[CHNOSZ-commits] r582 - in pkg/CHNOSZ: . demo inst inst/extdata inst/extdata/bison inst/extdata/protein man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Jul 25 08:48:32 CEST 2020
Author: jedick
Date: 2020-07-25 08:48:31 +0200 (Sat, 25 Jul 2020)
New Revision: 582
Added:
pkg/CHNOSZ/inst/extdata/bison/taxid_names.csv.xz
Removed:
pkg/CHNOSZ/demo/bugstab.R
pkg/CHNOSZ/inst/extdata/abundance/
pkg/CHNOSZ/inst/extdata/protein/microbial.aa.csv
pkg/CHNOSZ/inst/extdata/refseq/
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/demo/00Index
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/man/extdata.Rd
pkg/CHNOSZ/man/util.blast.Rd
Log:
Remove demo/bugstab.R
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2020-07-25 06:13:50 UTC (rev 581)
+++ pkg/CHNOSZ/DESCRIPTION 2020-07-25 06:48:31 UTC (rev 582)
@@ -1,6 +1,6 @@
Date: 2020-07-25
Package: CHNOSZ
-Version: 1.3.6-55
+Version: 1.3.6-56
Title: Thermodynamic Calculations and Diagrams for Geochemistry
Authors at R: c(
person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
Modified: pkg/CHNOSZ/demo/00Index
===================================================================
--- pkg/CHNOSZ/demo/00Index 2020-07-25 06:13:50 UTC (rev 581)
+++ pkg/CHNOSZ/demo/00Index 2020-07-25 06:48:31 UTC (rev 582)
@@ -17,7 +17,6 @@
contour Gold solubility contours on a log fO2 - pH diagram
sphalerite Solubility of sphalerite
dehydration log K of dehydration reactions; SVG file contains tooltips and links
-bugstab Formation potential of microbial proteins in colorectal cancer
Shh Affinities of transcription factors relative to Sonic hedgehog
saturation Equilibrium activity diagram showing activity ratios and mineral saturation limits
adenine HKF parameters regressed from heat capacity and volume of aqueous adenine
Deleted: pkg/CHNOSZ/demo/bugstab.R
===================================================================
--- pkg/CHNOSZ/demo/bugstab.R 2020-07-25 06:13:50 UTC (rev 581)
+++ pkg/CHNOSZ/demo/bugstab.R 2020-07-25 06:48:31 UTC (rev 582)
@@ -1,76 +0,0 @@
-# formation potential of microbial proteins in colorectal cancer
-# based on "bugstab" function in Supporting Information of Dick, 2016
-# (https://doi.org/10.7717/peerj.2238)
-
-# to reproduce the calculations in the paper, use superseded data for [Gly] and [UPBB] 20190206
-add.OBIGT("OldAA", c("[Gly]", "[UPBB]"))
-# set up graphics device
-layout(cbind(matrix(sapply(list(c(1, 2), c(3, 4)), function(x) rep(rep(x, each=3), 3)), nrow=6, byrow=TRUE),
- matrix(rep(c(0, 5, 5, 5, 5, 0), each=4), nrow=6, byrow=TRUE)))
-opar <- par(mar=c(3.3, 3.3, 1.5, 1.5), mgp=c(2.1, 0.7, 0), xaxs="i", yaxs="i", las=1, cex=0.9)
-# resolution for plots
-res <- 500
-# basis can be "QEC" or "CHNOS"
-basis <- "QEC"
-# read bioproject ids, species names
-mfile <- system.file("extdata/abundance/microbes.csv", package="CHNOSZ")
-bugs <- read.csv(mfile, as.is=TRUE)
