[Distr-commits] r1183 - in pkg/distrDoc: . inst man vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Jul 8 16:25:51 CEST 2018
Author: ruckdeschel
Date: 2018-07-08 16:25:50 +0200 (Sun, 08 Jul 2018)
New Revision: 1183
Modified:
pkg/distrDoc/DESCRIPTION
pkg/distrDoc/NAMESPACE
pkg/distrDoc/inst/CITATION
pkg/distrDoc/inst/NEWS
pkg/distrDoc/man/0distrDoc-package.Rd
pkg/distrDoc/vignettes/BiasType.pdf
pkg/distrDoc/vignettes/Confint.pdf
pkg/distrDoc/vignettes/Estimate.pdf
pkg/distrDoc/vignettes/EvaluationList.pdf
pkg/distrDoc/vignettes/NormType.pdf
pkg/distrDoc/vignettes/ParamFamParameter.pdf
pkg/distrDoc/vignettes/ProbFamily.pdf
pkg/distrDoc/vignettes/RiskType.pdf
pkg/distrDoc/vignettes/Symmetry.pdf
pkg/distrDoc/vignettes/dataclass.pdf
pkg/distrDoc/vignettes/distr.Rnw
pkg/distrDoc/vignettes/distribution.pdf
pkg/distrDoc/vignettes/evaluation.pdf
pkg/distrDoc/vignettes/parameter.pdf
pkg/distrDoc/vignettes/rspace.pdf
Log:
[distrDoc] merged branch 2.7 back to trunk
Modified: pkg/distrDoc/DESCRIPTION
===================================================================
--- pkg/distrDoc/DESCRIPTION 2018-07-08 14:24:29 UTC (rev 1182)
+++ pkg/distrDoc/DESCRIPTION 2018-07-08 14:25:50 UTC (rev 1183)
@@ -1,21 +1,25 @@
Package: distrDoc
-Version: 2.6.1
-Date: 2017-04-23
+Version: 2.7
+Date: 2015-11-07
Title: Documentation for 'distr' Family of R Packages
-Description: Provides documentation in form of a common vignette to packages 'distr', 'distrEx', 'distrMod', 'distrSim', 'distrTEst',
- 'distrTeach', and 'distrEllipse'.
-Authors at R: c(person("Florian", "Camphausen", role="ctb", comment="contributed as student to the documented packages in the initial
- phase --2005"), person("Matthias", "Kohl", role=c("aut", "cph")), person("Peter", "Ruckdeschel", role=c("cre", "cph"),
- email="peter.ruckdeschel at uni-oldenburg.de"), person("Thomas", "Stabla", role="ctb", comment="contributed as student to the
- documented packages in the initial phase --2005"))
+Description: Provides documentation in form of a common vignette to packages distr, distrEx,
+ distrMod, distrSim, distrTEst, distrTeach, and distrEllipse.
+Authors at R: c(person("Florian", "Camphausen", role="ctb", comment="contributed as student to the
+ documented packages in the initial phase --2005"), person("Matthias", "Kohl",
+ role=c("aut", "cph")), person("Peter", "Ruckdeschel", role=c("cre", "cph"),
+ email="peter.ruckdeschel at uni-oldenburg.de"), person("Thomas", "Stabla", role="ctb",
+ comment="contributed as student to the documented packages in the initial phase
+ --2005"))
Depends: R(>= 2.14.0)
-Imports: distr(>= 2.2.0), distrEx(>= 2.2.0), distrSim(>= 2.2.0), distrTEst(>= 2.2.0), distrTeach(>= 2.2.0), RandVar(>= 0.7),
- distrMod(>= 2.2.0), MASS, methods, SweaveListingUtils, startupmsg
-Suggests: Biobase
+Imports: distr(>= 2.2.0), distrEx(>= 2.2.0), distrSim(>= 2.2.0), distrTEst(>= 2.2.0),
+ distrTeach(>= 2.2.0), RandVar(>= 0.7), distrMod(>= 2.2.0), MASS, methods,
+ startupmsg
+Suggests: Biobase, knitr
+VignetteBuilder: knitr
ByteCompile: yes
Encoding: latin1
License: LGPL-3
URL: http://distr.r-forge.r-project.org/
LastChangedDate: {$LastChangedDate$}
LastChangedRevision: {$LastChangedRevision$}
-SVNRevision: 1133
+SVNRevision: 1080
Modified: pkg/distrDoc/NAMESPACE
===================================================================
--- pkg/distrDoc/NAMESPACE 2018-07-08 14:24:29 UTC (rev 1182)
+++ pkg/distrDoc/NAMESPACE 2018-07-08 14:25:50 UTC (rev 1183)
@@ -1,5 +1,4 @@
import("methods")
-import("SweaveListingUtils")
importFrom("startupmsg","buildStartupMessage")
import("MASS")
import("distr")
Modified: pkg/distrDoc/inst/CITATION
===================================================================
--- pkg/distrDoc/inst/CITATION 2018-07-08 14:24:29 UTC (rev 1182)
+++ pkg/distrDoc/inst/CITATION 2018-07-08 14:25:50 UTC (rev 1183)
@@ -1,4 +1,4 @@
-citHeader("To cite package distr in publications use:")
+citHeader("To cite package distrDoc (and other packages of the distr family of packages) in publications use:")
citEntry(entry="Article",
title = "S4 Classes for Distributions",
Modified: pkg/distrDoc/inst/NEWS
===================================================================
