[CHNOSZ-commits] r63 - in pkg/CHNOSZ: . R data inst inst/extdata/protein inst/tests man vignettes

[noreply at r-forge.r-project.org]

Author: jedick
Date: 2014-01-30 15:40:30 +0100 (Thu, 30 Jan 2014)
New Revision: 63

Added:
   pkg/CHNOSZ/inst/extdata/protein/DS11.csv
   pkg/CHNOSZ/inst/extdata/protein/DS13.csv
Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/affinity.R
   pkg/CHNOSZ/R/iprotein.R
   pkg/CHNOSZ/R/util.data.R
   pkg/CHNOSZ/data/protein.csv
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/inst/tests/test-affinity.R
   pkg/CHNOSZ/man/equilibrate.Rd
   pkg/CHNOSZ/vignettes/hotspring.Rnw
   pkg/CHNOSZ/vignettes/hotspring.lyx
   pkg/CHNOSZ/vignettes/vig.bib
Log:
update hotspring.Rnw: microbial abundances, knitr


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2014-01-12 15:17:43 UTC (rev 62)
+++ pkg/CHNOSZ/DESCRIPTION	2014-01-30 14:40:30 UTC (rev 63)
@@ -1,11 +1,11 @@
-Date: 2014-01-12
+Date: 2014-01-30
 Package: CHNOSZ
-Version: 1.0.3
+Version: 1.0.3-1
 Title: Chemical Thermodynamics and Activity Diagrams
 Author: Jeffrey Dick
 Maintainer: Jeffrey Dick <j3ffdick at gmail.com>
 Depends: R (>= 2.12.0)
-Suggests: limSolve, parallel, testthat
+Suggests: limSolve, parallel, testthat, knitr
 Description: This package includes functions and data sets to support chemical thermodynamic 
   modeling in biochemistry and low-temperature geochemistry. The features include calculation
   of the standard molal thermodynamic properties and chemical affinities of reactions involving 
@@ -17,4 +17,5 @@
 License: GPL (>= 2)
 BuildResaveData: no
 ZipData: no
+VignetteBuilder: knitr
 URL: http://www.chnosz.net/, http://chnosz.r-forge.r-project.org/

Modified: pkg/CHNOSZ/R/affinity.R
===================================================================
--- pkg/CHNOSZ/R/affinity.R	2014-01-12 15:17:43 UTC (rev 62)
+++ pkg/CHNOSZ/R/affinity.R	2014-01-30 14:40:30 UTC (rev 63)
@@ -43,6 +43,8 @@
     # to ionization calculations in energy() so no explicit accounting
     # is needed here
     if(!is.null(iprotein)) {
+      # check all proteins are available
+      if(!all(iprotein %in% 1:nrow(thermo$protein))) stop("some value(s) in iprotein not in rownumbers of thermo$protein")
       # add protein residues to the species list
       resnames <- c("H2O",aminoacids(3))
       # residue activities set to zero;

Modified: pkg/CHNOSZ/R/iprotein.R
===================================================================
--- pkg/CHNOSZ/R/iprotein.R	2014-01-12 15:17:43 UTC (rev 62)
+++ pkg/CHNOSZ/R/iprotein.R	2014-01-30 14:40:30 UTC (rev 63)
@@ -151,7 +151,8 @@
 
 read.aa <- function(file="protein.csv") {
   # 20090428 added colClasses here
-  aa <- read.csv(file,colClasses=c(rep("character",4),rep("numeric",21)))
+  # 20140128 added as.is=TRUE (in case numeric values are stored in ref or abbrv column)
+  aa <- read.csv(file, colClasses=c(rep("character", 2), NA, NA, rep("numeric", 21)), as.is=TRUE)
   if(!identical(colnames(aa), colnames(get("thermo")$protein)))
     stop(paste("format of", file, "is incompatible with thermo$protein"))
   return(aa)

Modified: pkg/CHNOSZ/R/util.data.R
===================================================================
--- pkg/CHNOSZ/R/util.data.R	2014-01-12 15:17:43 UTC (rev 62)
+++ pkg/CHNOSZ/R/util.data.R	2014-01-30 14:40:30 UTC (rev 63)
@@ -154,9 +154,9 @@
   thermo$obigt <- to1
   rownames(thermo$obigt) <- 1:nrow(thermo$obigt)
   assign("thermo", thermo, "CHNOSZ")
-  msgout("add.obigt: file has ", length(does.exist), " rows; made ", 
+  msgout("add.obigt: ", file, "\n")
+  msgout("add.obigt: read ", length(does.exist), " rows; made ", 
     nexist, " replacements, ", nrow(to2), " additions, units = ", E.units, "\n")
-  msgout("add.obigt: file was ", file, "\n")
   msgout("add.obigt: use data(thermo) to restore default database\n")
   return(invisible(inew))
 }

Modified: pkg/CHNOSZ/data/protein.csv
