From noreply at r-forge.r-project.org Tue Feb 23 15:47:03 2016 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Tue, 23 Feb 2016 15:47:03 +0100 (CET) Subject: [Vegan-commits] r2989 - pkg/vegan/R Message-ID: <20160223144703.AC1561879E0@r-forge.r-project.org> Author: jarioksa Date: 2016-02-23 15:47:03 +0100 (Tue, 23 Feb 2016) New Revision: 2989 Modified: pkg/vegan/R/betadiver.R pkg/vegan/R/linestack.R pkg/vegan/R/simper.R Log: Merge branch 'cran-2.3' into r-forge-svn-local Modified: pkg/vegan/R/betadiver.R =================================================================== --- pkg/vegan/R/betadiver.R 2016-01-12 14:16:01 UTC (rev 2988) +++ pkg/vegan/R/betadiver.R 2016-02-23 14:47:03 UTC (rev 2989) @@ -20,7 +20,7 @@ "co"="(a*c+a*b+2*b*c)/(2*(a+b)*(a+c))", "cc"="(b+c)/(a+b+c)", "g"="(b+c)/(a+b+c)", "-3"="pmin(b,c)/(a+b+c)", "l"="(b+c)/2", - "19"="2*(b*c+1)/((a+b+c)^2+(a+b+c))", + "19"="2*(b*c+1)/((a+b+c)^2-(a+b+c))", "hk"="(b+c)/(2*a+b+c)", "rlb"="a/(a+c)", "sim"="pmin(b,c)/(pmin(b,c)+a)", "gl"="2*abs(b-c)/(2*a+b+c)", Modified: pkg/vegan/R/linestack.R =================================================================== --- pkg/vegan/R/linestack.R 2016-01-12 14:16:01 UTC (rev 2988) +++ pkg/vegan/R/linestack.R 2016-02-23 14:47:03 UTC (rev 2989) @@ -2,14 +2,19 @@ function (x, labels, cex = 0.8, side = "right", hoff = 2, air = 1.1, at = 0, add = FALSE, axis = FALSE, ...) { + if (length(at) > 1 || length(hoff) > 1 || length(air) > 1 || length(cex) > 1) + stop("only one value accepted for arguments 'cex', 'hoff', 'air' and 'at'") x <- drop(x) n <- length(x) misslab <- missing(labels) if (misslab) { labels <- names(x) } + if (!is.character(labels)) + labels <- as.character(labels) nlab <- length(labels) - if (!misslab && nlab == 1L && pmatch(labels, c("right", "left"), nomatch = FALSE)) { + if (!misslab && nlab == 1L && pmatch(labels, c("right", "left"), + nomatch = FALSE)) { side <- labels labels <- NULL warning("argument 'label' is deprecated: use 'side'") @@ -30,7 +35,7 @@ plot(pos, x, type = "n", axes = FALSE, xlab = "", ylab = "", ...) } hoff <- hoff * strwidth("m") - ht <- air * strheight(names(x), cex = cex) + ht <- air * strheight(labels, cex = cex) mid <- (n + 1)%/%2 pos[mid] <- x[mid] if (n > 1) { Modified: pkg/vegan/R/simper.R =================================================================== --- pkg/vegan/R/simper.R 2016-01-12 14:16:01 UTC (rev 2988) +++ pkg/vegan/R/simper.R 2016-02-23 14:47:03 UTC (rev 2989) @@ -126,8 +126,8 @@ { if (ordered) { out <- lapply(object, function(z) - data.frame(contr = z$average, sd = z$sd, ratio = z$ratio, - av.a = z$ava, av.b = z$avb)[z$ord, ]) + data.frame(average = z$average, sd = z$sd, ratio = z$ratio, + ava = z$ava, avb = z$avb)[z$ord, ]) cusum <- lapply(object, function(z) z$cusum) for(i in seq_along(out)) { out[[i]]$cumsum <- cusum[[i]] From noreply at r-forge.r-project.org Thu Feb 25 13:09:52 2016 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 25 Feb 2016 13:09:52 +0100 (CET) Subject: [Vegan-commits] r2990 - in pkg/vegan: . R inst/doc man vignettes Message-ID: <20160225120952.441F2186C60@r-forge.r-project.org> Author: jarioksa Date: 2016-02-25 13:09:51 +0100 (Thu, 25 Feb 2016) New Revision: 2990 Added: pkg/vegan/vignettes/FAQ-vegan.Rmd pkg/vegan/vignettes/partitioning.Rnw pkg/vegan/vignettes/varpart23.pdf pkg/vegan/vignettes/varpart4.pdf Removed: pkg/vegan/inst/doc/partitioning.pdf pkg/vegan/vignettes/.install_extras pkg/vegan/vignettes/FAQ-vegan.texi pkg/vegan/vignettes/Makefile Modified: pkg/vegan/DESCRIPTION pkg/vegan/NAMESPACE pkg/vegan/R/vegandocs.R pkg/vegan/man/vegandocs.Rd Log: Merge branch 'cran-2.3' into r-forge-svn-local Modified: pkg/vegan/DESCRIPTION =================================================================== --- pkg/vegan/DESCRIPTION 2016-02-23 14:47:03 UTC (rev 2989) +++ pkg/vegan/DESCRIPTION 2016-02-25 12:09:51 UTC (rev 2990) @@ -6,9 +6,10 @@ Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens, Helene Wagner Maintainer: Jari Oksanen -Depends: permute (>= 0.8-0), lattice, R (>= 2.15.0) -Suggests: parallel, tcltk +Depends: permute (>= 0.8-0), lattice, R (>= 3.0.0) +Suggests: parallel, tcltk, knitr Imports: MASS, cluster, mgcv +VignetteBuilder: utils, knitr Description: Ordination methods, diversity analysis and other functions for community and vegetation ecologists. License: GPL-2 Modified: pkg/vegan/NAMESPACE =================================================================== --- pkg/vegan/NAMESPACE 2016-02-23 14:47:03 UTC (rev 2989) +++ pkg/vegan/NAMESPACE 2016-02-25 12:09:51 UTC (rev 2990) @@ -73,7 +73,8 @@ import(stats) import(graphics) import(permute) -importFrom(utils, browseURL, combn, flush.console, head, object.size, tail, str) +importFrom(utils, news, vignette, combn, flush.console, head, object.size, + tail, str) importFrom(tools, Rd2txt, startDynamicHelp) import(grDevices) ## too many functions to be listed separately import(lattice) Modified: pkg/vegan/R/vegandocs.R =================================================================== --- pkg/vegan/R/vegandocs.R 2016-02-23 14:47:03 UTC (rev 2989) +++ pkg/vegan/R/vegandocs.R 2016-02-25 12:09:51 UTC (rev 2990) @@ -1,29 +1,18 @@ `vegandocs` <- - function (doc = c("NEWS", "ONEWS", "FAQ-vegan.pdf", - "intro-vegan.pdf", "diversity-vegan.pdf", - "decision-vegan.pdf", "partitioning.pdf", "permutations.pdf")) + function (doc = c("NEWS", "ONEWS", "FAQ-vegan", + "intro-vegan", "diversity-vegan", + "decision-vegan", "partitioning", "permutations")) { doc <- match.arg(doc) - if (length(grep(".pdf", doc)) > 0) { - if (doc == "permutations.pdf") - doc <- file.path(system.file(package="permute"), "doc", doc) - else - doc <- file.path(system.file(package="vegan"), "doc", doc) - if (.Platform$OS.type == "windows") - shell.exec(doc) - else system(paste(getOption("pdfviewer"), doc, "&")) - } else if (doc == "NEWS") { - ## Try html - helptype <- getOption("help_type") - if (length(helptype) && helptype == "html") { - browseURL(paste("file://", - system.file(package="vegan", "doc", "NEWS.html"), - sep="")) - } else { - file.show(Rd2txt(file.path(system.file(package="vegan"), - "NEWS.Rd"), tempfile())) - } - } else { + if (doc == "NEWS") { + .Deprecated('news(package="vegan")') + news(package = "vegan") + } else if (doc %in% vignette(package="vegan")$results[, "Item"]) { + .Deprecated('browseVignettes("vegan")') + vignette(doc, package = "vegan") + } else if (doc == "permutations") { + .Deprecated('browseVignettes("permute")') + vignette(doc, package = "permute") + } else # last resort file.show(system.file(package="vegan", doc)) - } } Deleted: pkg/vegan/inst/doc/partitioning.pdf =================================================================== --- pkg/vegan/inst/doc/partitioning.pdf 2016-02-23 14:47:03 UTC (rev 2989) +++ pkg/vegan/inst/doc/partitioning.pdf 2016-02-25 12:09:51 UTC (rev 2990) @@ -1,984 +0,0 @@ -%PDF-1.4 -7 0 obj << -/Length 121 -/Filter /FlateDecode ->> -stream -x???? -?0 Dw?~???e?z/?????B??/U]??R$8??t?P2??z???> endobj -4 0 obj << -/Type /XObject -/Subtype /Form -/FormType 1 -/PTEX.FileName (./varpartv1.pdf) -/PTEX.PageNumber 1 -/PTEX.InfoDict 9 0 R -/Matrix [1.00000000 0.00000000 0.00000000 1.00000000 0.00000000 0.00000000] -/BBox [0.00000000 0.00000000 612.00000000 792.00000000] -/Resources << -/Font << /Fcpdf0 10 0 R /Fcpdf1 11 0 R /Fcpdf2 12 0 R /Fcpdf3 13 0 R /Fcpdf4 14 0 R >> -/ProcSet [ /PDF /Text ] ->> -/Length 2587 -/Filter /FlateDecode ->> -stream -x??ZK??8??Wpn ???oi???c?? fv ?? ???'?????????U|??e?I?M??XE~U?*i?e??j?e???????7??sI(-jr??????(Up?dUhI??w??????=?????+??B????\]?cuQ???d???0N????&??B??? -?`??5?nVv???H?@= -c?0? Y??F/@j@?+??f?U?3^E/????????h?SNL??4) ??xUT?i?"?XY*2-???~b?? -??"?? -???Lm??Q!???l%pQ??Jrj?d?uFhY?3?????th???????l=O&X?&?6?t`???,???vB??? -y?.?k????????pE???v$?(?????#?????z ???]?T???????8Q??????Y -y?A??h?z?Yxx??s?a"?!|????."l?V?Vd(?(!??d??bW?l????0q??*"?s?\???R3Q????SNXz?.?9X??|%5?f=?1g?jaBuU?}?!? ????c?3B?pv2K???????ksv?????L??????z?1W??ZLN?C?]?_3?5"b???k -??rX?i?\??+y=??r?????_fY???r??????????/??f?O???ZQd?_????X?& ;#???y?&?????u3#?rl? ?u??v??? -?q% -?%*?o???e??<>?K"??(L??y??V?R#O9/????M?e?E??????? @*??????3??????#~?5?????y9O&???z?Ea?y??8Oe??)*?"??Z????)*l???4????0?JQ|T-?D? O????x?t???????????f6?KRa?#???xa?l????9?????*A? ????fP?W?q???)*+,???0{?L?Z???+GeP? ???4I?2?h?0??K?*}???J9?-R? K?%s,?ej??t?2]??C????K?t ??.??X?Ha?-y??\K??L????D%?9????]?T??.Ms?e?3%?D??0?@?)n?W????a?FP???0??KN????:J???}????N?9A5i??:1?q.-???eiU???N?/?|i.k?????~??? ??O???*seTd???E!???t=???BQs~]? #????QX?wm?m??2??Y????l??????????LE????o??BmI0?????D???n? ;?m?Yf???F8?>r?:?^??????Q???????? -??!R? ???9:Q;DV??v???g??.???b?>?d? ?mE.?????:^|??,J[?r????????}r???????XK?,???h^?hpo_?K6? ??$????9?G????:?1??p|P????Gq? -?jtzx?# ??U,???~?5 t???6?fx?(d?}?O?u???[?