--- pkg/distrDoc/inst/NEWS 2018-07-08 14:24:29 UTC (rev 1182)
+++ pkg/distrDoc/inst/NEWS 2018-07-08 14:25:50 UTC (rev 1183)
@@ -8,6 +8,21 @@
information)
##############
+v 2.7
+##############
+
+user-visible CHANGES:
++ more precise formulation of how to use calls to q() for RStudio
+ and Jupyter IRKernel (i.e., use q.l)
++ switch from SweaveListingUtils to knitr in vignettes
++ replaced http://CRAN... by https://CRAN... (also in CITATION and similar files)
++ updated address (Oldenburg) in several vignettes
+
+under the hood:
++ fixed CITATION issue (raised by K.Hornik,(12.10., 12:26)
++ fixed omegahat.net issue (raised by K.Hornik,(24.10.2016, 18:08)
+
+##############
v 2.6
##############
@@ -18,7 +33,6 @@
+ updated references in vignette distr.Rnw
+ mention that pattern substitution can now be switched on and off in all plot
functions according to argument withSubst
-+ mention aliases p.r and q.l for RStudio
under the hood
+ fixed \VignetteKeyword issue detected as in mail by K. Hornik 2015-02-03
Modified: pkg/distrDoc/man/0distrDoc-package.Rd
===================================================================
--- pkg/distrDoc/man/0distrDoc-package.Rd 2018-07-08 14:24:29 UTC (rev 1182)
+++ pkg/distrDoc/man/0distrDoc-package.Rd 2018-07-08 14:25:50 UTC (rev 1183)
@@ -13,8 +13,8 @@
\details{
\tabular{ll}{
Package: \tab distrDoc \cr
-Version: \tab 2.6.1 \cr
-Date: \tab 2017-04-22 \cr
+Version: \tab 2.7 \cr
+Date: \tab 2015-11-07 \cr
Depends: \tab R(>= 2.14.0) \cr
Imports: \tab distr(>= 2.2.0), distrEx(>= 2.2.0), distrSim(>= 2.2.0), distrTEst(>= 2.2.0),
distrTeach(>= 2.2.0), RandVar(>= 0.7), distrMod(>= 2.2.0), MASS, methods,
@@ -23,7 +23,7 @@
ByteCompile: \tab yes \cr
License: \tab LGPL-3 \cr
URL: \tab http://distr.r-forge.r-project.org/\cr
-SVNRevision: \tab 1132 \cr
+SVNRevision: \tab 1080 \cr
}}
Modified: pkg/distrDoc/vignettes/BiasType.pdf
===================================================================
(Binary files differ)
Modified: pkg/distrDoc/vignettes/Confint.pdf
===================================================================
--- pkg/distrDoc/vignettes/Confint.pdf 2018-07-08 14:24:29 UTC (rev 1182)
+++ pkg/distrDoc/vignettes/Confint.pdf 2018-07-08 14:25:50 UTC (rev 1183)
@@ -1,98 +1,98 @@
-%PDF-1.4
-%Çì¢
-5 0 obj
-<</Length 6 0 R/Filter /FlateDecode>>
-stream
-xœ‘ÝNà ÇïÏSœ;]L°PJé.5Æ£™ö¡Sº²˜ùôž®u©™‰ ‡– ÿ°ÃŒq̆5MàöµÄu ‡×À%ã%¯«B3!1Wà y¥˜–£ƒ„f¹Tø G1|}¼äÚÛD“Éø¸Ÿ†
-xWƒ`Y©s¬-…ÒÈ+º(Ö
-Œa) ¤à¹B® -è(Àõý¦k|—õ<Ô°ú£È4q%%E.€þ1*©µƒ“VÁt™ëyð‚)UqI6’ ÍÁoÒaë–hßM46¹84˜K ÁTYbýD¨ K.ÑÄh‹«_ ›¶e®O>˜4HÒçÓ™àæÌÉöòìMض®÷_s¼Û½=SMÑ4›×ú>[ï}o:;×{Ù&¿éLû|Ò=>Þ
-¾ïÄ£àendstream
-endobj
-6 0 obj
-310
-endobj
-4 0 obj
-<</Type/Page/MediaBox [0 0 365 207]
-/Parent 3 0 R
-/Resources<</ProcSet[/PDF /Text]
-/ExtGState 10 0 R
-/Font 11 0 R
->>
-/Contents 5 0 R
->>
-endobj
-3 0 obj
-<< /Type /Pages /Kids [
-4 0 R
-] /Count 1
->>
-endobj
-1 0 obj
-<</Type /Catalog /Pages 3 0 R
-/Metadata 12 0 R
->>
-endobj
-7 0 obj
-<</Type/ExtGState
-/OPM 1>>endobj
-10 0 obj
-<</R7
-7 0 R>>
-endobj
-11 0 obj
-<</R9
-9 0 R/R8
-8 0 R>>
-endobj
-9 0 obj
-<</BaseFont/Courier/Type/Font
-/Subtype/Type1>>
-endobj
-8 0 obj
-<</BaseFont/Helvetica-Bold/Type/Font
-/Subtype/Type1>>
-endobj
-12 0 obj
-<</Type/Metadata
-/Subtype/XML/Length 1287>>stream
-<?xpacket begin='' id='W5M0MpCehiHzreSzNTczkc9d'?>
-<?adobe-xap-filters esc="CRLF"?>
-<x:xmpmeta xmlns:x='adobe:ns:meta/' x:xmptk='XMP toolkit 2.9.1-13, framework 1.6'>
-<rdf:RDF xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#' xmlns:iX='http://ns.adobe.com/iX/1.0/'>
-<rdf:Description rdf:about='ab2a2cd7-99ff-11e8-0000-b517b9d6e012' xmlns:pdf='http://ns.adobe.com/pdf/1.3/' pdf:Producer='GPL Ghostscript 8.61'/>
-<rdf:Description rdf:about='ab2a2cd7-99ff-11e8-0000-b517b9d6e012' xmlns:xap='http://ns.adobe.com/xap/1.0/' xap:ModifyDate='2008-08-04T07:06:39+02:00' xap:CreateDate='2008-08-04T07:06:39+02:00'><xap:CreatorTool>UnknownApplication</xap:CreatorTool></rdf:Description>
-<rdf:Description rdf:about='ab2a2cd7-99ff-11e8-0000-b517b9d6e012' xmlns:xapMM='http://ns.adobe.com/xap/1.0/mm/' xapMM:DocumentID='ab2a2cd7-99ff-11e8-0000-b517b9d6e012'/>