===================================================================
--- pkg/CHNOSZ/data/protein.csv	2014-01-12 15:17:43 UTC (rev 62)
+++ pkg/CHNOSZ/data/protein.csv	2014-01-30 14:40:30 UTC (rev 63)
@@ -368,111 +368,6 @@
 P53,HUMAN,BBA+03,P04637,1,24,10,20,30,11,23,12,8,20,32,12,14,44,15,27,38,22,18,4,9
 P53,MOUSE,BBA+03,P02340,1,23,12,17,32,13,24,11,9,24,35,10,8,38,14,24,35,23,20,3,12
 P53,PIG,BBA+03,Q9TUB2,1,26,10,18,29,13,20,9,7,20,36,8,16,39,11,27,42,22,19,4,10
-overall,bisonN,DS11,40360,1,14.922,1.746,9.16,15.878,9.257,14.468,3.411,12.241,13.563,22.487,3.948,6.265,8.939,5.484,12.167,10.655,8.555,15.743,2.533,7.708
-overall,bisonS,DS11,50497,1,15.319,1.65,8.579,13.934,8.039,13.773,3.237,10.99,10.765,20.255,3.731,5.498,8.829,5.331,12.249,9.791,8.318,15.013,2.728,6.318
-overall,bisonR,DS11,43250,1,19.316,1.657,8.762,13.901,7.537,15.218,3.896,9.579,7.465,23.088,3.705,5.264,11.017,7.404,14.92,9.139,9.375,14.71,3.232,6.3
-overall,bisonQ,DS11,83790,1,19.892,1.985,9.262,11.632,7.118,14.472,4.135,10.287,6.095,21.305,3.849,5.547,10.512,8.425,14.349,9.991,10.214,14.059,3.13,5.544
-overall,bisonP,DS11,74082,1,19.797,1.918,9.114,11.631,6.978,14.24,4.033,10.121,5.912,21.131,3.832,5.454,10.365,8.079,14.349,9.612,10.002,14.098,3.117,5.619
-transferase,bisonN,DS11,2384,1,17.826,2.457,11.129,19.789,12.771,18.434,4.725,15.546,17.168,27.834,4.84,7.492,11.625,5.86,14.44,12.782,9.646,19.8,2.825,9.815
-transferase,bisonS,DS11,2593,1,17.772,2.041,10.087,16.539,10.112,16.445,4.142,13.171,12.829,23.834,4.344,6.18,10.771,5.235,14.137,10.99,8.821,17.86,2.766,7.589
-transferase,bisonR,DS11,2257,1,21.817,2.032,9.397,15.504,8.257,16.694,4.755,10.564,7.948,25.194,4.069,4.967,12.629,6.997,16.736,8.958,9.28,16.79,3.235,6.857
-transferase,bisonQ,DS11,4398,1,23.621,2.664,10.704,12.761,8.009,16.814,5.453,11.893,6.195,24.446,4.475,5.343,12.729,8.637,17.03,10.21,10.656,16.528,3.619,6.563
-transferase,bisonP,DS11,4136,1,23.071,2.522,10.406,12.653,7.816,16.053,5.253,11.748,6.214,23.646,4.378,5.349,12.33,8.165,16.673,9.798,10.28,16.348,3.5,6.567
-transport,bisonN,DS11,1285,1,19.84,1.037,8.664,13.107,12.286,18.088,2.977,14.872,11.693,30.72,5.205,6.607,10.183,6.345,11.893,13.233,10.914,19.511,2.919,8.018
-transport,bisonS,DS11,1731,1,20.432,1.014,8.227,12.45,10.46,17.786,2.848,14.377,9.782,28.434,5.119,5.841,9.946,6.023,12.526,12.376,10.652,19.434,2.961,6.861
-transport,bisonR,DS11,1591,1,24.206,1.109,8.411,12.995,10.58,19.485,3.503,12.388,7.338,32.636,4.95,5.469,11.757,7.957,15.659,10.889,11.277,19.404,3.561,6.641
-transport,bisonQ,DS11,3429,1,24.82,1.574,9.253,11.534,9.986,18.959,3.673,14.514,6.053,29.968,5.453,6.138,11.688,9.195,14.985,12.312,12.625,19.244,3.799,5.789
-transport,bisonP,DS11,2993,1,23.869,1.497,9.027,11.186,9.606,18.133,3.492,13.929,6.056,28.76,5.293,6.043,11.137,8.797,14.775,11.666,12.144,18.628,3.543,5.825
-dehydrogenase,bisonN,DS11,1258,1,20.49,2.546,12.002,18.991,9.459,20.089,4.488,14.651,15.539,23.797,5.347,7.723,11.894,5.762,13.851,11.467,10.343,20.96,2.909,8.579
-dehydrogenase,bisonS,DS11,1651,1,21.414,2.419,11.078,17.543,8.291,19.552,4.568,13.631,12.705,21.668,5.062,6.806,11.258,5.51,14.398,10.644,10.259,20.231,2.933,7.357
-dehydrogenase,bisonR,DS11,1604,1,25.935,2.426,10.322,17.398,7.773,20.044,5.481,12.022,8.829,24.266,5.013,5.994,13.442,7.458,16.666,9.518,11.405,19.183,3.057,7.135
-dehydrogenase,bisonQ,DS11,2626,1,26.278,2.805,10.937,14.164,7.285,19.232,5.445,12.777,7.499,22.39,5.125,6.38,12.343,8.323,15.813,10.537,11.936,18.081,2.956,6.329
-dehydrogenase,bisonP,DS11,2428,1,26.05,2.764,10.894,14.44,7.251,19.02,5.441,12.445,7.376,21.996,5.027,6.362,12.259,8.044,15.853,10.046,11.795,18.069,2.873,6.435
-synthase,bisonN,DS11,1509,1,18.371,2.543,11.486,20.482,10.113,18.758,4.72,14.913,16.131,25.031,4.993,7.036,10.965,5.895,14.054,11.603,9.995,20.034,2.43,8.892
