1. metagenomeSeq
  2. NEWS
Browse code

Updated NEWS file for version 1.25.xx (2019)

Domenick Braccia authored on 11/07/2019 19:27:48 • hcorrada committed on 11/07/2019 20:25:39
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NEWS
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@@ -2,6 +2,7 @@ version 1.25.xx (2019)
2 2 
 	+ Added 'wrenchNorm' function
3 3 
 	+ Added option to use IHW as p-value adustment method in 'MRcoefs'
4 4 
 	+ Modified 'expSummary' slot in 'MRexperiment' object to be of class 'list' instead of 'environment'
5 
+	+ Added results classes for 'fitZig' and 'fitFeatureModel' results
5 6 
 version 1.21.xx (2018)
6 7 
 	+ Numerous changes. Added greater flexibility to fitFeatureModel
7 8 
 version 1.15.xx (2016)
Browse code

made various changes:

updated: DESCRIPTION, NAMESPACE, NEWS, metagenomeSeq vignette,
cumNorm and wrenchNorm code & man pages, and test-fitZig.R

Domenick Braccia authored on 19/04/2019 23:47:21
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1 
+version 1.25.xx (2019)
2 
+	+ Added 'wrenchNorm' function
3 
+	+ Added option to use IHW as p-value adustment method in 'MRcoefs'
4 
+	+ Modified 'expSummary' slot in 'MRexperiment' object to be of class 'list' instead of 'environment'
1 5 
 version 1.21.xx (2018)
2 6 
 	+ Numerous changes. Added greater flexibility to fitFeatureModel
3 7 
 version 1.15.xx (2016)
Browse code

added flexibility for fitFeatureModel

paulsoj1 authored on 09/04/2018 06:36:33
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1 
+version 1.21.xx (2018)
2 
+	+ Numerous changes. Added greater flexibility to fitFeatureModel
1 3 
 version 1.15.xx (2016)
2 4 
 	+ Added 'mergeMRexperiment' function
3 5 
 	+ Added 'normFactors' and 'libSize' generics
Browse code

Wrapper functions to visualize fitTimeSeries results

* update documents
* adding namespace
* add .git to .Rbuildignore
* version bump

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@122430 bc3139a8-67e5-0310-9ffc-ced21a209358

Hector Corrada Bravo authored on 14/10/2016 13:08:56
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1 1 
 version 1.15.xx (2016)
2 2 
 	+ Added 'mergeMRexperiment' function
3 3 
 	+ Added 'normFactors' and 'libSize' generics
4 
+	+ Added 'fitMultipleTimeSeries' function
4 5 
 	+ Replaced RUnit with testthat library for unit testing
5 6 
 	+ Adding multiple upgrades and changes throughout
6 7 
 	+ Deprecated the load_* functions and created load* function.
Browse code

Merge pull request #44 from HCBravoLab/normFactors

normFactor generics +

From: hcorrada <hcorrada@gmail.com>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@121986 bc3139a8-67e5-0310-9ffc-ced21a209358

Hector Corrada Bravo authored on 06/10/2016 18:53:27
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NEWS
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1 1 
 version 1.15.xx (2016)
2 2 
 	+ Added 'mergeMRexperiment' function
3 
+	+ Added 'normFactors' and 'libSize' generics
3 4 
 	+ Replaced RUnit with testthat library for unit testing
4 5 
 	+ Adding multiple upgrades and changes throughout
5 6 
 	+ Deprecated the load_* functions and created load* function.
Browse code

Merge pull request #40 from HCBravoLab/deprecate

Creating naming schemes consistency and deprecating the load_* functions.

From: Joseph N. Paulson <jpaulson@jimmy.harvard.edu>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@121795 bc3139a8-67e5-0310-9ffc-ced21a209358

Hector Corrada Bravo authored on 05/10/2016 10:10:48
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NEWS
History View file @ 552624f
... ... 
@@ -2,6 +2,7 @@ version 1.15.xx (2016)
2 2 
 	+ Added 'mergeMRexperiment' function
3 3 
 	+ Replaced RUnit with testthat library for unit testing
4 4 
 	+ Adding multiple upgrades and changes throughout
5 
+	+ Deprecated the load_* functions and created load* function.
5 6 
 version 1.13.xx (2015)
6 7 
 	+ Upgrade support for biom-format vs. 2.0
7 8 
 	+ Fixed issue - "MRtable, etc will report NA rows when user requests more features than available"
Browse code

adding mergeMRexperiment functions

From: nosson <jpaulson@umiacs.umd.edu>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@121104 bc3139a8-67e5-0310-9ffc-ced21a209358

Hector Corrada Bravo authored on 19/09/2016 03:09:25
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NEWS
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@@ -1,3 +1,7 @@
1 
+version 1.15.xx (2016)
2 
+	+ Added 'mergeMRexperiment' function
3 
+	+ Replaced RUnit with testthat library for unit testing
4 
+	+ Adding multiple upgrades and changes throughout
1 5 
 version 1.13.xx (2015)
2 6 
 	+ Upgrade support for biom-format vs. 2.0
3 7 
 	+ Fixed issue - "MRtable, etc will report NA rows when user requests more features than available"
Browse code

updated calculation of s2 in calcZeroComponent

From: jnpaulson <nosson@gmail.com>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@116424 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 17/04/2016 20:15:33
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NEWS
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@@ -1,6 +1,7 @@
1 1 
 version 1.13.xx (2015)
2 2 
 	+ Upgrade support for biom-format vs. 2.0
3 3 
 	+ Fixed issue - "MRtable, etc will report NA rows when user requests more features than available"
4 
+	+ Fixed s2 miscalculation in calcZeroComponent
4 5 
 version 1.11.xx (2015)
5 6 
 	+ Adding fitFeatureModel - a feature based zero-inflated log-normal model.
6 7 
 	+ Added MRcoefs,MRtable,MRfulltable support for fitFeatureModel output.
Browse code

closing https://github.com/HCBravoLab/metagenomeSeq/issues/7

From: jnpaulson <nosson@gmail.com>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@111515 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 15/12/2015 19:24:23
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NEWS
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@@ -1,3 +1,6 @@
1 
+version 1.13.xx (2015)
2 
+	+ Upgrade support for biom-format vs. 2.0
3 
+	+ Fixed issue - "MRtable, etc will report NA rows when user requests more features than available"
1 4 
 version 1.11.xx (2015)
2 5 
 	+ Adding fitFeatureModel - a feature based zero-inflated log-normal model.
3 6 
 	+ Added MRcoefs,MRtable,MRfulltable support for fitFeatureModel output.
Browse code

Upgrading w/o git svn bridge

From: jnpaulson <nosson@gmail.com>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@109105 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 02/10/2015 14:15:35
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NEWS
History View file @ 1870098
... ... 
@@ -2,6 +2,8 @@ version 1.11.xx (2015)
2 2 
 	+ Adding fitFeatureModel - a feature based zero-inflated log-normal model.
3 3 
 	+ Added MRcoefs,MRtable,MRfulltable support for fitFeatureModel output.
4 4 
 	+ Added mention in vignette.
5 
+	+ Added support for normalizing matrices instead of just MRexperiment objects.
6 
+	+ Fixed cumNormStat's non-default qFlag option
5 7 
 version 1.9.xx (2015)
6 8 
 	+ Added flexibility in formula choice for fitTimeSeries
7 9 
 	+ Added readability in ssPermAnalysis
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: a1b195cd9621682fb94068feb439e6d32e171b1b

addded mention in vignette



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@103925 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 18/05/2015 15:47:27
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NEWS
History View file @ 88ed5d7
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@@ -1,5 +1,7 @@
1 1 
 version 1.11.xx (2015)
2 2 
 	+ Adding fitFeatureModel - a feature based zero-inflated log-normal model.
3 
+	+ Added MRcoefs,MRtable,MRfulltable support for fitFeatureModel output.
4 
+	+ Added mention in vignette.
3 5 
 version 1.9.xx (2015)
4 6 
 	+ Added flexibility in formula choice for fitTimeSeries
5 7 
 	+ Added readability in ssPermAnalysis
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: c7faf0526a00f718e1fd9285d76f2216852ad115