-<rdf:Description rdf:about='ab2a2cd7-99ff-11e8-0000-b517b9d6e012' xmlns:dc='http://purl.org/dc/elements/1.1/' dc:format='application/pdf'><dc:title><rdf:Alt><rdf:li xml:lang='x-default'>Untitled</rdf:li></rdf:Alt></dc:title></rdf:Description>
-</rdf:RDF>
-</x:xmpmeta>
-
-
-<?xpacket end='w'?>
-endstream
-endobj
-2 0 obj
-<</Producer(GPL Ghostscript 8.61)
-/CreationDate(D:20080804070639+02'00')
-/ModDate(D:20080804070639+02'00')>>endobj
-xref
-0 13
-0000000000 65535 f
-0000000624 00000 n
-0000002294 00000 n
-0000000565 00000 n
-0000000414 00000 n
-0000000015 00000 n
-0000000395 00000 n
-0000000689 00000 n
-0000000861 00000 n
-0000000799 00000 n
-0000000730 00000 n
-0000000760 00000 n
-0000000930 00000 n
-trailer
-<< /Size 13 /Root 1 0 R /Info 2 0 R
-/ID [<AAC5262C4E5A9FAF4088CDC9CCF7AF82><AAC5262C4E5A9FAF4088CDC9CCF7AF82>]
->>
-startxref
-2417
-%%EOF
+%PDF-1.4
+%Çì¢
+5 0 obj
+<</Length 6 0 R/Filter /FlateDecode>>
+stream
+xœ‘ÝNà ÇïÏSœ;]L°PJé.5Æ£™ö¡Sº²˜ùôž®u©™‰ ‡– ÿ°ÃŒq̆5MàöµÄu ‡×À%ã%¯«B3!1Wà y¥˜–£ƒ„f¹Tø G1|}¼äÚÛD“Éø¸Ÿ†
+xWƒ`Y©s¬-…ÒÈ+º(Ö
+Œa) ¤à¹B® -è(Àõý¦k|—õ<Ô°ú£È4q%%E.€þ1*©µƒ“VÁt™ëyð‚)UqI6’ ÍÁoÒaë–hßM46¹84˜K ÁTYbýD¨ K.ÑÄh‹«_ ›¶e®O>˜4HÒçÓ™àæÌÉöòìMض®÷_s¼Û½=SMÑ4›×ú>[ï}o:;×{Ù&¿éLû|Ò=>Þ
+¾ïÄ£àendstream
+endobj
+6 0 obj
+310
+endobj
+4 0 obj
+<</Type/Page/MediaBox [0 0 365 207]
+/Parent 3 0 R
+/Resources<</ProcSet[/PDF /Text]
+/ExtGState 10 0 R
+/Font 11 0 R
+>>
+/Contents 5 0 R
+>>
+endobj
+3 0 obj
+<< /Type /Pages /Kids [
+4 0 R
+] /Count 1
+>>
+endobj
+1 0 obj
+<</Type /Catalog /Pages 3 0 R
+/Metadata 12 0 R
+>>
+endobj
+7 0 obj
+<</Type/ExtGState
+/OPM 1>>endobj
+10 0 obj
+<</R7
+7 0 R>>
+endobj
+11 0 obj
+<</R9
+9 0 R/R8
+8 0 R>>
+endobj
+9 0 obj
+<</BaseFont/Courier/Type/Font
+/Subtype/Type1>>
+endobj
+8 0 obj
+<</BaseFont/Helvetica-Bold/Type/Font
+/Subtype/Type1>>
+endobj
+12 0 obj
+<</Type/Metadata
+/Subtype/XML/Length 1287>>stream
+<?xpacket begin='' id='W5M0MpCehiHzreSzNTczkc9d'?>
+<?adobe-xap-filters esc="CRLF"?>
+<x:xmpmeta xmlns:x='adobe:ns:meta/' x:xmptk='XMP toolkit 2.9.1-13, framework 1.6'>
+<rdf:RDF xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#' xmlns:iX='http://ns.adobe.com/iX/1.0/'>
+<rdf:Description rdf:about='ab2a2cd7-99ff-11e8-0000-b517b9d6e012' xmlns:pdf='http://ns.adobe.com/pdf/1.3/' pdf:Producer='GPL Ghostscript 8.61'/>
+<rdf:Description rdf:about='ab2a2cd7-99ff-11e8-0000-b517b9d6e012' xmlns:xap='http://ns.adobe.com/xap/1.0/' xap:ModifyDate='2008-08-04T07:06:39+02:00' xap:CreateDate='2008-08-04T07:06:39+02:00'><xap:CreatorTool>UnknownApplication</xap:CreatorTool></rdf:Description>
+<rdf:Description rdf:about='ab2a2cd7-99ff-11e8-0000-b517b9d6e012' xmlns:xapMM='http://ns.adobe.com/xap/1.0/mm/' xapMM:DocumentID='ab2a2cd7-99ff-11e8-0000-b517b9d6e012'/>
+<rdf:Description rdf:about='ab2a2cd7-99ff-11e8-0000-b517b9d6e012' xmlns:dc='http://purl.org/dc/elements/1.1/' dc:format='application/pdf'><dc:title><rdf:Alt><rdf:li xml:lang='x-default'>Untitled</rdf:li></rdf:Alt></dc:title></rdf:Description>
+</rdf:RDF>
+</x:xmpmeta>
+
+
+<?xpacket end='w'?>
+endstream
+endobj
+2 0 obj
+<</Producer(GPL Ghostscript 8.61)
+/CreationDate(D:20080804070639+02'00')
+/ModDate(D:20080804070639+02'00')>>endobj
+xref
+0 13
+0000000000 65535 f
+0000000624 00000 n
+0000002294 00000 n
+0000000565 00000 n
+0000000414 00000 n
+0000000015 00000 n
+0000000395 00000 n
+0000000689 00000 n
+0000000861 00000 n
+0000000799 00000 n
+0000000730 00000 n
+0000000760 00000 n
+0000000930 00000 n
+trailer
+<< /Size 13 /Root 1 0 R /Info 2 0 R
+/ID [<AAC5262C4E5A9FAF4088CDC9CCF7AF82><AAC5262C4E5A9FAF4088CDC9CCF7AF82>]
+>>
+startxref
+2417
+%%EOF
Modified: pkg/distrDoc/vignettes/Estimate.pdf
===================================================================
(Binary files differ)
Modified: pkg/distrDoc/vignettes/EvaluationList.pdf
===================================================================
--- pkg/distrDoc/vignettes/EvaluationList.pdf 2018-07-08 14:24:29 UTC (rev 1182)
+++ pkg/distrDoc/vignettes/EvaluationList.pdf 2018-07-08 14:25:50 UTC (rev 1183)
@@ -1,68 +1,68 @@
-%PDF-1.2
-%Çì¢
-5 0 obj
-<</Length 6 0 R/Filter /FlateDecode>>
-stream
-xœ•ËjÃ0E÷ów׆ÂT£ÇÈβ`ºÉ&©~À§M‰SâºíïWrtÊ€4Ìãê aØz˜—¤HPb|%Vàa
-‰µaWÁÙÀÁbìiKÖ±
-¢ø¡Y›çÛ[/çÙü‘<‹ªÆ¹pwž=n"\ÍFmDÚfg¥%ÂA½‡ÍP!