-synthase,bisonS,DS11,1486,1,18.66,2.245,10.863,18.251,8.81,17.581,4.38,13.59,13.341,22.421,4.649,6.3,10.442,5.448,13.989,10.755,9.384,18.808,2.346,7.551
-synthase,bisonR,DS11,1206,1,23.016,2.061,10.304,17.033,7.735,18.004,5.31,11.715,8.744,24.674,4.641,5.219,12.451,7.054,16.362,9.416,10.366,17.314,2.48,6.867
-synthase,bisonQ,DS11,2323,1,24.109,2.678,11.151,14.443,7.532,17.815,5.737,12.635,7.205,23.575,4.784,5.874,12.35,9.04,16.23,10.512,11.628,16.704,2.759,6.558
-synthase,bisonP,DS11,2037,1,23.769,2.527,10.821,13.926,7.154,16.963,5.398,12.185,6.886,22.601,4.729,5.613,11.95,8.378,15.952,9.979,11.115,16.322,2.545,6.338
-ATPase,bisonN,DS11,1099,1,16.813,1.464,10.854,22.308,9.96,16.963,3.584,15.258,16.287,30.237,4.638,6.674,10.02,7.51,16.884,12.925,10.075,19.411,1.869,7.296
-ATPase,bisonS,DS11,1437,1,16.427,1.202,10.283,19.371,8.496,16.286,3.382,14.102,13.079,26.979,4.557,6.031,9.586,7.024,16.202,11.949,9.536,18.349,1.852,6.088
-ATPase,bisonR,DS11,1174,1,21.898,1.372,10.259,19.033,7.48,16.756,4.489,12.39,9.267,30.147,4.491,5.337,11.691,9.369,18.996,10.263,10.759,17.848,1.974,5.566
-ATPase,bisonQ,DS11,2235,1,22.826,1.753,11.458,16.338,7.383,16.647,4.888,13.645,7.743,28.441,5.008,6.03,11.392,11.146,18.409,11.835,12.236,17.422,2.128,5.078
-ATPase,bisonP,DS11,2038,1,22.99,1.694,11.194,16.487,7.119,16.254,4.872,13.245,7.558,28.283,4.924,5.828,11.048,10.811,18.672,11.174,11.879,17.582,2.009,5.152
-kinase,bisonN,DS11,677,1,16.511,1.818,10.617,18.4,9.625,17.768,3.872,13.498,14.539,25.739,4.168,6.26,8.846,5.529,14.093,11.572,8.861,18.31,1.852,6.882
-kinase,bisonS,DS11,836,1,18.638,1.821,10.422,16.734,8.284,17.706,3.78,12.522,11.354,23.611,4.12,5.683,9.296,5.562,14.764,11.002,9.315,17.92,2.169,5.589
-kinase,bisonR,DS11,819,1,24.486,1.764,10.426,17.683,7.592,18.879,4.972,11.294,7.768,28.418,4.343,5.125,12.371,8.369,18.432,9.884,10.906,17.79,2.773,5.543
-kinase,bisonQ,DS11,2040,1,25.404,2.379,12.046,15.717,7.421,18.296,5.591,13.392,6.95,27.756,4.741,6.24,12.689,11.192,18.016,12.251,12.713,17.947,2.768,5.503
-kinase,bisonP,DS11,1751,1,24.802,2.287,11.56,15.17,7.029,17.729,5.287,13.12,6.603,26.606,4.736,6.119,11.975,10.184,17.718,11.51,12.3,17.422,2.58,5.314
-synthetase,bisonN,DS11,1003,1,17.71,2.828,14.138,27.129,12.565,19.371,5.476,15.95,20.187,29.719,5.476,8.144,13.367,7.65,17.861,12.875,10.988,22.17,3.964,10.944
-synthetase,bisonS,DS11,1159,1,18.187,2.44,13.231,23.439,10.962,18.131,5.101,14.79,16.098,26.026,5.076,7.092,12.678,6.437,17.515,11.844,10.591,20.607,3.838,9.569
-synthetase,bisonR,DS11,891,1,22.727,2.574,12.952,22.348,10.497,18.761,5.941,13.478,12.154,28.167,5.228,6.772,15.007,9.015,19.727,10.164,11.758,18.761,3.981,9.429
-synthetase,bisonQ,DS11,1509,1,23.789,2.745,13.074,17.248,9.068,17.306,5.843,13.001,9.354,24.903,4.985,6.221,13.565,9.97,17.962,10.683,12.372,17.298,3.779,7.803
-synthetase,bisonP,DS11,1417,1,23.26,2.591,12.558,16.977,8.678,16.693,5.654,12.496,8.66,24.225,5.025,6.112,13.551,9.3,18.252,10.112,11.979,16.946,3.716,7.826
-membrane,bisonN,DS11,818,1,20.148,0.892,9.144,14.775,16.071,19.935,3.108,17.367,14.69,32.704,4.633,7.624,10.133,7.032,12.668,15.407,11.591,20.44,3.11,10.258
-membrane,bisonS,DS11,834,1,21.486,1.025,8.386,12.703,13.282,18.66,2.97,15.38,11.592,30.349,4.615,6.463,9.971,6.636,12.649,13.83,11.236,19.499,3.536,8.325
-membrane,bisonR,DS11,761,1,25.476,1.244,8.681,12.888,11.651,21.07,3.4,12.75,7.355,33.8,4.495,6.449,12.661,8.913,16.988,12.777,12.421,19.586,4.656,8.394
-membrane,bisonQ,DS11,1476,1,25.766,1.406,8.986,11.337,11.066,20.762,3.447,14.121,5.951,30.478,4.677,7.446,11.848,9.493,15.818,13.565,13.253,18.959,4.639,7.154
-membrane,bisonP,DS11,1305,1,25.992,1.349,8.741,10.794,10.684,20.141,3.458,13.569,5.726,30.691,4.731,6.804,11.668,8.904,15.9,13.017,13.036,19.05,4.746,7.251
-permease,bisonN,DS11,503,1,22.68,0.821,5.431,8.221,15.342,18.793,2.292,16.161,7.863,37.406,5.851,5.205,9.773,5.01,9.855,14.891,10.72,20.587,3.575,8.255
