diff --git a/docs/authors.html b/docs/authors.html index 919f8df..c3a6de3 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -60,7 +60,7 @@ catmaid - 0.9.8 + 0.9.9 diff --git a/docs/index.html b/docs/index.html index dd9bd79..e0a929c 100644 --- a/docs/index.html +++ b/docs/index.html @@ -33,7 +33,7 @@ catmaid - 0.9.8 + 0.9.9 diff --git a/docs/news/index.html b/docs/news/index.html index f8404dd..c625198 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -60,7 +60,7 @@ catmaid - 0.9.8 + 0.9.9 @@ -103,6 +103,14 @@

Changelog

Source: NEWS.md +
+

+catmaid 0.9.9

+ +

catmaid 0.9.8

@@ -324,6 +332,7 @@

Contents

    +
  • 0.9.9
  • 0.9.8
  • 0.9.7
  • 0.9.6
    • diff --git a/docs/reference/AV4b1.html b/docs/reference/AV4b1.html index 2611339..f19e127 100644 --- a/docs/reference/AV4b1.html +++ b/docs/reference/AV4b1.html @@ -63,7 +63,7 @@ catmaid - 0.9.8 + 0.9.9
diff --git a/docs/reference/as.catmaidmesh.html b/docs/reference/as.catmaidmesh.html index fa17f9f..5c29b9e 100644 --- a/docs/reference/as.catmaidmesh.html +++ b/docs/reference/as.catmaidmesh.html @@ -63,7 +63,7 @@ catmaid - 0.9.8 + 0.9.9

diff --git a/docs/reference/catmaid-package.html b/docs/reference/catmaid-package.html index 965fbbb..b7af202 100644 --- a/docs/reference/catmaid-package.html +++ b/docs/reference/catmaid-package.html @@ -68,7 +68,7 @@ catmaid - 0.9.8 + 0.9.9 diff --git a/docs/reference/catmaid_add_volume.html b/docs/reference/catmaid_add_volume.html index 5ab12db..ddeb8de 100644 --- a/docs/reference/catmaid_add_volume.html +++ b/docs/reference/catmaid_add_volume.html @@ -63,7 +63,7 @@ catmaid - 0.9.8 + 0.9.9 diff --git a/docs/reference/catmaid_connection_setenv.html b/docs/reference/catmaid_connection_setenv.html index 0caf0ce..ba40bf8 100644 --- a/docs/reference/catmaid_connection_setenv.html +++ b/docs/reference/catmaid_connection_setenv.html @@ -68,7 +68,7 @@ catmaid - 0.9.8 + 0.9.9 diff --git a/docs/reference/catmaid_entities_from_models.html b/docs/reference/catmaid_entities_from_models.html index 9a49bcb..53b5343 100644 --- a/docs/reference/catmaid_entities_from_models.html +++ b/docs/reference/catmaid_entities_from_models.html @@ -63,7 +63,7 @@ catmaid - 0.9.8 + 0.9.9 diff --git a/docs/reference/catmaid_fetch.html b/docs/reference/catmaid_fetch.html index 29ffe16..fa62afb 100644 --- a/docs/reference/catmaid_fetch.html +++ b/docs/reference/catmaid_fetch.html @@ -65,7 +65,7 @@ catmaid - 0.9.8 + 0.9.9 diff --git a/docs/reference/catmaid_get_annotationlist.html b/docs/reference/catmaid_get_annotationlist.html index 000ef55..d7b32d7 100644 --- a/docs/reference/catmaid_get_annotationlist.html +++ b/docs/reference/catmaid_get_annotationlist.html @@ -63,7 +63,7 @@ catmaid - 0.9.8 + 0.9.9 diff --git a/docs/reference/catmaid_get_annotations_for_skeletons.html b/docs/reference/catmaid_get_annotations_for_skeletons.html index d596a51..7c62a6f 100644 --- a/docs/reference/catmaid_get_annotations_for_skeletons.html +++ b/docs/reference/catmaid_get_annotations_for_skeletons.html @@ -68,7 +68,7 @@ catmaid - 0.9.8 + 0.9.9 diff --git a/docs/reference/catmaid_get_compact_skeleton.html b/docs/reference/catmaid_get_compact_skeleton.html index b4375f4..b4c168f 100644 --- a/docs/reference/catmaid_get_compact_skeleton.html +++ b/docs/reference/catmaid_get_compact_skeleton.html @@ -63,7 +63,7 @@ catmaid - 0.9.8 + 0.9.9 diff --git a/docs/reference/catmaid_get_connector_table.html b/docs/reference/catmaid_get_connector_table.html index 9938704..46ebfcf 100644 --- a/docs/reference/catmaid_get_connector_table.html +++ b/docs/reference/catmaid_get_connector_table.html @@ -63,7 +63,7 @@ catmaid - 0.9.8 + 0.9.9 diff --git a/docs/reference/catmaid_get_connectors.html b/docs/reference/catmaid_get_connectors.html index 901ad73..1544076 100644 --- a/docs/reference/catmaid_get_connectors.html +++ b/docs/reference/catmaid_get_connectors.html @@ -63,7 +63,7 @@ catmaid - 0.9.8 + 0.9.9 diff --git a/docs/reference/catmaid_get_connectors_between.html b/docs/reference/catmaid_get_connectors_between.html index 64cbc73..de70a44 100644 --- a/docs/reference/catmaid_get_connectors_between.html +++ b/docs/reference/catmaid_get_connectors_between.html @@ -63,7 +63,7 @@ catmaid - 0.9.8 + 0.9.9 diff --git a/docs/reference/catmaid_get_contributor_stats.html b/docs/reference/catmaid_get_contributor_stats.html index dc029b9..62baa34 100644 --- a/docs/reference/catmaid_get_contributor_stats.html +++ b/docs/reference/catmaid_get_contributor_stats.html @@ -63,7 +63,7 @@ catmaid - 0.9.8 + 0.9.9 diff --git a/docs/reference/catmaid_get_label_stats.html b/docs/reference/catmaid_get_label_stats.html index 03a08a3..fd00b10 100644 --- a/docs/reference/catmaid_get_label_stats.html +++ b/docs/reference/catmaid_get_label_stats.html @@ -65,7 +65,7 @@ catmaid - 0.9.8 + 0.9.9 @@ -171,8 +171,8 @@