-# where to keep the locations of healthy zones
-healthbugs <- list()
-if(basis=="CHNOS") {
- O2 <- c(-85, -65, res)
- H2O <- c(-15, 5, res)
-} else {
- O2 <- c(-75, -55, res)
- H2O <- c(-10, 10, res)
-}
-# the datasets that are considered
-datasets <- c("WCQ+12", "ZTV+14", "CTB+14", "FLJ+15")
-# colors
-blue <- "#4A6FE3"
-lightblue <- "#9DA8E2"
-neutral <- "#E2E2E2"
-lightred <- "#E495A5"
-red <- "#D33F6A"
-# labels
-logfO2lab <- expression(log*italic("f")[O[2]*group("(", italic("g"), ")")])
-logaH2Olab <- expression(log*italic("a")[H[2]*O*group("(", italic("liq"), ")")])
-for(i in 1:4) {
- ibug <- bugs$study==datasets[i] & (is.na(bugs$logodds) | abs(bugs$logodds) > 0.15)
- # get amino acid compositions
- aafile <- system.file("extdata/protein/microbial.aa.csv", package="CHNOSZ")
- microbial.aa <- read.csv(aafile, stringsAsFactors=FALSE)
- aa <- microbial.aa[match(bugs$bioproject[ibug], microbial.aa$organism), ]
- ip <- add.protein(aa)
- # set up system, calculate relative stabilities
- col <- ifelse(bugs$upcan[ibug], lightred, lightblue)
- basis(basis)
- a <- affinity(O2=O2, H2O=H2O, iprotein=ip, T=37)
- names <- bugs$abbrv[ibug]
- d <- diagram(a, names=names, fill=col, as.residue=TRUE, tplot=FALSE, xlab=logfO2lab, ylab=logaH2Olab, format.names=FALSE)
- if(i==1) title(main="Fecal 16S rRNA", cex.main=1)
- if(i==2) title(main="Fecal metagenome (ZTV+14)", cex.main=1)
- if(i==3) title(main="Co-abundance groups", cex.main=1)
- if(i==4) title(main="Fecal metagenome (FLJ+15)", cex.main=1)
- box()
- label.figure(LETTERS[i], yfrac=0.96, paren=FALSE, font=2, cex=1)
- # store locations of healthy bug zones
- p <- d$predominant
- p[p %in% which(bugs$upcan[ibug])] <- 0
- p[p != 0] <- 1
- healthbugs[[i]] <- p
-}
-# now show the healthy zones
-xs <- seq(O2[1], O2[2], length.out=O2[3])
-ys <- seq(H2O[1], H2O[2], length.out=H2O[3])
-hhh <- healthbugs[[1]] + healthbugs[[2]] + healthbugs[[3]] + healthbugs[[4]]
-image(xs, ys, hhh, col=c(red, lightred, neutral, lightblue, blue), useRaster=TRUE, xlab=logfO2lab, ylab=logaH2Olab)
-title(main="Cumulative stability count")
-box()
-label.figure("E", yfrac=0.96, paren=FALSE, font=2, cex=1)
-
-# reset graphics device to default
-par(opar)
-layout(1)
-# reset thermodynamic database
-reset()
Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd 2020-07-25 06:13:50 UTC (rev 581)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2020-07-25 06:48:31 UTC (rev 582)
@@ -124,7 +124,8 @@
\item Remove vignette \samp{hotspring.Rnw}, demo \samp{bison.R}, and
associated data files \samp{DS11.csv} and \samp{DS13.csv}. The plots are
now in the \samp{bison.Rmd} vignette in the \pkg{JMDplots} package
- (\url{https://github.com/jedick/JMDplots}).
+ (\url{https://github.com/jedick/JMDplots}). Also move the demo
+ \samp{bugstab.R} and supporting data files to \pkg{JMDplots}.
\item Add \samp{viglink} Rd macro so HTML versions of Rd files can link
to vignettes.
