Title: Microsoft Word, Microsoft Powerpoint and HTML Documents
Generation
Diff between ReporteRs versions 0.7.2 dated 2014-12-09 and 0.7.7 dated 2015-03-05
Description: Create Microsoft Word document (>=2007),
Microsoft Powerpoint document (>=2007) and HTML documents from R. There are
several features to let you format and present R outputs ; e.g. Editable
Vector Graphics, functions for complex tables reporting, reuse of corporate
template document (*.docx and *.pptx). You can use the package as a tool
for fast reporting and as a tool for reporting automation. The package does
not require any installation of Microsoft product to be able to write
Microsoft files (docx and pptx).
Author: David Gohel [aut, cre],
Bootstrap [ctb, cph] (Bootstrap development team),
jQuery [ctb, cph] (The jQuery Foundation),
Dmitry Baranovskiy [ctb, cph] (raphael javascript
libraries)
Maintainer: David Gohel
ReporteRs-0.7.2/ReporteRs/man/pot-add.Rd |only
ReporteRs-0.7.7/ReporteRs/DESCRIPTION | 8
ReporteRs-0.7.7/ReporteRs/MD5 | 489 +--
ReporteRs-0.7.7/ReporteRs/NAMESPACE | 317 +-
ReporteRs-0.7.7/ReporteRs/NEWS | 792 ++---
ReporteRs-0.7.7/ReporteRs/R/00_AllGeneric.R | 1097 +++---
ReporteRs-0.7.7/ReporteRs/R/01_tools.R | 496 +--
ReporteRs-0.7.7/ReporteRs/R/BootstrapMenu.R | 105
ReporteRs-0.7.7/ReporteRs/R/DropDownMenu.R | 44
ReporteRs-0.7.7/ReporteRs/R/FlexCell.R | 128
ReporteRs-0.7.7/ReporteRs/R/FlexRow.R | 185 -
ReporteRs-0.7.7/ReporteRs/R/FlexTable.R | 542 +--
ReporteRs-0.7.7/ReporteRs/R/FlexTableContentTools.R | 133
ReporteRs-0.7.7/ReporteRs/R/FlexTableFormatTools.R | 432 +-
ReporteRs-0.7.7/ReporteRs/R/FlexTablePublicAPI.R | 1573 ++++------
ReporteRs-0.7.7/ReporteRs/R/FlexTableUpdateTools.R | 156
ReporteRs-0.7.7/ReporteRs/R/FlexTable_theme.R | 139
ReporteRs-0.7.7/ReporteRs/R/FontMetric.R | 48
ReporteRs-0.7.7/ReporteRs/R/Footnote.R | 221 -
ReporteRs-0.7.7/ReporteRs/R/Lists.R | 209 -
ReporteRs-0.7.7/ReporteRs/R/RScript.R | 390 +-
ReporteRs-0.7.7/ReporteRs/R/ReporteRs.R | 233 -
ReporteRs-0.7.7/ReporteRs/R/Section.R | 110
ReporteRs-0.7.7/ReporteRs/R/add.plot.interactivity.R | 208 -
ReporteRs-0.7.7/ReporteRs/R/addBootstrapMenu.R | 56
ReporteRs-0.7.7/ReporteRs/R/addDate.pptx.R | 104
ReporteRs-0.7.7/ReporteRs/R/addDocument.docx.R | 73
ReporteRs-0.7.7/ReporteRs/R/addFlexTable.bsdoc.R | 83
ReporteRs-0.7.7/ReporteRs/R/addFlexTable.docx.R | 83
ReporteRs-0.7.7/ReporteRs/R/addFlexTable.pptx.R | 153
ReporteRs-0.7.7/ReporteRs/R/addFooter.bsdoc.R | 115
ReporteRs-0.7.7/ReporteRs/R/addFooter.pptx.R | 83
ReporteRs-0.7.7/ReporteRs/R/addIframe.bsdoc.R | 63
ReporteRs-0.7.7/ReporteRs/R/addImage.bsdoc.R | 88
ReporteRs-0.7.7/ReporteRs/R/addImage.docx.R | 96
ReporteRs-0.7.7/ReporteRs/R/addImage.pptx.R | 141
ReporteRs-0.7.7/ReporteRs/R/addLinkItem.R | 117
ReporteRs-0.7.7/ReporteRs/R/addMarkdown.bsdoc.R | 209 -
ReporteRs-0.7.7/ReporteRs/R/addMarkdown.docx.R | 201 -
ReporteRs-0.7.7/ReporteRs/R/addMarkdown.pptx.R | 207 -
ReporteRs-0.7.7/ReporteRs/R/addPageBreak.docx.R | 39
ReporteRs-0.7.7/ReporteRs/R/addPageNumber.pptx.R | 103
ReporteRs-0.7.7/ReporteRs/R/addParagraph.bsdoc.R | 134
ReporteRs-0.7.7/ReporteRs/R/addParagraph.docx.R | 179 -
ReporteRs-0.7.7/ReporteRs/R/addParagraph.pptx.R | 259 -
ReporteRs-0.7.7/ReporteRs/R/addPlot.bsdoc.R | 187 -
ReporteRs-0.7.7/ReporteRs/R/addPlot.docx.R | 249 -
ReporteRs-0.7.7/ReporteRs/R/addPlot.pptx.R | 437 +-
ReporteRs-0.7.7/ReporteRs/R/addRScript.bsdoc.R | 79
ReporteRs-0.7.7/ReporteRs/R/addRScript.docx.R | 106
ReporteRs-0.7.7/ReporteRs/R/addRScript.pptx.R | 94
ReporteRs-0.7.7/ReporteRs/R/addSlide.pptx.R | 227 -
ReporteRs-0.7.7/ReporteRs/R/addSubtitle.pptx.R | 71
ReporteRs-0.7.7/ReporteRs/R/addTOC.bsdoc.R | 66
ReporteRs-0.7.7/ReporteRs/R/addTOC.docx.R | 129
ReporteRs-0.7.7/ReporteRs/R/addTitle.bsdoc.R | 105
ReporteRs-0.7.7/ReporteRs/R/addTitle.docx.R | 112
ReporteRs-0.7.7/ReporteRs/R/addTitle.pptx.R | 67
ReporteRs-0.7.7/ReporteRs/R/as.FlexTable.sessionInfo.R |only
ReporteRs-0.7.7/ReporteRs/R/as.html.FlexTable.R | 40
ReporteRs-0.7.7/ReporteRs/R/bootstrap.copy.R | 44
ReporteRs-0.7.7/ReporteRs/R/borderProperties.R | 243 -
ReporteRs-0.7.7/ReporteRs/R/bsdoc.R | 237 -
ReporteRs-0.7.7/ReporteRs/R/cellProperties.R | 1064 +++---
ReporteRs-0.7.7/ReporteRs/R/deleteBookmark.R | 106
ReporteRs-0.7.7/ReporteRs/R/dim.docx.R | 41
ReporteRs-0.7.7/ReporteRs/R/dim.pptx.R | 53
ReporteRs-0.7.7/ReporteRs/R/docx.R | 160 -
ReporteRs-0.7.7/ReporteRs/R/drawingML.R | 198 -
ReporteRs-0.7.7/ReporteRs/R/format.properties.R | 532 +--
ReporteRs-0.7.7/ReporteRs/R/is.color.R | 38
ReporteRs-0.7.7/ReporteRs/R/java_description.R | 90
ReporteRs-0.7.7/ReporteRs/R/markdown.api.R | 1394 ++++----
ReporteRs-0.7.7/ReporteRs/R/parProperties.R | 700 ++--
ReporteRs-0.7.7/ReporteRs/R/pot.R | 330 +-
ReporteRs-0.7.7/ReporteRs/R/pptx.R | 192 -
ReporteRs-0.7.7/ReporteRs/R/print.docx.R | 60
ReporteRs-0.7.7/ReporteRs/R/print.pptx.R | 66
ReporteRs-0.7.7/ReporteRs/R/raphael.html.R | 122
ReporteRs-0.7.7/ReporteRs/R/setHeaderStyle.docx.R | 77
ReporteRs-0.7.7/ReporteRs/R/set_of_pot.R | 149
ReporteRs-0.7.7/ReporteRs/R/slide.layouts.pptx.R | 87
ReporteRs-0.7.7/ReporteRs/R/styles.docx.R | 58
ReporteRs-0.7.7/ReporteRs/R/textProperties.R | 509 +--
ReporteRs-0.7.7/ReporteRs/R/text_extract.R |only
ReporteRs-0.7.7/ReporteRs/R/toc.options.R | 65
ReporteRs-0.7.7/ReporteRs/R/writeDoc.bsdoc.R | 95
ReporteRs-0.7.7/ReporteRs/R/writeDoc.docx.R | 82
ReporteRs-0.7.7/ReporteRs/R/writeDoc.pptx.R | 91
ReporteRs-0.7.7/ReporteRs/inst/COPYRIGHTS | 178 -
ReporteRs-0.7.7/ReporteRs/inst/Rmd/example.Rmd | 180 -
ReporteRs-0.7.7/ReporteRs/inst/bootstrap/css/bootstrap.min.css | 10
