diff --git a/DESCRIPTION b/DESCRIPTION index d56084f..a22d7c4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: catmaid Type: Package Title: R access to the API for the CATMAID web image annotation tool -Version: 0.9.7 +Version: 0.9.8 Authors@R: person("Gregory","Jefferis", email="jefferis@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-0587-9355")) Maintainer: Gregory Jefferis diff --git a/NEWS.md b/NEWS.md index 10485e7..f46bcd9 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,11 @@ +# catmaid 0.9.8 + +* Fix bug in `catmaid_get_connectors_between()` when getting neuron names. + There was an off by one error for the postsynaptic partner name (#109). + Thanks to @mmc46 for the bug report. + # catmaid 0.9.7 + * New `catmaid_userids()` function converts user login names to ids. * `catmaid_connection()` gets a new `config` argument to allow curl options to be set (#108). diff --git a/docs/authors.html b/docs/authors.html index 0165abf..919f8df 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -60,7 +60,7 @@ catmaid - 0.9.7 + 0.9.8 diff --git a/docs/index.html b/docs/index.html index c3cd489..dd9bd79 100644 --- a/docs/index.html +++ b/docs/index.html @@ -33,7 +33,7 @@ catmaid - 0.9.7 + 0.9.8 diff --git a/docs/news/index.html b/docs/news/index.html index 5ead727..f8404dd 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -60,7 +60,7 @@ catmaid - 0.9.7 + 0.9.8 @@ -103,6 +103,13 @@

Changelog

Source: NEWS.md +
+

+catmaid 0.9.8

+ +

catmaid 0.9.7

@@ -317,6 +324,7 @@

Contents

    +
  • 0.9.8
  • 0.9.7
  • 0.9.6
  • 0.9.5
    • diff --git a/docs/reference/AV4b1.html b/docs/reference/AV4b1.html index 1eabd4d..2611339 100644 --- a/docs/reference/AV4b1.html +++ b/docs/reference/AV4b1.html @@ -63,7 +63,7 @@ catmaid - 0.9.7 + 0.9.8
diff --git a/docs/reference/as.catmaidmesh.html b/docs/reference/as.catmaidmesh.html index 1be6b78..fa17f9f 100644 --- a/docs/reference/as.catmaidmesh.html +++ b/docs/reference/as.catmaidmesh.html @@ -63,7 +63,7 @@ catmaid - 0.9.7 + 0.9.8