-t ùn÷_í´û8¬vŸS.,Ò;5‰Ö.×Ù›—Šƒ“ÒÍ‘ùÏà’¿Èȵÿ¬-jjÇF\œý? Ú¡_¢{kǶ›ú±x÷žÕÛÌ·ÊýfŸ¡–(çâ¦_…Ò` endstream
-endobj
-6 0 obj
-232
-endobj
-4 0 obj
-<</Type/Page/MediaBox [0 0 612 792]
-/Rotate 0/Parent 3 0 R
-/Resources<</ProcSet[/PDF /Text]
-/Font 9 0 R
->>
-/Contents 5 0 R
->>
-endobj
-3 0 obj
-<< /Type /Pages /Kids [
-4 0 R
-] /Count 1
->>
-endobj
-1 0 obj
-<</Type /Catalog /Pages 3 0 R
->>
-endobj
-9 0 obj
-<</R7
-7 0 R/R8
-8 0 R>>
-endobj
-7 0 obj
-<</BaseFont/Helvetica-Bold/Type/Font
-/Subtype/Type1>>
-endobj
-8 0 obj
-<</BaseFont/Courier/Type/Font
-/Subtype/Type1>>
-endobj
-2 0 obj
-<</Producer(GPL Ghostscript 8.56)
-/CreationDate(D:20070711222628Z)
-/ModDate(D:20070711222628Z)>>endobj
-xref
-0 10
-0000000000 65535 f
-0000000536 00000 n
-0000000753 00000 n
-0000000477 00000 n
-0000000336 00000 n
-0000000015 00000 n
-0000000317 00000 n
-0000000622 00000 n
-0000000691 00000 n
-0000000584 00000 n
-trailer
-<< /Size 10 /Root 1 0 R /Info 2 0 R
-/ID [<E1D2E012CEF9FA49770F81D9A9F3D26E><E1D2E012CEF9FA49770F81D9A9F3D26E>]
->>
-startxref
-864
-%%EOF
+%PDF-1.2
+%Çì¢
+5 0 obj
+<</Length 6 0 R/Filter /FlateDecode>>
+stream
+xœ•ËjÃ0E÷ów׆ÂT£ÇÈβ`ºÉ&©~À§M‰SâºíïWrtÊ€4Ìãê aØz˜—¤HPb|%Vàa
+‰µaWÁÙÀÁbìiKÖ±
+¢ø¡Y›çÛ[/çÙü‘<‹ªÆ¹pwž=n"\ÍFmDÚfg¥%ÂA½‡ÍP!
+t ùn÷_í´û8¬vŸS.,Ò;5‰Ö.×Ù›—Šƒ“ÒÍ‘ùÏà’¿Èȵÿ¬-jjÇF\œý? Ú¡_¢{kǶ›ú±x÷žÕÛÌ·ÊýfŸ¡–(çâ¦_…Ò` endstream
+endobj
+6 0 obj
+232
+endobj
+4 0 obj
+<</Type/Page/MediaBox [0 0 612 792]
+/Rotate 0/Parent 3 0 R
+/Resources<</ProcSet[/PDF /Text]
+/Font 9 0 R
+>>
+/Contents 5 0 R
+>>
+endobj
+3 0 obj
+<< /Type /Pages /Kids [
+4 0 R
+] /Count 1
+>>
+endobj
+1 0 obj
+<</Type /Catalog /Pages 3 0 R
+>>
+endobj
+9 0 obj
+<</R7
+7 0 R/R8
+8 0 R>>
+endobj
+7 0 obj
+<</BaseFont/Helvetica-Bold/Type/Font
+/Subtype/Type1>>
+endobj
+8 0 obj
+<</BaseFont/Courier/Type/Font
+/Subtype/Type1>>
+endobj
+2 0 obj
+<</Producer(GPL Ghostscript 8.56)
+/CreationDate(D:20070711222628Z)
+/ModDate(D:20070711222628Z)>>endobj
+xref
+0 10
+0000000000 65535 f
+0000000536 00000 n
+0000000753 00000 n
+0000000477 00000 n
+0000000336 00000 n
+0000000015 00000 n
+0000000317 00000 n
+0000000622 00000 n
+0000000691 00000 n
+0000000584 00000 n
+trailer
+<< /Size 10 /Root 1 0 R /Info 2 0 R
+/ID [<E1D2E012CEF9FA49770F81D9A9F3D26E><E1D2E012CEF9FA49770F81D9A9F3D26E>]
+>>
+startxref
+864
+%%EOF
Modified: pkg/distrDoc/vignettes/NormType.pdf
===================================================================
(Binary files differ)
Modified: pkg/distrDoc/vignettes/ParamFamParameter.pdf
===================================================================
--- pkg/distrDoc/vignettes/ParamFamParameter.pdf 2018-07-08 14:24:29 UTC (rev 1182)
+++ pkg/distrDoc/vignettes/ParamFamParameter.pdf 2018-07-08 14:25:50 UTC (rev 1183)
@@ -1,9 +1,101 @@
-%PDF-1.4
-%Çì¢
-5 0 obj
-<</Length 6 0 R/Filter /FlateDecode>>
-stream
-xœRÉNÃ0½û+æÆ&
-™ñÞ#pa'?…‚šB+ø|&MR¨TµB>زß̼Åï AÒaÏkuúàáùCt«}V–döÀÖYÔré9"èè0m¡Jŵqð©–ÍàárŸ²Ç-CÞõçaËk8Kc +µi.¬P”JfHKÕ³%ð98
-ì½Öêð.k³º˜íQúªÎSu¿A Â`W¤8h4Žz-{€v2OPt†À=õd1x ~S·Ù‹g¬
-Æ–ÔO
+%PDF-1.4
+%Çì¢
+5 0 obj
+<</Length 6 0 R/Filter /FlateDecode>>
+stream
+xœRÉNÃ0½û+æÆ&
+™ñÞ#pa'?…‚šB+ø|&MR¨TµB>زß̼Åï AÒaÏkuúàáùCt«}V–döÀÖYÔré9"èè0m¡Jŵqð©–ÍàárŸ²Ç-CÞõçaËk8Kc +µi.¬P”JfHKÕ³%ð98
+ì½Öêð.k³º˜íQúªÎSu¿A Â`W¤8h4Žz-{€v2OPt†À=õd1x ~S·Ù‹g¬
+Æ–ÔOa>üE$äAò!zQŠp¶ëiìÚÃ{áküïeJ´âÉ!éžFï/²zK#¹q ÉE§Ñ;·®` è_2@ç"™å7²ÉAUÍšE]´UÞñ é®3:/®\ua-ª¬É%°Û·y5k²éÍPt°6ü𤬾Š§Ý°y›•³ \gó¶úšµ‹&ï
+×[¨½A/Y8‘
+Ô«›ñ«NÅ• £Ùš
+h2‰C‰v*6‡€äV˜©*ÿV÷"“ïÕ7À-ò÷endstream
+endobj
+6 0 obj
+404
+endobj
+4 0 obj
+<</Type/Page/MediaBox [0 0 275 298]
+/Parent 3 0 R
+/Resources<</ProcSet[/PDF /Text]
+/ExtGState 10 0 R
+/Font 11 0 R
+>>
+/Contents 5 0 R
+>>
+endobj
+3 0 obj
+<< /Type /Pages /Kids [
+4 0 R
+] /Count 1
+>>
+endobj
+1 0 obj
+<</Type /Catalog /Pages 3 0 R
+/Metadata 12 0 R
+>>
+endobj
+7 0 obj