*?Ykendstream -endobj -9 0 obj -<< -/Creator (Canvas\222 3.0.3) -/CreationDate (D:20020223175104) -/Subject () -/Title () -/Author (P. Legendre) -/Producer (Acrobat PDFWriter 4.0 for Power Macintosh) -/Keywords () -/ModDate (D:20050821141706-04'00') ->> -endobj -10 0 obj -<< -/Type /Font -/Subtype /Type1 -/Name /Fcpdf0 -/BaseFont /Times-Bold -/Encoding /MacRomanEncoding ->> -endobj -11 0 obj -<< -/Type /Font -/Subtype /Type1 -/Name /Fcpdf1 -/BaseFont /Times-BoldItalic -/Encoding /MacRomanEncoding ->> -endobj -12 0 obj -<< -/Type /Font -/Subtype /Type1 -/Name /Fcpdf2 -/BaseFont /Times-Roman -/Encoding /MacRomanEncoding ->> -endobj -13 0 obj -<< -/Type /Font -/Subtype /Type1 -/Name /Fcpdf3 -/BaseFont /Times-Italic -/Encoding /MacRomanEncoding ->> -endobj -14 0 obj -<< -/Type /Font -/Subtype /Type1 -/Name /Fcpdf4 -/BaseFont /Symbol ->> -endobj -5 0 obj << -/XObject << /Im4 4 0 R >> -/ProcSet [ /PDF ] ->> endobj -21 0 obj << -/Length 121 -/Filter /FlateDecode ->> -stream -x???? -?0 Dw?~???e?x/???? ?B??/U]??R$8??t?P2??z??M?-?A??7????Ow?{???6???IN? -?L?2???? kX?#b??I~?F7v?P????%/Z86endstream -endobj -20 0 obj << -/Type /Page -/Contents 21 0 R -/Resources 19 0 R -/MediaBox [0 0 611.9985 791.9981] -/Parent 8 0 R ->> endobj -18 0 obj << -/Type /XObject -/Subtype /Form -/FormType 1 -/PTEX.FileName (./varpart23.pdf) -/PTEX.PageNumber 1 -/PTEX.InfoDict 22 0 R -/Matrix [1.00000000 0.00000000 0.00000000 1.00000000 0.00000000 0.00000000] -/BBox [0.00000000 0.00000000 612.00000000 792.00000000] -/Resources << -/ProcSet [ /PDF /Text ] -/ColorSpace << -/Cs1 23 0 R ->>/Font << /F1.0 24 0 R/F1.1 25 0 R>> ->> -/Length 26 0 R -/Filter /FlateDecode ->> -stream -x??]?s9r~?_1??$??I -?`?U?Te/~J??n??R?(j$1I/E?????????z?}??-?4?w7?d?~?x??|?U?U???Vu]??bZ????m??w???~|???%??/??~????????f???en~?????>o?OrYUe? ?}^?|Z?5k??]e?????%[???????]gU^g?g?W??'>?3???????c???}????>?M ????f?ue15??5X?,??'{K?jZ??`???[???????|???????g??9Os?R?U ?8?'?????j?m>????wB??*????~c -?:/?*?Q???7VD?H?<3v???2????t?w???Nm? -?????Y?h?cf2???.7h&?P??????y???t2Y??f??rnuc?p?. ???Y+??????YG %c?2J?G{?l?x??????m??R?(T-b????h???y???6?o??????g??? ??~????nUT??*???????w?k?_.????/#???Xf2??K?U???3C??g??F?m????:????????g?z???} v??H<"N???iH:??K?4?X??#??j????m?=??|+?2???xkH?5b?"P??0?s????? -B??J? ?z5????c??? -??`#??>s????]?E????0(~L$??~6????/?K?&?????B?"?`?x7>?b?????B,???qn??I1??v?U_^??D#V?????kA?Uo?,]?A??s???4??b?{?t????m??}E????8S?I????A??h0???y?6//6???\+?]l???~??[???|mB#?]?2?UU?~?BP?.={?z?aA???? -?c?4?E -7{??w=?m??(?n??????5????????]s?m??h'?.???????Uy?,??????????F???????"?X(v\?N',B???U????f?K????l??????$???@(F&u?z?@??????jB?k???:=9u??(???|^???? -1???q?|0b?^ +??M -t2???Tm??fR???[~y??HESB???fg7?SL?b???????x?q.?z???4FF3??.?8?????d>U?sW??????,????{Qs???r???l???*T?pWo?-d??4J?},fve\??Q?Rk???4"6??k??&(?$])P???f???E???2????????????iSZ?$]????????b??(at??????5kA???<&??K?q3??? -X??^\?yn???g???????#?????????? Y??#\f???U+?#-.5;?k:????k2?4??o?????????AZxn??????l????.??????`hE& ->?4?!z??xiP?qiH,? -?L??"?????Z?w?`$???m??,xL?Ri??????CZ?????jZ??yJ????HDd*\??7+?^??U??2??????????H3???as??3[????Q????????ee???5Bq^JYG7B??Yl????f?]??5?E????#!?Y??#??{A??????~?2????X??????x?iB?iB?@?#?F[?? ??Q?MbB???Q<Zc7????;RNg?>???6-??y+?Te-????W6??vs??7??z??)Rw($ ?x?SpAr??h#??Q??ZS????K?????????|:?W??b????$???n?~?0???a|??_`J????_><4???G?r?^?-?????oM?????!W?????]?$??3w_"W???y????%??K? /??h??????????}XY???a?)-??]~?<=?P?G?0fv???S??W?#??u??m.iU%5?Q??WOE'f?mW?8??r9% ? -J??%|??u9?V????]?X?B?,??K??b+@??z?G????L??7?u?mS??Dg}?L??5/j?????= ?}??j?g?\?? -??w?4????@?1SO?~:???G_??a ???5???3eW6kr5???hX8??3D?f?3??????82?6kh1;??W+?'?;?G?? ???B"2????> W??0?Z??-??$?4seTK???(?????R?NE ?|7?yS???????j????B ????G?b?>@??u]??d"??A??z?Qm ????IN;??a???KC? `?{???:?%??,l??0??#??XW???"??????2g????>a,???"??@_?t???d>X??8;w?z??????u? ??;f=?B??4??4??????????^,? -a?f?m? -??Q???"???W??=;k?Y+E?"g -?u??u?l?Z????M???p????|?1????0??2?,=?1?????u'9?r#?_?????K?O?.??R?T>????=?r?w?X\ -g???l? -?:T?)GR???????d.ZC???????? ?|?|?MDd??-????????6?X??86&???4 W?f?????j????I/??9k??`??E5?>|?l bh?}b???>?c?{???ic??d0?#v ?C??qd??S??$?E:)f?????L2D1?d?9kz??dH1?dH?K??? ???C~ ? ?????!R??O? ??l???L2?]2?c??YX?,???3C??O>??Q?N4??g?_?u`W??,????e{?w-??^?U?Sr??|&??y){?y?p;+M?k??I?yI,0?A???m???]?A????8L]??@?=????????????7????~?%ql???z? ??GVv?Z?G?|???? ??J=?V???O???"ij??M????????e -???,}??M??p??b???M??G/,o?????n(??x?n?eh?C@?F]?G?jn?x??&X???????}???xB?7;?7C=!7a?&I9?F'??t?`yS??t??-??????l(?@`??^+?T6 P?t???rrV?o???bl?.A????'