Copied: pkg/CHNOSZ/inst/extdata/bison/taxid_names.csv.xz (from rev 581, pkg/CHNOSZ/inst/extdata/refseq/taxid_names.csv.xz)
===================================================================
(Binary files differ)
Deleted: pkg/CHNOSZ/inst/extdata/protein/microbial.aa.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/protein/microbial.aa.csv 2020-07-25 06:13:50 UTC (rev 581)
+++ pkg/CHNOSZ/inst/extdata/protein/microbial.aa.csv 2020-07-25 06:48:31 UTC (rev 582)
@@ -1,69 +0,0 @@
-protein,organism,ref,abbrv,chains,Ala,Cys,Asp,Glu,Phe,Gly,His,Ile,Lys,Leu,Met,Asn,Pro,Gln,Arg,Ser,Thr,Val,Trp,Tyr
-mean,PRJNA13225,NA,NA,1,22.0408163265306,1.68673469387755,16.7071428571429,18.8836734693878,14.0489795918367,18.5051020408163,5.78112244897959,22.8658163265306,21.9331632653061,29.9397959183673,7.16428571428572,14.3311224489796,9.32448979591837,12.0540816326531,11.5459183673469,18.5683673469388,16.5933673469388,19.4790816326531,2.57704081632653,11.3882653061225
-mean,PRJNA13378,NA,NA,1,25.6036900369003,4.84969249692498,20.3945879458796,24.7416974169742,17.0792127921279,25.5567035670357,7.4029520295203,25.7269372693727,25.4361623616236,33.7136531365314,10.5645756457565,19.5377613776139,13.9052890528905,12.7448954489544,17.5675276752767,22.4142681426814,20.7950799507996,23.5758917589175,5.00123001230015,16.9778597785979
-mean,PRJNA13485,NA,NA,1,26.0537662337662,4.43012987012987,20.8332467532467,24.4075324675324,17.518961038961,25.718961038961,6.78051948051948,26.1615584415584,24.1888311688311,35.0501298701298,10.2651948051948,18.6194805194805,14.6511688311688,12.3592207792208,17.9098701298701,23.6522077922078,20.6431168831169,24.4311688311688,4.65142857142856,16.6955844155844
-mean,PRJNA13799,NA,NA,1,20.9127031908489,1.53100541842264,16.3756773028296,19.151715833835,12.8121613485852,18.4455147501505,5.30042143287177,20.6387718242023,19.1896447922938,27.6616496086695,7,12.7814569536424,9.12703190848886,10.524984948826,11.4954846478025,17.3257074051776,15.8609271523179,19.9554485249849,2.32510535821794,10.4274533413606
-mean,PRJNA1419,NA,NA,1,14.272,2.13066666666667,14.608,21.2093333333334,12.9333333333333,16.7755555555556,3.18933333333334,26.4719999999999,27.2102222222223,24.5857777777777,6.37333333333333,17.2204444444444,6.82933333333332,5.88399999999999,8.85822222222225,15.824,13.0933333333334,15.9266666666666,1.77422222222222,11.936
-mean,PRJNA15579,NA,NA,1,16.6505867014342,3.78031290743155,19.5834419817471,21.8826597131682,11.480443285528,19.0977835723598,5.45436766623207,33.1981747066493,26.27444589309,26.9393741851369,7.32855280312908,24.1786179921773,10.1975228161669,8.32268578878747,9.73272490221643,20.1675358539765,21.6988265971317,20.2979139504563,1.77835723598436,13.9406779661017
-mean,PRJNA165425,NA,NA,1,25.6383207750269,3.20452099031216,19.1103336921421,26.272874058127,14.6130247578041,25.3573735199139,7.43702906350914,23.4720129171152,22.1167922497309,36.3304628632939,9.33907427341227,15.2238966630786,14.6286329386437,13.694833153929,18.3509149623251,22.9305705059204,19.7395048439182,23.7922497308934,4.14693218514532,15.2039827771798
-mean,PRJNA169488,NA,NA,1,40.9726368159204,4.13723051409618,18.3793532338308,21.4195688225539,14.301824212272,27.1762023217247,6.51492537313433,18.7039800995025,16.1455223880597,35.2927031509121,8.893864013267,10.8370646766169,16.6504975124378,11.0841625207297,21.4825870646766,21.0290215588723,19.297263681592,25.3897180762852,4.71641791044776,8.46227197346601