+<</Type/ExtGState
+/OPM 1>>endobj
+10 0 obj
+<</R7
+7 0 R>>
+endobj
+11 0 obj
+<</R9
+9 0 R/R8
+8 0 R>>
+endobj
+9 0 obj
+<</BaseFont/Courier/Type/Font
+/Subtype/Type1>>
+endobj
+8 0 obj
+<</BaseFont/Helvetica-Bold/Type/Font
+/Subtype/Type1>>
+endobj
+12 0 obj
+<</Type/Metadata
+/Subtype/XML/Length 1287>>stream
+<?xpacket begin='' id='W5M0MpCehiHzreSzNTczkc9d'?>
+<?adobe-xap-filters esc="CRLF"?>
+<x:xmpmeta xmlns:x='adobe:ns:meta/' x:xmptk='XMP toolkit 2.9.1-13, framework 1.6'>
+<rdf:RDF xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#' xmlns:iX='http://ns.adobe.com/iX/1.0/'>
+<rdf:Description rdf:about='4ed87dd1-b03a-11e8-0000-05261415641d' xmlns:pdf='http://ns.adobe.com/pdf/1.3/' pdf:Producer='GPL Ghostscript 8.61'/>
+<rdf:Description rdf:about='4ed87dd1-b03a-11e8-0000-05261415641d' xmlns:xap='http://ns.adobe.com/xap/1.0/' xap:ModifyDate='2008-09-01T14:01:50+02:00' xap:CreateDate='2008-09-01T14:01:50+02:00'><xap:CreatorTool>UnknownApplication</xap:CreatorTool></rdf:Description>
+<rdf:Description rdf:about='4ed87dd1-b03a-11e8-0000-05261415641d' xmlns:xapMM='http://ns.adobe.com/xap/1.0/mm/' xapMM:DocumentID='4ed87dd1-b03a-11e8-0000-05261415641d'/>
+<rdf:Description rdf:about='4ed87dd1-b03a-11e8-0000-05261415641d' xmlns:dc='http://purl.org/dc/elements/1.1/' dc:format='application/pdf'><dc:title><rdf:Alt><rdf:li xml:lang='x-default'>Untitled</rdf:li></rdf:Alt></dc:title></rdf:Description>
+</rdf:RDF>
+</x:xmpmeta>
+
+
+<?xpacket end='w'?>
+endstream
+endobj
+2 0 obj
+<</Producer(GPL Ghostscript 8.61)
+/CreationDate(D:20080901140150+02'00')
+/ModDate(D:20080901140150+02'00')>>endobj
+xref
+0 13
+0000000000 65535 f
+0000000718 00000 n
+0000002388 00000 n
+0000000659 00000 n
+0000000508 00000 n
+0000000015 00000 n
+0000000489 00000 n
+0000000783 00000 n
+0000000955 00000 n
+0000000893 00000 n
+0000000824 00000 n
+0000000854 00000 n
+0000001024 00000 n
+trailer
+<< /Size 13 /Root 1 0 R /Info 2 0 R
+/ID [<ABCDB6122A7E63B2B97239E06EBB5975><ABCDB6122A7E63B2B97239E06EBB5975>]
+>>
+startxref
+2511
+%%EOF
Modified: pkg/distrDoc/vignettes/ProbFamily.pdf
===================================================================
(Binary files differ)
Modified: pkg/distrDoc/vignettes/RiskType.pdf
===================================================================
(Binary files differ)
Modified: pkg/distrDoc/vignettes/Symmetry.pdf
===================================================================
(Binary files differ)
Modified: pkg/distrDoc/vignettes/dataclass.pdf
===================================================================
(Binary files differ)
Modified: pkg/distrDoc/vignettes/distr.Rnw
===================================================================
--- pkg/distrDoc/vignettes/distr.Rnw 2018-07-08 14:24:29 UTC (rev 1182)
+++ pkg/distrDoc/vignettes/distr.Rnw 2018-07-08 14:25:50 UTC (rev 1183)
@@ -4,6 +4,7 @@
%\VignetteKeyword{simulation}
%\VignetteKeyword{estimation}
%\VignettePackage{distr}
+%\VignetteEngine{knitr::knitr}
%
\documentclass[11pt]{article}
%
@@ -57,7 +58,7 @@
\usepackage{amssymb}
\usepackage{url}
\usepackage[%
-baseurl={http://www.bioconductor.org},%
+baseurl={https://www.bioconductor.org},%
pdftitle={S4 Classes for Distributions---a manual for packages distr, distrSim, distrTEst, distrEx,
distrMod, and distrTeach},%
pdfauthor={Peter Ruckdeschel, Matthias Kohl, Thomas Stabla, Florian Camphausen},%
@@ -71,20 +72,25 @@
\RequirePackage{listings}
%\usepackage{Sweave} no longer needed
% -------------------------------------------------------------------------------
-\SweaveOpts{keep.source=TRUE}
-% -------------------------------------------------------------------------------
\definecolor{distrCol}{rgb}{0.0,0.4,0.4}
-<<SweaveListingsPreparations, results=tex, echo=FALSE>>=
-require(SweaveListingUtils)