Merge branch 'wgs'


Commit id: dd46fdfd9565c673f0a5ae2a885bd3050b31586f

adding required namespace, description, etc


Commit id: 3a1d5b7a1d44c18bd9962b223030964927660d8b

Merge branch 'wgs' of https://github.com/nosson/metagenomeSeq into wgs


Commit id: bf5591aaa1af549293fd17a14f31a7602d78585c

Adding fitFeatureModel to wgs branch


Commit id: fb291bfd25b2301ea0be95a2b16d87bed922a21b

adding citation


Commit id: 2575df5ef4e5deaa4b373e222f03be2f6b1da8c7

Updating requirements in DESCRIPTION


Commit id: 9261688c0f34b0ee86ffc4daaccee0feb327bee0

Adding fitFeatureModel to wgs branch


Commit id: efab9f028c91f4ba32b73992160cf6530fa67f02

modify zero M-step


Commit id: 6a38ca85a2e9a1605afc1bf781ab00e35ebdb082

keeping zeroLM



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@103667 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 12/05/2015 00:07:46
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NEWS
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1 
+version 1.11.xx (2015)
2 
+	+ Adding fitFeatureModel - a feature based zero-inflated log-normal model.
1 3 
 version 1.9.xx (2015)
2 4 
 	+ Added flexibility in formula choice for fitTimeSeries
3 5 
 	+ Added readability in ssPermAnalysis
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: ecfca4d5b491c1bec2a57bd81c9ed7ccfe193970

renaming fitMeta -> fitLogNormal (more appropriately named)



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@101722 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 01/04/2015 17:15:11
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NEWS
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@@ -6,6 +6,7 @@ version 1.9.xx (2015)
6 6 
 	+ Removed interactiveDisplay to namespace - moved to suggests
7 7 
 	+ Fixed ordering of MRtable,MRfulltable first four columns
8 8 
 	+ modified df estimated through responsibilities
9 
+	+ renamed fitMeta to fitLogNormal - a more appropriate name
9 10 
 version 1.7.xx (2014-05-07)
10 11 
 	+ Added function plotBubble
11 12 
 	+ Added parallel (multi-core) options to fitPA, fitDO
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: aa5e246702c60b5de8a4b203bb4652d0260371e7

adding fixes due to updates for mouseData taxonomy



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@100580 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 12/03/2015 02:37:31
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NEWS
History View file @ 86e0352
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@@ -5,6 +5,7 @@ version 1.9.xx (2015)
5 5 
 	+ Added fitTimeSeries vignette
6 6 
 	+ Removed interactiveDisplay to namespace - moved to suggests
7 7 
 	+ Fixed ordering of MRtable,MRfulltable first four columns
8 
+	+ modified df estimated through responsibilities
8 9 
 version 1.7.xx (2014-05-07)
9 10 
 	+ Added function plotBubble
10 11 
 	+ Added parallel (multi-core) options to fitPA, fitDO
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 1 commit.

Commit information:

Commit id: bf9545aeaf599afe2c4df8f87b440e72dc2b45f8

uptick

Committed by: nosson
Author Name: nosson
Commit date: 2015-02-07 17:26:11 -0500
Author date: 2015-02-07 17:26:11 -0500


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@99197 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 07/02/2015 22:26:19
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NEWS
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@@ -1,6 +1,7 @@
1 1 
 version 1.9.xx (2015)
2 2 
 	+ Added flexibility in formula choice for fitTimeSeries
3 3 
 	+ Added readability in ssPermAnalysis
4 
+	+ Fixed default in plotClassTimeSeries (include = c("1",...))
4 5 
 	+ Added fitTimeSeries vignette
5 6 
 	+ Removed interactiveDisplay to namespace - moved to suggests
6 7 
 	+ Fixed ordering of MRtable,MRfulltable first four columns
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 1 commit.

Commit information:

Commit id: 91095e5380cc1cc8e62af3850af012809a8c93b3

cleaning up ssPermAnalysis

Committed by: nosson
Author Name: nosson
Commit date: 2015-02-03 16:29:10 -0500
Author date: 2015-02-03 16:29:10 -0500


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@99013 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 03/02/2015 21:29:20
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NEWS
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1 
-version 1.9.xx (2014)
1 
+version 1.9.xx (2015)
2 2 
 	+ Added flexibility in formula choice for fitTimeSeries
3 
+	+ Added readability in ssPermAnalysis
3 4 
 	+ Added fitTimeSeries vignette
4 5 
 	+ Removed interactiveDisplay to namespace - moved to suggests
5 6 
 	+ Fixed ordering of MRtable,MRfulltable first four columns
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 1 commit.

Commit information:

Commit id: 1af619fef6dbf88a8803fab65d4859b52b1d1eb6

upgraded fitTimeSeries to allow for various models

Committed by: nosson
Author Name: nosson
Commit date: 2015-01-31 02:11:27 -0500
Author date: 2015-01-31 02:11:27 -0500


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@98935 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 31/01/2015 07:11:37
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NEWS
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@@ -1,4 +1,5 @@
1 1 
 version 1.9.xx (2014)
2 
+	+ Added flexibility in formula choice for fitTimeSeries
2 3 
 	+ Added fitTimeSeries vignette
3 4 
 	+ Removed interactiveDisplay to namespace - moved to suggests
4 5 
 	+ Fixed ordering of MRtable,MRfulltable first four columns
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 1 commit.

Commit information:

Commit id: 3bf3dbe989866f8e6f1dd332affe99d82fd6ef16

Adding separate fitTimeSeries vignette

Committed by: nosson
Author Name: nosson
Commit date: 2014-11-12 22:56:12 -0500
Author date: 2014-11-12 22:56:12 -0500


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@96710 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 13/11/2014 03:56:27
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NEWS
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@@ -1,4 +1,5 @@
1 1 
 version 1.9.xx (2014)
2 
+	+ Added fitTimeSeries vignette
2 3 
 	+ Removed interactiveDisplay to namespace - moved to suggests
3 4 
 	+ Fixed ordering of MRtable,MRfulltable first four columns
4 5 
 version 1.7.xx (2014-05-07)
Browse code

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Commit information:

Commit id: 4bc5c8251031ecfd6ffdff3177a46dcbedc8c3a2

same time points bug

Committed by: nosson
Author Name: nosson
Commit date: 2014-11-12 22:10:29 -0500
Author date: 2014-11-12 22:10:29 -0500


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@96709 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 13/11/2014 03:10:42
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NEWS
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@@ -1,3 +1,6 @@
1 
+version 1.9.xx (2014)
2 
+	+ Removed interactiveDisplay to namespace - moved to suggests
3 
+	+ Fixed ordering of MRtable,MRfulltable first four columns
1 4 
 version 1.7.xx (2014-05-07)
2 5 
 	+ Added function plotBubble
3 6 
 	+ Added parallel (multi-core) options to fitPA, fitDO
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 1 commit.