?t]['????>6] ???l?,F??>??????+1?MW?W? ??t]??6]??yZ -???%?l???tVo?4???}??%?z?^?%??P??eS -K?wIC??Z?j?-???M???F?v??xwC????%G@??c.?Vx????AL?M?~??!6???????l*)?D????[M?w??5??@g]??-kV??b??*????L@???G*V;????HZH?0?U?d???????#?C??V???f??????8??????jH2?("???g??????????m]?????`????Xk???o?? ?,h??????????o]?o?????>S?2?fy=???V??:N??????0??Y?3???{O??p???F??$#W??????&?Gk5?y?U?d%??Q??X???????z|?q?Q?????^?G??Q4?(?????B;?"?zT??????W??????z?%N??(?????0s????y6 at Z:?)]U?h??S<u??vPU?T??????B?U??N&??y??U?@?+\????^???-????y?-W??P??s??S)(???????5?R?9?&?^?Y ??Q??S?8x??M????????dz?S`??????^?Izb???^x?'?????P???(?????A?,.5?`l???????od?k????"v??X?s9l?mo????+???6/M???VG]???{??H ? -?,???????n??,??????CQF?us??/??[?1e???_n??n/?,????????]6 -???????l??m???z???.)??_iM?n???f?????D??n`?W??_?L?W???2?vendstream -endobj -22 0 obj -<< -/Author (legendre) -/Creator (BBEdit Lite) -/CreationDate (D:20051128165431-05'00') -/ModDate (D:20051128165431-05'00') -/Producer (Mac OS X 10.4.3 Quartz PDFContext) -/Title (Varpart2-3 procedures \(65%\).txt) ->> -endobj -23 0 obj -[/ICCBased 27 0 R] -endobj -24 0 obj -<< -/Type /Font -/Subtype /TrueType -/BaseFont /FFYBXK#2BMonaco -/FontDescriptor 28 0 R -/Widths 29 0 R -/FirstChar 32 -/LastChar 124 -/Encoding /MacRomanEncoding ->> -endobj -25 0 obj -<< -/Type /Font -/Subtype /TrueType -/BaseFont /ZBLSFD#2BMonaco -/FontDescriptor 30 0 R -/Widths 31 0 R -/FirstChar 33 -/LastChar 34 -/ToUnicode 32 0 R ->> -endobj -26 0 obj -7226 -endobj -27 0 obj -<< -/Length 33 0 R -/N 3 -/Alternate /DeviceRGB -/Filter /FlateDecode ->> -stream -x?}?OHQ???%B?e&R?N?W?`???o???k??????????n%B?.A?1?X?I:??b]"?(????73?????7?3????{@](m?z?y???(?;>??7P?A+?Xf$?v?lqd?}????????] -?U???????x????iO:???b??M??1?W?g?>??q?[ -?2?M?'?"()Y'??ld4?????2??'&??Sg^???}8??&????w????,? \V:k???;?i?R;;\??u????V?????\???\?C9?u?(J?I????]????BS?s_ QP5??Fz?????G?%?t{3qW?D?0vz ?? \}\?$??u??m???+??????C?;X?9:Y?^g?B?,?\?ACioci]g?????(?L;?z???9?An???I? -?????4?I?????x#?{z?wA??j}????????Q????=??8?m??? -?(?o{1?c??d5?U???g??t????la??i"??\.5???????^?8tph0?k?!?~D? ?T?hd????6??????:>f??&?m?????x?A4????L?&????%???k???i??????Cq????m?&/?By#???%i??'?W??:?Xl?Err?'?=_???)?i7??????,?F|?N?????6?rm?^?? ???U?HW?????5;?????hendstream -endobj -28 0 obj -<< -/Type /FontDescriptor -/Ascent 1000 -/CapHeight 769 -/Descent -250 -/Flags 33 -/FontBBox [ -144 -422 748 1223] -/FontName /FFYBXK#2BMonaco -/ItalicAngle 0 -/StemV 0 -/Leading 83 -/MaxWidth 600 -/XHeight 553 -/FontFile2 34 0 R ->> -endobj -29 0 obj -[ 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600 600] -endobj -30 0 obj -<< -/Type /FontDescriptor -/Ascent 1000 -/CapHeight 769 -/Descent -250 -/Flags 5 -/FontBBox [ -144 -422 748 1223] -/FontName /ZBLSFD#2BMonaco -/ItalicAngle 0 -/StemV 0 -/Leading 83 -/MaxWidth 600 -/XHeight 553 -/FontFile2 35 0 R ->> -endobj -31 0 obj -[ 600 600] -endobj -32 0 obj -<< -/Length 36 0 R -/Filter /FlateDecode ->> -stream -x?]PAj?0??{LA?(9AI??6??dim?J?????$?)?0???YF????%????F,???[?F?q??j??????Iy?S?[??SK???a???9?o????g??`?4?????I?x??R??I ???]?5!?=?&?6????s|?A^o??38{?1(?5U%??U2$?O[?v???Q+???;N?%?k????? -?B*W?RZ?>??y9?|N<??sUendstream -endobj -33 0 obj -706 -endobj -34 0 obj -<< -/Length 37 0 R -/Length1 19156 -/Filter /FlateDecode ->> -stream -x??| `E?wU?=g?L?N23??!I?@H?A?A#?w$? -?+??Q9A -?0P?U?vW???3p</j>#>?? `??R??9???L??}??}??i3?5?l????*4F?= ?m??#???B_??6?Oq?N$??#I?&?1Q?0f83?]%4?)??Z??V??L? 0R?+?? -r????SO??},??&?@?|???t????|???????@?o@?? S???'?yx n?G???,?_???k???D????2#23???*fs????????????????????????f-?6U?eh-? -3???A'?Y???K0????`3?a .E????[???<O??0?Z????0?F|??3?????Udy??#_????"??R?6????E0'??2???????r??ea??5??it G???m?q???F???,H?m?f?=?I? -????8??.??=?????Y????RS????q?/6&??q??{??j??&?A??D??X?`??$XZ?oH?l`?}?????8?0?? ? -~?Tzg????gKZN???J??????T???_?7?)?????GAyuqp???U+??l?vb??@??????p????t?????b???,??wB??@=????h? 2????,.ip??:&?d????w?*)???;5?>??P?w?9-r??s?????]??R?J??No??j????4????q??j`??????58?? -??-??NMx??Q -R?&???:?4% LJU??^???o????S??U?=u -h??@?????)?? - 4y???G??BuC?w+~??5???????J?E???p?????yK??;????t????????0?QA7z????&t?f????????:?;?,? ?u? ??`????2.r?O?A?H??Cl????????? -3?T?C+?.??w??? -???/? - -w??? ????lR?x8iXr??????6"%3mt??5o??????%?5?WA&h0?? &v??e??dJ????TWi??X ?|5??D?>?\ C??6? -?D? -1 ?HC?[l??0F??????????U???9T????l K??%?s?!?U^?p#:?g?b?????%U? ?z?5{?,??M6???Q?0???/{???R]Z?W -\r??????7|F???\F?"??? ?????O???>?Y??[ /`?ah????=?m4u -?e'?W????{z?.|??]T?u??us???_7? ?f???????+?????j?