diff --git a/docs/reference/catmaid-package.html b/docs/reference/catmaid-package.html index 7a895c2..965fbbb 100644 --- a/docs/reference/catmaid-package.html +++ b/docs/reference/catmaid-package.html @@ -68,7 +68,7 @@ catmaid - 0.9.7 + 0.9.8 diff --git a/docs/reference/catmaid_add_volume.html b/docs/reference/catmaid_add_volume.html index c8a87fe..5ab12db 100644 --- a/docs/reference/catmaid_add_volume.html +++ b/docs/reference/catmaid_add_volume.html @@ -63,7 +63,7 @@ catmaid - 0.9.7 + 0.9.8 diff --git a/docs/reference/catmaid_connection_setenv.html b/docs/reference/catmaid_connection_setenv.html index 9383ed9..0caf0ce 100644 --- a/docs/reference/catmaid_connection_setenv.html +++ b/docs/reference/catmaid_connection_setenv.html @@ -68,7 +68,7 @@ catmaid - 0.9.7 + 0.9.8 diff --git a/docs/reference/catmaid_entities_from_models.html b/docs/reference/catmaid_entities_from_models.html index 65427aa..9a49bcb 100644 --- a/docs/reference/catmaid_entities_from_models.html +++ b/docs/reference/catmaid_entities_from_models.html @@ -63,7 +63,7 @@ catmaid - 0.9.7 + 0.9.8 diff --git a/docs/reference/catmaid_fetch.html b/docs/reference/catmaid_fetch.html index 9ac7362..29ffe16 100644 --- a/docs/reference/catmaid_fetch.html +++ b/docs/reference/catmaid_fetch.html @@ -65,7 +65,7 @@ catmaid - 0.9.7 + 0.9.8 diff --git a/docs/reference/catmaid_get_annotationlist.html b/docs/reference/catmaid_get_annotationlist.html index 23b852e..000ef55 100644 --- a/docs/reference/catmaid_get_annotationlist.html +++ b/docs/reference/catmaid_get_annotationlist.html @@ -63,7 +63,7 @@ catmaid - 0.9.7 + 0.9.8 diff --git a/docs/reference/catmaid_get_annotations_for_skeletons.html b/docs/reference/catmaid_get_annotations_for_skeletons.html index 7194aaa..d596a51 100644 --- a/docs/reference/catmaid_get_annotations_for_skeletons.html +++ b/docs/reference/catmaid_get_annotations_for_skeletons.html @@ -68,7 +68,7 @@ catmaid - 0.9.7 + 0.9.8 diff --git a/docs/reference/catmaid_get_compact_skeleton.html b/docs/reference/catmaid_get_compact_skeleton.html index 20babc5..b4375f4 100644 --- a/docs/reference/catmaid_get_compact_skeleton.html +++ b/docs/reference/catmaid_get_compact_skeleton.html @@ -63,7 +63,7 @@ catmaid - 0.9.7 + 0.9.8 diff --git a/docs/reference/catmaid_get_connector_table.html b/docs/reference/catmaid_get_connector_table.html index 9c0d42e..9938704 100644 --- a/docs/reference/catmaid_get_connector_table.html +++ b/docs/reference/catmaid_get_connector_table.html @@ -63,7 +63,7 @@ catmaid - 0.9.7 + 0.9.8 diff --git a/docs/reference/catmaid_get_connectors.html b/docs/reference/catmaid_get_connectors.html index 06d8057..901ad73 100644 --- a/docs/reference/catmaid_get_connectors.html +++ b/docs/reference/catmaid_get_connectors.html @@ -63,7 +63,7 @@ catmaid - 0.9.7 + 0.9.8 diff --git a/docs/reference/catmaid_get_connectors_between.html b/docs/reference/catmaid_get_connectors_between.html index 8d66283..64cbc73 100644 --- a/docs/reference/catmaid_get_connectors_between.html +++ b/docs/reference/catmaid_get_connectors_between.html @@ -63,7 +63,7 @@ catmaid - 0.9.7 + 0.9.8 diff --git a/docs/reference/catmaid_get_contributor_stats.html b/docs/reference/catmaid_get_contributor_stats.html index 85875c7..dc029b9 100644 --- a/docs/reference/catmaid_get_contributor_stats.html +++ b/docs/reference/catmaid_get_contributor_stats.html @@ -63,7 +63,7 @@ catmaid - 0.9.7 + 0.9.8 diff --git a/docs/reference/catmaid_get_label_stats.html b/docs/reference/catmaid_get_label_stats.html index 50d7913..03a08a3 100644 --- a/docs/reference/catmaid_get_label_stats.html +++ b/docs/reference/catmaid_get_label_stats.html @@ -65,7 +65,7 @@ catmaid - 0.9.7 + 0.9.8 @@ -171,8 +171,8 @@