Commit information:

Commit id: 950cecd82a11fd4f62b6d1223b0b968933b972d9

Requiring interactiveDisplay

Committed by: nosson
Author Name: nosson
Commit date: 2014-09-10 01:22:14 -0400
Author date: 2014-09-10 01:22:14 -0400


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@93963 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 10/09/2014 05:22:33
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NEWS
History View file @ c8c0ac8
... ... 
@@ -10,6 +10,7 @@ version 1.7.xx (2014-05-07)
10 10 
 	+ (1.7.20) Fixed minor bug for OTU level time series analyses and added plotClassTimeSeries
11 11 
 	+ (1.7.26) Added warning / fix if any samples are empty in cumNormStat
12 12 
 	+ (1.7.27) Added a few unit tests
13 
+	+ (1.7.29) Added interactiveDisplay to namespace (display function allows interactive exploration / plots through browser)
13 14 
 version 1.5.xx (2014-04-17)
14 15 
 	+ Incorporating biom-format support with the biom2MRexperiment, MRexperiment2biom and load_biome function.
15 16 
 	+ Added uniqueFeatures, filterData, aggregateByTaxonomy / aggTax, plotFeature and calculateEffectiveSamples functions.
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Commit information:

Commit id: 7b60c60385d23f54b10aa6546e075de850d7a6f9
Commit message: Adding a few unit tests
Committed by: Umiacs
Author Name: Umiacs
Commit date: 2014-08-13 14:59:55 -0400
Author date: 2014-08-13 14:59:55 -0400



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@93352 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 13/08/2014 19:00:07
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NEWS
History View file @ 58e2f30
... ... 
@@ -9,6 +9,7 @@ version 1.7.xx (2014-05-07)
9 9 
 	+ (1.7.18) fitTimeSeries Including times series method for differentially abundant time intervals
10 10 
 	+ (1.7.20) Fixed minor bug for OTU level time series analyses and added plotClassTimeSeries
11 11 
 	+ (1.7.26) Added warning / fix if any samples are empty in cumNormStat
12 
+	+ (1.7.27) Added a few unit tests
12 13 
 version 1.5.xx (2014-04-17)
13 14 
 	+ Incorporating biom-format support with the biom2MRexperiment, MRexperiment2biom and load_biome function.
14 15 
 	+ Added uniqueFeatures, filterData, aggregateByTaxonomy / aggTax, plotFeature and calculateEffectiveSamples functions.
Browse code

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Commit information:

Commit id: d006758610f926051693590da955624ff3afc5c3
Commit message: Added fix for absent samples in cumnormstat/fast
Committed by: Umiacs
Author Name: Umiacs
Commit date: 2014-08-13 11:03:25 -0400
Author date: 2014-08-13 11:03:25 -0400



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@93343 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 13/08/2014 15:03:36
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NEWS
History View file @ f98b43d
... ... 
@@ -8,6 +8,7 @@ version 1.7.xx (2014-05-07)
8 8 
 	+ (1.7.16) plotMRheatmap allows for sorting by any stat (not just sd)
9 9 
 	+ (1.7.18) fitTimeSeries Including times series method for differentially abundant time intervals
10 10 
 	+ (1.7.20) Fixed minor bug for OTU level time series analyses and added plotClassTimeSeries
11 
+	+ (1.7.26) Added warning / fix if any samples are empty in cumNormStat
11 12 
 version 1.5.xx (2014-04-17)
12 13 
 	+ Incorporating biom-format support with the biom2MRexperiment, MRexperiment2biom and load_biome function.
13 14 
 	+ Added uniqueFeatures, filterData, aggregateByTaxonomy / aggTax, plotFeature and calculateEffectiveSamples functions.
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Commit information:

Commit id: 6a5a4df47720fc57683207310311271b3fbfb560
Commit message: Added plotClassTimeSeries, auto remove 0 features
Committed by: nosson
Author Name: nosson
Commit date: 2014-07-17 15:17:39 -0400
Author date: 2014-07-17 15:17:39 -0400



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@92601 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 17/07/2014 19:17:55
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... ... 
@@ -7,6 +7,7 @@ version 1.7.xx (2014-05-07)
7 7 
 	+ (1.7.15) Output of fitZig (eb) is now a result of limma::eBayes instead of limma::ebayes
8 8 
 	+ (1.7.16) plotMRheatmap allows for sorting by any stat (not just sd)
9 9 
 	+ (1.7.18) fitTimeSeries Including times series method for differentially abundant time intervals
10 
+	+ (1.7.20) Fixed minor bug for OTU level time series analyses and added plotClassTimeSeries
10 11 
 version 1.5.xx (2014-04-17)
11 12 
 	+ Incorporating biom-format support with the biom2MRexperiment, MRexperiment2biom and load_biome function.
12 13 
 	+ Added uniqueFeatures, filterData, aggregateByTaxonomy / aggTax, plotFeature and calculateEffectiveSamples functions.
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 14 commits.

Commit information:

Commit id: bd56b3467846f55b07019b3365efac5dac59123b
Commit message: Merge pull request #11 from nosson/timeseries
Time series method added
Committed by: Joseph N. Paulson
Author Name: Joseph N. Paulson
Commit date: 2014-07-10 16:32:44 -0400
Author date: 2014-07-10 16:32:44 -0400

Commit id: 9ee0799a0e4c8c4d7f8dfadacbfe507495e81301
Commit message: time-series multiple methods
Committed by: Umiacs
Author Name: Umiacs
Commit date: 2014-07-10 16:30:00 -0400
Author date: 2014-07-10 16:30:00 -0400

Commit id: 03f4cc9f4aa9b187e04e154b2bc1fc2c1c138c85
Commit message: Adding plotTimeSeries in vignette
Committed by: Umiacs
Author Name: Umiacs
Commit date: 2014-07-10 13:06:56 -0400
Author date: 2014-07-10 13:06:56 -0400

Commit id: 869b6ab60e92aa21eb4337cc42d490c469b2e155
Commit message: predict on second class + no interval fix
Committed by: Umiacs
Author Name: Umiacs
Commit date: 2014-07-10 12:58:54 -0400
Author date: 2014-07-10 12:58:54 -0400

Commit id: 621f52347cbd252186fcda26783311b3d938ee02
Commit message: Fixed no interval errors
Committed by: Umiacs
Author Name: Umiacs
Commit date: 2014-07-10 12:33:32 -0400
Author date: 2014-07-10 12:33:32 -0400

Commit id: 9822bd6bad1a6492b6fe8e452bd7a42cdb41355c
Commit message: Merge branch 'timeseries' of https://github.com/nosson/metagenomeSeq into timeseries
Committed by: Umiacs
Author Name: Umiacs
Commit date: 2014-07-10 12:21:22 -0400
Author date: 2014-07-10 12:21:22 -0400

Commit id: 8ddc0a0ad6f5b2337446886a4bddfeba392abe38
Commit message: Squashed commit of the following:
commit 4854dd14140e5c4635cefddc9c7afccb1ac1fadf
Author: Umiacs <nosson@gmail.com>
Date: Thu Jul 10 12:18:51 2014 -0400

updating rd, adding plotTimeSeries and fixing fitTimeSeries abs

commit b002aeda586e2ef3dca8abe535edfbc2e0af8da0
Author: unknown <nosson@gmail.com>
Date: Wed Jul 9 10:38:48 2014 -0400