ReporteRs-0.7.7/ReporteRs/inst/bootstrap/css/docs.min.css | 444 +-
ReporteRs-0.7.7/ReporteRs/inst/bootstrap/fonts/glyphicons-halflings-regular.svg | 456 +-
ReporteRs-0.7.7/ReporteRs/inst/bootstrap/js/bootstrap.min.js | 10
ReporteRs-0.7.7/ReporteRs/inst/bootstrap/js/docs.min.js | 46
ReporteRs-0.7.7/ReporteRs/inst/bootstrap/js/html5shiv.min.js | 6
ReporteRs-0.7.7/ReporteRs/inst/bootstrap/js/ie-emulation-modes-warning.js | 102
ReporteRs-0.7.7/ReporteRs/inst/bootstrap/js/ie10-viewport-bug-workaround.js | 44
ReporteRs-0.7.7/ReporteRs/inst/bootstrap/js/ie8-responsive-file-warning.js | 26
ReporteRs-0.7.7/ReporteRs/inst/bootstrap/js/jquery.min.js | 6
ReporteRs-0.7.7/ReporteRs/inst/bootstrap/js/raphael-min.js | 20
ReporteRs-0.7.7/ReporteRs/inst/bootstrap/js/respond.min.js | 8
ReporteRs-0.7.7/ReporteRs/inst/java/ReporteRs-0.7.jar |binary
ReporteRs-0.7.7/ReporteRs/java/ReporteRs-0.7-src.jar |binary
ReporteRs-0.7.7/ReporteRs/man/BootstrapMenu.Rd | 107
ReporteRs-0.7.7/ReporteRs/man/DropDownMenu.Rd | 61
ReporteRs-0.7.7/ReporteRs/man/FlexCell.Rd | 93
ReporteRs-0.7.7/ReporteRs/man/FlexRow-alter.Rd | 66
ReporteRs-0.7.7/ReporteRs/man/FlexRow.Rd | 88
ReporteRs-0.7.7/ReporteRs/man/FlexTable-alter.Rd | 261 -
ReporteRs-0.7.7/ReporteRs/man/FlexTable.Rd | 600 +--
ReporteRs-0.7.7/ReporteRs/man/FontMetric.Rd | 32
ReporteRs-0.7.7/ReporteRs/man/Footnote.Rd | 238 -
ReporteRs-0.7.7/ReporteRs/man/RScript.Rd | 149
ReporteRs-0.7.7/ReporteRs/man/ReporteRs-package.Rd | 206 -
ReporteRs-0.7.7/ReporteRs/man/add.plot.interactivity.Rd | 202 -
ReporteRs-0.7.7/ReporteRs/man/add.pot.Rd | 55
ReporteRs-0.7.7/ReporteRs/man/addBootstrapMenu.Rd | 84
ReporteRs-0.7.7/ReporteRs/man/addColumnBreak.Rd | 54
ReporteRs-0.7.7/ReporteRs/man/addColumnBreak.docx.Rd | 72
ReporteRs-0.7.7/ReporteRs/man/addDate.Rd | 55
ReporteRs-0.7.7/ReporteRs/man/addDate.pptx.Rd | 109
ReporteRs-0.7.7/ReporteRs/man/addDocument.Rd | 50
ReporteRs-0.7.7/ReporteRs/man/addDocument.docx.Rd | 106
ReporteRs-0.7.7/ReporteRs/man/addFlexTable.Rd | 67
ReporteRs-0.7.7/ReporteRs/man/addFlexTable.bsdoc.Rd | 367 +-
ReporteRs-0.7.7/ReporteRs/man/addFlexTable.docx.Rd | 377 +-
ReporteRs-0.7.7/ReporteRs/man/addFlexTable.pptx.Rd | 421 +-
ReporteRs-0.7.7/ReporteRs/man/addFooter.Rd | 52
ReporteRs-0.7.7/ReporteRs/man/addFooter.bsdoc.Rd | 109
ReporteRs-0.7.7/ReporteRs/man/addFooter.pptx.Rd | 91
ReporteRs-0.7.7/ReporteRs/man/addFooterRow.Rd | 132
ReporteRs-0.7.7/ReporteRs/man/addHeaderRow.Rd | 164 -
ReporteRs-0.7.7/ReporteRs/man/addIframe.Rd | 44
ReporteRs-0.7.7/ReporteRs/man/addIframe.bsdoc.Rd | 65
ReporteRs-0.7.7/ReporteRs/man/addImage.Rd | 63
ReporteRs-0.7.7/ReporteRs/man/addImage.bsdoc.Rd | 123
ReporteRs-0.7.7/ReporteRs/man/addImage.docx.Rd | 147
ReporteRs-0.7.7/ReporteRs/man/addImage.pptx.Rd | 168 -
ReporteRs-0.7.7/ReporteRs/man/addJavascript.Rd | 45
ReporteRs-0.7.7/ReporteRs/man/addLinkItem.Rd | 113
ReporteRs-0.7.7/ReporteRs/man/addMarkdown.Rd | 72
ReporteRs-0.7.7/ReporteRs/man/addMarkdown.bsdoc.Rd | 311 -
ReporteRs-0.7.7/ReporteRs/man/addMarkdown.docx.Rd | 309 -
ReporteRs-0.7.7/ReporteRs/man/addMarkdown.pptx.Rd | 325 +-
ReporteRs-0.7.7/ReporteRs/man/addPageBreak.Rd | 54
ReporteRs-0.7.7/ReporteRs/man/addPageBreak.docx.Rd | 57
ReporteRs-0.7.7/ReporteRs/man/addPageNumber.Rd | 54
ReporteRs-0.7.7/ReporteRs/man/addPageNumber.pptx.Rd | 100
ReporteRs-0.7.7/ReporteRs/man/addParagraph.Footnote.Rd | 68
ReporteRs-0.7.7/ReporteRs/man/addParagraph.Rd | 71
ReporteRs-0.7.7/ReporteRs/man/addParagraph.bsdoc.Rd | 219 -
ReporteRs-0.7.7/ReporteRs/man/addParagraph.docx.Rd | 269 -
ReporteRs-0.7.7/ReporteRs/man/addParagraph.pptx.Rd | 357 +-
ReporteRs-0.7.7/ReporteRs/man/addPlot.Rd | 112
ReporteRs-0.7.7/ReporteRs/man/addPlot.bsdoc.Rd | 205 -
ReporteRs-0.7.7/ReporteRs/man/addPlot.docx.Rd | 196 -
ReporteRs-0.7.7/ReporteRs/man/addPlot.pptx.Rd | 217 -
ReporteRs-0.7.7/ReporteRs/man/addPostCommand.Rd | 36
ReporteRs-0.7.7/ReporteRs/man/addRScript.Rd | 72
ReporteRs-0.7.7/ReporteRs/man/addRScript.bsdoc.Rd | 100
ReporteRs-0.7.7/ReporteRs/man/addRScript.docx.Rd | 119
ReporteRs-0.7.7/ReporteRs/man/addRScript.pptx.Rd | 115
ReporteRs-0.7.7/ReporteRs/man/addSection.Rd | 51
ReporteRs-0.7.7/ReporteRs/man/addSection.docx.Rd | 144
ReporteRs-0.7.7/ReporteRs/man/addSlide.Rd | 51
ReporteRs-0.7.7/ReporteRs/man/addSlide.pptx.Rd | 215 -
ReporteRs-0.7.7/ReporteRs/man/addSubtitle.Rd | 51
ReporteRs-0.7.7/ReporteRs/man/addSubtitle.pptx.Rd | 87
ReporteRs-0.7.7/ReporteRs/man/addTOC.Rd | 55
ReporteRs-0.7.7/ReporteRs/man/addTOC.bsdoc.Rd | 99
ReporteRs-0.7.7/ReporteRs/man/addTOC.docx.Rd | 171 -
ReporteRs-0.7.7/ReporteRs/man/addTitle.Rd | 62
ReporteRs-0.7.7/ReporteRs/man/addTitle.bsdoc.Rd | 98
ReporteRs-0.7.7/ReporteRs/man/addTitle.docx.Rd | 125
ReporteRs-0.7.7/ReporteRs/man/addTitle.pptx.Rd | 83
ReporteRs-0.7.7/ReporteRs/man/as.FlexTable.Rd |only
ReporteRs-0.7.7/ReporteRs/man/as.FlexTable.sessionInfo.Rd |only
ReporteRs-0.7.7/ReporteRs/man/as.html.FlexTable.Rd | 99
ReporteRs-0.7.7/ReporteRs/man/as.html.RScript.Rd | 55
ReporteRs-0.7.7/ReporteRs/man/as.html.Rd | 51
ReporteRs-0.7.7/ReporteRs/man/as.html.pot.Rd | 56
ReporteRs-0.7.7/ReporteRs/man/borderDashed.Rd | 55
ReporteRs-0.7.7/ReporteRs/man/borderDotted.Rd | 55
ReporteRs-0.7.7/ReporteRs/man/borderNone.Rd | 55
ReporteRs-0.7.7/ReporteRs/man/borderProperties.Rd | 57
ReporteRs-0.7.7/ReporteRs/man/borderSolid.Rd | 55
ReporteRs-0.7.7/ReporteRs/man/bsdoc.Rd | 366 +-
ReporteRs-0.7.7/ReporteRs/man/cellProperties.Rd | 282 -
ReporteRs-0.7.7/ReporteRs/man/chprop.Rd | 55
ReporteRs-0.7.7/ReporteRs/man/chprop.borderProperties.Rd | 69
ReporteRs-0.7.7/ReporteRs/man/chprop.cellProperties.Rd | 265 -
ReporteRs-0.7.7/ReporteRs/man/chprop.parProperties.Rd | 148