*?o? ??O'mg???B@=N?u??o??S ?!8???c?E0?"'??Q??@v,N????(?$A)???"Y???b?I?,F,??????85(-??????w????r?8?x{?#?s???D&N?????O????S;w>uwy?????o??&?PO?|???%???t?????????????g???|Q???????? ??????~??3???i????>\????4??>q?-???J??D???? ???b\\ 33?*?q??S??) f?uM`????????p?b?t??o?????????o??t??"????Lk?5?)#m??? -??'V??a?w????!YX??????E?r"0??)eH?bI??%%???????LIDT?oqx)|L8?''d???B???T???'??%[BMbP???!???Y?X??z[? ?wJ]??F?????>?????N??? ???R*c?X??Yg?0??f?'[9??7?le???????D#?T?**?n? bL?&?wP?,?"???C???x??]m7??c???Sg>M?????????{?C?$????t??cr?? 6"???8G=S?????O}???~?!k?=o??a??c?^u????6??????|Kmi???BB ??X??11[??O?`[P????K?&??ca?????L|v3????????.u ????I??X}?N??? ???????4??u?*?y?$O?^????????+F??5la?u`???z?????O-???:*CH?9z?Q 8l?e??Xw}?&?h=?[9 -?#??)%z??I??D!Q,?? ???L??3-v?oF`?????[]?0v?oA`?????bOz???n?m?8.??0?%?????MM??~?k?G=???R?I????????z]X?Z4???&???30s(?eg?P?N???J0:? -6?M -?Ny?R??????/??z?X ?i&p`????l>??y???WO{`qh???&e????_?. ?uq??????:???_???o???~6??ue??6T?Z???G??k?m??????|rZs????????8??O???h?$????c???|l??????`4???21?!{Dq"????4???b6e???@?? ?,?R????q???.??W1{?= ???`\R5ad??2U??~<O{Z??a???=????6??I"??h?]??W?{/???#?:E?aR?w?PzG)???????4?????D4?C??z??????4\0X??4}?7??????7?<)a9???<9?????`F~??? ?4??????:;?T?s??A????,??,???|>}???V?M=???c?2?v??A?#????????p????????v??E '.?C)?nL7{i?T?? -?b?T+?????#<#n?O2??s?%???Kg??&2y 6Yo? 6?c???2??gTH ?/???qyc??H'???????+`1???|h]???Qa$??j.? -hDy?b-"]?*?Z?????`\T???????n?g???>>8ebe??m?r???G?;R[?????O??uh?J -w,????15???!????1hd???????3??y??7??N????o?o$N'??, ?DobR>S?-?.?)M(M,N*M+??=,qX?????U???i?i????????)?&f????<=g?n?wV???YI ?kSj?k;??,??e??_2F??ar????y??s.F_???}???????^?lf?*??N???0?d??5????????????E????&??yN??Ho???????>4?J?l6???ae???O?]?Z????:o?t9???N>\\??????dS???w?????Lk~&0??_1??C?[?*f?????('??`?a???V9v?u{??26?/? -????]??n?W??x?_q???????=3? ?????t??Cm?t????V[CJV???@??}f??a?nW$$??*?G}g`??^???????#l???>v9???#Sn}???????p?# `V??c??4~???E\y4??og og????6 -???@b@??Z?$????;S?Vq ??e?Uy???F?~?)Bd???&???s?(?zD?2X?~??7??R???6???????aAY??w? ??}[?? ??eg%??U?????{???????CG?? -%e?a#??a??gw3;?=?f#gH?X?M?????7?Z%^?G?vE/,??R??<2czzM)#?m??(2??? -W? m?'?zVB?? \F? -VN c?@????9I0? Nr?n??HB?57?.?gy????>?J?]f?m{!??????r??Jr???Q??b??EG_???d" !?5?/?%q? ??????\???CQlD|??(]???'???4?Y ?E2?!?`/????`?t??Q?R???g ?????xn?f?????l|??????e9I/$???e???hu???d6?[ -?AF???%Yd3?d4b? ??3&i??F_?U?3?? -:??D]Pl???| ?/(h??????*?????;?&;i??H??d-0????}??z{?}?X??pq? ??PN?#_M?2I<8?H?@???q???-?O ?0`???&???????=/.??p??qC???????xcv????W??y???~?z????c?e????????x?? -?`?m?A??Qb?? -?q&????R???????*5e0h?RF???V?\??=`r??D?V;?Q??2]??*^?~1qi?>?"?u)F????$????aD??6? -??ceNX=A?b?J -?d???Qp???? -[?%*??m? -?4???}V??O???{???y?&wj?????0{o????v???C?H?/???EtR??/|$|+2?(??2I\?,.@p??s? \S??R`?aBR???e?x(p??,?(B=???!????&?????C????? ????????\v;{?maE?-?????p -U?V??????????X?msB???Dw?V???H(???F??+??q5??????)??? &??s[n?=:?R'????{?4r1?=q?Ro?$??>1?~F??=??]??ew???9?{|I?p3f??/!K?'?'?5d -?????$?yx?x+f9L8?3?x?? ?q ? ?Ps?????Md??7B???? ?*????.R,? ??!X??YA??(?r???-??tK????'$m??)x?ZK??U????}?U?4?9]?hx?? Af?L?? ??B[d??@???D???f??v? RZ?W_???/o??Im_????( -?? ??'??+??`w{????X??}`D???wxaL?????l??Xs?+?? 6?.?;?G6?5?j?????y5Vl??y?kx?????Y??tmC????????:4??N????O?a???-ySQ4? -H??AK??~?(V???-g}?^??v ???Q???Jm7? +N???3??X??Qd?v???&??r???????#??? ??^\4x?_n?????????????????Z??G?zq?????m??{????b?1???^???K\??w??~??DX?O?? ??????.???????#?.?]????3???????????GE??zQ?M??r??C????-?????=?9o??q)?'{??hb-G1?????s??KJL$??4??m?l??W}?????3dss????.|? |??C????????Fn#?????]?????E?'o????g??!&&:???5??????o???????5F?????}%??+?xf4??}IT? ??8?0?:V? -?_??5??`~h?????\([?%:???B??;T!*|????uqK????????????m?x{????;s???mh[??? -&=???????J??6?????rW? -??h>??v{`q?L????Ro7???N????HD?8?=b?????Y??s?,??I??-AZ?Xm,gc-????*G??;-?????7^?1l???OO}????#S?????VFn ????t?I|??dOr??S?)?)?)?)?)?????d?I?Ig+n?Z??M|????/???h -??!???? K?=?????5p??}??N?N?? G?G(i??3??7wS?;??YX??"???(.ip??PR?? ??D&_V?????a???O??ohh?jk????6u_?w???????}G? u {?N?? ???[?Y?q ????????~??!|??!?aD??e???6?D)Xx@?z??~??'????-?????2?[a??/????S??)??0??????Nx?m?fX?? u oV?o?4(&?a?5)%??????:?$???Y=E"^&???z??\B?/"1??d?_??+ =b?z?a?I??????P?_?j^nRb&IL -o????;>?p??????#W????Q?~???'?????????/]?Ji???|???~=?)N??3=9w???k???{haA||fFQy??????R%?i/?8r?Z?V?Vp??????s??qIc?????D?? oTt? ?GS?5?????3????????o[1?RA_??'?%P7????;k?F6????*?#????"/-??'?????u?? ? -?f??jV??[?>??}LC>^?????j?3s???y???V??}Z?=-|a#>??k??z?Vo'>???kN?????2????#??}%bt?o??._Tp????y?k????|-K}-?w_?A?? ?,?w?ja;7??????)?k??]?V???K]??=?HMhx????J??V??h????Y??????&~5C?w+?DY?z??