Adding vignette + seealso in

commit 6fc0766ceadc28e43032e8f4a47c08e6b6d66157
Author: nosson <nosson@gmail.com>
Date: Mon Jul 7 16:21:38 2014 -0400

Updating NEWS

commit c7542026ca588b0117effac1a577d7a0d92a29ec
Author: nosson <nosson@gmail.com>
Date: Mon Jul 7 16:19:29 2014 -0400

Updating man pages

commit 92e5e345a2eef4e9d51592c392f3270ea9c5b681
Author: nosson <nosson@gmail.com>
Date: Mon Jul 7 16:04:22 2014 -0400

Fixed build issues due to time series changes

commit 1a1c071a46239a8d7f8d1a468d633b3e4fa91528
Author: nosson <nosson@gmail.com>
Date: Mon Jul 7 15:43:32 2014 -0400

Fixing citation

commit 219a263363260d67bb153a4745d05e4cb5fe378a
Author: nosson <nosson@gmail.com>
Date: Mon Jul 7 15:41:06 2014 -0400

Adding ss-anova functions
Committed by: Umiacs
Author Name: Umiacs
Commit date: 2014-07-10 12:20:57 -0400
Author date: 2014-07-10 12:20:57 -0400

Commit id: 4854dd14140e5c4635cefddc9c7afccb1ac1fadf
Commit message: updating rd, adding plotTimeSeries and fixing fitTimeSeries abs
Committed by: Umiacs
Author Name: Umiacs
Commit date: 2014-07-10 12:18:51 -0400
Author date: 2014-07-10 12:18:51 -0400

Commit id: b002aeda586e2ef3dca8abe535edfbc2e0af8da0
Commit message: Adding vignette + seealso in
Committed by: unknown
Author Name: unknown
Commit date: 2014-07-09 10:38:48 -0400
Author date: 2014-07-09 10:38:48 -0400

Commit id: 6fc0766ceadc28e43032e8f4a47c08e6b6d66157
Commit message: Updating NEWS
Committed by: nosson
Author Name: nosson
Commit date: 2014-07-07 16:21:38 -0400
Author date: 2014-07-07 16:21:38 -0400

Commit id: c7542026ca588b0117effac1a577d7a0d92a29ec
Commit message: Updating man pages
Committed by: nosson
Author Name: nosson
Commit date: 2014-07-07 16:19:29 -0400
Author date: 2014-07-07 16:19:29 -0400

Commit id: 92e5e345a2eef4e9d51592c392f3270ea9c5b681
Commit message: Fixed build issues due to time series changes
Committed by: nosson
Author Name: nosson
Commit date: 2014-07-07 16:04:22 -0400
Author date: 2014-07-07 16:04:22 -0400

Commit id: 1a1c071a46239a8d7f8d1a468d633b3e4fa91528
Commit message: Fixing citation
Committed by: nosson
Author Name: nosson
Commit date: 2014-07-07 15:43:32 -0400
Author date: 2014-07-07 15:43:32 -0400

Commit id: 219a263363260d67bb153a4745d05e4cb5fe378a
Commit message: Adding ss-anova functions
Committed by: nosson
Author Name: nosson
Commit date: 2014-07-07 15:41:06 -0400
Author date: 2014-07-07 15:41:06 -0400



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@92401 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 10/07/2014 20:36:34
Showing 1 changed files
NEWS
History View file @ e093bc6
... ... 
@@ -6,6 +6,7 @@ version 1.7.xx (2014-05-07)
6 6 
 	+ (1.7.10) Added short description on how to do multiple group comparisons
7 7 
 	+ (1.7.15) Output of fitZig (eb) is now a result of limma::eBayes instead of limma::ebayes
8 8 
 	+ (1.7.16) plotMRheatmap allows for sorting by any stat (not just sd)
9 
+	+ (1.7.18) fitTimeSeries Including times series method for differentially abundant time intervals
9 10 
 version 1.5.xx (2014-04-17)
10 11 
 	+ Incorporating biom-format support with the biom2MRexperiment, MRexperiment2biom and load_biome function.
11 12 
 	+ Added uniqueFeatures, filterData, aggregateByTaxonomy / aggTax, plotFeature and calculateEffectiveSamples functions.
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 1 commit.

Commit information:

Commit id: bc502d7aa3919a874f9221631ab95f9e9d4fb7ba
Commit message: update plotMRheatmap
Committed by: nosson
Author Name: nosson
Commit date: 2014-06-23 14:35:40 -0400
Author date: 2014-06-23 14:35:40 -0400



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@91756 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 23/06/2014 18:35:50
Showing 1 changed files
NEWS
History View file @ 2ddba19
... ... 
@@ -4,7 +4,8 @@ version 1.7.xx (2014-05-07)
4 4 
 	+ Fixed bug for fitMeta when useCSSoffset=FALSE and model matrix ncol==2
5 5 
 	+ (1.7.10) Updated default quantile estimate (.5) for low estimates
6 6 
 	+ (1.7.10) Added short description on how to do multiple group comparisons
7 
-	+ (1.7.15) Output of fitZig (eb) is now a result of limma::eBayes instead of limma::ebayes.
7 
+	+ (1.7.15) Output of fitZig (eb) is now a result of limma::eBayes instead of limma::ebayes
8 
+	+ (1.7.16) plotMRheatmap allows for sorting by any stat (not just sd)
8 9 
 version 1.5.xx (2014-04-17)
9 10 
 	+ Incorporating biom-format support with the biom2MRexperiment, MRexperiment2biom and load_biome function.
10 11 
 	+ Added uniqueFeatures, filterData, aggregateByTaxonomy / aggTax, plotFeature and calculateEffectiveSamples functions.
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 1 commit.

Commit information:

Commit id: adce455f6c326b6ef1d6420cf61102597e6e8cb2
Commit message: Output of fitZig (eb) is now a result of limma::eBayes instead of limma::ebayes
Committed by: nosson
Author Name: nosson
Commit date: 2014-06-13 11:35:33 -0400
Author date: 2014-06-13 11:35:33 -0400



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@91372 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 13/06/2014 15:35:42
Showing 1 changed files
NEWS
History View file @ bc4a927
... ... 
@@ -4,6 +4,7 @@ version 1.7.xx (2014-05-07)
4 4 
 	+ Fixed bug for fitMeta when useCSSoffset=FALSE and model matrix ncol==2
5 5 
 	+ (1.7.10) Updated default quantile estimate (.5) for low estimates
6 6 
 	+ (1.7.10) Added short description on how to do multiple group comparisons
7 
+	+ (1.7.15) Output of fitZig (eb) is now a result of limma::eBayes instead of limma::ebayes.
7 8 
 version 1.5.xx (2014-04-17)
8 9 
 	+ Incorporating biom-format support with the biom2MRexperiment, MRexperiment2biom and load_biome function.
9 10 
 	+ Added uniqueFeatures, filterData, aggregateByTaxonomy / aggTax, plotFeature and calculateEffectiveSamples functions.
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 1 commit.