ReporteRs-0.7.7/ReporteRs/man/chprop.textProperties.Rd | 127
ReporteRs-0.7.7/ReporteRs/man/declareTitlesStyles.Rd | 57
ReporteRs-0.7.7/ReporteRs/man/declareTitlesStyles.docx.Rd | 104
ReporteRs-0.7.7/ReporteRs/man/deleteBookmark.Rd | 39
ReporteRs-0.7.7/ReporteRs/man/deleteBookmarkNextContent.Rd | 39
ReporteRs-0.7.7/ReporteRs/man/dim.docx.Rd | 48
ReporteRs-0.7.7/ReporteRs/man/dim.pptx.Rd | 50
ReporteRs-0.7.7/ReporteRs/man/doc-list-settings.Rd | 149
ReporteRs-0.7.7/ReporteRs/man/docx-bookmark.Rd | 217 -
ReporteRs-0.7.7/ReporteRs/man/docx.Rd | 397 +-
ReporteRs-0.7.7/ReporteRs/man/is.color.Rd | 47
ReporteRs-0.7.7/ReporteRs/man/light.table.Rd | 48
ReporteRs-0.7.7/ReporteRs/man/list_bookmarks.Rd |only
ReporteRs-0.7.7/ReporteRs/man/parCenter.Rd | 55
ReporteRs-0.7.7/ReporteRs/man/parJustify.Rd | 55
ReporteRs-0.7.7/ReporteRs/man/parLeft.Rd | 55
ReporteRs-0.7.7/ReporteRs/man/parProperties.Rd | 182 -
ReporteRs-0.7.7/ReporteRs/man/parRight.Rd | 55
ReporteRs-0.7.7/ReporteRs/man/plus-.pot.Rd |only
ReporteRs-0.7.7/ReporteRs/man/pot.Rd | 102
ReporteRs-0.7.7/ReporteRs/man/pptx.Rd | 308 -
ReporteRs-0.7.7/ReporteRs/man/print.FlexTable.Rd |only
ReporteRs-0.7.7/ReporteRs/man/print.Footnote.Rd |only
ReporteRs-0.7.7/ReporteRs/man/print.bsdoc.Rd | 53
ReporteRs-0.7.7/ReporteRs/man/print.docx.Rd | 53
ReporteRs-0.7.7/ReporteRs/man/print.pot.Rd |only
ReporteRs-0.7.7/ReporteRs/man/print.pptx.Rd | 53
ReporteRs-0.7.7/ReporteRs/man/print.textProperties.Rd | 45
ReporteRs-0.7.7/ReporteRs/man/raphael.html.Rd | 117
ReporteRs-0.7.7/ReporteRs/man/registerRaphaelGraph.Rd | 32
ReporteRs-0.7.7/ReporteRs/man/setColumnsColors.Rd | 64
ReporteRs-0.7.7/ReporteRs/man/setFlexTableBackgroundColors.Rd | 128
ReporteRs-0.7.7/ReporteRs/man/setFlexTableBorders.Rd | 112
ReporteRs-0.7.7/ReporteRs/man/setFlexTableWidths.Rd | 52
ReporteRs-0.7.7/ReporteRs/man/setRowsColors.Rd | 64
ReporteRs-0.7.7/ReporteRs/man/setZebraStyle.Rd | 68
ReporteRs-0.7.7/ReporteRs/man/set_of_paragraphs.Rd | 67
ReporteRs-0.7.7/ReporteRs/man/slide.layouts.Rd | 46
ReporteRs-0.7.7/ReporteRs/man/slide.layouts.pptx.Rd | 96
ReporteRs-0.7.7/ReporteRs/man/spanFlexTableColumns.Rd | 93
ReporteRs-0.7.7/ReporteRs/man/spanFlexTableRows.Rd | 93
ReporteRs-0.7.7/ReporteRs/man/styles.Rd | 49
ReporteRs-0.7.7/ReporteRs/man/styles.docx.Rd | 63
ReporteRs-0.7.7/ReporteRs/man/textBold.Rd | 55
ReporteRs-0.7.7/ReporteRs/man/textBoldItalic.Rd | 55
ReporteRs-0.7.7/ReporteRs/man/textItalic.Rd | 55
ReporteRs-0.7.7/ReporteRs/man/textNormal.Rd | 55
ReporteRs-0.7.7/ReporteRs/man/textProperties.Rd | 144
ReporteRs-0.7.7/ReporteRs/man/text_extract.Rd |only
ReporteRs-0.7.7/ReporteRs/man/toc.options.Rd | 54
ReporteRs-0.7.7/ReporteRs/man/toc.options.docx.Rd | 73
ReporteRs-0.7.7/ReporteRs/man/triggerPostCommand.Rd | 28
ReporteRs-0.7.7/ReporteRs/man/vanilla.table.Rd | 48
ReporteRs-0.7.7/ReporteRs/man/writeDoc.Rd | 57
ReporteRs-0.7.7/ReporteRs/man/writeDoc.bsdoc.Rd | 93
ReporteRs-0.7.7/ReporteRs/man/writeDoc.docx.Rd | 68
ReporteRs-0.7.7/ReporteRs/man/writeDoc.pptx.Rd | 77
251 files changed, 18490 insertions(+), 18572 deletions(-)
Title: Tools for Analyzing QTL Experiments
Diff between qtl versions 1.35-3 dated 2014-12-15 and 1.36-6 dated 2015-03-05
Description: Analysis of experimental crosses to identify genes
(called quantitative trait loci, QTLs) contributing to variation in
quantitative traits.
Author: Karl W Broman
Maintainer: Karl W Broman
DESCRIPTION | 14 +++----
MD5 | 70 ++++++++++++++++++++-----------------
NAMESPACE | 5 ++
R/phyloqtl_util.R | 56 +++++++++++++++++++++++-------
R/plot.R | 51 ++++++++++++++++++---------
R/read.cross.mq.R | 11 +++--
R/scanonevar.R | 2 -
R/scanonevar.meanperm.R |only
R/scanonevar.varperm.R |only
R/summary.scantwo.old.R | 2 -
R/util.R | 74 +++++++++++++++++++++++++++++++++++++---
R/write.cross.mq.R | 2 -
build/vignette.rds |binary
data/badorder.RData |binary
data/bristle3.RData |binary
data/bristleX.RData |binary
data/fake.4way.RData |binary
data/fake.bc.RData |binary
data/fake.f2.RData |binary
data/hyper.RData |binary
data/listeria.RData |binary
data/locations.RData |binary
data/map10.RData |binary
data/mapthis.RData |binary
data/multitrait.RData |binary
inst/INSTALL_ME.txt | 12 +++---
inst/README.md | 2 -
inst/STATUS.txt | 35 ++++++++++++++++++
inst/TODO.txt | 13 +++----
inst/doc/rqtltour.pdf |binary
man/flip.order.Rd |only
man/geno.image.Rd | 6 +--
man/hyper.Rd | 18 ++++-----
man/plot.pxg.Rd | 9 ++--
man/scanonevar.meanperm.Rd |only
man/scanonevar.varperm.Rd |only
man/summary.scantwo.old.Rd | 11 ++---
man/switch.order.Rd | 12 +++---
tests/testthat/test-fliporder.R |only
39 files changed, 281 insertions(+), 124 deletions(-)
Title: Constrained Nonlinear Optimization
Diff between alabama versions 2014.12-1 dated 2014-12-01 and 2015.3-1 dated 2015-03-05
Description: Augmented Lagrangian Adaptive Barrier Minimization
Algorithm for optimizing smooth nonlinear objective functions
with constraints. Linear or nonlinear equality and inequality
constraints are allowed.
Author: Ravi Varadhan (with contributions from Gabor Grothendieck)
Maintainer: Ravi Varadhan
DESCRIPTION | 8 +--
MD5 | 10 +--
NEWS | 8 +++
R/auglag.R | 126 +++++++++++++++++++++++++++++++++++--------------
man/alabama-package.Rd | 8 +--
man/auglag.Rd | 18 +++++--
6 files changed, 126 insertions(+), 52 deletions(-)
Title: Population and Evolutionary Genetics Analysis System
Diff between pegas versions 0.6 dated 2014-08-21 and 0.7 dated 2015-03-05
Description: Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, and for the analysis of population nucleotide sequences and micro-satellites including coalescence analyses.
