-
Notifications
You must be signed in to change notification settings - Fork 7
/
Copy pathCHANGELOG
128 lines (115 loc) · 4.41 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
Changes from Version 0.0.8-13 to 1.0 [February 2021]
* Update maintainer email
* Transition of Rnw to Rmd [WIP]
* the first stable version
Changes from Version 0.0.8-11 to 0.0.8-12 [February 02 2018]
* Improved plot of humanrater
* Fixed function poc in amptester
* Improved documentation for amptester
* adopted the fairly new CRAN requirements
* removed natbib.sty from vignettes
* some improvements to grammar and spelling
Changes from Version 0.0.8-10 to 0.0.8-11 [April 31 2015]
* further CRAN changes, VideoScan -> 'VideoScan', HCU -> 'HCU'
* some further test of validity for the th.cyc function
Changes from Version 0.0.8-9 to 0.0.8-10 [April 8 2015]
* further CRAN changes
Changes from Version 0.0.8-7 to 0.0.8-9 [April 4 2015]
* further CRAN changes
* Less confusing error messages from th.cyc
* Removed arrow warning in plot.eff
* assorted documentation improvements
Changes from Version 0.0.8-6 to 0.0.8-7 [March 12 2015]
* New data sets
* further CRAN changes
Changes from Version 0.0.8-3 to 0.0.8-6 [February 22 2015]
* Add citation("chipPCR")
* Improved vignette
* Improved documentation
* Improved examples
* removed calculation of dB from CPP function
* new plot option for MFIaggr function
* several bug fixes
* Reference Spiess et al. 2015 added to documentation
* New contributor Konstantin A. Blagodatskikh
* Adaption to new CRAN policies
Changes from Version 0.0.8-2 to 0.0.8-3 [September 28 2014]
* build uses now: R CMD build --resave-data --compact-vignettes="gs+qpdf" chipPCR
* reduced size of bitmap images
Changes from Version 0.0.8-1 to 0.0.8-2 [September 26 2014]
* suggest RDML package
* update of the vignette
* fix of several annoying bugs
* update and improvement of the GUIs
* minmax parameter renamed to minm
Changes from Version 0.0.8 to 0.0.8-1 [August 26 2014]
* Fix CRAN issue
Changes from Version 0.0.7 to 0.0.8-1 [August 25 2014]
* Numerous bug fixes (see change-log at https://github.com/michbur/chipPCR)
* New function th.cyc (threshold cycle method)
* New function humanrater
* New pco test for amptester
* New function plotCurves
* New "Depends"/"Imports" to/from bptest {lmtest}
* effcalc with improved plot and analysis methods
* Considerably enhanced shiny GUIs
- New function amptester.gui
- New function MFIaggr.gui
- New function lm.coefs (moved from CPP as independent function)
* smoother function has parallelization option now
- normalization algorithm moved from CPP as independent function normalizer
- parameter norm of CPP renamed to method.norm
- parameter rob.reg of CPP renamed to method.reg
* MFIaggr
- improved plot and analysis methods
- Breusch-Pagan to test against heteroskedasticity
* Documentation
- preprocess -> pre-process in docs
- inclusion of more examples
- documentation fixes
Changes from Version 0.0.6 to 0.0.7 [June 26 2014]
* From S3 to S4
* Dependency to qpcR and MBmca packages removed
* New "Depends"/"Imports" to/from MASS, ptw, quantreg and shiny, methods
* Many bug fixes
* Better sanity check of input variables
* Code optimized for speed and less memory usage
* Improved some examples
* New function MFIaggr and class refMFI
* New function effcalc
* amptester
- flexible head and tail now
- nonlinearity test to detect positive amplifications
- t.test exchanged by wilcox.test to compare levels of head and tail
region
- tests for noise (based on Shapiro-Wilk test) and linearity
* smoother
- Support for weighted Whittaker smoother
- Argument "spline" as parameter for internal fixNA detracted
- Uses splines in fixNA exclusively
* CPP
- has further normalization methods
- new regression methods (rank-based estimation models, quantile
regression)
- argument "minmax" detracted and substituted by more powerful
method "norm"
* Added methods to fixNA
* NOTE: new naming convention in inder
* bg.max
- uses inder method by default now
- better tests for estimated start and end of exponential
amplification region
* Added rounder function for rounding results of inder
* New data set added
* testxy function added for unformalized testing of x and y values
* Added methods for CPP, inder, bg.max and effcalc
* Added amptest, der and bg classes.
* Assorted improvements to AmpSim
* Added AmpSim.gui
* Many updates and correction to descriptions in manual
* New data sets
Changes from Version 0.0.5 to 0.0.6 [April 24 2014]
* Several bug fixes
* Improved some examples
* Minor code improvements
* New data sets added