Commit information:

Commit id: 327abd1208eaef0aadfa55bc9130ab829c188902
Commit message: added parallel fitDO, fixed desc of fitPA,DO, fixed plotBubble
Committed by: nosson
Author Name: nosson
Commit date: 2014-05-27 19:24:00 -0400
Author date: 2014-05-27 19:24:00 -0400



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@90755 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 27/05/2014 23:24:27
Showing 1 changed files
NEWS
History View file @ 7ec77ed
... ... 
@@ -1,6 +1,6 @@
1 1 
 version 1.7.xx (2014-05-07)
2 2 
 	+ Added function plotBubble
3 
-	+ Added parallel (multi-core) options to fitPA
3 
+	+ Added parallel (multi-core) options to fitPA, fitDO
4 4 
 	+ Fixed bug for fitMeta when useCSSoffset=FALSE and model matrix ncol==2
5 5 
 	+ (1.7.10) Updated default quantile estimate (.5) for low estimates
6 6 
 	+ (1.7.10) Added short description on how to do multiple group comparisons
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 2 commits.

Commit information:

Commit id: 7e670b70d71ee1885afbc59bede1e2578001e04c
Commit message: minor tweaks
Committed by: nosson
Author Name: nosson
Commit date: 2014-05-14 14:12:52 -0400
Author date: 2014-05-14 14:12:52 -0400

Commit id: 12b2c7015aef06911fae7b2ff37bfacbe1fa7049
Commit message: Updated vignette and default quantile
Committed by: nosson
Author Name: nosson
Commit date: 2014-05-14 14:10:07 -0400
Author date: 2014-05-14 14:10:07 -0400



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@90332 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 14/05/2014 18:13:14
Showing 1 changed files
NEWS
History View file @ e54e12a
... ... 
@@ -1,6 +1,9 @@
1 1 
 version 1.7.xx (2014-05-07)
2 
-	+ Added function plotContingency
3 
-	+ Fixed fitMeta in cases where useCSSoffset=FALSE and the design matrix had only 2 covariates
2 
+	+ Added function plotBubble
3 
+	+ Added parallel (multi-core) options to fitPA
4 
+	+ Fixed bug for fitMeta when useCSSoffset=FALSE and model matrix ncol==2
5 
+	+ (1.7.10) Updated default quantile estimate (.5) for low estimates
6 
+	+ (1.7.10) Added short description on how to do multiple group comparisons
4 7 
 version 1.5.xx (2014-04-17)
5 8 
 	+ Incorporating biom-format support with the biom2MRexperiment, MRexperiment2biom and load_biome function.
6 9 
 	+ Added uniqueFeatures, filterData, aggregateByTaxonomy / aggTax, plotFeature and calculateEffectiveSamples functions.
Browse code

conflicts resolved while setting up Git-SVN bridge

From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@90051 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 07/05/2014 19:29:30
Showing 1 changed files
NEWS
History View file @ 65e0e07
... ... 
@@ -1,3 +1,6 @@
1 
+version 1.7.xx (2014-05-07)
2 
+	+ Added function plotContingency
3 
+	+ Fixed fitMeta in cases where useCSSoffset=FALSE and the design matrix had only 2 covariates
1 4 
 version 1.5.xx (2014-04-17)
2 5 
 	+ Incorporating biom-format support with the biom2MRexperiment, MRexperiment2biom and load_biome function.
3 6 
 	+ Added uniqueFeatures, filterData, aggregateByTaxonomy / aggTax, plotFeature and calculateEffectiveSamples functions.
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 1 commit(s).

Commit information:

Commit id: 8a76fc6a8d9083369a8b8d59c8f354197f13a0af
Commit message:
added uniqueFeatures, plotFeature, updated vignettes
Committed by Joseph N. Paulson <jpaulson at umiacs.umd.edu>
Commit date: 2014-03-17T16:38:06-04:00

From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@87534 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 17/03/2014 20:38:32
Showing 1 changed files
NEWS
History View file @ 240ea47
... ... 
@@ -1,6 +1,6 @@
1 1 
 version 1.5.xx (2014-04-17)
2 2 
 	+ Incorporating biom-format support with the biom2MRexperiment, MRexperiment2biom and load_biome function.
3 
-	+ Added filterData, aggregateByTaxonomy / aggTax and calculateEffectiveSamples functions.
3 
+	+ Added uniqueFeatures, filterData, aggregateByTaxonomy / aggTax, plotFeature and calculateEffectiveSamples functions.
4 4 
 	+ Renamed MRfisher to fitPA (presence-absence fisher test).
5 5 
 	+ Added warnings for normalization
6 6 
 	+ Added fitDO (Discovery odds ratio test) and fitMeta (original metastats).
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 1 commit(s).

Commit information:

Commit id: ba9ee022fd44ab0267ac21eb9015cb16170f66d6
Commit message:
Added warning and override for low norm quantile estimate
Committed by Joseph N. Paulson <jpaulson at umiacs.umd.edu>
Commit date: 2014-03-17T15:27:01-04:00

From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@87528 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 17/03/2014 19:27:18
Showing 1 changed files
NEWS
History View file @ 63ecea0
... ... 
@@ -1,9 +1,11 @@
1 
-version 1.5.xx (2013-11-12)
1 
+version 1.5.xx (2014-04-17)
2 2 
 	+ Incorporating biom-format support with the biom2MRexperiment, MRexperiment2biom and load_biome function.
3 3 
 	+ Added filterData, aggregateByTaxonomy / aggTax and calculateEffectiveSamples functions.
4 4 
 	+ Renamed MRfisher to fitPA (presence-absence fisher test).
5 
+	+ Added warnings for normalization
5 6 
 	+ Added fitDO (Discovery odds ratio test) and fitMeta (original metastats).
6 7 
 	+ Added match.call() info to fitZig output
8 
+	+ Fixed missing E-Step bounds
7 9 
 version 1.2.xx (2013-08-20)
8 10 
 	+ Our paper got accepted and is available!
9 11 
         + Added methods for MRexperiment objects (colSums,colMeans,rowSums,rowMeans, usage is for example colSums(obj) or colSums(obj,norm=TRUE)) (09-25)
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 2 commit(s).

Commit information:

Commit id: 252a7e23fde3c29a0e343308a66a56bdc7054203
Commit message:
Added MRexperiment2biom - now files can be converted/written out to biom format.
Committed by nosson <nosson at gmail.com>
Commit date: 2014-03-03T23:26:05-08:00

Commit id: adead6fb5ea9d4bc1dd235055b92f2e7d82d468b
Commit message:
Merge branch 'master' of https://github.com/nosson/metagenomeSeq
Committed by nosson <nosson at gmail.com>
Commit date: 2014-03-03T23:26:12-08:00

From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@86997 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 04/03/2014 07:26:28
Showing 1 changed files
NEWS
History View file @ 218839b
... ... 
@@ -1,6 +1,6 @@
1 1 
 version 1.5.xx (2013-11-12)
2 
-	+ Incorporating biome format support with the biom2MRexperiment and load_biome function.
3 
-	+ Added filterData, aggregateByTaxonomy(aggTax), calculateEffectiveSamples, functions.
2 
+	+ Incorporating biom-format support with the biom2MRexperiment, MRexperiment2biom and load_biome function.
3 
+	+ Added filterData, aggregateByTaxonomy / aggTax and calculateEffectiveSamples functions.
4 4 
 	+ Renamed MRfisher to fitPA (presence-absence fisher test).
5 5 
 	+ Added fitDO (Discovery odds ratio test) and fitMeta (original metastats).
6 6 
 	+ Added match.call() info to fitZig output
Browse code