>cX??FO?:f???u??l?7 -/3{???&?0{?;??????9?RS?@?X???j????[Y?g??????F???3%????<.?qc?????y? ?2?6`c???6Z#t????s?????SO??????w????R???K??\?GQ=????}??Y5???f?lfJo?S}?s?vWic/?? ????I???bf>?o1t??]??? -??K??!?m?|?ok????????g,k.?????7??;;r?_?w)?k?}"R???Q??m?R;j??}?3h-K??3?  '|r??@???? ????"?i??????i?)r???}oG?~i>??p????????/???G?U??Gq??~??L??rn?]???HA????2?T?`?]0?Ah0? -AC?0?7F?Q`??{??h??????2^??fN?\?5?????|?4?????9??????E5??@? -??p\?2$ -?c$?V?bg????g???>?'??>?d????????? 5??F-;N?^F?&>??????#"??h??Hc????? -}?p?/?jjL\ -?????A?!???l?????????@c|4??Ooi8???'*G?N??a??pjcz??????8? D?Xd?!?E_?w?{????`?? -h}8X?k -v??????=?mC?????x-{!?m -6a?? 6?n??%????`???6?????}??e?2_?`?Wz????M8???n???@3E?? ?? ?h?=|?]?KZ????RX3HX?k -?5???,aM??&UX+D?VQ0`u?(?"+?7?????R?4??4?Yzd??L?7L?xL_B ?^c??????u??????E?"k?%???w??c????V???(0}?h<$??|????j?h5kh????5?WL???CG5?3??3-???????P????]xgI?a??F?:?l??J?????????a??J?m??h3?c??f??p?x?m?C3h?VP??.????n?x_I?>?Ok?T?x??xg??n3$???km:/AC?6C:/??5Nk B??A? >??Z? >?u??[m??mL???1=?m??M???S?{?E?????? ?TA?lX9??a?x???E??H??a -??U5, -V7L???\?;??iu?`?>??d??}??????J???????3?|????x??????`??@?????S=?Vg?gM???L???dh?*?:???z??ys??|???g?Sendstream -endobj -35 0 obj -<< -/Length 38 0 R -/Length1 4236 -/Filter /FlateDecode ->> -stream [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/vegan -r 2990 From noreply at r-forge.r-project.org Thu Feb 25 13:36:24 2016 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 25 Feb 2016 13:36:24 +0100 (CET) Subject: [Vegan-commits] r2991 - in pkg/vegan: . inst Message-ID: <20160225123624.2D40118760D@r-forge.r-project.org> Author: jarioksa Date: 2016-02-25 13:36:23 +0100 (Thu, 25 Feb 2016) New Revision: 2991 Modified: pkg/vegan/DESCRIPTION pkg/vegan/inst/NEWS.Rd Log: Merge branch 'cran-2.3' into r-forge-svn-local Modified: pkg/vegan/DESCRIPTION =================================================================== --- pkg/vegan/DESCRIPTION 2016-02-25 12:09:51 UTC (rev 2990) +++ pkg/vegan/DESCRIPTION 2016-02-25 12:36:23 UTC (rev 2991) @@ -1,7 +1,7 @@ Package: vegan Title: Community Ecology Package Version: 2.3-4 -Date: 2016-01-12 +Date: 2016-02-26 Author: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre, Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens, Helene Wagner Modified: pkg/vegan/inst/NEWS.Rd =================================================================== --- pkg/vegan/inst/NEWS.Rd 2016-02-25 12:09:51 UTC (rev 2990) +++ pkg/vegan/inst/NEWS.Rd 2016-02-25 12:36:23 UTC (rev 2991) @@ -2,6 +2,56 @@ \title{vegan News} \encoding{UTF-8} +\section{Changes in version 2.3-4}{ + + \subsection{BUG FIXES}{ + \itemize{ + + \item \code{betadiver} index \code{19} had wrong sign in one of + its terms. + + \item \code{linestack} failed when the \code{labels} were given, + but the input scores had no names. Reported by Jeff Wood (ANU, + Canberra, ACT). + + } %itemize + } % bug fixes + + \subsection{DEPRECATED}{ + \itemize{ + + \item \code{vegandocs} is deprecated. Current \R{} provides better + tools for seeing extra documentation. + + } %itemize + } %deprecated + + \subsection{VIGNETTES}{ + \itemize{ + + \item All vignettes are built with standard \R{} tools and can be + browsed with \code{browseVignettes}. Earlier \code{FAQ-vegan} and + \code{partitioning} were only accessible with \code{vegandocs} + function. + + } %itemize + } %vignettes + + \subsection{BUILDING}{ + \itemize{ + + \item Dependence on external software \code{texi2dvi} was + removed. Version 6.1 of \code{texi2dvi} was incompatible with \R{} + and prevented building \pkg{vegan}. The \code{FAQ-vegan} that was + earlier built with \code{texi2dvi} uses now \pkg{knitr}. Because + of this, \pkg{vegan} is now dependent on \R-3.0.0. + + } %itemize + } % building + + +} % v2.3-4 + \section{Changes in version 2.3-3}{ \subsection{BUG FIXES}{ \itemize{ From noreply at r-forge.r-project.org Thu Feb 25 13:37:23 2016 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 25 Feb 2016 13:37:23 +0100 (CET) Subject: [Vegan-commits] r2992 - www Message-ID: <20160225123723.2929018760D@r-forge.r-project.org> Author: jarioksa Date: 2016-02-25 13:37:22 +0100 (Thu, 25 Feb 2016) New Revision: 2992 Modified: www/NEWS.html Log: update NEWS Modified: www/NEWS.html =================================================================== --- www/NEWS.html 2016-02-25 12:36:23 UTC (rev 2991) +++ www/NEWS.html 2016-02-25 12:37:22 UTC (rev 2992) @@ -7,6 +7,68 @@