-mean,PRJNA169707,NA,NA,1,24.8824163969795,4.54422869471413,19.4867853290183,24.1957928802589,15.925836030205,23.7036138079828,6.8435814455232,24.8357605177993,24.7667206040993,32.1639697950378,9.98975188781014,18.1637001078749,13.0687702265372,12.2545846817691,16.4983818770226,21.11380798274,19.7918015102481,22.5404530744337,4.38754045307443,15.8149946062568
-mean,PRJNA174975,NA,NA,1,33.798286090969,4.59129861568886,20.9881344759393,22.8058668424522,15.5527356624918,28.3388266315095,6.51549110085696,20.9545154911008,17.5840474620962,32.3576137112722,9.45352669742914,14.5906394199077,15.2007251153592,11.387936717205,22.9119973632169,20.5959129861569,21.1064601186553,25.2788398154252,4.90079103493739,15.2943309162821
-mean,PRJNA18169,NA,NA,1,14.7210965435042,3.14481525625745,17.3224076281287,23.5488676996424,15.9201430274136,18.2061978545888,3.67997616209774,29.3569725864124,30.3802145411204,27.3843861740167,7.37067938021454,19.6174016686531,7.51132300357569,6.28665077473183,10.0625744934446,19.2514898688915,14.5023837902265,19.6066746126341,1.9362336114422,12.6573301549464
-mean,PRJNA18175,NA,NA,1,20.7852315394243,4.21426783479349,15.3411764705882,21.2443053817272,10.8272841051314,19.8002503128911,4.87133917396746,20.4105131414268,19.2187734668335,24.2190237797247,8.91914893617022,11.0685857321652,9.17421777221527,8.93391739674594,12.9862327909887,15.2250312891114,14.1624530663329,18.3344180225282,2.51163954943679,11.2352941176471
-mean,PRJNA18179,NA,NA,1,19.6966521850243,4.18936877076412,14.416304625607,22.3163812931255,11.3074367492972,19.0337337081523,4.87733197035523,19.9207768975211,19.884998722208,24.6746741630462,8.7868642984922,11.5502172246358,8.77689752108356,10.0981344237158,12.4444160490672,15.4099156657296,14.7794531050345,18.7937643751597,2.68387426526962,11.3559928443649
-mean,PRJNA18183,NA,NA,1,23.1068702290076,4.45580554439534,15.0176777822418,21.4521896343913,12.107472880675,22.392527119325,4.71313780634793,20.7567296102853,17.9439533949377,26.5359582161511,9.29188429087987,11.4777018883086,10.4244676576938,8.77340297308157,14.3182000803535,16.9887505022097,15.1488549618321,19.3475291281639,2.66834069907593,11.2089192446766
-mean,PRJNA18193,NA,NA,1,21.4787864963504,3.74817518248175,16.944799270073,19.9450273722628,14.4270072992701,21.1142791970803,5.65396897810219,21.035355839416,20.3599452554744,28.1270529197081,8.47217153284673,15.2338047445256,11.8398722627737,10.2294708029197,14.6475821167884,18.5647810218978,16.8496806569343,20.0335310218978,3.82709854014599,13.4206204379562
-mean,PRJNA18195,NA,NA,1,22.7550932875831,4.1559082135964,17.0581170920008,20.3622131674887,14.5496461505469,21.9221531203088,6.19601115161913,20.6041175209093,20.0068625348488,28.7469440274501,8.96161269568946,15.3892343984559,11.9182929444564,10.7014797340768,15.1520480377439,18.7973407677461,17.4550718421617,20.5382800772035,4.14346986918294,14.0160840660519
-mean,PRJNA18201,NA,NA,1,19.7837069782128,4.11398800126302,17.0606251973476,22.0779917903379,12.353646984528,20.0274707925481,5.51215661509315,24.022102936533,25.1594568992738,25.3009156930849,9.67035048942217,13.4840543100726,8.93337543416483,9.98231765077361,11.6769813703821,16.6832964951058,16.1834543732239,19.9538995895169,2.43542784970003,12.6450899905273