Author: Emmanuel Paradis [aut, cre, cph],
Klaus Schliep [aut, cph],
Alastair Potts [aut, cph],
David Winter [aut, cph]
Maintainer: Emmanuel Paradis
DESCRIPTION | 15 -
MD5 | 36 +--
NAMESPACE | 17 -
NEWS | 38 +++
R/IO.R | 6
R/geo.R |only
R/haplotype.R | 532 ++++++++++++++++++++++++++-------------------
R/zzz.R |only
build/vignette.rds |binary
inst/doc/ReadingFiles.Rnw | 2
inst/doc/ReadingFiles.pdf |binary
man/diffHaplo.Rd |only
man/geoTrans.Rd |only
man/geod.Rd |only
man/haploNet.Rd | 35 ++
man/haplotype.Rd | 3
man/pegas-package.Rd | 2
man/read.loci.Rd | 2
man/read.vcf.Rd | 44 +++
man/replot.Rd |only
src |only
vignettes/ReadingFiles.Rnw | 2
22 files changed, 463 insertions(+), 271 deletions(-)
Title: Simultaneous Inference in General Parametric Models
Diff between multcomp versions 1.3-9 dated 2015-02-18 and 1.4-0 dated 2015-03-05
Description: Simultaneous tests and confidence intervals
for general linear hypotheses in parametric models, including
linear, generalized linear, linear mixed effects, and survival models.
The package includes demos reproducing analyzes presented
in the book "Multiple Comparisons Using R" (Bretz, Hothorn,
Westfall, 2010, CRC Press).
Author: Torsten Hothorn [aut, cre],
Frank Bretz [aut],
Peter Westfall [aut],
Richard M. Heiberger [ctb],
Andre Schuetzenmeister [ctb],
Susan Scheibe [ctb]
Maintainer: Torsten Hothorn
DESCRIPTION | 16
MD5 | 16
NAMESPACE | 1
R/expressions.R | 468 +++++++++++++++++++++++++++--
inst/NEWS | 7
inst/doc/chfls1.pdf |binary
inst/doc/generalsiminf.pdf |binary
inst/doc/multcomp-examples.pdf |binary
tests/regtest-interface-extended.R |only
tests/regtest-interface-extended.Rout.save |only
10 files changed, 465 insertions(+), 43 deletions(-)
Title: Performing Continuous-Time Microsimulation
Diff between MicSim versions 1.0.7 dated 2015-02-27 and 1.0.8 dated 2015-03-05
Description: This entry-level toolkit allows performing generic continuous-time microsimulation for a wide range of demograhic applications.
Author: Sabine Zinn
Maintainer: Sabine Zinn
DESCRIPTION | 10 +++++-----
MD5 | 8 ++++----
NAMESPACE | 10 ++++++++--
inst/NEWS.Rd | 5 +++++
man/MicSim-package.Rd | 4 ++--
5 files changed, 24 insertions(+), 13 deletions(-)
Title: Multivariate Dependence with Copulas
Diff between copula versions 0.999-12 dated 2014-10-02 and 0.999-13 dated 2015-03-05
Description: Classes (S4) of commonly used elliptical, Archimedean, extreme
value and some more copula families. Methods for density, distribution,
random number generation, bivariate dependence measures, perspective and
contour plots. Fitting copula models including variance estimates.
Independence and serial (univariate and multivariate) independence tests,
and other copula related tests. Empirical copula and multivariate CDF.
Goodness-of-fit tests for copulas based on multipliers, the parametric
bootstrap with several transformation options.
Merged former package 'nacopula' for nested Archimedean copulas: Efficient
sampling algorithms, various estimators, goodness-of-fit tests and related
tools and special functions.
Author: Marius Hofert
Maintainer: Martin Maechler
DESCRIPTION | 13 +++++----
MD5 | 57 +++++++++++++++++++++---------------------
NAMESPACE | 21 ++++++++++-----
R/aux-acopula.R | 2 -
R/empcop.R | 4 +--
R/estimation.R | 15 +++++------
R/gofTrafos.R | 14 ++++++----
R/pairsRosenblatt.R | 2 -
R/special-func.R | 43 ++++++++++++++++++++++++++------
TODO | 3 ++
build/vignette.rds |binary
demo/00Index | 38 ++++++++++++++--------------
demo/dDiag-plots.R | 4 +--
demo/qrng.R | 60 +++++++++++++++++++++++++++++++++++++++++++++
demo/tail_compatibility.R |only
inst/CITATION | 4 +--
inst/NEWS.Rd | 10 ++++++-
inst/doc/Frank-Rmpfr.R | 1
inst/doc/Frank-Rmpfr.pdf |binary
inst/doc/nacopula-pkg.R | 1
inst/doc/nacopula-pkg.pdf |binary
inst/doc/rhoAMH-dilog.R | 1
inst/doc/rhoAMH-dilog.Rnw | 4 +--
inst/doc/rhoAMH-dilog.pdf |binary
man/cCopula.Rd | 10 +++----
man/device.Rd | 18 ++++++-------
man/emle.Rd | 10 +++----
man/evTestA.Rd | 9 +++---
tests/Stirling-etc.R | 28 +++++++++++++++++++++
vignettes/rhoAMH-dilog.Rnw | 4 +--
30 files changed, 256 insertions(+), 120 deletions(-)
Title: A Package for Running 'JAGS' from R
Diff between R2jags versions 0.05-01 dated 2015-01-09 and 0.05-03 dated 2015-03-05
Description: Using this package to call 'JAGS' from R.
Author: Yu-Sung Su
Maintainer: Yu-Sung Su
CHANGELOG | 3 +++
DESCRIPTION | 12 ++++++------
MD5 | 16 ++++++++--------
NAMESPACE | 4 ++--
R/as.mcmc.R | 2 +-
man/attach.jags.Rd | 14 +++++++-------
man/autojags.Rd | 18 +++++++++---------
man/jags.Rd | 14 ++++++++------
man/traceplot.Rd | 6 +++---
9 files changed, 47 insertions(+), 42 deletions(-)
Title: Dynamic Assembly Model of Colonization, Local Extinction and
Speciation
Diff between DAMOCLES versions 1.0 dated 2014-10-29 and 1.1 dated 2015-03-05
Description: Simulates and computes (maximum) likelihood of a dynamical model of community assembly that takes into account phylogenetic history.
Author: Rampal S. Etienne & Alex L. Pigot
Maintainer: Rampal S. Etienne
DESCRIPTION | 15 +--
MD5 | 24 ++---
NAMESPACE | 2
R/DAMOCLES_ML.R | 24 +++--
R/DAMOCLES_bootstrap.R |only
R/DAMOCLES_loglik.R | 1
R/DAMOCLES_sim.R | 197 ++++++++++++++++++++++++++++++---------------
data/NWPrimates_data.RData |binary
man/DAMOCLES-internal.Rd | 6 -
man/DAMOCLES-package.Rd | 17 ++-
man/DAMOCLES_ML.Rd | 5 -
man/DAMOCLES_bootstrap.Rd |only
man/DAMOCLES_loglik.Rd | 2
man/DAMOCLES_sim.Rd | 16 +--
14 files changed, 198 insertions(+), 111 deletions(-)
Title: Multi-Class Discriminant Analysis using Binary Predictors
Diff between binda versions 1.0.1 dated 2014-11-14 and 1.0.2 dated 2015-03-05
Description: The "binda" package implements functions for multi-class
discriminant analysis using binary predictors, for corresponding
variable selection, and for dichotomizing continuous data.
Author: Sebastian Gibb and Korbinian Strimmer.
Maintainer: Korbinian Strimmer
DESCRIPTION | 8 +++---
MD5 | 24 ++++++++++----------
NAMESPACE | 2 +
NEWS | 11 ++++++++-
R/binda.R | 59 +++++++++++++++++++++++----------------------------
R/binda.ranking.R | 57 ++++++++++++++++++-------------------------------
R/dichotomize.R | 6 ++---
R/getClassMeans.R | 21 ++++--------------
R/is.binaryMatrix.R | 12 ++++++----
man/binda.Rd | 11 +++++++++
man/binda.package.Rd | 4 +++
man/binda.ranking.Rd | 7 +++++-
man/dichotomize.Rd | 8 ++++++
13 files changed, 119 insertions(+), 111 deletions(-)
Title: Predict Presence of Signal Peptides
Diff between signal.hsmm versions 1.1 dated 2014-09-29 and 1.2 dated 2015-03-05
Description: Predicts presence of signal peptides in eukaryotic protein using
hidden semi-Markov models. The implemented algorithm can be accessed both
from command line and GUI.
