurons = hemibrain_settags(neurons, antennal.lobe = TRUE)
#> Error in hemibrain_settags(neurons, antennal.lobe = TRUE): object 'neurons' not found
@@ -237,7 +243,7 @@

Contents

-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/hemibrain_type_plot.html b/docs/reference/hemibrain_type_plot.html index 60327115..23d48402 100644 --- a/docs/reference/hemibrain_type_plot.html +++ b/docs/reference/hemibrain_type_plot.html @@ -81,13 +81,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/hemibrain_use_splitpoints.html b/docs/reference/hemibrain_use_splitpoints.html index 94dd72e3..5696c89c 100644 --- a/docs/reference/hemibrain_use_splitpoints.html +++ b/docs/reference/hemibrain_use_splitpoints.html @@ -80,13 +80,19 @@ hemibrainr - 0.2.0 + 0.3.0
#> Re-rooting 2 neurons without a soma
#> Removing synapses outside the hemibrain neuropil volume for 5 neurons
#> Warning: invalid factor level, NA generated
#> Warning: invalid factor level, NA generated
#> Warning: invalid factor level, NA generated
#> Warning: invalid factor level, NA generated
#> Warning: invalid factor level, NA generated
#> Warning: invalid factor level, NA generated
+
#> Re-rooting 2 neurons without a soma
#> Removing synapses outside the hemibrain neuropil volume for 5 neurons
# Split neuron ## These are the recommended parameters for hemibrain neurons neurons.flow = flow_centrality(neurons.checked, polypre = TRUE, @@ -253,7 +259,7 @@

Contents

-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/hemibrain_view.html b/docs/reference/hemibrain_view.html index d2c1b6b8..5b643f24 100644 --- a/docs/reference/hemibrain_view.html +++ b/docs/reference/hemibrain_view.html @@ -80,13 +80,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/hemibrainr-package.html b/docs/reference/hemibrainr-package.html index 4983c235..d0a09749 100644 --- a/docs/reference/hemibrainr-package.html +++ b/docs/reference/hemibrainr-package.html @@ -81,13 +81,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/hemibrainr_googledrive_data.html b/docs/reference/hemibrainr_googledrive_data.html index 7aa2abe2..ee2b05ed 100644 --- a/docs/reference/hemibrainr_googledrive_data.html +++ b/docs/reference/hemibrainr_googledrive_data.html @@ -86,13 +86,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/hemibrainr_set_drive.html b/docs/reference/hemibrainr_set_drive.html index c2481bea..046d32ec 100644 --- a/docs/reference/hemibrainr_set_drive.html +++ b/docs/reference/hemibrainr_set_drive.html @@ -85,13 +85,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/hemilineages.html b/docs/reference/hemilineages.html index 3757e602..3102b6ea 100644 --- a/docs/reference/hemilineages.html +++ b/docs/reference/hemilineages.html @@ -81,13 +81,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/index.html b/docs/reference/index.html index 0431f469..55381b50 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -79,13 +79,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/info.html b/docs/reference/info.html index 7bfbf6d9..0c87678a 100644 --- a/docs/reference/info.html +++ b/docs/reference/info.html @@ -83,13 +83,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/lineage_clones.html b/docs/reference/lineage_clones.html index 84427d9a..f090bc1f 100644 --- a/docs/reference/lineage_clones.html +++ b/docs/reference/lineage_clones.html @@ -81,13 +81,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/manually_assign_labels.html b/docs/reference/manually_assign_labels.html index 1ed29233..6d517c17 100644 --- a/docs/reference/manually_assign_labels.html +++ b/docs/reference/manually_assign_labels.html @@ -82,13 +82,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/matches_update.html b/docs/reference/matches_update.html index 6ef5db1e..7d41327a 100644 --- a/docs/reference/matches_update.html +++ b/docs/reference/matches_update.html @@ -82,13 +82,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/paper_colours.html b/docs/reference/paper_colours.html index b2607dec..452727ba 100644 --- a/docs/reference/paper_colours.html +++ b/docs/reference/paper_colours.html @@ -80,13 +80,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/plot3d_split.html b/docs/reference/plot3d_split.html index 55a32d36..9dd47475 100644 --- a/docs/reference/plot3d_split.html +++ b/docs/reference/plot3d_split.html @@ -80,13 +80,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/plot_inspirobot.html b/docs/reference/plot_inspirobot.html index 3b927984..18190e10 100644 --- a/docs/reference/plot_inspirobot.html +++ b/docs/reference/plot_inspirobot.html @@ -82,13 +82,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/primary_neurite.html b/docs/reference/primary_neurite.html index b9eda133..aea295e4 100644 --- a/docs/reference/primary_neurite.html +++ b/docs/reference/primary_neurite.html @@ -87,13 +87,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/prune_vertices.neuprintneuron.html b/docs/reference/prune_vertices.neuprintneuron.html index f931af75..08d214f7 100644 --- a/docs/reference/prune_vertices.neuprintneuron.html +++ b/docs/reference/prune_vertices.neuprintneuron.html @@ -80,13 +80,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/randomwords.html b/docs/reference/randomwords.html index dc7a6542..e5114b90 100644 --- a/docs/reference/randomwords.html +++ b/docs/reference/randomwords.html @@ -81,13 +81,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html index 6ca4401e..892361af 100644 --- a/docs/reference/reexports.html +++ b/docs/reference/reexports.html @@ -89,13 +89,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/standardise.html b/docs/reference/standardise.html index d55caa7d..419da877 100644 --- a/docs/reference/standardise.html +++ b/docs/reference/standardise.html @@ -80,13 +80,19 @@ hemibrainr - 0.2.0 + 0.3.0
-

Site built with pkgdown 1.6.1.9000.

+

Site built with pkgdown 1.6.1.