-mean,PRJNA188796,NA,NA,1,27.4694505494505,3.90373626373626,16.9920879120879,19.9547252747253,12.5802197802198,24.3010989010989,6.73846153846154,19.5446153846154,19.6228571428572,30.0843956043956,9.59692307692308,10.556043956044,12.5665934065934,9.39252747252747,15.5854945054945,17.2114285714286,17.4892307692308,21.9762637362637,2.9389010989011,10.5327472527473
-mean,PRJNA19423,NA,NA,1,37.9142670157068,3.6053664921466,23.0130890052356,21.6302356020942,12.348167539267,27.6236910994764,8.59489528795812,19.1708115183246,12.9155759162304,31.2840314136126,10.1086387434555,12.3965968586387,16.6753926701571,13.0013089005236,22.0130890052356,20.7284031413613,20.8527486910995,27.6969895287958,4.71989528795812,9.64267015706807
-mean,PRJNA19655,NA,NA,1,23.0047410649161,3.74507658643326,15.4959883296864,18.8778264040846,12.2687819110139,19.7396061269147,4.87490882567469,18.0525164113786,15.27352297593,25.0295404814004,7.17906637490883,11.2407002188184,11.2053245805981,8.99161196207148,17.0568927789934,16.0853391684901,15.6622902990518,18.6520787746171,3.10612691466084,10.9055433989788
-mean,PRJNA197159,NA,NA,1,23.3324423655195,4.17641162712997,16.1660541262947,21.5599732709656,11.5910457734714,21.6204477113264,5.01002338790511,19.6184430337454,19.2746408286001,25.0831941196124,9.26227865018376,11.729368526562,9.9605746742399,8.41129301703976,13.1319746074173,16.2034747744738,15.8606749081189,19.8703641830939,2.6321416638824,11.0350818576679
-mean,PRJNA197168,NA,NA,1,25.0603585205355,4.41093714545042,20.2473337871568,24.2167007034264,16.5200816882233,24.7077376900386,6.55139550714771,25.3253914227365,24.714091218516,32.4878602223735,9.96687088722487,19.2407533469481,13.5883821193556,12.669616519174,16.2645790787384,22.5203085999546,20.7585659178579,22.9897889720898,4.87542545949627,16.8123439981847
-mean,PRJNA20527,NA,NA,1,21.351048269137,1.6611409068747,16.526084836665,18.8347147732813,12.5841053144807,17.900048756704,5.2457337883959,20.4310092637738,19.7591418820088,27.008288639688,7.1496830814237,13.0360799609946,8.65870307167235,10.1452949780595,10.7469527059971,17.1131155533886,16.0141394441736,19.8035104826914,2.33788395904437,10.4275962944905
-mean,PRJNA212635,NA,NA,1,26.2762969332187,4.6262539409573,20.8601318429349,25.4800802522213,17.6864431069074,25.9492691315563,6.94640298079679,27.2032100888507,26.1126397248495,34.8096875895672,10.3983949555747,20.1338492404701,14.445113212955,13.2662654055603,17.3098308971052,23.4130123244482,21.5333906563485,24.633992548008,4.93035253654343,17.3195758096876
-mean,PRJNA212673,NA,NA,1,25.3055091819699,3.27935447968836,18.5386755703951,20.4691151919866,12.2487479131886,23.2309404563161,7.22426265998886,24.328324986088,19.1452420701169,28.5982192543127,9.52643294379519,13.9855314412911,11.841958820256,10.8436282693378,13.9265442404006,18.1107401224263,18.4056761268781,24.0372843628269,3.00556483027266,11.8219254312743
-mean,PRJNA223063,NA,NA,1,33.3793103448275,4.83926147162638,16.7705674721694,20.1830029866957,13.0323106163454,26.9940266087429,6.5164268259571,17.1306000543035,13.8400760249796,34.2112408362748,9.0529459679609,9.70730382840075,16.5495519956557,9.94759706760792,20.2468096660331,18.4713548737442,16.8050502307901,23.0494162367634,4.12163996741787,8.55063806679337