vegan News

+

Changes in version 2.3-4

+ + + +

BUG FIXES

+ + +
    +

  • betadiver index 19 had wrong sign in one of +its terms. +

    +
    • +

  • linestack failed when the labels were given, +but the input scores had no names. Reported by Jeff Wood (ANU, +Canberra, ACT). +

    +
+ + + + +

DEPRECATED

+ + +
    +

  • vegandocs is deprecated. Current R provides better +tools for seeing extra documentation. +

    +
+ + + + +

VIGNETTES

+ + +
    +

  • All vignettes are built with standard R tools and can be +browsed with browseVignettes. Earlier FAQ-vegan and +partitioning were only accessible with vegandocs +function. +

    +
+ + + + +

BUILDING

+ + +
    +

  • Dependence on external software texi2dvi was +removed. Version 6.1 of texi2dvi was incompatible with R +and prevented building vegan. The FAQ-vegan that was +earlier built with texi2dvi uses now knitr. Because +of this, vegan is now dependent on R-3.0.0. +

    +
+ + + +

Changes in version 2.3-3

From noreply at r-forge.r-project.org Thu Feb 25 13:51:14 2016 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 25 Feb 2016 13:51:14 +0100 (CET) Subject: [Vegan-commits] r2993 - pkg/vegan Message-ID: <20160225125114.157A91875DE@r-forge.r-project.org> Author: jarioksa Date: 2016-02-25 13:51:13 +0100 (Thu, 25 Feb 2016) New Revision: 2993 Modified: pkg/vegan/DESCRIPTION Log: Merge branch 'cran-2.3' into r-forge-svn-local Modified: pkg/vegan/DESCRIPTION =================================================================== --- pkg/vegan/DESCRIPTION 2016-02-25 12:37:22 UTC (rev 2992) +++ pkg/vegan/DESCRIPTION 2016-02-25 12:51:13 UTC (rev 2993) @@ -14,4 +14,4 @@ functions for community and vegetation ecologists. License: GPL-2 BugReports: https://github.com/vegandevs/vegan/issues -URL: http://cran.r-project.org, https://github.com/vegandevs/vegan +URL: https://cran.r-project.org, https://github.com/vegandevs/vegan From noreply at r-forge.r-project.org Fri Feb 26 12:04:06 2016 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 26 Feb 2016 12:04:06 +0100 (CET) Subject: [Vegan-commits] r2994 - in pkg/vegan: inst man Message-ID: <20160226110406.288F818441E@r-forge.r-project.org> Author: jarioksa Date: 2016-02-26 12:04:05 +0100 (Fri, 26 Feb 2016) New Revision: 2994 Modified: pkg/vegan/inst/NEWS.Rd pkg/vegan/man/cca.Rd pkg/vegan/man/diversity.Rd pkg/vegan/man/nestedtemp.Rd pkg/vegan/man/oecosimu.Rd pkg/vegan/man/plot.cca.Rd pkg/vegan/man/simper.Rd pkg/vegan/man/specpool.Rd pkg/vegan/man/varpart.Rd pkg/vegan/man/vegan-package.Rd Log: Merge branch 'cran-2.3' into r-forge-svn-local Modified: pkg/vegan/inst/NEWS.Rd =================================================================== --- pkg/vegan/inst/NEWS.Rd 2016-02-25 12:51:13 UTC (rev 2993) +++ pkg/vegan/inst/NEWS.Rd 2016-02-26 11:04:05 UTC (rev 2994) @@ -21,7 +21,8 @@ \itemize{ \item \code{vegandocs} is deprecated. Current \R{} provides better - tools for seeing extra documentation. + tools for seeing extra documentation (\code{news()} and + \code{browseVignettes()}). } %itemize } %deprecated @@ -30,9 +31,9 @@ \itemize{ \item All vignettes are built with standard \R{} tools and can be - browsed with \code{browseVignettes}. Earlier \code{FAQ-vegan} and + browsed with \code{browseVignettes}. \code{FAQ-vegan} and \code{partitioning} were only accessible with \code{vegandocs} - function. + function. } %itemize } %vignettes @@ -44,7 +45,9 @@ removed. Version 6.1 of \code{texi2dvi} was incompatible with \R{} and prevented building \pkg{vegan}. The \code{FAQ-vegan} that was earlier built with \code{texi2dvi} uses now \pkg{knitr}. Because - of this, \pkg{vegan} is now dependent on \R-3.0.0. + of this, \pkg{vegan} is now dependent on \R-3.0.0. Fixes issue + \href{https://github.com/vegandevs/vegan/issues/158}{#158} in + Github. } %itemize } % building Modified: pkg/vegan/man/cca.Rd =================================================================== --- pkg/vegan/man/cca.Rd 2016-02-25 12:51:13 UTC (rev 2993) +++ pkg/vegan/man/cca.Rd 2016-02-26 11:04:05 UTC (rev 2994) @@ -271,10 +271,6 @@ data(dune.env) dune.Manure <- rda(dune ~ Manure, dune.env) plot(dune.Manure) -## For further documentation: -\dontrun{ -vegandocs("decision") } -} \keyword{ multivariate } Modified: pkg/vegan/man/diversity.Rd =================================================================== --- pkg/vegan/man/diversity.Rd 2016-02-25 12:51:13 UTC (rev 2993) +++ pkg/vegan/man/diversity.Rd 2016-02-26 11:04:05 UTC (rev 2994) @@ -79,12 +79,12 @@ \seealso{These functions calculate only some basic indices, but many others can be derived with them (see Examples). Facilities related to diversity are discussed in a \pkg{vegan} vignette that can be read - with command \code{vegandocs("diversity")}. Functions - \code{\link{renyi}} and \code{\link{tsallis}} estimate a series of - generalized diversity indices. Function \code{\link{rarefy}} finds - estimated number of species for given sample size. Beta diversity can - be estimated with \code{\link{betadiver}}. Diversities can be - partitioned with \code{\link{adipart}} and \code{\link{multipart}}. } + with \code{browseVignettes("vegan")}. Functions \code{\link{renyi}} + and \code{\link{tsallis}} estimate a series of generalized diversity + indices. Function \code{\link{rarefy}} finds estimated number of + species for given sample size. Beta diversity can be estimated with + \code{\link{betadiver}}. Diversities can be partitioned with + \code{\link{adipart}} and \code{\link{multipart}}. } \author{ Jari Oksanen and Bob O'Hara (\code{fisher.alpha}).} Modified: pkg/vegan/man/nestedtemp.Rd =================================================================== --- pkg/vegan/man/nestedtemp.Rd 2016-02-25 12:51:13 UTC (rev 2993) +++ pkg/vegan/man/nestedtemp.Rd 2016-02-26 11:04:05 UTC (rev 2994) @@ -93,7 +93,7 @@ cautious in interpreting the results. The details of calculations are explained in the \code{\link{vignette}} \emph{Design decisions and implementation} that you can read using functions - \code{\link{vignette}} or \code{\link{vegandocs}}. Function + \code{\link{browseVignettes}}. Function \code{\link[bipartite]{nestedness}} in the \pkg{bipartite} package is a direct port of the BINMATNEST programme of \enc{Rodr?guez-Giron?s}{Rodriguez-Girones} & Santamaria (2006). Modified: pkg/vegan/man/oecosimu.Rd =================================================================== --- pkg/vegan/man/oecosimu.Rd 2016-02-25 12:51:13 UTC (rev 2993) +++ pkg/vegan/man/oecosimu.Rd 2016-02-26 11:04:05 UTC (rev 2994) @@ -80,8 +80,7 @@ processing. The parallel processing is done with \pkg{parallel} package. If you define a \code{nestfun} in Windows that needs other \R packages than \pkg{vegan} or \pkg{permute}, you must set up a - socket cluster before the call. See \code{\link{vegandocs}} - \code{decision-vegan} for details. } + socket cluster before the call. } \item{x}{An \code{oecosimu} result object.} \item{\dots}{Other arguments to functions.} Modified: pkg/vegan/man/plot.cca.Rd =================================================================== --- pkg/vegan/man/plot.cca.Rd 2016-02-25 12:51:13 UTC (rev 2993) +++ pkg/vegan/man/plot.cca.Rd 2016-02-26 11:04:05 UTC (rev 2994) @@ -88,9 +88,10 @@ \item{const}{General scaling constant to \code{rda} scores. The default is to use a constant that gives biplot scores, that is, scores that approximate original data (see \code{\link{vignette}} - \samp{decision-vegan.pdf} with \code{\link{vegandocs}} for details - and discussion). If \code{const} is a vector of two items, the first - is used for species, and the second item for site scores.} + on \sQuote{Design Decisions} with \code{browseVignettes("vegan")} + for details and discussion). If \code{const} is a vector of two + items, the first is used for species, and the second item for site + scores.} \item{axis.bp}{Draw \code{\link{axis}} for biplot arrows.} \item{axes}{Number of axes in summaries.} \item{digits}{Number of digits in output.} Modified: pkg/vegan/man/simper.Rd =================================================================== --- pkg/vegan/man/simper.Rd 2016-02-25 12:51:13 UTC (rev 2993) +++ pkg/vegan/man/simper.Rd 2016-02-26 11:04:05 UTC (rev 2994) @@ -31,9 +31,7 @@ \item{digits}{Number of digits in output.} \item{parallel}{Number of parallel processes or a predefined socket cluster. With \code{parallel = 1} uses ordinary, non-parallel - processing. The parallel processing is done with \pkg{parallel} - package. See \code{\link{vegandocs}} \code{decision-vegan} for - details.} + processing.} \item{...