-SweaveListingPreparations()
-setToBeDefinedPkgs(pkgs = c("distr","distrEx","distrTEst","distrSim",
- "distrDoc","distrTeach","distrMod","RandVar"),
- keywordstyles = "\\bf\\color{distrCol}")
-@
+%%
+%% ------------------------------------------------------------------------------
+%% before version 2.7, we used package SweaveListingUtils for syntax highlighting
+%% from version 2.7 on, we switch to knitR
+%% ------------------------------------------------------------------------------
+%%
+%%#(ll)SweaveListingsPreparations, results="asis", echo=FALSE(ggeq)
+%%#require(SweaveListingUtils)
+%%#SweaveListingPreparations()
+%%#setToBeDefinedPkgs(pkgs = c("distr","distrEx","distrTEst","distrSim",
+%%# "distrDoc","distrTeach","distrMod","RandVar"),
+%%# keywordstyles = "\\bf\\color{distrCol}")
+%%#(at)
+%%
+%% ------------------------------------------------------------------------------
%
% -------------------------------------------------------------------------------
-\renewcommand{\pkgversion}{{\tt 2.6}}
-\newcommand{\pkgExversion}{{\tt 2.6}}
+\newcommand{\pkgExversion}{{\tt 2.7}}
\newcommand{\Reals}{\mathbb{R}}
\newcommand{\R}{\mathbb{R}}
\newcommand{\N}{\mathbb{N}}
@@ -100,18 +106,52 @@
% -------------------------------------------------------------------------------
\begin{document}
% -------------------------------------------------------------------------------
-\title{{\tt S4} Classes for Distributions---a manual for packages \pkg{distr},
+<<knitRPreparations,include=FALSE>>=
+library(knitr)
+opts_chunk$set(tidy=FALSE)
+@
+% -------------------------------------------------------------------------------
+\lstdefinelanguage{Rd}[common]{TeX}%
+{moretexcs={acronym,alias,arguments,author,bold,cite,%
+ code,command,concept,cr,deqn,describe,%
+ description,details,dfn,doctype,dots,%
+ dontrun,dontshow,donttest,dQuote,%
+ email,emph,enc,encoding,enumerate,env,eqn,%
+ examples,file,format,if,ifelse,item,itemize,kbd,keyword,%
+ ldots,link,linkS4class,method,name,note,%
+ option,out,pkg,preformatted,R,Rdopts,Rdversion,%
+ references,S3method,S4method,Sexpr,samp,section,%
+ seealso,source,sp,special,sQuote,strong,%
+ subsection,synopsis,tab,tabular,testonly,%
+ title,url,usage,value,var,verb},
+ sensitive=true,%
+ morecomment=[l]\%% 2008/9 Peter Ruckdeschel
+}[keywords,comments]%%
+\lstdefinestyle{Rdstyle}{fancyvrb=TRUE,language=Rd, keywordstyle={\bf},%
+ basicstyle={\color{black}\footnotesize},%
+ commentstyle={\ttfamily\itshape},%
+ alsolanguage=R}%
+\global\def\Rdlstset{\lstset{style=Rdstyle}}%
+% -------------------------------------------------------------------------------
+\lstset{language=R,basicstyle={\color{Rcolor}\footnotesize},keywordstyle={\bf}}
+\let\code\lstinline
+\def\Code#1{{\tt\color{Rcolor} #1}}
+\def\file#1{{\tt #1}}
+\def\pkg#1{{\tt"#1"}}
+\newcommand{\pkgversion}{{\tt 2.7}}
+% -------------------------------------------------------------------------------
+\title{{\tt S4} Classes for Distributions---a manual for packages \pkg{distr},
\pkg{distrEx}, \pkg{distrEllipse}, \pkg{distrMod}, \pkg{distrSim},
\pkg{distrTEst}, \pkg{distrTeach},
version \pkgversion}
%,version \pkgExversion}
\author{\small Peter Ruckdeschel\thanks{Carl von Ossietzky Universit\"at Oldenburg}
\\[-.5ex]
-\small Matthias Kohl\thanks{FH Furtwangen}
+\small Matthias Kohl\thanks{Hochschule Furtwangen}
\\[-.5ex]
\small Thomas Stabla\thanks{Graf-M\"unster-Gymnasium, Bayreuth}
\\[-.5ex]
-\small Florian Camphausen\thanks{West-LB, London}
+\small Florian Camphausen\thanks{European Central Bank, Frankfurt}
\smallskip\\
\small Institute for Mathematics\\[-.5ex]
\small School of Mathematics and Science\\[-.5ex]
@@ -179,7 +219,7 @@
\pkg{RobExtremes}. This concerns the Gumbel, Weibull, Pareto distributions.