Examp arrange(desc(n)) multiple_soma_info = soma_labels %>% - filter(skeletonID%in% multiple_soma$skeletonID)
head(catmaid_get_all_labels())
#> [1] "ends" "synapse?" "TO LEFT ANTE BRANCH" -#> [4] "TO RIGHT ANTE BRANCH" "synapse onto glia?" "TO RIGHT POST BRANCH"
+ filter(skeletonID%in% multiple_soma$skeletonID)
head(catmaid_get_all_labels())
#> [1] "ends" "not a branch" "end of series" "uncertain end" +#> [5] "lost" "nucleus"
diff --git a/docs/reference/catmaid_get_neuronnames.html b/docs/reference/catmaid_get_neuronnames.html index a9dc705..0ab6ccc 100644 --- a/docs/reference/catmaid_get_neuronnames.html +++ b/docs/reference/catmaid_get_neuronnames.html @@ -63,7 +63,7 @@ catmaid - 0.9.7 + 0.9.8 diff --git a/docs/reference/catmaid_get_node_count.html b/docs/reference/catmaid_get_node_count.html index a9afbfb..1686ce0 100644 --- a/docs/reference/catmaid_get_node_count.html +++ b/docs/reference/catmaid_get_node_count.html @@ -63,7 +63,7 @@ catmaid - 0.9.7 + 0.9.8 diff --git a/docs/reference/catmaid_get_review_status.html b/docs/reference/catmaid_get_review_status.html index 90d59f6..c9b90da 100644 --- a/docs/reference/catmaid_get_review_status.html +++ b/docs/reference/catmaid_get_review_status.html @@ -63,7 +63,7 @@ catmaid - 0.9.7 + 0.9.8 diff --git a/docs/reference/catmaid_get_treenode_table.html b/docs/reference/catmaid_get_treenode_table.html index 087c176..9fba8b9 100644 --- a/docs/reference/catmaid_get_treenode_table.html +++ b/docs/reference/catmaid_get_treenode_table.html @@ -63,7 +63,7 @@ catmaid - 0.9.7 + 0.9.8 diff --git a/docs/reference/catmaid_get_treenodes_detail.html b/docs/reference/catmaid_get_treenodes_detail.html index 5fe2b64..426c445 100644 --- a/docs/reference/catmaid_get_treenodes_detail.html +++ b/docs/reference/catmaid_get_treenodes_detail.html @@ -63,7 +63,7 @@ catmaid - 0.9.7 + 0.9.8 @@ -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        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
+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
 #>   edition_time user_id
-#> 1   1496315535      18
-#> 2   1525270313      71
-#> 3   1523630041      18

+#> 1   1498514622     113
+#> 2   1521466478     134
+#> 3   1496347172     150

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

See a

Examples

- 
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
+ 
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
diff --git a/docs/reference/catmaid_get_volumelist.html b/docs/reference/catmaid_get_volumelist.html index 5eccff4..a61ed14 100644 --- a/docs/reference/catmaid_get_volumelist.html +++ b/docs/reference/catmaid_get_volumelist.html @@ -63,7 +63,7 @@ catmaid - 0.9.7 + 0.9.8 diff --git a/docs/reference/catmaid_login.html b/docs/reference/catmaid_login.html index c4a6431..1f598a0 100644 --- a/docs/reference/catmaid_login.html +++ b/docs/reference/catmaid_login.html @@ -74,7 +74,7 @@ catmaid - 0.9.7 + 0.9.8 diff --git a/docs/reference/catmaid_parse_url.html b/docs/reference/catmaid_parse_url.html index 53cf8b5..dbcfeed 100644 --- a/docs/reference/catmaid_parse_url.html +++ b/docs/reference/catmaid_parse_url.html @@ -63,7 +63,7 @@ catmaid - 0.9.7 + 0.9.8 diff --git a/docs/reference/catmaid_query_by_name.html b/docs/reference/catmaid_query_by_name.html index 1bd4033..5226015 100644 --- a/docs/reference/catmaid_query_by_name.html +++ b/docs/reference/catmaid_query_by_name.html @@ -74,7 +74,7 @@ catmaid - 0.9.7 + 0.9.8 diff --git a/docs/reference/catmaid_query_connected.html b/docs/reference/catmaid_query_connected.html index ba3a354..cb5667d 100644 --- a/docs/reference/catmaid_query_connected.html +++ b/docs/reference/catmaid_query_connected.html @@ -63,7 +63,7 @@ catmaid - 0.9.7 + 0.9.8 diff --git a/docs/reference/catmaid_rename_neuron.html b/docs/reference/catmaid_rename_neuron.html index 428d903..c1e7460 100644 --- a/docs/reference/catmaid_rename_neuron.html +++ b/docs/reference/catmaid_rename_neuron.html @@ -63,7 +63,7 @@ catmaid - 0.9.7 + 0.9.8 diff --git a/docs/reference/catmaid_skids.html b/docs/reference/catmaid_skids.html index 68db9bb..46fe345 100644 --- a/docs/reference/catmaid_skids.html +++ b/docs/reference/catmaid_skids.html @@ -64,7 +64,7 @@ catmaid - 0.9.7 + 0.9.8 diff --git a/docs/reference/catmaid_user_history.html b/docs/reference/catmaid_user_history.html index 4c64c8a..efe4a1d 100644 --- a/docs/reference/catmaid_user_history.html +++ b/docs/reference/catmaid_user_history.html @@ -63,7 +63,7 @@ catmaid - 0.9.7 + 0.9.8 diff --git a/docs/reference/catmaid_version.html b/docs/reference/catmaid_version.html index 46da57b..f7fd948 100644 --- a/docs/reference/catmaid_version.html +++ b/docs/reference/catmaid_version.html @@ -63,7 +63,7 @@ catmaid - 0.9.7 + 0.9.8 diff --git a/docs/reference/connectors.html b/docs/reference/connectors.html index fe2d4c7..d9a4a55 100644 --- a/docs/reference/connectors.html +++ b/docs/reference/connectors.html @@ -65,7 +65,7 @@ catmaid - 0.9.7 + 0.9.8 diff --git a/docs/reference/copy_tags_connectors.html b/docs/reference/copy_tags_connectors.html index 3943363..7faca26 100644 --- a/docs/reference/copy_tags_connectors.html +++ b/docs/reference/copy_tags_connectors.html @@ -65,7 +65,7 @@ catmaid - 0.9.7 + 0.9.8 diff --git a/docs/reference/index.html b/docs/reference/index.html index de63dfc..76caeba 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -60,7 +60,7 @@ catmaid - 0.9.7 + 0.9.8 diff --git a/docs/reference/nsoma.html b/docs/reference/nsoma.html index c7075b8..d2e1d3f 100644 --- a/docs/reference/nsoma.html +++ b/docs/reference/nsoma.html @@ -63,7 +63,7 @@ catmaid - 0.9.7 + 0.9.8 @@ -166,19 +166,7 @@