Author: Michal Burdukiewicz [cre, aut],
Piotr Sobczyk [aut]
Maintainer: Michal Burdukiewicz
signal.hsmm-1.1/signal.hsmm/R/degenerate.R |only
signal.hsmm-1.1/signal.hsmm/man/degenerate.Rd |only
signal.hsmm-1.2/signal.hsmm/DESCRIPTION | 8 -
signal.hsmm-1.2/signal.hsmm/MD5 | 63 +++++++-------
signal.hsmm-1.2/signal.hsmm/NAMESPACE | 6 -
signal.hsmm-1.2/signal.hsmm/R/datasets.R | 15 +--
signal.hsmm-1.2/signal.hsmm/R/duration_viterbi.R | 37 ++++----
signal.hsmm-1.2/signal.hsmm/R/find_nhc.R | 8 -
signal.hsmm-1.2/signal.hsmm/R/hsmm_pred.R | 2
signal.hsmm-1.2/signal.hsmm/R/predict.seq_hsmm.R |only
signal.hsmm-1.2/signal.hsmm/R/read_txt.R | 2
signal.hsmm-1.2/signal.hsmm/R/read_uniprot.R | 6 -
signal.hsmm-1.2/signal.hsmm/R/run_signal.hsmm.R | 6 -
signal.hsmm-1.2/signal.hsmm/R/signal.hsmm.R | 1
signal.hsmm-1.2/signal.hsmm/R/train_hsmm.R |only
signal.hsmm-1.2/signal.hsmm/README.md | 6 -
signal.hsmm-1.2/signal.hsmm/data/aaaggregation.rda |binary
signal.hsmm-1.2/signal.hsmm/inst/CITATION |only
signal.hsmm-1.2/signal.hsmm/man/aaaggregation.Rd | 6 -
signal.hsmm-1.2/signal.hsmm/man/benchmark_dat.Rd | 7 -
signal.hsmm-1.2/signal.hsmm/man/duration_viterbi.Rd | 3
signal.hsmm-1.2/signal.hsmm/man/find_nhc.Rd | 9 +-
signal.hsmm-1.2/signal.hsmm/man/gui_signal.hsmm.Rd | 8 -
signal.hsmm-1.2/signal.hsmm/man/hsmm_pred.Rd | 5 -
signal.hsmm-1.2/signal.hsmm/man/hsmm_pred_list.Rd | 3
signal.hsmm-1.2/signal.hsmm/man/is_protein.Rd | 3
signal.hsmm-1.2/signal.hsmm/man/plot.hsmm_pred.Rd | 3
signal.hsmm-1.2/signal.hsmm/man/pred2df.Rd | 3
signal.hsmm-1.2/signal.hsmm/man/predict.sighsmm_model.Rd |only
signal.hsmm-1.2/signal.hsmm/man/read_txt.Rd | 5 -
signal.hsmm-1.2/signal.hsmm/man/read_uniprot.Rd | 9 +-
signal.hsmm-1.2/signal.hsmm/man/run_signal.hsmm.Rd | 3
signal.hsmm-1.2/signal.hsmm/man/signal.hsmm.Rd | 3
signal.hsmm-1.2/signal.hsmm/man/summary.hsmm_pred.Rd | 3
signal.hsmm-1.2/signal.hsmm/man/summary.hsmm_pred_list.Rd | 3
signal.hsmm-1.2/signal.hsmm/man/train_hsmm.Rd |only
36 files changed, 125 insertions(+), 111 deletions(-)
Title: Tools for Phoneticians and Phonologists
Diff between phonR versions 0.4-2 dated 2013-03-25 and 1.0-1 dated 2015-03-05
Description: Tools for phoneticians and phonologists, including functions for normalization and plotting of vowels.
Author: Daniel R. McCloy
Maintainer: Daniel R. McCloy
phonR-0.4-2/phonR/R/ellipse.R |only
phonR-0.4-2/phonR/R/phonR.r |only
phonR-0.4-2/phonR/data/indoVowelData.rda |only
phonR-0.4-2/phonR/man/ellipse.Rd |only
phonR-0.4-2/phonR/man/normalizeVowels.Rd |only
phonR-1.0-1/phonR/DESCRIPTION | 16 -
phonR-1.0-1/phonR/MD5 | 20 +-
phonR-1.0-1/phonR/NAMESPACE | 22 +-
phonR-1.0-1/phonR/R/phonR.R |only
phonR-1.0-1/phonR/data/indoVowels.rda |only
phonR-1.0-1/phonR/inst/CITATION | 4
phonR-1.0-1/phonR/man/indo.Rd | 15 -
phonR-1.0-1/phonR/man/normVowels.Rd |only
phonR-1.0-1/phonR/man/plotVowels.Rd | 281 ++++++++++++++++++++++---------
phonR-1.0-1/phonR/man/repulsiveForce.Rd |only
phonR-1.0-1/phonR/man/vowelSpaceArea.Rd |only
16 files changed, 247 insertions(+), 111 deletions(-)
Title: Compares the Distribution of Sister Clades Through a Phylogeny
Diff between nodiv versions 1.0.1 dated 2015-01-06 and 1.0.2 dated 2015-03-05
Description: An implementation of the nodiv algorithm, (see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. DOI: 10.1111/2041-210X.12283. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped using the SOS statistic.
Author: Michael Krabbe Borregaard
Maintainer: Michael Krabbe Borregaard
DESCRIPTION | 8 +++---
MD5 | 12 +++++-----
R/Methods_for_data_objects.R | 50 +++++++++++++++++++++++++------------------
R/Node_based_analysis.R | 19 ++++++++++++----
R/Prepare_data.R | 38 ++++++++++++++++++++++++++++----
man/distrib_data.Rd | 2 -
man/nodiv-package.Rd | 4 +--
7 files changed, 91 insertions(+), 42 deletions(-)
Title: Linear Group Fixed Effects
Diff between lfe versions 2.1-1620 dated 2015-03-02 and 2.1-1629 dated 2015-03-05
Description: Transforms away factors with many levels prior to doing an OLS.
Useful for estimating linear models with multiple group fixed effects, and for
estimating linear models which uses factors as pure control variables.
Includes support for instrumental variables, conditional F statistics for weak instruments,
robust and multi-way clustered standard errors, as well as limited mobility bias correction.
Author: Simen Gaure, Ragnar Frisch Centre for Economic Research
Maintainer: Simen Gaure
DESCRIPTION | 8 +-
MD5 | 24 +++----
R/felm.R | 138 +++++++++++++++++++++++++++++++++++---------
R/generics.R | 10 ++-
R/oldfelm.R | 45 +++++++-------
R/utils.R | 16 ++++-
inst/doc/identification.pdf |binary
inst/doc/lfehow.pdf |binary
inst/doc/speed.pdf |binary
man/felm.Rd | 48 ++++++++++-----
src/demean.c | 2
src/lfe.c | 1
src/lfe.h | 1
13 files changed, 208 insertions(+), 85 deletions(-)
Title: Biodiversity Assessment Tools
Diff between BAT versions 1.2 dated 2015-02-12 and 1.2.1 dated 2015-03-05
Description: Includes algorithms to assess alpha and beta
diversity in all their dimensions (taxon, phylogenetic and functional
diversity), whether communities are completely sampled or not. It allows
performing a number of analyses based on either species identities or
ultrametric trees depicting species relationships.
Author: Pedro Cardoso, Francois Rigal, Jose Carlos Carvalho
Maintainer: Pedro Cardoso
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
R/BAT.R | 15 ++++++++++++---
3 files changed, 18 insertions(+), 9 deletions(-)
Title: Flexible Regression Models for Survival Data
Diff between timereg versions 1.8.6 dated 2014-11-18 and 1.8.7 dated 2015-03-05
Description: Programs for Martinussen and Scheike (2006), `Dynamic Regression
Models for Survival Data', Springer Verlag. Plus more recent developments.
Additive survival model, semiparametric proportional odds model, fast cumulative
residuals, excess risk models and more. Flexible competing risks regression
including GOF-tests. Two-stage frailty modelling.
PLS for the additive risk model. Lasso in ahaz package.
Author: Thomas Scheike with contributions from Torben Martinussen, Jeremy Silver
and Klaus Holst
Maintainer: Thomas Scheike
timereg-1.8.6/timereg/R/Gprop-odds-subdist.r |only
timereg-1.8.6/timereg/R/faster.reshape.r |only
timereg-1.8.6/timereg/man/Gprop.odds.subdist.Rd |only
timereg-1.8.7/timereg/DESCRIPTION | 26 ++--
timereg-1.8.7/timereg/MD5 | 75 ++++++-------
timereg-1.8.7/timereg/NAMESPACE | 19 +++
timereg-1.8.7/timereg/R/base.r | 38 ++++++
timereg-1.8.7/timereg/R/comprisk.ipw.r |only
timereg-1.8.7/timereg/R/comprisk.r | 27 +++-
timereg-1.8.7/timereg/R/cox.ipw.r | 4
timereg-1.8.7/timereg/R/dynadd.r | 10 +
timereg-1.8.7/timereg/R/kmplot.r | 2
timereg-1.8.7/timereg/R/mgresid.r | 9 -
timereg-1.8.7/timereg/R/new.cox-aalen.r | 4
timereg-1.8.7/timereg/R/new.prop-excess.r | 2
timereg-1.8.7/timereg/R/new.timecox.r | 4
timereg-1.8.7/timereg/R/prop-excess.r | 12 +-
timereg-1.8.7/timereg/R/restricted.residual.mean.r | 14 +-
timereg-1.8.7/timereg/R/timecox.r | 20 +--
timereg-1.8.7/timereg/man/Gprop.odds.Rd | 2
timereg-1.8.7/timereg/man/dynreg.Rd | 1
timereg-1.8.7/timereg/man/internal-addreg.Rd | 4
timereg-1.8.7/timereg/man/krylow.pls.Rd | 3
timereg-1.8.7/timereg/man/plot.dynreg.Rd | 1
timereg-1.8.7/timereg/man/predict.timereg.Rd | 2
timereg-1.8.7/timereg/man/prop.excess.Rd | 23 +---
timereg-1.8.7/timereg/man/prop.odds.subdist.Rd | 3
timereg-1.8.7/timereg/man/restricted.residual.mean.Rd | 4
timereg-1.8.7/timereg/man/timecox.Rd | 3
timereg-1.8.7/timereg/man/wald.test.Rd |only
timereg-1.8.7/timereg/src/Makevars | 1
timereg-1.8.7/timereg/src/aalen.c | 1
timereg-1.8.7/timereg/src/aalenC.c | 31 +++--
timereg-1.8.7/timereg/src/comprisk.c | 35 ++++--
timereg-1.8.7/timereg/src/cox-aalen.c | 7 -
timereg-1.8.7/timereg/src/dynadd.c | 17 +--
timereg-1.8.7/timereg/src/matrix.h | 3
timereg-1.8.7/timereg/src/pe-sasieni.c | 2
timereg-1.8.7/timereg/src/prop-excess.c | 52 ++++-----
timereg-1.8.7/timereg/src/smooth.c | 12 +-
timereg-1.8.7/timereg/src/timecox.c | 100 ++++++++++--------
41 files changed, 328 insertions(+), 245 deletions(-)
Title: Work with Hyperspectral Data, i.e. Spectra + Meta Information
(Spatial, Time, Concentration, ...)