Updated fitPA,aggTax and added fitMeta and fitDO

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@85736 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 23/01/2014 04:33:54
Showing 1 changed files
NEWS
History View file @ b327ef5
... ... 
@@ -2,6 +2,7 @@ version 1.5.xx (2013-11-12)
2 2 
 	+ Incorporating biome format support with the biom2MRexperiment and load_biome function.
3 3 
 	+ Added filterData, aggregateByTaxonomy(aggTax), calculateEffectiveSamples, functions.
4 4 
 	+ Renamed MRfisher to fitPA (presence-absence fisher test).
5 
+	+ Added fitDO (Discovery odds ratio test) and fitMeta (original metastats).
5 6 
 	+ Added match.call() info to fitZig output
6 7 
 version 1.2.xx (2013-08-20)
7 8 
 	+ Our paper got accepted and is available!
Browse code

added match.call() to fitZig

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@84983 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 23/12/2013 18:34:11
Showing 1 changed files
NEWS
History View file @ 927898e
... ... 
@@ -2,6 +2,7 @@ version 1.5.xx (2013-11-12)
2 2 
 	+ Incorporating biome format support with the biom2MRexperiment and load_biome function.
3 3 
 	+ Added filterData, aggregateByTaxonomy(aggTax), calculateEffectiveSamples, functions.
4 4 
 	+ Renamed MRfisher to fitPA (presence-absence fisher test).
5 
+	+ Added match.call() info to fitZig output
5 6 
 version 1.2.xx (2013-08-20)
6 7 
 	+ Our paper got accepted and is available!
7 8 
         + Added methods for MRexperiment objects (colSums,colMeans,rowSums,rowMeans, usage is for example colSums(obj) or colSums(obj,norm=TRUE)) (09-25)
Browse code

many minor updates

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@84391 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 12/12/2013 19:16:19
Showing 1 changed files
NEWS
History View file @ 679d906
... ... 
@@ -1,6 +1,7 @@
1 1 
 version 1.5.xx (2013-11-12)
2 2 
 	+ Incorporating biome format support with the biom2MRexperiment and load_biome function.
3 
-	+ Added filterData, aggregateByTaxonomy(aggTax) function.
3 
+	+ Added filterData, aggregateByTaxonomy(aggTax), calculateEffectiveSamples, functions.
4 
+	+ Renamed MRfisher to fitPA (presence-absence fisher test).
4 5 
 version 1.2.xx (2013-08-20)
5 6 
 	+ Our paper got accepted and is available!
6 7 
         + Added methods for MRexperiment objects (colSums,colMeans,rowSums,rowMeans, usage is for example colSums(obj) or colSums(obj,norm=TRUE)) (09-25)
Browse code

updated news

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@84096 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 09/12/2013 23:52:07
Showing 1 changed files
NEWS
History View file @ c1b24a3
... ... 
@@ -1,6 +1,6 @@
1 1 
 version 1.5.xx (2013-11-12)
2 2 
 	+ Incorporating biome format support with the biom2MRexperiment and load_biome function.
3 
-	+ Added filterData function.
3 
+	+ Added filterData, aggregateByTaxonomy(aggTax) function.
4 4 
 version 1.2.xx (2013-08-20)
5 5 
 	+ Our paper got accepted and is available!
6 6 
         + Added methods for MRexperiment objects (colSums,colMeans,rowSums,rowMeans, usage is for example colSums(obj) or colSums(obj,norm=TRUE)) (09-25)
Browse code

added filterData

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@84025 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 07/12/2013 21:15:22
Showing 1 changed files
NEWS
History View file @ c33e874
... ... 
@@ -1,5 +1,6 @@
1 1 
 version 1.5.xx (2013-11-12)
2 2 
 	+ Incorporating biome format support with the biom2MRexperiment and load_biome function.
3 
+	+ Added filterData function.
3 4 
 version 1.2.xx (2013-08-20)
4 5 
 	+ Our paper got accepted and is available!
5 6 
         + Added methods for MRexperiment objects (colSums,colMeans,rowSums,rowMeans, usage is for example colSums(obj) or colSums(obj,norm=TRUE)) (09-25)
Browse code

load_biom/biom2MRexperiment

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@83242 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 13/11/2013 03:11:38
Showing 1 changed files
NEWS
History View file @ b521381
... ... 
@@ -1,5 +1,5 @@
1 1 
 version 1.5.xx (2013-11-12)
2 
-	+ Incorporating biome format support with biom2MRexperiment function.
2 
+	+ Incorporating biome format support with the biom2MRexperiment and load_biome function.
3 3 
 version 1.2.xx (2013-08-20)
4 4 
 	+ Our paper got accepted and is available!
5 5 
         + Added methods for MRexperiment objects (colSums,colMeans,rowSums,rowMeans, usage is for example colSums(obj) or colSums(obj,norm=TRUE)) (09-25)
Browse code

included biom2MRexperiment format function

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@83212 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 12/11/2013 17:38:00
Showing 1 changed files
NEWS
History View file @ 194e546
... ... 
@@ -1,3 +1,5 @@
1 
+version 1.5.xx (2013-11-12)
2 
+	+ Incorporating biome format support with biom2MRexperiment function.
1 3 
 version 1.2.xx (2013-08-20)
2 4 
 	+ Our paper got accepted and is available!
3 5 
         + Added methods for MRexperiment objects (colSums,colMeans,rowSums,rowMeans, usage is for example colSums(obj) or colSums(obj,norm=TRUE)) (09-25)
Browse code

reformatted news, added Rd for package

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@81367 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 09/10/2013 14:50:59
Showing 1 changed files
NEWS
History View file @ 57a36c3
... ... 
@@ -1,23 +1,24 @@
1 1 
 version 1.2.xx (2013-08-20)
2 
-        Added methods for MRexperiment objects (colSums,colMeans,rowSums,rowMeans, usage is for example colSums(obj) or colSums(obj,norm=TRUE)) (09-25)
3 
-        Added two new functions, plotOrd and plotRare - a function to plot PCA/MDS coordinates and rarefaction effect (09-04,09-18)
4 
-        Updated MRfisher to include thresholding for presence-absence testing (08-19)
5 
-	Updated comments (roxygen2) style for all the functions using the Rd2roxygen package (07-13)
6 
-	Updated plotCorr and plotMRheatmap to allow various colors/not require trials(07-13)
7 
-	Rewrote vignette (and switched to knitr)
2 
+	+ Our paper got accepted and is available!
3 
+        + Added methods for MRexperiment objects (colSums,colMeans,rowSums,rowMeans, usage is for example colSums(obj) or colSums(obj,norm=TRUE)) (09-25)
4 
+        + Added two new functions, plotOrd and plotRare - a function to plot PCA/MDS coordinates and rarefaction effect (09-04,09-18)
5 
+        + Updated MRfisher to include thresholding for presence-absence testing (08-19)
6 
+	+ Updated comments (roxygen2) style for all the functions using the Rd2roxygen package (07-13)
7 
+	+ Updated plotCorr and plotMRheatmap to allow various colors/not require trials(07-13)
8 
+	+ Rewrote vignette (and switched to knitr)
8 9
9 10 
 version 1.1.xx (last update 2013-06-25)
10 
-	Rewrote load_meta and load_metaQ to be faster/use less memory
11 
-	Modified cumNormStat to remove NA samples from calculations (example would be samples without any counts)
12 
-	Re-added plotGenus' jitter
13 
-	Fixed uniqueNames call in the MR tables
11 
+	+ Rewrote load_meta and load_metaQ to be faster/use less memory
12 
+	+ Modified cumNormStat to remove NA samples from calculations (example would be samples without any counts)
13 
+	+ Re-added plotGenus' jitter
14 
+	+ Fixed uniqueNames call in the MR tables
14 15
15 
-	Changed thanks to Kasper Daniel Hansen's suggestions the following:
16 
+	+ Changed thanks to Kasper Daniel Hansen's suggestions the following:
16 17 
 		plotOTU and plotGenus both have much better auto-generated axis
17 18 
 		MRtable, MRfulltable, MRcoefs have a sort by p-value option now
18 19 
 		MRtable, MRfulltable, MRcoefs now have an extra option to include unique numbers for OTU features (default would automatically add them previously)
19 20 
 		cumNorm.R - now returns the object as well - not just replacing the environment
20 
-	Still need to turn the fitZig output to S3, consider subsetting function address low p-values
21 
+	0 Still need to turn the fitZig output to S3, consider subsetting function address low p-values
21 22
22 23 
 version 1.0.0: (2013-03-29)
23 
-	-- release!
24 
+	+ Release!
Browse code