Examp #> 0 0 0 0 0 0 0 0 0 0 0 #> TL4R TS7L TT27R VA15R VA20R VB37L VB58L #> 0 0 0 0 0 0 0
data("AV4b1") -nsoma(AV4b1)
#> [1] 1
nsoma("ORN PNs")
#> -#> 3486381 8021456 4354933 4493199 4651929 7843730 8399890 7515491 -#> 1 1 1 1 1 1 1 1 -#> 7092417 7107433 7198338 7852250 7845346 7851153 7864823 7865652 -#> 1 1 1 1 1 1 1 1 -#> 7865696 7865767 7873135 7916593 7934904 7935088 8140109 8243455 -#> 1 1 1 1 1 1 1 1 -#> 8244723 8244823 8245014 8245146 8245513 8245692 8245869 8246081 -#> 1 1 2 1 1 1 1 1 -#> 8246750 8247451 8248631 8252067 8253413 8256186 11279244 13589251 -#> 1 1 1 1 1 1 1 1 -#> 14604028 16259595 -#> 1 1
# NOT RUN { +nsoma(AV4b1)
#> [1] 1
nsoma("ORN PNs")
#> Warning: Assumed you want a complete annotation but found no matches for query "annotation:^ORN PNs$"!
#> integer(0)
# NOT RUN { nsoma(3486381) # } diff --git a/docs/reference/plot3d.catmaidneuron.html b/docs/reference/plot3d.catmaidneuron.html index 859a480..3728fd9 100644 --- a/docs/reference/plot3d.catmaidneuron.html +++ b/docs/reference/plot3d.catmaidneuron.html @@ -63,7 +63,7 @@ catmaid - 0.9.7 + 0.9.8 diff --git a/docs/reference/read.neuron.catmaid.html b/docs/reference/read.neuron.catmaid.html index 7294943..d86a0b7 100644 --- a/docs/reference/read.neuron.catmaid.html +++ b/docs/reference/read.neuron.catmaid.html @@ -65,7 +65,7 @@ catmaid - 0.9.7 + 0.9.8 diff --git a/docs/reference/read_catmaid_selection.html b/docs/reference/read_catmaid_selection.html index 479287c..7d1975f 100644 --- a/docs/reference/read_catmaid_selection.html +++ b/docs/reference/read_catmaid_selection.html @@ -63,7 +63,7 @@ catmaid - 0.9.7 + 0.9.8 diff --git a/docs/reference/write_catmaid_selection.html b/docs/reference/write_catmaid_selection.html index 5be9bb2..08cbb66 100644 --- a/docs/reference/write_catmaid_selection.html +++ b/docs/reference/write_catmaid_selection.html @@ -63,7 +63,7 @@ catmaid - 0.9.7 + 0.9.8