Examp arrange(desc(n)) multiple_soma_info = soma_labels %>% - filter(skeletonID%in% multiple_soma$skeletonID)
head(catmaid_get_all_labels())
#> [1] "ends" "not a branch" "end of series" "uncertain end" -#> [5] "lost" "nucleus"
+ filter(skeletonID%in% multiple_soma$skeletonID)
head(catmaid_get_all_labels())
#> [1] "ends" "synapse?" "TO LEFT ANTE BRANCH" +#> [4] "TO RIGHT ANTE BRANCH" "synapse onto glia?" "TO RIGHT POST BRANCH"
diff --git a/docs/reference/catmaid_get_neuronnames.html b/docs/reference/catmaid_get_neuronnames.html index 0ab6ccc..e073e7d 100644 --- a/docs/reference/catmaid_get_neuronnames.html +++ b/docs/reference/catmaid_get_neuronnames.html @@ -63,7 +63,7 @@ catmaid - 0.9.8 + 0.9.9 diff --git a/docs/reference/catmaid_get_node_count.html b/docs/reference/catmaid_get_node_count.html index 1686ce0..d78523e 100644 --- a/docs/reference/catmaid_get_node_count.html +++ b/docs/reference/catmaid_get_node_count.html @@ -63,7 +63,7 @@ catmaid - 0.9.8 + 0.9.9 diff --git a/docs/reference/catmaid_get_review_status.html b/docs/reference/catmaid_get_review_status.html index c9b90da..6328b79 100644 --- a/docs/reference/catmaid_get_review_status.html +++ b/docs/reference/catmaid_get_review_status.html @@ -63,7 +63,7 @@ catmaid - 0.9.8 + 0.9.9 diff --git a/docs/reference/catmaid_get_treenode_table.html b/docs/reference/catmaid_get_treenode_table.html index 9fba8b9..c747c49 100644 --- a/docs/reference/catmaid_get_treenode_table.html +++ b/docs/reference/catmaid_get_treenode_table.html @@ -63,7 +63,7 @@ catmaid - 0.9.8 + 0.9.9 diff --git a/docs/reference/catmaid_get_treenodes_detail.html b/docs/reference/catmaid_get_treenodes_detail.html index 426c445..c7a07c9 100644 --- a/docs/reference/catmaid_get_treenodes_detail.html +++ b/docs/reference/catmaid_get_treenodes_detail.html @@ -63,7 +63,7 @@ catmaid - 0.9.8 + 0.9.9 @@ -190,16 +190,16 @@

See a

Examples

# details for 3 nodes from two different skeletons
-catmaid_get_treenodes_detail(c(9943214L, 25069047L, 12829015L))
#>   treenode_id parent_id      x      y      z confidence radius    skid
-#> 1     9943214   9943217 419085 175627 120280          5     -1 4116825
-#> 2    25069047  25069046 426264 244230 143920          5     -1 7138957
-#> 3    12829015  12829013 442500 147757 175160          5     -1 3821611
+catmaid_get_treenodes_detail(c(9943214L, 25069047L, 12829015L))
#>   treenode_id parent_id       x       y     z confidence radius     skid
+#> 1     9943214        NA 65439.8 20611.2 41250          5   1911  4453485
+#> 2    25069047  10983327 53296.5 14791.1 42650          5     -1  4453485
+#> 3    12829015  12829014 59222.2 65869.2 51150          5     -1 10418394
 #>   edition_time user_id
-#> 1   1498514622     113
-#> 2   1521466478     134
-#> 3   1496347172     150