%\noindent The latter two of them require package \pkg{setRNG} by
%\href{mailto:pgilbert at bank-banque-canada.ca}{Paul Gilbert}
-%to be installed from \href{https://cran.r-project.org/mirrors.html}{\tt CRAN}.
+%to be installed from \href{https://cran.r-project.org/mirrors.html}{\tt CRAN}.
% \\
%\noindent Additionally, mainly contributed by \cite{MK:05}, in \pkg{distrEx} we
@@ -227,8 +267,9 @@
function $f\colon \Reals^2 \to \Reals$ which is already realized as a function
in {\sf R}.\\
This is possible with package \pkg{distr}. As an example, try
-<<echo=false,results=hide>>=
-## preparation: set option withSweave to true
+
+<<echo = FALSE, results = "hide">>=
+## preparation: set option withSweave to TRUE
require(distrTEst)
require(distrEx)
require(distrTeach)
@@ -236,7 +277,8 @@
distroptions(withSweave = TRUE)
options("newDevice" = TRUE)
@
-<<exam1, eval = TRUE, fig = TRUE>>=
+
+<<exam1, eval = TRUE, fig.width=8.0, fig.height=4.5>>=
require(distr)
N <- Norm(mean = 2, sd = 1.3)
P <- Pois(lambda = 1.2)
@@ -245,18 +287,27 @@
plot(Z)
p(Z)(0.4)
q(Z)(0.3)
+## in RStudio or Jupyter IRKernel, use q.l(.)(.) instead of q(.)(.)
Zs <- r(Z)(50)
Zs
@
\par
\begin{small}
-Due to a non-conformal implementation of function \code{q} in \texttt{RStudio},
-our approach to overload function \code{q} by method dispatch does not work
-from an \texttt{RStudio} console (it does work, though, within a function
-environment). To overcome this, from version 2.6 on, we have aliases
-\code{p.r} and \code{q.l} for functions \code{p} and \code{q}, respectively,
-alluding to the right (resp. left) continous form of the cdf and the quantile
-function. These two aliases (in particular \code{q.l}) do work in \texttt{RStudio}.
+In the environments of \texttt{RStudio}, see \url{https://www.rstudio.com/} and
+\texttt{Jupyter IRKernel}, see \url{https://github.com/IRkernel/IRkernel},
+calls to \code{q} are caught away from standard {\sf R} evaluation and are treated
+in a non-standard way. This non-standard evaluation in particular throws
+errors at calls to our accessor methods \code{q} to slot \code{q} of the
+respective distribution object. For \texttt{RStudio}, this holds for calls from the
+console (i.e., in the \code{.GlobalEnv} environment) only, while calls
+to our accessor \code{q} in different environment are not affected. This
+is not true in \texttt{IRKernel}, where all calls to our accessor \code{q} are
+affected. To amend this, from version 2.6 on, we provide function \code{q.l}
+(for left-continuous quantile function) as alias to our accessors \code{q}, so
+that all our package functionality also becomes available in \texttt{RStudio}
+and \texttt{IRKernel}. The same holds, albeit with less consequences in
+\texttt{RStudio} and \texttt{IRKernel} for accessor \code{p}: Here we have an
+alias \code{p.r} (for the right-continuous cdf) for it.\\
\end{small}
\par
\begin{small}
@@ -386,9 +437,9 @@
% -------------------------------------------------------------------------------
\subsubsection{Subclasses}
% -------------------------------------------------------------------------------
-To begin with, we have considered univariate distributions giving the
+To begin with, we consider univariate distributions giving
{\tt S4}-class \code{UnivariateDistribution}, and as typical subclasses, we
-have introduced classes for absolutely continuous and discrete distributions
+introduce classes for absolutely continuous and discrete distributions
---\code{AbscontDistribution} and \code{DiscreteDistribution}.\\
The former, from version 1.9 on, has a slot \code{gaps} of class
@@ -443,20 +494,20 @@
the corresponding help. E.g., to produce a discrete distribution with
support $(1,5,7,21)$ with corresponding probabilities $(0.1,0.1,0.6,0.2)$
we may write
-<<DiscrDist, eval = TRUE, fig = TRUE>>=
+<<DiscrDist, eval = TRUE>>=
D <- DiscreteDistribution(supp = c(1,5,7,21), prob = c(0.1,0.1,0.6,0.2))
D
plot(D)
@
-\newline
+%\newline
and to generate an absolutely continuos distribution with density proportional
to $e^{-|x|^3}$, we write
-<<AbscDist, eval = TRUE, fig = TRUE>>=
+<<AbscDist, eval = TRUE>>=
AC <- AbscontDistribution(d = function(x) exp(-abs(x)^3), withStand = TRUE)
AC
plot(AC)
@
-\newline
+%\newline
As subclasses of these absolutely continuous and discrete classes, we have
implemented all parametric families which already exist in the \pkg{stats}
package of {\sf R} in form of
@@ -1142,24 +1193,24 @@
Having implemented a class for Lebesgue decomposed distributions, we have been
able to realize further binary operators, in particular we have exact
analytical constructions for multiplication, division, exponentiation:
-<<arith2v1, eval = TRUE, fig = TRUE>>=
+<<arith2v1, eval = TRUE>>=
A1 <- Norm(); A2 <- Unif()
A1A2 <- A1*A2
plot(A1A2)
@
-<<arith2v2, eval = TRUE, fig = TRUE>>=
+<<arith2v2, eval = TRUE>>=
A12 <- 1/(A2 + .3)
plot(A12)
@
-<<arith2v3, eval = TRUE, fig = TRUE>>=
+<<arith2v3, eval = TRUE>>=
B <- Binom(5,.2)+1
A1B <- A1^B
plot(A1B, xlim=c(-3,3))
@
-<<arith2V4, fig = TRUE>>=
+<<arith2v4>>=
plot(1.2^A1)
@
-<<arith2v5, fig = TRUE>>=
+<<arith2v5>>=
plot(B^A1)
@
%
@@ -1170,23 +1221,23 @@
the last three could not be realized in a completely satisfactory manour,
as Lebesgue decomposed distributions had not been available before.