}{Parameters passed to other functions. In \code{simper} the extra parameters are passed to \code{\link[permute]{shuffleSet}} if permutations are used.} Modified: pkg/vegan/man/specpool.Rd =================================================================== --- pkg/vegan/man/specpool.Rd 2016-02-25 12:51:13 UTC (rev 2993) +++ pkg/vegan/man/specpool.Rd 2016-02-26 11:04:05 UTC (rev 2994) @@ -121,18 +121,17 @@ the number of individuals in rare species. - Functions estimate the standard errors of the estimates. These - only concern the number of added species, and assume that there is - no variance in the observed richness. The equations of standard - errors are too complicated to be reproduced in this help page, but - they can be studied in the \R source code of the function and are - discussed in the \code{\link{vignette}} \dQuote{diversity-vegan} - that can be read with the \code{\link{vegandocs}} command. The - standard error are based on the following sources: Chiu et - al. (2014) for the Chao estimates and Smith and van Belle (1984) - for the first-order Jackknife and the bootstrap (second-order - jackknife is still missing). For the variance estimator of - \eqn{S_{ace}}{S_ace} see O'Hara (2005). + Functions estimate the standard errors of the estimates. These only + concern the number of added species, and assume that there is no + variance in the observed richness. The equations of standard errors + are too complicated to be reproduced in this help page, but they can + be studied in the \R source code of the function and are discussed + in the \code{\link{vignette}} that can be read with the + \code{browseVignettes("vegan")}. The standard error are based on the + following sources: Chiu et al. (2014) for the Chao estimates and + Smith and van Belle (1984) for the first-order Jackknife and the + bootstrap (second-order jackknife is still missing). For the + variance estimator of \eqn{S_{ace}}{S_ace} see O'Hara (2005). Functions \code{poolaccum} and \code{estaccumR} are similar to \code{\link{specaccum}}, but estimate extrapolated richness indices Modified: pkg/vegan/man/varpart.Rd =================================================================== --- pkg/vegan/man/varpart.Rd 2016-02-25 12:51:13 UTC (rev 2993) +++ pkg/vegan/man/varpart.Rd 2016-02-26 11:04:05 UTC (rev 2994) @@ -92,10 +92,9 @@ explained by the explanatory table. The identifiable fractions are designated by lower case alphabets. The - meaning of the symbols can be found in the separate document - "partitioning.pdf" (which can be read using \code{\link{vegandocs}}), - or can be displayed graphically using function - \code{showvarparts}. + meaning of the symbols can be found in the separate document (use + \code{browseVignettes("vegan")}), or can be displayed graphically + using function \code{showvarparts}. A fraction is testable if it can be directly expressed as an RDA model. In these cases the printed output also @@ -107,9 +106,9 @@ the number of estimated models. An abridged explanation of the alphabetic symbols for the individual - fractions follows, but computational details should be checked in - "partitioning.pdf" (readable with \code{\link{vegandocs}}) or in the - source code. + fractions follows, but computational details should be checked in the + vignette (readable with \code{browseVignettes("vegan")}) or in the + source code. With two explanatory tables, the fractions explained uniquely by each of the two tables are \code{[a]} and @@ -209,11 +208,11 @@ \note{ - You can use command \code{\link{vegandocs}} to display document - "partitioning.pdf" which presents Venn diagrams showing the fraction - names in partitioning the variation of Y with respect to 2, 3, and 4 - tables of explanatory variables, as well as the equations used in - variation partitioning. + You can use command \code{browseVignettes("vegan")} to display + document which presents Venn diagrams showing the fraction names in + partitioning the variation of Y with respect to 2, 3, and 4 tables of + explanatory variables, as well as the equations used in variation + partitioning. The functions frequently give negative estimates of variation. Adjusted \eqn{R^2}{R-squared} can be negative for any fraction; @@ -252,11 +251,6 @@ data(mite.env) data(mite.pcnm) -## See detailed documentation: -\dontrun{ -vegandocs("partition") -} - # Two explanatory matrices -- Hellinger-transform Y # Formula shortcut "~ ." means: use all variables in 'data'. mod <- varpart(mite, ~ ., mite.pcnm, data=mite.env, transfo="hel") Modified: pkg/vegan/man/vegan-package.Rd =================================================================== --- pkg/vegan/man/vegan-package.Rd 2016-02-25 12:51:13 UTC (rev 2993) +++ pkg/vegan/man/vegan-package.Rd 2016-02-26 11:04:05 UTC (rev 2994) @@ -12,31 +12,26 @@ multivariate tools can be used for other data types as well. } \details{The functions in the \pkg{vegan} package contain tools for -diversity analysis (see \code{\link{vignette}} -\code{vegandocs("diversity")}), ordination and analysis of -dissimilarities (see \code{\link{vignette}} -\code{vegandocs("intro")}). Together with the \pkg{labdsv} package, -the \pkg{vegan} package provides most standard tools of descriptive -community analysis. Package \pkg{ade4} provides an alternative -comprehensive package, and several other packages complement -\pkg{vegan} and provide tools for deeper analysis in specific -fields. Package \pkg{BiodiversityR} provides a GUI for a large subset -of \pkg{vegan} functionality. +diversity analysis, ordination methods and tools for the analysis of +dissimilarities. Together with the \pkg{labdsv} package, the \pkg{vegan} +package provides most standard tools of descriptive community +analysis. Package \pkg{ade4} provides an alternative comprehensive +package, and several other packages complement \pkg{vegan} and provide +tools for deeper analysis in specific fields. Package +\pkg{BiodiversityR} provides a GUI for a large subset of \pkg{vegan} +functionality. The \pkg{vegan} package is developed at GitHub (\url{https://github.com/vegandevs/vegan/}). GitHub provides up-to-date information and forums for bug reports. -The \pkg{vegan} documents can be read with \code{\link{vegandocs}} -function. In addition to \code{\link{vignette}}s of basic usage, you -can read \code{NEWS} on the new features and bug fixes in the release -version (\code{vegandocs("NEWS")}), and more technical and fine -grained \code{ChangeLog} (\code{vegandocs("Change")}). Several -frequently asked questions really are answered in the vegan FAQ -(\code{vegandocs("FAQ")}). The discussion on design decisions can be -read with \code{vegandocs("decision")}. A tutorial of the package at -\url{http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf} -provides a more thorough introduction to the package. +Most important changes in \pkg{vegan} documents can be read with +\code{news(package="vegan")} and vignettes can be browsed with +\code{browseVignettes("vegan")}. The vignettes include a \pkg{vegan} +FAQ, discussion on design decisions, short introduction to ordination +and discussion on diversity methods. A tutorial of the package at +\url{http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf} provides +a more thorough introduction to the package. To see the preferable citation of the package, type \code{citation("vegan")}. From noreply at r-forge.r-project.org Fri Feb 26 12:05:24 2016 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 26 Feb 2016 12:05:24 +0100 (CET) Subject: [Vegan-commits] r2995 - www Message-ID: <20160226110524.98E1F18441E@r-forge.r-project.org> Author: jarioksa Date: 2016-02-26 12:05:24 +0100 (Fri, 26 Feb 2016) New Revision: 2995 Modified: www/NEWS.html Log: update NEWS Modified: www/NEWS.html =================================================================== --- www/NEWS.html 2016-02-26 11:04:05 UTC (rev 2994) +++ www/NEWS.html 2016-02-26 11:05:24 UTC (rev 2995) @@ -33,7 +33,8 @@

  • vegandocs is deprecated. Current R provides better -tools for seeing extra documentation. +tools for seeing extra documentation (news() and +browseVignettes()).

@@ -45,9 +46,9 @@

  • All vignettes are built with standard R tools and can be -browsed with browseVignettes. Earlier FAQ-vegan and +browsed with browseVignettes. FAQ-vegan and partitioning were only accessible with vegandocs -function. +function.

@@ -62,7 +63,9 @@ removed. Version 6.1 of texi2dvi was incompatible with R and prevented building vegan. The FAQ-vegan that was earlier built with texi2dvi uses now knitr. Because -of this, vegan is now dependent on R-3.0.0. +of this, vegan is now dependent on R-3.0.0. Fixes issue +#158 in +Github.