-permease,bisonS,DS11,748,1,23.842,0.822,5.341,7.723,13.509,19.119,2.31,15.983,6.215,34.941,5.928,4.862,9.765,5.054,10.658,13.749,11.215,20.584,3.77,7.566
-permease,bisonR,DS11,698,1,27.186,0.744,5.477,8.457,13.714,21.416,2.603,12.689,4.542,40.755,5.383,4.585,11.58,6.524,13.824,11.841,11.212,20.264,4.688,7.029
-permease,bisonQ,DS11,1568,1,26.457,1.239,6.206,7.508,12.466,20.071,2.57,16.172,3.781,35.101,5.985,5.13,11.049,7.531,13.226,12.999,12.55,20.295,5.073,5.96
-permease,bisonP,DS11,1369,1,25.953,1.272,5.938,7.226,12.197,19.419,2.506,15.758,3.751,34.306,5.959,5.154,10.633,7.143,13.053,12.316,12.066,20.11,4.627,5.995
-hydrolase,bisonN,DS11,558,1,15.842,2.172,10.697,17.595,9.084,15.803,5.828,12.461,13.468,23.165,4.296,6.272,10.061,5.242,13.043,9.975,8.669,16.918,2.618,7.763
-hydrolase,bisonS,DS11,684,1,17.148,2.124,10.975,16.136,8.883,15.718,5.7,11.997,11.254,21.924,4.3,5.844,10.224,5.291,13.674,9.838,8.782,16.635,2.983,6.798
-hydrolase,bisonR,DS11,632,1,21.331,1.962,10.419,15.812,7.782,16.6,6.272,10.253,7.551,23.709,4.149,5.245,12.642,6.91,16.212,9.114,9.418,15.426,3.435,6.845
-hydrolase,bisonQ,DS11,1271,1,22.438,2.541,11.737,13.408,7.784,16.308,6.747,11.338,6.266,22.988,4.5,5.597,12.578,8.581,16.017,10.11,11.027,15.505,3.596,6.773
-hydrolase,bisonP,DS11,1181,1,21.707,2.419,11.209,12.801,7.232,15.679,6.481,10.672,5.887,21.804,4.392,5.272,11.986,7.621,15.56,9.362,10.37,14.733,3.442,6.274
-oxidoreductase,bisonN,DS11,637,1,20.545,3.339,9.948,16.159,14.201,19.962,4.846,15.57,13.835,29.706,6.424,6.658,12.013,5.953,12.407,12.851,10.765,20.959,3.931,10.914
-oxidoreductase,bisonS,DS11,806,1,19.947,3.124,9.061,14.65,11.452,18.187,4.314,13.49,11.356,25.295,5.852,5.8,11.266,5.416,12.556,11.039,9.881,18.677,3.615,8.648
-oxidoreductase,bisonR,DS11,475,1,22.105,3.225,7.754,14.065,10.305,18.667,4.465,11.215,8.371,26.863,5.724,5.175,12.221,6.28,13.528,9.419,9.385,16.613,3.928,7.92
-oxidoreductase,bisonQ,DS11,1035,1,23.552,3.589,9.329,12.511,9.813,18.391,4.726,12.643,6.772,25.654,6.181,5.646,12.47,7.604,14.17,10.739,11.202,16.961,3.759,7.238
-oxidoreductase,bisonP,DS11,850,1,22.975,3.327,8.98,12.325,9.489,18.242,4.535,12.387,6.978,24.821,6.075,5.562,11.731,7.2,13.728,10.288,10.844,16.789,3.657,7.287
-transcription,bisonN,DS11,470,1,14.906,1.715,7.692,15.449,6.238,11.498,3.517,10.353,10.294,20.883,3.806,4.687,7.421,5.911,13.249,9.309,7.534,13.715,1.577,5.204
-transcription,bisonS,DS11,603,1,15.464,1.758,7.756,14.028,5.72,11.604,3.265,9.735,9.128,20.101,3.746,4.164,7.806,5.97,13.882,9.066,7.743,13.542,1.751,4.703
-transcription,bisonR,DS11,509,1,19.521,1.497,8.234,16.656,5.639,12.878,4.271,8.835,7.531,24.713,3.658,3.731,10.358,7.586,17.475,8.623,8.77,13.697,2.035,5.297
-transcription,bisonQ,DS11,1127,1,20.441,2.002,9.895,14.477,5.851,12.53,4.808,10.532,6.184,23.698,4.239,4.801,10.147,9.392,17.06,10.815,10.209,13.877,2.163,4.996
-transcription,bisonP,DS11,1038,1,20.12,1.922,9.512,14.456,5.677,12.502,4.765,10.48,6.075,23.203,4.24,4.793,10.063,9.13,17.133,10.284,10.011,13.978,2.158,5.06
-peptidase,bisonN,DS11,472,1,18.053,1.303,11.561,18.903,10.434,19.576,4.138,14.803,16.225,25.225,4.816,7.538,11.153,6.343,14.155,13.032,10.485,19.22,3.021,9.672
-peptidase,bisonS,DS11,497,1,20.153,1.493,12.042,17.519,9.859,19.517,4.531,14.322,13.879,24.062,4.708,7.411,11.662,6.672,15.099,12.678,10.928,19.141,3.519,8.519
-peptidase,bisonR,DS11,612,1,27.964,1.722,12.894,19.021,9.912,22.132,5.479,12.719,8.954,30.214,4.994,7.726,15.943,9.861,20.652,12.476,13.515,20.033,4.533,9.088
-peptidase,bisonQ,DS11,1064,1,26.028,1.784,12.69,15.317,9.222,20.119,5.567,12.978,7.626,26.306,4.822,7.545,14.358,10.104,17.995,12.93,13.752,17.482,3.949,8.602
-peptidase,bisonP,DS11,990,1,25.312,1.856,12.347,15.217,8.714,19.308,5.467,12.648,6.953,25.637,4.778,7.121,14.083,9.651,18.093,12.07,13.104,17.332,3.829,8.007
-ribosomal,bisonN,DS11,597,1,10.01,0.965,5.385,10.951,4.327,10.544,2.581,8.779,14.353,12.692,2.93,3.851,6.58,3.9,10.67,5.493,5.36,12.844,1.343,4.457