+#> 1   1496315535      18
+#> 2   1525270313      71
+#> 3   1523630041      18

 # example label search
-tosoma=catmaid_get_treenodes_detail("to soma")
#> Error in catmaid_error_check(nodeinfo): invalid literal for int() with base 10: 'to soma'	type: ValueError
+tosoma=catmaid_get_treenodes_detail("to soma")
#> Error in catmaid_get_treenodes_detail("to soma"): Unexpected return format catmaid_get_treenodes_detail!
@@ -155,13 +155,20 @@

See a

Examples

- 
head(catmaid_get_user_list())
#>    id         login full_name first_name last_name                        color
-#> 1  79 rfranconville                                1.000000, 0.156985, 0.439778
-#> 2 243       wolskyd                                0.290622, 0.213735, 1.000000
-#> 3 159   WT_outreach                                1.000000, 0.631121, 0.678050
-#> 4  87    tavosanisg                                0.257581, 0.049968, 1.000000
-#> 5 265     obrusnikt                                0.505058, 1.000000, 0.828322
-#> 6 274      buhmannj                                1.000000, 0.900653, 0.208175
catmaid_userids(1)
#> [1] 1
catmaid_userids('greg')
#> [1] NA
+ 
head(catmaid_get_user_list())
#>   id         login                full_name      first_name   last_name
+#> 1 -1 AnonymousUser                                                     
+#> 2 20         bruno             Bruno Afonso           Bruno      Afonso
+#> 3 65    mballstars a Mushroom Body All-star a Mushroom Body    All-star
+#> 4  6        ingrid           Ingrid Andrade          Ingrid     Andrade
+#> 5 84       rebecca           Rebecca Arruda         Rebecca      Arruda
+#> 6 45          aref         Aref Arzan Zarin            Aref Arzan Zarin
+#>                          color
+#> 1                0.2, 0.2, 0.2
+#> 2 0.751444, 1.000000, 0.997314
+#> 3 0.728931, 1.000000, 0.002305
+#> 4                      1, 1, 0
+#> 5 1.000000, 0.292329, 0.570369
+#> 6                0.0, 0.7, 0.0
catmaid_userids(1)
#> [1] 1
catmaid_userids('greg')
#> [1] 51
diff --git a/docs/reference/catmaid_get_volumelist.html b/docs/reference/catmaid_get_volumelist.html index a61ed14..78a7566 100644 --- a/docs/reference/catmaid_get_volumelist.html +++ b/docs/reference/catmaid_get_volumelist.html @@ -63,7 +63,7 @@ catmaid - 0.9.8 + 0.9.9 diff --git a/docs/reference/catmaid_login.html b/docs/reference/catmaid_login.html index 1f598a0..737f706 100644 --- a/docs/reference/catmaid_login.html +++ b/docs/reference/catmaid_login.html @@ -74,7 +74,7 @@ catmaid - 0.9.8 + 0.9.9 diff --git a/docs/reference/catmaid_parse_url.html b/docs/reference/catmaid_parse_url.html index dbcfeed..e055214 100644 --- a/docs/reference/catmaid_parse_url.html +++ b/docs/reference/catmaid_parse_url.html @@ -63,7 +63,7 @@ catmaid - 0.9.8 + 0.9.9 diff --git a/docs/reference/catmaid_query_by_name.html b/docs/reference/catmaid_query_by_name.html index 5226015..e389a60 100644 --- a/docs/reference/catmaid_query_by_name.html +++ b/docs/reference/catmaid_query_by_name.html @@ -74,7 +74,7 @@ catmaid - 0.9.8 + 0.9.9 diff --git a/docs/reference/catmaid_query_connected.html b/docs/reference/catmaid_query_connected.html index cb5667d..11e97f5 100644 --- a/docs/reference/catmaid_query_connected.html +++ b/docs/reference/catmaid_query_connected.html @@ -63,7 +63,7 @@ catmaid - 0.9.8 + 0.9.9 @@ -113,9 +113,9 @@

Find neurons connected to a starting neuron

- 
catmaid_query_connected(skids, minimum_synapses = 1,
-  boolean_op = c("OR", "AND"), pid = 1, raw = FALSE, conn = NULL,
-  ...)
+ 
catmaid_query_connected(skids, minimum_synapses = 1L,
+  minimum_confidence = 1L, boolean_op = c("OR", "AND"), pid = 1,
+  raw = FALSE, conn = NULL, ...)

Arguments

@@ -127,12 +127,17 @@

Arg

- + + + + - @@ -162,7 +167,7 @@

Arg

Value

-

A list containing two data.frames (incoming, outgoing), each +

A list containing two data.frames (incoming, outgoing), each data.frame having one row for each partner neuron and the following columns

minimum_synapses

Must be at least this number of synapses between +

Must be at least this number of synapses between starter neuron and returned partners

minimum_confidence

The minimum confidence score (1-5, where 5 is high) +of the reported connections.
boolean_op

Whether returned neurons can be connected to any +

Whether returned neurons can be connected to any character vector (boolean_op="OR", the default) or must be connected to all the specified neurons (boolean_op="AND").