-mean,PRJNA257718,NA,NA,1,25.0828220858896,4.40720858895705,20.3046395705522,24.0761119631902,16.6715874233129,25.0124616564417,6.58454754601227,25.4158358895705,24.8778757668712,32.5776457055215,10.0427530674847,19.7302530674847,13.6144555214724,12.8293711656442,16.354486196319,22.8843941717791,21.1209739263804,23.1708205521472,5.03604294478528,17.0901073619632
-mean,PRJNA27827,NA,NA,1,24.6030719482619,4.39450282942603,18.589329021827,22.2403664780383,15.6725949878739,23.6009161950957,6.5313931554837,23.3777957423875,22.4653732147669,31.0215575316626,9.53570466181622,17.3190514686068,12.8978711937483,11.5295068714632,16.2842899488009,20.2872541094045,19.0573969280517,22.1172190784155,4.37267582861763,15.102937213689
-mean,PRJNA27831,NA,NA,1,22.8658880386629,4.38018525976641,18.3014498590415,21.9981876761981,15.3308497784938,22.8755537656061,6.68445428916633,23.3153443415223,22.8515908175594,30.2388240032219,9.54289166331053,17.5795408779702,12.4454289166331,11.619412001611,15.594039468385,20.2072090213452,18.7466774063633,21.2450664518727,4.56081353201771,15.2869512686267
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-mean,PRJNA39383,NA,NA,1,25.8332058148432,5.56648814078042,19.0586074980872,26.9473603672533,15.4959449120123,25.3937260902831,5.89410864575364,24.0509563886764,21.1473603672532,33.0111706197398,10.8644223412395,14.5121652639633,12.5998469778118,11.4339709257842,16.7851568477429,20.5776587605203,17.8168324407039,22.1825554705432,4.13312930374904,15.1963274674828
-mean,PRJNA39397,NA,NA,1,26.703572033181,4.41171491450821,15.4691044523447,19.5268325715253,10.2310817673946,21.975960724564,5.13932622312511,14.6380565430844,12.8943626206196,27.5840528186897,7.32791603182665,9.28068393431522,12.0722871169799,9.82038259691891,16.7282884713053,15.3360419840867,15.6023362112747,19.2911799559845,3.27916031826646,10.1200270865075
-mean,PRJNA40027,NA,NA,1,22.9425170068027,4.27448979591837,17.7017006802721,25.7044217687075,12.4704081632653,22.0357142857143,5.12040816326531,22.4278911564626,23.7071428571429,26.3608843537415,9.228231292517,13.5625850340136,9.75204081632653,9.87959183673469,13.8636054421769,17.8078231292517,17.2925170068027,21.4663265306122,2.81360544217687,12.7972789115646
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-mean,PRJNA46383,NA,NA,1,25.6406069602507,5.07075705096488,17.8292924294904,23.0277090549233,12.7097146627082,25.2874814448293,5.63796800263896,21.9800428830612,18.3902358568366,29.0349661883556,10.9130793336632,12.3219528286327,11.6518225301006,10.7720600362857,16.1616361537193,18.8550222662049,16.9325416460498,22.0936829952169,3.24047501237012,12.7690912089725
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-mean,PRJNA48497,NA,NA,1,27.4627408215194,3.99018538713195,15.612141039622,20.0577971646674,13.7041075972374,22.8171573973101,5.43984005816067,18.9596510359869,20.2126499454744,30.4311159578335,7.66121410396219,12.5696110505271,13.4354780079971,10.3845874227554,15.4478371501272,19.7062886223192,15.9462013813159,21.6045074518357,3.63649581970193,8.65030897855325
-mean,PRJNA48501,NA,NA,1,24.1164588528679,4.62418952618455,18.7526184538654,21.7364089775562,14.8279301745636,23.5496259351621,6.50498753117205,19.3102244389028,19.7476309226932,29.0438902743141,9.2199501246883,15.0468827930175,12.4655860349127,10.9546134663341,17.3618453865337,19.2598503740649,18.6441396508729,22.3413965087281,4.46758104738152,14.7159600997506