-ribosomal,bisonS,DS11,716,1,9.582,0.75,4.747,9.605,3.521,9.71,2.461,7.993,12.284,11.105,2.788,3.325,6.226,3.719,11.166,5.324,5.275,11.814,1.208,3.87
-ribosomal,bisonR,DS11,543,1,10.785,0.726,4.842,9.827,3.503,10.158,2.735,7.867,11.309,11.521,2.691,3.694,6.694,4.481,12.494,5.14,5.902,10.91,1.168,3.462
-ribosomal,bisonQ,DS11,882,1,11.863,0.87,5.268,9.034,3.349,9.821,2.951,7.934,9.705,11.274,2.967,3.89,6.298,5.355,12.477,5.797,6.717,10.444,1.177,3.102
-ribosomal,bisonP,DS11,860,1,11.72,0.887,5.187,9.138,3.386,10.077,2.973,7.877,9.765,11.305,2.865,3.815,6.47,5.167,12.776,5.78,6.442,10.681,1.194,3.364
-protease,bisonN,DS11,377,1,19.454,1.554,10.708,17.931,11.215,20.926,3.687,16.984,14.804,27.785,5.122,7.963,11.676,6.894,13.899,13.658,10.692,20.743,2.706,9.029
-protease,bisonS,DS11,470,1,19.645,1.515,10.268,16.328,9.5,18.498,3.385,15.411,12.409,24.492,4.428,7.33,10.977,7.015,13.434,12.296,9.755,19.128,2.717,7.4
-protease,bisonR,DS11,418,1,27.601,1.457,11.859,16.725,9.294,21.737,4.258,13.694,9.45,30.093,4.593,7.433,15.108,10.325,18.203,11.792,12.301,20.799,3.639,8.148
-protease,bisonQ,DS11,930,1,25.572,1.696,12.102,14.799,8.734,20.469,4.405,14.098,7.323,27.489,4.732,7.536,13.888,10.513,17.848,12.922,12.725,19.148,3.545,6.825
-protease,bisonP,DS11,734,1,25.296,1.471,11.764,14.461,8.307,19.868,4.256,13.463,7.315,26.264,4.681,7.356,13.522,10.012,17.403,12.008,12.164,19.114,3.456,6.674
-reductase,bisonN,DS11,536,1,18.961,4.028,11.519,20.405,10.235,19.69,4.722,15.506,17.452,24.302,5.646,8.237,11.116,6.349,13.843,12.498,10.64,19.886,3.19,9.623
-reductase,bisonS,DS11,531,1,19.207,3.522,10.251,17.416,8.889,17.94,4.377,13.343,13.638,21.166,4.949,6.799,10.339,6.213,13.348,11.205,9.917,18.337,3.055,7.332
-reductase,bisonR,DS11,378,1,20.796,2.677,9.362,15.548,7.762,17.132,4.741,11.058,8.614,21.492,4.511,5.622,11.167,6.841,15.138,9.257,9.849,16.696,2.894,7.04
-reductase,bisonQ,DS11,785,1,24.408,3.29,11.14,15.006,8.688,18.804,5.968,13.119,8.454,22.766,5.082,6.679,12.162,9.043,16.046,11.373,12.434,17.525,3.299,6.913
-reductase,bisonP,DS11,675,1,24.147,3.033,10.738,14.644,8.332,18.042,5.424,12.698,8.09,21.997,4.964,6.717,11.539,8.807,15.856,10.612,11.821,17.304,3.102,6.804
-transposase,bisonN,DS11,471,1,17.076,1.399,7.898,18.423,7.471,13.072,5.507,12.711,24.958,26.503,3.741,8.8,7.361,7.809,17.047,11.573,10.161,15.412,4.824,9.482
-transposase,bisonS,DS11,425,1,16.892,1.772,8.365,16.546,7.511,13.445,5.139,12.271,22.064,24.04,4.122,8.125,7.84,6.828,18.668,11.337,9.304,14.904,4.734,8.744
-transposase,bisonR,DS11,314,1,18.914,1.796,7.506,15.955,7.003,17.162,4.803,6.764,14.283,26.309,3.618,5.516,9.933,6.911,21.618,10.44,7.971,15.647,4.494,7.226
-transposase,bisonQ,DS11,1085,1,18.263,4.134,8.288,10.426,6.362,12.923,5.043,9.03,12.761,18.747,3.159,7.355,8.219,10.573,20.88,11.635,9.959,13.338,3.713,5.854
-transposase,bisonP,DS11,550,1,16.042,3.642,7.653,10.522,6.366,12.027,5.104,8.178,11.295,18.916,3.509,5.855,8.091,8.584,18.289,9.909,8.798,13.042,3.853,5.596
-periplasmic,bisonN,DS11,313,1,18.473,1.038,12.304,15.441,10.502,17.438,3.144,13.566,15.693,24.131,4.505,7.968,13.077,7.505,13.137,12.396,10.629,19.214,3.042,10.326
-periplasmic,bisonS,DS11,409,1,20.159,1.23,11.621,14.668,9.306,17.716,2.905,13.553,14.205,22.007,4.205,7.501,12.716,7.672,12.883,12.24,10.746,19.467,3.249,8.614
-periplasmic,bisonR,DS11,440,1,22.902,1.121,12.064,14.055,9.502,19.802,3.234,11.616,10.386,24.632,4.159,7.048,14.766,9.65,17.727,10.934,11.755,18.757,3.959,8.277
-periplasmic,bisonQ,DS11,850,1,25.292,1.418,13.372,13.453,9.034,19.272,3.292,12.875,8.955,23.404,4.208,8.377,14.853,10.484,15.908,12.673,13.488,18.094,3.978,7.245
-periplasmic,bisonP,DS11,772,1,24.144,1.339,12.953,12.882,8.589,18.782,3.276,12.034,8.744,22.184,4.133,7.948,14.29,9.956,15.784,12.2,12.912,17.553,3.965,7.153