Now these illustrations have moved into the package itself:
-<<Hub, eval = TRUE, fig = TRUE>>=
+<<Hub, eval = TRUE>>=
H <- Huberize(Norm(),lower=-1,upper=2)
plot(H)
@
-<<Trun, eval = TRUE, fig = TRUE>>=
+<<Trun, eval = TRUE>>=
T <- Truncate(Norm(),lower=-1,upper=2)
plot(T)
@
-<<Min1, eval = TRUE, fig = TRUE>>=
+<<Min1, eval = TRUE>>=
M1 <- Maximum(Unif(0,1), Minimum(Unif(0,1), Unif(0,1)))
plot(M1)
@
-<<Min2, eval = TRUE, fig = TRUE>>=
+<<Min2, eval = TRUE>>=
M2 <- Minimum(Exp(4),4)
plot(M2)
@
-<<Min3, eval = TRUE, fig = TRUE>>=
+<<Min3, eval = TRUE>>=
M3 <- Minimum(Norm(2,2), Pois(3))
plot(M3)
@
@@ -1271,7 +1322,7 @@
Note that in the result, slots \code{p} and \code{q} are not replaced but
rather taken unchanged from the argument:
-<<makeAC, eval = TRUE, fig = TRUE>>=
+<<makeAC, eval = TRUE>>=
par(mfrow=c(2,3))
plot(makeAbscontDistribution(Nbinom(5,.5)),mfColRow=FALSE)
plot(makeAbscontDistribution(HN),mfColRow=FALSE)
@@ -1323,10 +1374,10 @@
\paragraph{\code{xlim} argument:} More importantly, you may also
override the automatically chosen $x$-region by passing an \code{xlim} argument:
-<<cauchy1, eval = TRUE, fig = TRUE>>=
+<<cauchy1, eval = TRUE>>=
plot(Cauchy())
@
-<<cauchy2, eval = TRUE, fig = TRUE>>=
+<<cauchy2, eval = TRUE>>=
plot(Cauchy(),xlim=c(-4,4))
@
From version 2.1, the automatic choice of the x-range of \code{plot}
@@ -1383,7 +1434,7 @@
\begin{figure}[p]
\begin{center}
-<<plotex1, eval = TRUE, fig = TRUE, width=8.0,height=4.5>>=
+<<plotex1, eval = TRUE, fig.width=8.0, fig.height=4.5>>=
plot(Binom(size = 4, prob = 0.3))
@
\caption{\label{plotexPic1}{Standard plot for discrete distributions
@@ -1397,7 +1448,7 @@
gives Figure~\ref{plotexPic2}.
\begin{figure}[p]
\begin{center}
-<<plotex2, eval = TRUE, fig = TRUE, width=8.0,height=4.5>>=
+<<plotex2, eval = TRUE, fig.width=8.0, fig.height=4.5>>=
plot(Binom(size = 4, prob = 0.3), do.points = FALSE, verticals = FALSE)
@
\caption{\label{plotexPic2}{Plot for discrete distributions without
@@ -1414,7 +1465,7 @@
\begin{figure}[p]
\begin{center}
-<<plotex3, eval = TRUE, fig = TRUE, width=8.0,height=4.5>>=
+<<plotex3, eval = TRUE, fig.width=8.0, fig.height=4.5>>=
plot(Binom(size = 4, prob = 0.3), main = TRUE, inner = FALSE, cex.main = 1.6,
tmar = 6)
@
@@ -1431,7 +1482,7 @@
\begin{figure}[p]
\begin{center}
-<<plotex4, eval = TRUE, fig = TRUE, width=8.0,height=4.5>>=
+<<plotex4, eval = TRUE, fig.width=8.0, fig.height=4.5>>=
plot(Binom(size = 4, prob = 0.3), cex.points = 1.2, pch = 20, lwd = 2)
@
\caption{\label{plotexPic4}{Plot for discrete distributions using panel
@@ -1450,7 +1501,7 @@
\begin{figure}[p]
\begin{center}
-<<plotex5, eval = TRUE, fig = TRUE, width=8.0,height=4.5>>=
+<<plotex5, eval = TRUE, fig.width=8.0, fig.height=4.5>>=
B <- Binom(size = 4, prob = 0.3)
plot(B, col="red", col.points = "green", main = TRUE, col.main="blue",
col.sub = "orange", sub = TRUE, cex.sub = 0.6, col.inner = "brown")
@@ -1468,7 +1519,7 @@
\begin{figure}[p]
\begin{center}
-<<plotex6, eval = TRUE, fig = TRUE, width=8.0,height=4.5>>=
+<<plotex6, eval = TRUE, fig.width=8.0, fig.height=4.5>>=
plot(Nbinom(size = 4,prob = 0.3), cex.points = 1.2, pch.u = 20, pch.a = 10)
@
\caption{\label{plotexPic6}{Plot for discrete distributions with different
@@ -1483,7 +1534,7 @@
\begin{figure}[p]
\begin{center}
-<<plotex7, eval = TRUE, fig = TRUE, width=8.0,height=4.5>>=
+<<plotex7, eval = TRUE, fig.width=8.0, fig.height=4.5>>=
plot(Chisq(), log = "xy", ngrid = 100)
@
\caption{\label{plotexPic7}{Plot for absolutely continuous distributions
@@ -1498,7 +1549,7 @@
Figure~\ref{plotexPic8}.
\begin{figure}[p]
\begin{center}
-<<plotex8, eval = TRUE, fig = TRUE, width=8.0,height=4.5>>=
+<<plotex8, eval = TRUE, fig.width=8.0, fig.height=4.5>>=
plot(Norm(), lwd=3, col = "red", ngrid = 200, lty = 3, las = 2)
@
\caption{\label{plotexPic8}{Plot for absolutely continuous distributions
@@ -1514,7 +1565,7 @@
\begin{figure}[p]
\begin{center}
-<<plotex9, eval = TRUE, fig = TRUE, width=8.0,height=4.5>>=
+<<plotex9, eval = TRUE, fig.width=8.0, fig.height=4.5>>=
plot(Norm(), panel.first = grid(), main = "my Distribution: %A",
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/distr -r 1183
More information about the Distr-commits
mailing list