Added four methods for MRexperiment object

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@80740 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 25/09/2013 04:45:29
Showing 1 changed files
NEWS
History View file @ 7654e34
... ... 
@@ -1,41 +1,23 @@
1 1 
 version 1.2.xx (2013-08-20)
2 
+        Added methods for MRexperiment objects (colSums,colMeans,rowSums,rowMeans, usage is for example colSums(obj) or colSums(obj,norm=TRUE)) (09-25)
3 
+        Added two new functions, plotOrd and plotRare - a function to plot PCA/MDS coordinates and rarefaction effect (09-04,09-18)
4 
+        Updated MRfisher to include thresholding for presence-absence testing (08-19)
2 5 
 	Updated comments (roxygen2) style for all the functions using the Rd2roxygen package (07-13)
3 6 
 	Updated plotCorr and plotMRheatmap to allow various colors/not require trials(07-13)
4 
-	Updated MRfisher to include thresholding for presence-absence testing (08-19)
5 
-	Included Presence-Absence in vignette
6 
-	Added two new functions, plotOrd and plotRare - a function to plot PCA/MDS coordinates and rarefaction effect (09-04,09-18)
7 
+	Rewrote vignette (and switched to knitr)
7 8
8 
-version 1.1.9 (2013-06-25)
9 
-
10 
-	Modified load_meta and load_metaQ to be faster/use less memory
9 
+version 1.1.xx (last update 2013-06-25)
10 
+	Rewrote load_meta and load_metaQ to be faster/use less memory
11 11 
 	Modified cumNormStat to remove NA samples from calculations (example would be samples without any counts)
12 
-
13 
-version 1.1.7 (2013-06-11)
14 
-
15 
-	Changed modified date on vignette
16 
-
17 
-version 1.1.6 (2013-06-11)
18 
-
19 12 
 	Re-added plotGenus' jitter
20 
-	Fixed vignette with the new plotOTU and plotGenus call
21 13 
 	Fixed uniqueNames call in the MR tables
22 14
23 
-version 1.1.5 (2013-06-11)
24 
-
25 
-Changed thanks to Kasper Daniel Hansen's suggestions the following:
26 
-
27 
-	plotOTU and plotGenus both have much better auto-generated axis
28 
-	MRtable, MRfulltable, MRcoefs have a sort by p-value option now
29 
-	MRtable, MRfulltable, MRcoefs now have an extra option to include unique numbers for OTU features (default would automatically add them previously)
30 
-
31 
-Still need to turn the fitZig output to S3, consider subsetting function address low p-values
32 
-
33 
-version 1.1.3 (2013-06-01)
34 
-
35 
-Changed thanks to Kasper Daniel Hansen's suggestions the following:
36 
-
37 
-	cumNorm.R - now returns the object as well - not just replacing the environment
15 
+	Changed thanks to Kasper Daniel Hansen's suggestions the following:
16 
+		plotOTU and plotGenus both have much better auto-generated axis
17 
+		MRtable, MRfulltable, MRcoefs have a sort by p-value option now
18 
+		MRtable, MRfulltable, MRcoefs now have an extra option to include unique numbers for OTU features (default would automatically add them previously)
19 
+		cumNorm.R - now returns the object as well - not just replacing the environment
20 
+	Still need to turn the fitZig output to S3, consider subsetting function address low p-values
38 21
39 22 
 version 1.0.0: (2013-03-29)
40 
-
41 23 
 	-- release!
Browse code

Added new function - plotRare

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@80564 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 18/09/2013 23:13:11
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NEWS
History View file @ d0c17b8
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@@ -1,9 +1,9 @@
1 
-version 1.2.2x (2013-08-20)
1 
+version 1.2.xx (2013-08-20)
2 2 
 	Updated comments (roxygen2) style for all the functions using the Rd2roxygen package (07-13)
3 3 
 	Updated plotCorr and plotMRheatmap to allow various colors/not require trials(07-13)
4 4 
 	Updated MRfisher to include thresholding for presence-absence testing (08-19)
5 5 
 	Included Presence-Absence in vignette
6 
-	Added a new function plotOrd - a function to plot PCA/MDS coordinates (09-04)
6 
+	Added two new functions, plotOrd and plotRare - a function to plot PCA/MDS coordinates and rarefaction effect (09-04,09-18)
7 7
8 8 
 version 1.1.9 (2013-06-25)
9 9
Browse code

updated all of the plotting functions and included a new plot function, plotOrd

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@80039 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 04/09/2013 20:26:47
Showing 1 changed files
NEWS
History View file @ 127827e
... ... 
@@ -3,6 +3,7 @@ version 1.2.2x (2013-08-20)
3 3 
 	Updated plotCorr and plotMRheatmap to allow various colors/not require trials(07-13)
4 4 
 	Updated MRfisher to include thresholding for presence-absence testing (08-19)
5 5 
 	Included Presence-Absence in vignette
6 
+	Added a new function plotOrd - a function to plot PCA/MDS coordinates (09-04)
6 7
7 8 
 version 1.1.9 (2013-06-25)
8 9
Browse code

updated plotMRheatmap

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@79600 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 20/08/2013 16:10:00
Showing 1 changed files
NEWS
History View file @ 72d9022
... ... 
@@ -1,6 +1,6 @@
1 
-version 1.2.2x (2013-08-19)
1 
+version 1.2.2x (2013-08-20)
2 2 
 	Updated comments (roxygen2) style for all the functions using the Rd2roxygen package (07-13)
3 
-	Updated plotCorr and plotMRheatmap to allow various colors (07-13)
3 
+	Updated plotCorr and plotMRheatmap to allow various colors/not require trials(07-13)
4 4 
 	Updated MRfisher to include thresholding for presence-absence testing (08-19)
5 5 
 	Included Presence-Absence in vignette
6 6
Browse code

adjusted vignette 2

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@79573 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 19/08/2013 20:08:40
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NEWS
History View file @ 97bacfd
... ... 
@@ -1,7 +1,7 @@
1 
-version 1.2.2x (2013-08-16)
1 
+version 1.2.2x (2013-08-19)
2 2 
 	Updated comments (roxygen2) style for all the functions using the Rd2roxygen package (07-13)
3 3 
 	Updated plotCorr and plotMRheatmap to allow various colors (07-13)
4 
-	Updated MRfisher to include thresholding for presence-absence testing (08-16)
4 
+	Updated MRfisher to include thresholding for presence-absence testing (08-19)
5 5 
 	Included Presence-Absence in vignette
6 6
7 7 
 version 1.1.9 (2013-06-25)
Browse code