Diff between hyperSpec versions 0.98-20140523 dated 2014-05-23 and 0.98-20150304 dated 2015-03-05
Description: Comfortable ways to work with hyperspectral data sets.
I.e. spatially or time-resolved spectra, or spectra with any other kind
of information associated with each of the spectra. The spectra can be data
as obtained in XRF, UV/VIS, Fluorescence, AES, NIR, IR, Raman, NMR, MS,
etc. More generally, any data that is recorded over a discretized variable,
e.g. absorbance = f (wavelength), stored as a vector of absorbance values
for discrete wavelengths is suitable.
Author: Claudia Beleites
Maintainer: Claudia Beleites
hyperSpec-0.98-20140523/hyperSpec/R/logbook.R |only
hyperSpec-0.98-20140523/hyperSpec/R/logentry.R |only
hyperSpec-0.98-20140523/hyperSpec/R/sel.poly.R |only
hyperSpec-0.98-20140523/hyperSpec/man/logbook.Rd |only
hyperSpec-0.98-20140523/hyperSpec/man/logentry.Rd |only
hyperSpec-0.98-20140523/hyperSpec/man/map.sel.poly.Rd |only
hyperSpec-0.98-20140523/hyperSpec/vignettes/Rplots.pdf |only
hyperSpec-0.98-20150304/hyperSpec/DESCRIPTION | 74 -
hyperSpec-0.98-20150304/hyperSpec/MD5 | 406 ++++------
hyperSpec-0.98-20150304/hyperSpec/NAMESPACE | 33
hyperSpec-0.98-20150304/hyperSpec/R/Arith.R | 87 +-
hyperSpec-0.98-20150304/hyperSpec/R/Compare.R | 3
hyperSpec-0.98-20150304/hyperSpec/R/DollarNames.R | 4
hyperSpec-0.98-20150304/hyperSpec/R/Math.R | 41 -
hyperSpec-0.98-20150304/hyperSpec/R/Summary.R | 2
hyperSpec-0.98-20150304/hyperSpec/R/aggregate.R | 19
hyperSpec-0.98-20150304/hyperSpec/R/all.equal.R | 110 +-
hyperSpec-0.98-20150304/hyperSpec/R/apply.R | 13
hyperSpec-0.98-20150304/hyperSpec/R/as.data.frame.R | 4
hyperSpec-0.98-20150304/hyperSpec/R/barbiturates.R | 2
hyperSpec-0.98-20150304/hyperSpec/R/bind.R | 28
hyperSpec-0.98-20150304/hyperSpec/R/chondro.R | 24
hyperSpec-0.98-20150304/hyperSpec/R/colMeans.R | 57 -
hyperSpec-0.98-20150304/hyperSpec/R/collapse.R | 54 -
hyperSpec-0.98-20150304/hyperSpec/R/cov.R | 1
hyperSpec-0.98-20150304/hyperSpec/R/decomposition.R | 58 +
hyperSpec-0.98-20150304/hyperSpec/R/dimnames.R | 4
hyperSpec-0.98-20150304/hyperSpec/R/empty.R | 11
hyperSpec-0.98-20150304/hyperSpec/R/extract.R | 23
hyperSpec-0.98-20150304/hyperSpec/R/fileio.optional.R |only
hyperSpec-0.98-20150304/hyperSpec/R/flu.R | 15
hyperSpec-0.98-20150304/hyperSpec/R/hyperspec-class.R | 24
hyperSpec-0.98-20150304/hyperSpec/R/hyperspec-package.R | 9
hyperSpec-0.98-20150304/hyperSpec/R/initialize.R | 40
hyperSpec-0.98-20150304/hyperSpec/R/labels.R | 12
hyperSpec-0.98-20150304/hyperSpec/R/levelplot.R | 5
hyperSpec-0.98-20150304/hyperSpec/R/map.identify.R | 6
hyperSpec-0.98-20150304/hyperSpec/R/map.sel.poly.R | 87 +-
hyperSpec-0.98-20150304/hyperSpec/R/mark.dendrogram.R | 2
hyperSpec-0.98-20150304/hyperSpec/R/matlab.palette.R | 2
hyperSpec-0.98-20150304/hyperSpec/R/mean_sd.R | 56 -
hyperSpec-0.98-20150304/hyperSpec/R/merge.R | 16
hyperSpec-0.98-20150304/hyperSpec/R/mvtnorm.R | 5
hyperSpec-0.98-20150304/hyperSpec/R/normalize01.R | 22
hyperSpec-0.98-20150304/hyperSpec/R/options.R | 21
hyperSpec-0.98-20150304/hyperSpec/R/orderwl.R | 10
hyperSpec-0.98-20150304/hyperSpec/R/plot.R | 2
hyperSpec-0.98-20150304/hyperSpec/R/plotc.R | 3
hyperSpec-0.98-20150304/hyperSpec/R/plotmap.R | 2
hyperSpec-0.98-20150304/hyperSpec/R/plotmat.R | 16
hyperSpec-0.98-20150304/hyperSpec/R/plotspc.R | 15
hyperSpec-0.98-20150304/hyperSpec/R/plotvoronoi.R | 12
hyperSpec-0.98-20150304/hyperSpec/R/qplot.R | 9
hyperSpec-0.98-20150304/hyperSpec/R/qplotmixmap.R | 45 -
hyperSpec-0.98-20150304/hyperSpec/R/quantile.R |only
hyperSpec-0.98-20150304/hyperSpec/R/rbind.fill.R | 2
hyperSpec-0.98-20150304/hyperSpec/R/read.ENVI.Nicolet.R | 46 -
hyperSpec-0.98-20150304/hyperSpec/R/read.ENVI.R | 47 -
hyperSpec-0.98-20150304/hyperSpec/R/read.cytomat.R | 4
hyperSpec-0.98-20150304/hyperSpec/R/read.jdx.R | 16
hyperSpec-0.98-20150304/hyperSpec/R/read.jdx.Shimadzu.R | 46 -
hyperSpec-0.98-20150304/hyperSpec/R/read.spc.Kaiser.R | 28
hyperSpec-0.98-20150304/hyperSpec/R/read.spc.R | 76 -
hyperSpec-0.98-20150304/hyperSpec/R/read.txt.Horiba.R | 2
hyperSpec-0.98-20150304/hyperSpec/R/read.txt.long.R | 2
hyperSpec-0.98-20150304/hyperSpec/R/read.txt.wide.R | 4
hyperSpec-0.98-20150304/hyperSpec/R/replace.R | 32
hyperSpec-0.98-20150304/hyperSpec/R/sample.R | 25
hyperSpec-0.98-20150304/hyperSpec/R/scan.txt.Renishaw.R | 11
hyperSpec-0.98-20150304/hyperSpec/R/scan.txt.Witec.R | 28
hyperSpec-0.98-20150304/hyperSpec/R/seq.R | 18
hyperSpec-0.98-20150304/hyperSpec/R/show.R | 60 -
hyperSpec-0.98-20150304/hyperSpec/R/spc.NA.approx.R | 11
hyperSpec-0.98-20150304/hyperSpec/R/spc.bin.R | 10
hyperSpec-0.98-20150304/hyperSpec/R/spc.fit.poly.R | 30
hyperSpec-0.98-20150304/hyperSpec/R/spc.identify.R | 9
hyperSpec-0.98-20150304/hyperSpec/R/spc.loess.R | 6
hyperSpec-0.98-20150304/hyperSpec/R/spc.rubberband.R | 2
hyperSpec-0.98-20150304/hyperSpec/R/split.R | 31
hyperSpec-0.98-20150304/hyperSpec/R/subset.R | 12
hyperSpec-0.98-20150304/hyperSpec/R/sweep.R | 42 -
hyperSpec-0.98-20150304/hyperSpec/R/sysdata.rda |binary
hyperSpec-0.98-20150304/hyperSpec/R/trellis.factor.key.R | 1
hyperSpec-0.98-20150304/hyperSpec/R/unittest.R | 7
hyperSpec-0.98-20150304/hyperSpec/R/validate.R | 4
hyperSpec-0.98-20150304/hyperSpec/R/vandermonde.R | 5
hyperSpec-0.98-20150304/hyperSpec/R/wl.R | 8
hyperSpec-0.98-20150304/hyperSpec/R/wleval.R | 2
hyperSpec-0.98-20150304/hyperSpec/R/write.txt.long.R | 5
hyperSpec-0.98-20150304/hyperSpec/build/vignette.rds |binary
hyperSpec-0.98-20150304/hyperSpec/data/barbiturates.rda |binary
hyperSpec-0.98-20150304/hyperSpec/data/flu.rda |binary
