-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathchangelog.txt
78 lines (70 loc) · 3.49 KB
/
changelog.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
TaxCI Changelog:
================
0.5-1
-----
- class removed from imported ape-function is.binary.tree
0.5-0
-----
- tci() now uses phangorn::CI instead of own R-functions to calculate consistency indices. This makes it substantially faster.
- retention indices are no longer offered
- parallel computing is no longer needed. doSNOW is removed from dependencies
- fixed bug when integer was given as sp.col-argument in BCCluster
0.4.5
-----
- tci() & BCCluster(): implemented check that x is a data.frame / convert it into one
- BCCluster(): implemented check that 'sp.col' is in names of 'x' if it is not integer
- BCCluster(): implemented check that DNA-data is a matrix and convert into one (as.matrix) if not
- added internal function to check for whole numbers (see ?is.integer) and fixed previous check in transform_user_table()
0.4.4
-----
fixes
- implemented handling of BCCluster-method "external" to TaxCIsummary
- fixed an error in transform_user_table()
- some minor issues in the man pages
0.4.3
-----
new functions
- parse_mPTP for parsing output of the species delimitation program mPTP
changes
- renamed most functions: periods in non-generic-S3-methods were deleted and subsequent character changed to uppercase
- added S3 print method for BCCluster (former bc.cluster)
- added class "BCCluster" for output of the BCCluster function (former bc.cluster)
- BCCluster (former bc.cluster): new option 'method' for choosing a user-supplied clustering (e.g. from mPTP)
fixes
- some minor changes in the example
- TaxCIplot (former PlotCI): error occured when info=NA which was the default; replaced by ""
- added missing plotParamTCI (former plot.param.tci) argument in plotParamBCC (former plot.param.bcc) manpage
0.4.2
-----
fixes
- "Rhyssemus germanus - Problem" splitted homogeneous clusters were not marked with penalty point 5 if the respective species occured in an heterogeneous cluster, too.
- renamed find.in.clusters to find.species.in.clusters
- new function find.in.clusters: same as above but really directly search in bc.cluster.result$clusters
- changed plot-legend point 3 to "Species in heterogeneous cluster and in more than one cluster" (analogously)
- added option 'cluster.nodes' to plot.param.bcc and alterd 'vis.clusters' from PlotCI. Nodes CAN now be searched along with plot.param.bcc and vis.clusters is takes Boolean values or a vector of node numbers which should be marked.
- Added documentation for Carabidae dataset
- invisibly return clusters in find.in.clusters-functions
- Added verbose option to find.in.clusters-functions
0.4.1
-----
fixes
- fixed match ration calculation in summarize.TaxCI; now: 2*perfect cluster / (no. morphospecies + no. clusters); perfect clusters are non-splitted homogeneous
changes
- PlotCI: added "alternative.tiplabels" - option (e.g. for use with mixedFontLabel{ape})
- PlotCI: added experimental option 'box.placement' for automatic placement of boxes and tip labels
- PlotCI: added option 'vis.clades' to switch clade-dots off
minor changes
- changed colors of boxes
- plot.param.tci, PlotCI: fixed 'taxa-not-in-tree' warning
- removed sp.col from PlotCI arguments; was unused
- changed number of tips per page calculation from 'ntips / npages' to 'as.integer(ntips / npages) + 1' (whole number plus 1)
0.4.0
-----
new functions
- no.morphospecies
- find.in.clusters
- summarize.TaxCI
minor changes
- PlotCI: added dots to common nodes of each cluster
- TaxCI-script: set timestamp decimals to 2 and corrected units
- added $cluster output of bcc.cluster also to plot.param.bcc result-list