-signal,bisonN,DS11,297,1,18.165,1.852,12.586,18.966,11.694,17.748,3.387,14.865,17.347,26.889,4.966,8.024,10.956,6.875,14.603,13.195,10.717,20.047,2.391,8.593
-signal,bisonS,DS11,408,1,18.223,1.855,10.838,15.23,8.821,16.436,3.527,12.441,12.466,22.679,4.407,6.549,10.115,6.586,14.525,10.885,10.11,18.191,2.691,5.993
-signal,bisonR,DS11,299,1,25.181,1.896,11.134,19.144,9.087,19.813,4.84,12.334,10.141,32.217,5.037,6.244,12.809,11.037,19.913,11.234,12.555,19.04,3.284,6.054
-signal,bisonQ,DS11,732,1,25.425,2.034,12.243,16.406,8.213,18.031,5.303,14.452,7.981,29.495,4.984,7.357,12.855,12.869,18.719,13.465,13.715,18.519,3.143,5.496
-signal,bisonP,DS11,641,1,23.841,1.93,11.376,15.476,7.746,16.665,5.027,13.732,7.173,28.257,4.927,6.877,11.594,11.892,18.028,12.516,12.719,17.493,2.816,4.952
-phosphatase,bisonN,DS11,364,1,15.077,1.761,11.187,16.135,9.159,15.843,4.052,11.256,12.462,22.055,3.747,5.478,9.03,4.253,11.808,10.148,8.332,16.382,2.508,7.291
-phosphatase,bisonS,DS11,372,1,15.065,1.554,9.559,14.817,8.091,14.712,3.586,10.194,10.605,19.575,3.495,4.656,7.995,4.051,11.269,9.057,7.554,15.215,2.352,5.586
-phosphatase,bisonR,DS11,324,1,19.599,1.321,9.056,13.978,7.269,16.281,4.386,9.611,7.355,22.256,3.84,4.617,9.87,5.79,12.926,8.395,8.577,13.978,2.769,5.707
-phosphatase,bisonQ,DS11,642,1,21.611,2.195,10.724,12.88,6.941,16.322,4.883,10.908,5.777,21.86,4.241,5.204,10.332,7.777,14.927,9.96,10.382,14.522,2.843,5.556
-phosphatase,bisonP,DS11,558,1,21.842,1.909,10.256,12.24,6.808,16.332,4.876,10.871,5.298,21.597,4.074,5.335,9.686,7.634,14.124,9.919,9.815,14.787,2.794,5.292
 HBA,HUMAN,BBA+03,"Hemoglobin (P69905)",1,21,1,8,4,7,7,10,0,11,18,2,4,7,1,3,11,9,13,1,3
 ALBU,HUMAN,BBA+03,"Albumin (P02768)",1,62,35,36,62,31,12,16,8,59,61,6,17,24,20,24,24,28,41,1,18
 IGHG1,HUMAN,BBA+03,"IgG Total (P01857)",1,13,9,13,17,10,18,9,5,28,26,2,15,31,11,6,39,26,35,5,12

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2014-01-12 15:17:43 UTC (rev 62)
+++ pkg/CHNOSZ/inst/NEWS	2014-01-30 14:40:30 UTC (rev 63)
@@ -1,3 +1,13 @@
+CHANGES IN CHNOSZ 1.0.3-1 (2014-01-30)
+--------------------------------------
+
+- Add files with average amino acid compositions of proteins from Bison
+  Pool grouped according to annotation keyword (DS11.csv) (moved here
+  from main protein.csv) or phylum assignment (DS13.csv).
+
+- Convert hotspring.Rnw to use knitr, and add example calculations of
+  relative abundances of microbial phyla from Dick and Shock, 2013.
+
 CHANGES IN CHNOSZ 1.0.3 (2014-01-12)
 ------------------------------------
 

Added: pkg/CHNOSZ/inst/extdata/protein/DS11.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/protein/DS11.csv	                        (rev 0)
+++ pkg/CHNOSZ/inst/extdata/protein/DS11.csv	2014-01-30 14:40:30 UTC (rev 63)
@@ -0,0 +1,106 @@
+"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"
+"overall","bisonN","",40360,1,14.922,1.746,9.16,15.878,9.257,14.468,3.411,12.241,13.563,22.487,3.948,6.265,8.939,5.484,12.167,10.655,8.555,15.743,2.533,7.708
+"overall","bisonS","",50497,1,15.319,1.65,8.579,13.934,8.039,13.773,3.237,10.99,10.765,20.255,3.731,5.498,8.829,5.331,12.249,9.791,8.318,15.013,2.728,6.318
+"overall","bisonR","",43250,1,19.316,1.657,8.762,13.901,7.537,15.218,3.896,9.579,7.465,23.088,3.705,5.264,11.017,7.404,14.92,9.139,9.375,14.71,3.232,6.3
+"overall","bisonQ","",83790,1,19.892,1.985,9.262,11.632,7.118,14.472,4.135,10.287,6.095,21.305,3.849,5.547,10.512,8.425,14.349,9.991,10.214,14.059,3.13,5.544
+"overall","bisonP","",74082,1,19.797,1.918,9.114,11.631,6.978,14.24,4.033,10.121,5.911,21.131,3.832,5.454,10.365,8.079,14.349,9.612,10.002,14.098,3.117,5.619
+"transferase","bisonN","",2384,1,17.826,2.457,11.129,19.789,12.771,18.434,4.725,15.546,17.168,27.834,4.84,7.492,11.625,5.86,14.44,12.781,9.646,19.799,2.825,9.815
+"transferase","bisonS","",2593,1,17.772,2.041,10.087,16.539,10.111,16.445,4.142,13.171,12.829,23.834,4.344,6.18,10.771,5.235,14.137,10.99,8.821,17.86,2.766,7.589