hyperSpec-0.98-20150304/hyperSpec/data/laser.rda |binary
hyperSpec-0.98-20150304/hyperSpec/data/paracetamol.rda |binary
hyperSpec-0.98-20150304/hyperSpec/inst/CITATION | 36
hyperSpec-0.98-20150304/hyperSpec/inst/doc/baseline.R | 11
hyperSpec-0.98-20150304/hyperSpec/inst/doc/baseline.Rnw | 33
hyperSpec-0.98-20150304/hyperSpec/inst/doc/baseline.pdf |binary
hyperSpec-0.98-20150304/hyperSpec/inst/doc/chondro.Rnw | 2
hyperSpec-0.98-20150304/hyperSpec/inst/doc/fileio.Rnw | 2
hyperSpec-0.98-20150304/hyperSpec/inst/doc/fileio.pdf |binary
hyperSpec-0.98-20150304/hyperSpec/inst/doc/flu.Rnw | 4
hyperSpec-0.98-20150304/hyperSpec/inst/doc/flu.pdf |binary
hyperSpec-0.98-20150304/hyperSpec/inst/doc/introduction.R | 272 ++----
hyperSpec-0.98-20150304/hyperSpec/inst/doc/introduction.Rnw | 75 -
hyperSpec-0.98-20150304/hyperSpec/inst/doc/introduction.pdf |binary
hyperSpec-0.98-20150304/hyperSpec/inst/doc/laser.Rnw | 4
hyperSpec-0.98-20150304/hyperSpec/inst/doc/laser.pdf |binary
hyperSpec-0.98-20150304/hyperSpec/inst/doc/plotting.R | 157 +--
hyperSpec-0.98-20150304/hyperSpec/inst/doc/plotting.Rnw | 139 +--
hyperSpec-0.98-20150304/hyperSpec/inst/doc/plotting.pdf |binary
hyperSpec-0.98-20150304/hyperSpec/inst/doc/vignettes.defs | 15
hyperSpec-0.98-20150304/hyperSpec/man/Arith.Rd | 154 ++-
hyperSpec-0.98-20150304/hyperSpec/man/Comparison.Rd | 146 +--
hyperSpec-0.98-20150304/hyperSpec/man/aggregate.Rd | 87 --
hyperSpec-0.98-20150304/hyperSpec/man/apply.Rd | 85 --
hyperSpec-0.98-20150304/hyperSpec/man/asdataframe.Rd | 111 +-
hyperSpec-0.98-20150304/hyperSpec/man/barbiturates.Rd | 11
hyperSpec-0.98-20150304/hyperSpec/man/baselines.Rd | 70 -
hyperSpec-0.98-20150304/hyperSpec/man/bind.Rd | 88 --
hyperSpec-0.98-20150304/hyperSpec/man/chk.hy.Rd | 17
hyperSpec-0.98-20150304/hyperSpec/man/chondro.Rd | 30
hyperSpec-0.98-20150304/hyperSpec/man/colSums.Rd | 57 -
hyperSpec-0.98-20150304/hyperSpec/man/collapse.Rd | 35
hyperSpec-0.98-20150304/hyperSpec/man/cov.Rd | 38
hyperSpec-0.98-20150304/hyperSpec/man/decomposition.Rd | 118 +-
hyperSpec-0.98-20150304/hyperSpec/man/dim.Rd | 67 -
hyperSpec-0.98-20150304/hyperSpec/man/dimnames.Rd | 49 -
hyperSpec-0.98-20150304/hyperSpec/man/dollarnames.Rd | 18
hyperSpec-0.98-20150304/hyperSpec/man/empty.Rd | 30
hyperSpec-0.98-20150304/hyperSpec/man/extractreplace.Rd | 191 ++--
hyperSpec-0.98-20150304/hyperSpec/man/flu.Rd | 8
hyperSpec-0.98-20150304/hyperSpec/man/hyperSpec-package.Rd | 38
hyperSpec-0.98-20150304/hyperSpec/man/initialize.Rd | 93 --
hyperSpec-0.98-20150304/hyperSpec/man/labels.Rd | 57 -
hyperSpec-0.98-20150304/hyperSpec/man/laser.Rd | 6
hyperSpec-0.98-20150304/hyperSpec/man/levelplot.Rd | 201 ++--
hyperSpec-0.98-20150304/hyperSpec/man/makeraster.Rd | 47 -
hyperSpec-0.98-20150304/hyperSpec/man/map-sel-poly.Rd | 65 +
hyperSpec-0.98-20150304/hyperSpec/man/mark.dendrogram.Rd | 44 -
hyperSpec-0.98-20150304/hyperSpec/man/math.Rd | 85 --
hyperSpec-0.98-20150304/hyperSpec/man/mean_sd.Rd | 92 --
hyperSpec-0.98-20150304/hyperSpec/man/merge.Rd | 40
hyperSpec-0.98-20150304/hyperSpec/man/normalize01.Rd | 38
hyperSpec-0.98-20150304/hyperSpec/man/options.Rd | 50 -
hyperSpec-0.98-20150304/hyperSpec/man/orderwl.Rd | 21
hyperSpec-0.98-20150304/hyperSpec/man/palettes.Rd | 30
hyperSpec-0.98-20150304/hyperSpec/man/paracetamol.Rd | 8
hyperSpec-0.98-20150304/hyperSpec/man/pearson.dist.Rd | 25
hyperSpec-0.98-20150304/hyperSpec/man/plot.Rd | 90 +-
hyperSpec-0.98-20150304/hyperSpec/man/plotc.Rd | 55 -
hyperSpec-0.98-20150304/hyperSpec/man/plotmat.Rd | 38
hyperSpec-0.98-20150304/hyperSpec/man/plotspc.Rd | 279 ++----
hyperSpec-0.98-20150304/hyperSpec/man/qplotc.Rd | 36
hyperSpec-0.98-20150304/hyperSpec/man/qplotmap.Rd | 39
hyperSpec-0.98-20150304/hyperSpec/man/qplotmix.Rd | 122 +--
hyperSpec-0.98-20150304/hyperSpec/man/qplotmixmap.Rd | 18
hyperSpec-0.98-20150304/hyperSpec/man/qplotspc.Rd | 35
hyperSpec-0.98-20150304/hyperSpec/man/quickdf.Rd | 14
hyperSpec-0.98-20150304/hyperSpec/man/rbind-fill.Rd | 71 -
hyperSpec-0.98-20150304/hyperSpec/man/read-cytomat.Rd | 34
hyperSpec-0.98-20150304/hyperSpec/man/read-ini.Rd | 27
hyperSpec-0.98-20150304/hyperSpec/man/read-spc-Kaiser.Rd | 64 -
hyperSpec-0.98-20150304/hyperSpec/man/read-spc.Rd | 100 +-
hyperSpec-0.98-20150304/hyperSpec/man/read.jdx.Rd | 75 -
hyperSpec-0.98-20150304/hyperSpec/man/read.txt.Horiba.Rd | 41 -
hyperSpec-0.98-20150304/hyperSpec/man/read.txt.Shimadzu.Rd | 24
hyperSpec-0.98-20150304/hyperSpec/man/readENVI.Rd | 190 ++--
hyperSpec-0.98-20150304/hyperSpec/man/rmmvnorm.Rd | 43 -
hyperSpec-0.98-20150304/hyperSpec/man/sample.Rd | 63 -
hyperSpec-0.98-20150304/hyperSpec/man/scale.Rd | 41 -
hyperSpec-0.98-20150304/hyperSpec/man/scan-txt-Renishaw.Rd | 89 +-
hyperSpec-0.98-20150304/hyperSpec/man/scan.dat.Witec.Rd | 57 -
hyperSpec-0.98-20150304/hyperSpec/man/seq.Rd | 47 -
hyperSpec-0.98-20150304/hyperSpec/man/show.Rd | 71 -
hyperSpec-0.98-20150304/hyperSpec/man/spc-bin.Rd | 44 -
hyperSpec-0.98-20150304/hyperSpec/man/spc-identify.Rd | 202 ++--
hyperSpec-0.98-20150304/hyperSpec/man/spc-loess.Rd | 35
hyperSpec-0.98-20150304/hyperSpec/man/spc-rubberband.Rd | 36
hyperSpec-0.98-20150304/hyperSpec/man/spc-spline.Rd | 25
hyperSpec-0.98-20150304/hyperSpec/man/spc.NA.linapprox.Rd | 22
hyperSpec-0.98-20150304/hyperSpec/man/split.Rd | 28
hyperSpec-0.98-20150304/hyperSpec/man/subset.Rd | 22
hyperSpec-0.98-20150304/hyperSpec/man/summary.Rd | 43 -
hyperSpec-0.98-20150304/hyperSpec/man/sweep.Rd | 55 -
hyperSpec-0.98-20150304/hyperSpec/man/textio.Rd | 231 ++---
hyperSpec-0.98-20150304/hyperSpec/man/trellis.factor.key.Rd | 20