-mean,PRJNA48505,NA,NA,1,28.0241860465116,4.40372093023256,15.4288372093023,19.3762790697674,11.5055813953488,21.5311627906977,5.52604651162791,19.1995348837209,19.1241860465116,28.7920930232558,9.10232558139535,11.8144186046512,10.7148837209302,10.466976744186,13.2562790697674,15.0297674418605,14.7223255813953,21.4037209302326,2.52558139534884,10.4260465116279
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-mean,PRJNA57669,NA,NA,1,21.5707720588235,1.95435049019608,14.5024509803922,21.9669117647059,13.5370710784314,19.078125,5.02297794117648,21.2944240196078,20.8511029411765,28.828431372549,7.62745098039216,13.8566176470588,10.4604779411765,13.3149509803922,11.0692401960784,16.9874387254902,18.374080882353,20.3351715686274,2.79074754901961,10.8125
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-mean,PRJNA71551,NA,NA,1,18.8432397126061,2.39124755062051,17.0306988896146,24.0352710646636,14.430437622469,19.161985630307,4.61267145656434,27.9621162638798,28.0581319399086,29.9431743958197,7.25734813847159,18.1972566949706,8.3847158719791,8.11038536903984,10.800783801437,18.6316133246244,16.6165904637492,21.3670803396473,2.01045068582625,13.5088177661659
Modified: pkg/CHNOSZ/man/extdata.Rd
===================================================================
--- pkg/CHNOSZ/man/extdata.Rd 2020-07-25 06:13:50 UTC (rev 581)
+++ pkg/CHNOSZ/man/extdata.Rd 2020-07-25 06:48:31 UTC (rev 582)
@@ -22,15 +22,12 @@
\item The \code{testing} directory contains data files based on Berman and Aranovich (1996). These are used to demonstrate the addition of data from a user-supplied file (see \code{\link{berman}}).
}
- Files in \code{abundance} contain protein abundance and microbial occurrence data:
- \itemize{
- \item \code{microbes.csv} has data for microbial occurrence (i.e. relative enrichement) in colorectal cancer and normal tissue. The file is from the Supporting Information of Dick (2016). This file is used by \code{demo("bugstab")}.
- }
-
Files in \code{bison} contain BLAST results and taxonomic information for an environmental metagenome from the Bison Pool hot spring in Yellowstone National Park:
\itemize{
\item \code{bisonN_vs_refseq57.blast.xz}, \code{bisonS...}, \code{bisonR...}, \code{bisonQ...}, \code{bisonP...} are partial tabular BLAST results for proteins in the Bison Pool Environmental Genome. Protein sequences predicted in the metagenome were downloaded from the Joint Genome Institute's IMG/M system on 2009-05-13. The target database for the searches was constructed from microbial protein sequences in National Center for Biotechnology Information (NCBI) RefSeq database version 57, representing 7415 microbial genomes. The \sQuote{blastall} command was used with the default setting for E value cuttoff (10.0) and options to make a tabular output file consisting of the top 20 hits for each query sequence. The function \code{\link{read.blast}} was used to extract only those hits with E values less than or equal to 1e-5 and with sequence similarity (percent identity) at least 30 percent, and to keep only the first hit for each query sequence. The function \code{\link{write.blast}} was used to save partial BLAST files (only selected columns). The files provided with CHNOSZ contain the first 1000 hits for each sampling site at Bison Pool, representing between about 1.5 to 3 percent of the first BLAST hits after similarity and E value filtering.
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/chnosz -r 582
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