/
ChangeLog
130 lines (60 loc) · 2.53 KB
/
ChangeLog
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
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
CHANGES IN ADEPHYLO VERSION 1.1-15
FIXES
o Update authors, description of tha spackage and add references
o remove dontrun as required by CRAN
CHANGES IN ADEPHYLO VERSION 1.1-7
FIXES
o sp.tips now returns ordered paths between tips
FRESH BLOOD
o Anders Ellern Bilgrau has joined the development team!
CHANGES IN ADEPHYLO VERSION 1.1-5
FIXES
o the new NAMESPACE selectively imports procedures to avoid
conflicts between ape, phylobase, and ade4. Thes packages are no
longer attached when loading adephylo
o most dataset examples have been 'dontrun-ed' to save time during
checks of the package on CRAN
CHANGES IN ADEPHYLO VERSION 1.1-4
NEW FEATURES
o added the function bullseye to plot fan-like phylogenies and
associated traits.
o added new methods for dibas.
CHANGES IN ADEPHYLO VERSION 1.1-3
NEW FEATURES
o added dibas, a new (and still under development) method for
describing/testing phylogenetic clusters
BUG FIXES
o replaced the use of .First.lib and library.dynam by more
up-to-date procedures
o replaced a call to a C procedure from ade4 to the same procedure
in adephylo
o replaced instances of 'printf' by 'Rprintf' in C procedures
CHANGES IN ADEPHYLO VERSION 1.1-1
BUG FIXES
o fixed the citation to be used for adephylo.
CHANGES IN ADEPHYLO VERSION 1.1-0
NEW FEATURES
o the phylogenetic Principal Component Analysis (pPCA, Jombart et
al. 2010) has been implemented in adephylo. See ?ppca for more
information.
o phylogenetic distances and proximities are now computed using
compiled C code, speeding up dramatically computations and making
the functions applicable to large trees (thousands of tips).
o table.phylo4d has now a color mode which allows using colors to
represent values of traits; this is usefull for large trees.
CHANGES IN ADEPHYLO VERSION 1.0-2
BUG FIXES
o standardization of variables in abouheif.moran is now performed using
uniform weights (instead of marginal phylogenetic weights)
CHANGES IN ADEPHYLO VERSION 1.0-1
NEW FEATURES
o first release on CRAN, first stable version
o compatible with the first stable release of the phylobase package
CHANGES IN ADEPHYLO VERSION 1.0-0
NEW FEATURES
o first release of the package with unstable status. Compatible
with phylobase (in development) and ape packages; package
only released on R-Forge, not CRAN.
o re-implements all phylogenetic methods and datasets available in ade4
o add new features to compute phylogenetic distances/proximities,
pPCA, tree walks, ...