+"transferase","bisonR","",2257,1,21.817,2.031,9.397,15.504,8.257,16.694,4.755,10.564,7.948,25.194,4.069,4.967,12.629,6.997,16.736,8.957,9.28,16.79,3.235,6.857
+"transferase","bisonQ","",4398,1,23.621,2.664,10.704,12.761,8.009,16.814,5.453,11.892,6.195,24.446,4.475,5.343,12.729,8.637,17.03,10.21,10.656,16.528,3.618,6.563
+"transferase","bisonP","",4136,1,23.071,2.522,10.406,12.653,7.816,16.052,5.253,11.748,6.214,23.646,4.378,5.349,12.33,8.165,16.673,9.798,10.279,16.348,3.5,6.567
+"transport","bisonN","",1285,1,19.84,1.037,8.664,13.107,12.286,18.088,2.977,14.872,11.693,30.72,5.205,6.607,10.183,6.345,11.893,13.233,10.914,19.511,2.919,8.018
+"transport","bisonS","",1731,1,20.432,1.014,8.227,12.449,10.46,17.786,2.848,14.377,9.782,28.434,5.119,5.841,9.946,6.023,12.526,12.376,10.652,19.434,2.961,6.861
+"transport","bisonR","",1591,1,24.206,1.109,8.411,12.995,10.58,19.485,3.503,12.388,7.338,32.636,4.95,5.469,11.757,7.957,15.659,10.889,11.277,19.404,3.561,6.64
+"transport","bisonQ","",3429,1,24.82,1.574,9.253,11.534,9.986,18.959,3.673,14.514,6.053,29.968,5.453,6.138,11.688,9.195,14.985,12.311,12.625,19.244,3.799,5.789
+"transport","bisonP","",2993,1,23.869,1.496,9.027,11.186,9.606,18.133,3.492,13.929,6.056,28.76,5.293,6.043,11.137,8.797,14.775,11.666,12.144,18.628,3.543,5.825
+"dehydrogenase","bisonN","",1258,1,20.49,2.546,12.002,18.99,9.459,20.089,4.488,14.651,15.539,23.797,5.347,7.723,11.893,5.762,13.851,11.467,10.343,20.96,2.909,8.579
+"dehydrogenase","bisonS","",1651,1,21.414,2.419,11.078,17.543,8.291,19.552,4.568,13.631,12.705,21.667,5.062,6.806,11.258,5.51,14.398,10.644,10.259,20.231,2.933,7.357
+"dehydrogenase","bisonR","",1604,1,25.935,2.426,10.322,17.398,7.773,20.044,5.481,12.022,8.829,24.266,5.012,5.994,13.442,7.458,16.666,9.518,11.405,19.183,3.057,7.135
+"dehydrogenase","bisonQ","",2626,1,26.278,2.805,10.937,14.164,7.284,19.232,5.445,12.777,7.498,22.39,5.125,6.38,12.343,8.323,15.813,10.537,11.936,18.081,2.956,6.329
+"dehydrogenase","bisonP","",2428,1,26.05,2.764,10.894,14.439,7.251,19.02,5.441,12.445,7.376,21.996,5.027,6.362,12.259,8.044,15.853,10.046,11.795,18.069,2.873,6.435
+"synthase","bisonN","",1509,1,18.371,2.543,11.486,20.482,10.113,18.758,4.72,14.913,16.131,25.031,4.993,7.036,10.965,5.895,14.054,11.603,9.995,20.034,2.43,8.892
+"synthase","bisonS","",1486,1,18.66,2.245,10.863,18.251,8.81,17.581,4.38,13.59,13.341,22.421,4.649,6.299,10.441,5.448,13.989,10.755,9.384,18.808,2.346,7.55
+"synthase","bisonR","",1206,1,23.016,2.061,10.303,17.033,7.735,18.004,5.31,11.715,8.744,24.674,4.641,5.219,12.451,7.054,16.362,9.416,10.366,17.314,2.48,6.867
+"synthase","bisonQ","",2323,1,24.109,2.678,11.151,14.443,7.532,17.814,5.737,12.635,7.205,23.575,4.784,5.874,12.35,9.04,16.23,10.512,11.628,16.704,2.759,6.558
+"synthase","bisonP","",2037,1,23.769,2.527,10.821,13.926,7.154,16.963,5.398,12.185,6.886,22.601,4.729,5.613,11.95,8.378,15.952,9.979,11.115,16.322,2.545,6.338
+"ATPase","bisonN","",1099,1,16.813,1.464,10.854,22.308,9.96,16.963,3.584,15.258,16.287,30.237,4.638,6.674,10.02,7.51,16.884,12.924,10.075,19.411,1.869,7.296
+"ATPase","bisonS","",1437,1,16.427,1.202,10.283,19.371,8.496,16.286,3.382,14.102,13.079,26.979,4.557,6.031,9.586,7.024,16.202,11.949,9.536,18.349,1.852,6.088
+"ATPase","bisonR","",1174,1,21.898,1.372,10.259,19.033,7.48,16.756,4.489,12.39,9.267,30.147,4.491,5.337,11.691,9.369,18.996,10.263,10.759,17.848,1.974,5.566
+"ATPase","bisonQ","",2235,1,22.826,1.753,11.458,16.338,7.383,16.647,4.888,13.645,7.743,28.441,5.008,6.03,11.391,11.146,18.409,11.835,12.236,17.421,2.128,5.078
+"ATPase","bisonP","",2038,1,22.99,1.694,11.194,16.487,7.119,16.254,4.872,13.245,7.558,28.283,4.924,5.828,11.048,10.811,18.672,11.174,11.879,17.581,2.009,5.152
+"kinase","bisonN","",677,1,16.511,1.818,10.617,18.4,9.625,17.768,3.871,13.498,14.539,25.739,4.168,6.26,8.846,5.529,14.093,11.572,8.861,18.31,1.852,6.882