hyperSpec-0.98-20150304/hyperSpec/man/unittests.Rd | 20
hyperSpec-0.98-20150304/hyperSpec/man/vanderMonde.Rd | 47 -
hyperSpec-0.98-20150304/hyperSpec/man/wc.Rd | 18
hyperSpec-0.98-20150304/hyperSpec/man/wl.Rd | 72 -
hyperSpec-0.98-20150304/hyperSpec/man/wl.eval.Rd | 28
hyperSpec-0.98-20150304/hyperSpec/man/wl2i.Rd | 49 -
hyperSpec-0.98-20150304/hyperSpec/vignettes/Makefile | 69 -
hyperSpec-0.98-20150304/hyperSpec/vignettes/baseline-pkg.bib |only
hyperSpec-0.98-20150304/hyperSpec/vignettes/baseline.Rnw | 33
hyperSpec-0.98-20150304/hyperSpec/vignettes/chondro.Rnw | 2
hyperSpec-0.98-20150304/hyperSpec/vignettes/chondro.tex | 2
hyperSpec-0.98-20150304/hyperSpec/vignettes/fig-3D.png |binary
hyperSpec-0.98-20150304/hyperSpec/vignettes/fileio.Rnw | 2
hyperSpec-0.98-20150304/hyperSpec/vignettes/fileio.tex | 2
hyperSpec-0.98-20150304/hyperSpec/vignettes/flu.Rnw | 4
hyperSpec-0.98-20150304/hyperSpec/vignettes/introduction-pkg.bib | 4
hyperSpec-0.98-20150304/hyperSpec/vignettes/introduction.Rnw | 75 -
hyperSpec-0.98-20150304/hyperSpec/vignettes/laser-pkg.bib | 75 -
hyperSpec-0.98-20150304/hyperSpec/vignettes/laser.Rnw | 4
hyperSpec-0.98-20150304/hyperSpec/vignettes/plotting-pkg.bib | 12
hyperSpec-0.98-20150304/hyperSpec/vignettes/plotting.Rnw | 139 +--
hyperSpec-0.98-20150304/hyperSpec/vignettes/vignettes.defs | 15
209 files changed, 3849 insertions(+), 4575 deletions(-)
Title: Spatial Visualization with Google Maps and OpenStreetMap
Diff between ggmap versions 2.3 dated 2013-04-13 and 2.4 dated 2015-03-05
Description: Easily visualize of spatial data and models on top of Google Maps,
OpenStreetMaps, Stamen Maps, or CloudMade Maps with ggplot2.
Author: David Kahle [aut, cre],
Hadley Wickham [aut]
Maintainer: David Kahle
ggmap-2.3/ggmap/inst/PH.txt |only
ggmap-2.3/ggmap/man/geocodeQueryCheck.Rd |only
ggmap-2.4/ggmap/DESCRIPTION | 37 -
ggmap-2.4/ggmap/MD5 | 116 +++--
ggmap-2.4/ggmap/NAMESPACE | 9
ggmap-2.4/ggmap/NEWS | 57 ++
ggmap-2.4/ggmap/R/OSM_scale_lookup.R | 68 +--
ggmap-2.4/ggmap/R/bb2bbox.R |only
ggmap-2.4/ggmap/R/calc_zoom.r |only
ggmap-2.4/ggmap/R/file_drawer.R |only
ggmap-2.4/ggmap/R/geocode.R | 419 ++++++++++++++-------
ggmap-2.4/ggmap/R/get_cloudmademap.R | 268 ++++++-------
ggmap-2.4/ggmap/R/get_googlemap.R | 577 +++++++++++++++--------------
ggmap-2.4/ggmap/R/get_map.R | 367 +++++++++---------
ggmap-2.4/ggmap/R/get_navermap.R |only
ggmap-2.4/ggmap/R/get_openstreetmap.R | 183 +++++----
ggmap-2.4/ggmap/R/get_stamenmap.R | 601 +++++++++++++++++++++----------
ggmap-2.4/ggmap/R/ggimage.R | 52 +-
ggmap-2.4/ggmap/R/gglocator.R | 50 +-
ggmap-2.4/ggmap/R/ggmap.R | 448 ++++++++++++-----------
ggmap-2.4/ggmap/R/ggplot2.R |only
ggmap-2.4/ggmap/R/help.R | 2
ggmap-2.4/ggmap/R/mapdist.R | 156 ++++----
ggmap-2.4/ggmap/R/qmap.R | 275 +++++++-------
ggmap-2.4/ggmap/R/qmplot.R | 369 ++++++++++++-------
ggmap-2.4/ggmap/R/revgeocode.R | 83 ++--
ggmap-2.4/ggmap/R/route.R | 307 +++++++--------
ggmap-2.4/ggmap/R/zips.R | 6
ggmap-2.4/ggmap/R/zzz.R |only
ggmap-2.4/ggmap/README.md |only
ggmap-2.4/ggmap/inst/CITATION |only
ggmap-2.4/ggmap/man/LonLat2XY.Rd | 26 -
ggmap-2.4/ggmap/man/OSM_scale_lookup.Rd | 57 +-
ggmap-2.4/ggmap/man/XY2LonLat.Rd | 30 -
ggmap-2.4/ggmap/man/bb2bbox.Rd |only
ggmap-2.4/ggmap/man/calc_zoom.Rd |only
ggmap-2.4/ggmap/man/crime.Rd | 10
ggmap-2.4/ggmap/man/distQueryCheck.Rd | 12
ggmap-2.4/ggmap/man/file_drawer.Rd |only
ggmap-2.4/ggmap/man/geocode.Rd | 82 ++--
ggmap-2.4/ggmap/man/geom_leg.Rd | 27 -
ggmap-2.4/ggmap/man/get_cloudmademap.Rd | 92 +---
ggmap-2.4/ggmap/man/get_googlemap.Rd | 189 ++++-----
ggmap-2.4/ggmap/man/get_map.Rd | 127 ++----
ggmap-2.4/ggmap/man/get_navermap.Rd |only
ggmap-2.4/ggmap/man/get_openstreetmap.Rd | 96 ++--
ggmap-2.4/ggmap/man/get_stamenmap.Rd | 213 ++++++++--
ggmap-2.4/ggmap/man/ggimage.Rd | 26 -
ggmap-2.4/ggmap/man/gglocator.Rd | 31 -
ggmap-2.4/ggmap/man/ggmap.Rd | 124 +++---
ggmap-2.4/ggmap/man/ggmapplot.Rd | 32 -
ggmap-2.4/ggmap/man/hadley.Rd | 7
ggmap-2.4/ggmap/man/inset.Rd | 30 -
ggmap-2.4/ggmap/man/inset_raster.Rd | 19
ggmap-2.4/ggmap/man/legs2route.Rd | 12
ggmap-2.4/ggmap/man/make_bbox.Rd | 17
ggmap-2.4/ggmap/man/mapdist.Rd | 51 --
ggmap-2.4/ggmap/man/qmap.Rd | 50 +-
ggmap-2.4/ggmap/man/qmplot.Rd | 255 +++++++++----
ggmap-2.4/ggmap/man/revgeocode.Rd | 43 --
ggmap-2.4/ggmap/man/route.Rd | 86 +---
ggmap-2.4/ggmap/man/routeQueryCheck.Rd | 12
ggmap-2.4/ggmap/man/theme_inset.Rd | 13
ggmap-2.4/ggmap/man/theme_nothing.Rd | 15
ggmap-2.4/ggmap/man/wind.Rd | 16
ggmap-2.4/ggmap/man/zips.Rd | 11
66 files changed, 3548 insertions(+), 2713 deletions(-)
Title: Calculate Cluster-Robust p-Values and Confidence Intervals
Diff between clusterSEs versions 1.0 dated 2015-03-03 and 1.1 dated 2015-03-05
Description: Calculate p-values and confidence intervals using cluster-adjusted standard errors (based on Ibragimov and Muller 2010, Journal of Business and Economic Statistics 28(4)), pairs cluster bootstrapped t-statistics, and wild cluster bootstrapped t-statistics for the GLM and mlogit models (the latter two techniques based on Cameron, Gelbach, and Miller 2008, Review of Economics and Statistics 90(3)).
Author: Justin Esarey [aut, cre]
Maintainer: Justin Esarey
DESCRIPTION | 10 +-
MD5 | 18 ++-
NAMESPACE | 1
R/clusterBS.R | 27 ++++-
R/clusterBSmlogit.R |only
R/clusterIMmlogit.R | 9 +
R/clusterwild.R | 226 +++++++++++++++++++++++++++++++++--------------
man/cluster.bs.Rd | 7 +
man/cluster.bs.mlogit.Rd |only
man/cluster.im.mlogit.Rd | 9 +
man/cluster.wild.Rd | 31 ++++--
11 files changed, 241 insertions(+), 97 deletions(-)