adjusted vignette

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@79572 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 19/08/2013 20:06:00
Showing 1 changed files
NEWS
History View file @ 1bb6910
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@@ -1,6 +1,8 @@
1 
-version 1.2.2 (2013-07-13)
2 
-	Updated comments (roxygen2) style for all the functions using the Rd2roxygen package
3 
-	Updated plotCorr and plotMRheatmap to allow various colors
1 
+version 1.2.2x (2013-08-16)
2 
+	Updated comments (roxygen2) style for all the functions using the Rd2roxygen package (07-13)
3 
+	Updated plotCorr and plotMRheatmap to allow various colors (07-13)
4 
+	Updated MRfisher to include thresholding for presence-absence testing (08-16)
5 
+	Included Presence-Absence in vignette
4 6
5 7 
 version 1.1.9 (2013-06-25)
6 8
Browse code

updated plotting functions

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@79410 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 13/08/2013 19:37:58
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@@ -1,4 +1,8 @@
1 
-version 1.1.9 (2103-06-25)
1 
+version 1.2.2 (2013-07-13)
2 
+	Updated comments (roxygen2) style for all the functions using the Rd2roxygen package
3 
+	Updated plotCorr and plotMRheatmap to allow various colors
4 
+
5 
+version 1.1.9 (2013-06-25)
2 6
3 7 
 	Modified load_meta and load_metaQ to be faster/use less memory
4 8 
 	Modified cumNormStat to remove NA samples from calculations (example would be samples without any counts)
Browse code

Updated news/load/cumnormstat

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@77912 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 25/06/2013 18:52:00
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NEWS
History View file @ 205ba79
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@@ -1,6 +1,7 @@
1 
-version 1.1.8 (2103-06-25)
1 
+version 1.1.9 (2103-06-25)
2 2
3 
-	Modified load_meta and load_metaQ to be faster/use less memory.
3 
+	Modified load_meta and load_metaQ to be faster/use less memory
4 
+	Modified cumNormStat to remove NA samples from calculations (example would be samples without any counts)
4 5
5 6 
 version 1.1.7 (2013-06-11)
6 7
Browse code

changed load matrix files

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@77911 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 25/06/2013 18:40:43
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NEWS
History View file @ 2ad5c18
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@@ -1,14 +1,18 @@
1 
-versions 1.1.7 (2013-06-11)
1 
+version 1.1.8 (2103-06-25)
2 
+
3 
+	Modified load_meta and load_metaQ to be faster/use less memory.
4 
+
5 
+version 1.1.7 (2013-06-11)
2 6
3 7 
 	Changed modified date on vignette
4 8
5 
-versions 1.1.6 (2013-06-11)
9 
+version 1.1.6 (2013-06-11)
6 10
7 11 
 	Re-added plotGenus' jitter
8 12 
 	Fixed vignette with the new plotOTU and plotGenus call
9 13 
 	Fixed uniqueNames call in the MR tables
10 14
11 
-versions 1.1.5 (2013-06-11)
15 
+version 1.1.5 (2013-06-11)
12 16
13 17 
 Changed thanks to Kasper Daniel Hansen's suggestions the following:
14 18
... ... 
@@ -18,7 +22,7 @@ Changed thanks to Kasper Daniel Hansen's suggestions the following:
18 22
19 23 
 Still need to turn the fitZig output to S3, consider subsetting function address low p-values
20 24
21 
-versions 1.1.3 (2013-06-01)
25 
+version 1.1.3 (2013-06-01)
22 26
23 27 
 Changed thanks to Kasper Daniel Hansen's suggestions the following:
24 28
Browse code

updating to 1.1.7, changes in NEWS

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@77422 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 12/06/2013 00:52:35
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NEWS
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@@ -1,6 +1,12 @@
1 
+versions 1.1.7 (2013-06-11)
2 
+
3 
+	Changed modified date on vignette
4 
+
1 5 
 versions 1.1.6 (2013-06-11)
2 6
3 
-	Re-added plotGenus' jitter, fixed vignette with the new plotOTU and plotGenus calls
7 
+	Re-added plotGenus' jitter
8 
+	Fixed vignette with the new plotOTU and plotGenus call
9 
+	Fixed uniqueNames call in the MR tables
4 10
5 11 
 versions 1.1.5 (2013-06-11)
6 12
Browse code

updating to 1.1.6, changes in NEWS

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@77421 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 12/06/2013 00:49:55
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NEWS
History View file @ 03d3c28
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@@ -1,4 +1,8 @@
1 
-versions 1.1.5 (2013-06-11)
1 
+versions 1.1.6 (2013-06-11)
2 
+
3 
+	Re-added plotGenus' jitter, fixed vignette with the new plotOTU and plotGenus calls
4 
+
5 
+versions 1.1.5 (2013-06-11)
2 6
3 7 
 Changed thanks to Kasper Daniel Hansen's suggestions the following:
4 8
Browse code

updating to 1.1.5, changes in NEWS

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@77398 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 11/06/2013 15:30:22
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NEWS
History View file @ 82c621a
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@@ -1,7 +1,19 @@
1 
+versions 1.1.5 (2013-06-11)
2 
+
3 
+Changed thanks to Kasper Daniel Hansen's suggestions the following:
4 
+
5 
+	plotOTU and plotGenus both have much better auto-generated axis
6 
+	MRtable, MRfulltable, MRcoefs have a sort by p-value option now
7 
+	MRtable, MRfulltable, MRcoefs now have an extra option to include unique numbers for OTU features (default would automatically add them previously)
8 
+
9 
+Still need to turn the fitZig output to S3, consider subsetting function address low p-values
10 
+
1 11 
 versions 1.1.3 (2013-06-01)
2 12
3 
-cumNorm.R - now returns the object as well - not just replacing the environment
13 
+Changed thanks to Kasper Daniel Hansen's suggestions the following:
14 
+
15 
+	cumNorm.R - now returns the object as well - not just replacing the environment
4 16
5 17 
 version 1.0.0: (2013-03-29)
6 18
19 
+	-- release!
Browse code

cumnorm now returns the object, updated vignette too

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@77138 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 03/06/2013 20:00:43
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NEWS
History View file @ 598bec8
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@@ -1,6 +1,6 @@
1 1 
 versions 1.1.3 (2013-06-01)
2 2
3 
-cumNorm.R - now returns a vector of the normalization factors as well
3 
+cumNorm.R - now returns the object as well - not just replacing the environment
4 4
5 5 
 version 1.0.0: (2013-03-29)
6 6
Browse code

cumnorm now stores norm factors and returns them as an object

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@77132 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 03/06/2013 19:43:57
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History View file @ bed02ed
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@@ -1,3 +1,7 @@
1 
+versions 1.1.3 (2013-06-01)
2 
+
3 
+cumNorm.R - now returns a vector of the normalization factors as well
4 
+
1 5 
 version 1.0.0: (2013-03-29)
2 6
3 7 
 -- release!
Browse code

firstcommit

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@75067 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 30/03/2013 01:32:54
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1 
-version 1.0.0: (2013-00-00)
1 
+version 1.0.0: (2013-03-29)
2 2
3 3 
\ No newline at end of file
4 
+-- release!
Browse code

Adds DASiR, metagenomeSeq to the repos and manifest.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@74804 bc3139a8-67e5-0310-9ffc-ced21a209358

Marc Carlson authored on 25/03/2013 18:40:33
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new file mode 100644
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+version 1.0.0: (2013-00-00)
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+
3 
+-- release!
0 4 
\ No newline at end of file