+"kinase","bisonS","",836,1,18.638,1.821,10.422,16.734,8.283,17.706,3.78,12.522,11.354,23.611,4.12,5.683,9.295,5.562,14.764,11.002,9.315,17.92,2.169,5.589
+"kinase","bisonR","",819,1,24.486,1.764,10.426,17.683,7.592,18.879,4.972,11.294,7.768,28.418,4.343,5.125,12.371,8.369,18.432,9.884,10.906,17.79,2.773,5.543
+"kinase","bisonQ","",2040,1,25.404,2.379,12.046,15.717,7.421,18.296,5.591,13.392,6.95,27.756,4.741,6.24,12.689,11.192,18.016,12.251,12.713,17.947,2.768,5.503
+"kinase","bisonP","",1751,1,24.802,2.287,11.56,15.17,7.029,17.729,5.287,13.12,6.603,26.606,4.736,6.119,11.975,10.184,17.718,11.51,12.3,17.422,2.58,5.314
+"synthetase","bisonN","",1003,1,17.71,2.828,14.138,27.129,12.565,19.371,5.476,15.95,20.187,29.719,5.476,8.144,13.367,7.65,17.861,12.875,10.988,22.169,3.964,10.944
+"synthetase","bisonS","",1159,1,18.187,2.44,13.231,23.439,10.962,18.131,5.101,14.79,16.098,26.026,5.076,7.091,12.678,6.437,17.515,11.844,10.591,20.607,3.838,9.569
+"synthetase","bisonR","",891,1,22.727,2.574,12.952,22.348,10.497,18.761,5.941,13.478,12.154,28.167,5.228,6.772,15.007,9.015,19.727,10.164,11.758,18.761,3.981,9.429
+"synthetase","bisonQ","",1509,1,23.789,2.745,13.074,17.248,9.068,17.306,5.843,13.001,9.354,24.903,4.985,6.221,13.565,9.97,17.962,10.683,12.372,17.298,3.779,7.803
+"synthetase","bisonP","",1417,1,23.26,2.591,12.558,16.977,8.677,16.693,5.654,12.496,8.66,24.225,5.025,6.112,13.551,9.3,18.252,10.112,11.979,16.946,3.716,7.826
+"membrane","bisonN","",818,1,20.148,0.892,9.144,14.775,16.071,19.935,3.108,17.367,14.689,32.704,4.633,7.623,10.133,7.032,12.667,15.407,11.59,20.44,3.11,10.258
+"membrane","bisonS","",834,1,21.486,1.025,8.386,12.703,13.282,18.659,2.97,15.38,11.592,30.349,4.615,6.463,9.971,6.635,12.649,13.83,11.236,19.499,3.536,8.325
+"membrane","bisonR","",761,1,25.476,1.244,8.681,12.888,11.65,21.07,3.399,12.75,7.355,33.8,4.495,6.449,12.661,8.913,16.988,12.777,12.42,19.586,4.656,8.394
+"membrane","bisonQ","",1476,1,25.766,1.406,8.986,11.337,11.066,20.762,3.447,14.121,5.951,30.478,4.677,7.446,11.848,9.493,15.818,13.565,13.253,18.959,4.639,7.154
+"membrane","bisonP","",1305,1,25.992,1.349,8.741,10.794,10.684,20.141,3.458,13.569,5.726,30.691,4.731,6.804,11.668,8.904,15.9,13.017,13.036,19.05,4.746,7.251
+"permease","bisonN","",503,1,22.68,0.821,5.431,8.221,15.342,18.793,2.292,16.161,7.863,37.406,5.851,5.205,9.773,5.01,9.855,14.891,10.72,20.586,3.575,8.254
+"permease","bisonS","",748,1,23.842,0.822,5.341,7.723,13.509,19.119,2.31,15.983,6.215,34.941,5.928,4.862,9.765,5.053,10.658,13.749,11.215,20.584,3.77,7.566
+"permease","bisonR","",698,1,27.186,0.744,5.477,8.457,13.713,21.415,2.603,12.689,4.542,40.755,5.383,4.585,11.58,6.524,13.824,11.841,11.212,20.264,4.688,7.029
+"permease","bisonQ","",1568,1,26.457,1.239,6.206,7.508,12.466,20.071,2.57,16.172,3.781,35.101,5.985,5.13,11.049,7.531,13.226,12.999,12.55,20.295,5.073,5.96
+"permease","bisonP","",1369,1,25.953,1.272,5.938,7.226,12.197,19.419,2.506,15.758,3.751,34.306,5.959,5.154,10.633,7.143,13.053,12.316,12.066,20.11,4.627,5.995
+"hydrolase","bisonN","",558,1,15.842,2.172,10.697,17.595,9.084,15.803,5.828,12.461,13.468,23.165,4.296,6.272,10.061,5.242,13.043,9.975,8.668,16.918,2.618,7.763
+"hydrolase","bisonS","",684,1,17.148,2.124,10.975,16.136,8.883,15.718,5.7,11.997,11.254,21.924,4.3,5.844,10.224,5.291,13.674,9.838,8.782,16.635,2.982,6.798
+"hydrolase","bisonR","",632,1,21.331,1.962,10.419,15.812,7.782,16.6,6.272,10.253,7.551,23.709,4.149,5.245,12.642,6.91,16.212,9.114,9.418,15.426,3.435,6.845
+"hydrolase","bisonQ","",1271,1,22.437,2.541,11.737,13.408,7.784,16.308,6.747,11.338,6.266,22.988,4.5,5.597,12.578,8.581,16.017,10.11,11.027,15.505,3.596,6.773
+"hydrolase","bisonP","",1181,1,21.707,2.419,11.209,12.801,7.232,15.679,6.481,10.671,5.887,21.804,4.392,5.272,11.986,7.621,15.56,9.362,10.37,14.733,3.442,6.273
+"oxidoreductase","bisonN","",637,1,20.545,3.339,9.948,16.159,14.201,19.962,4.846,15.57,13.835,29.706,6.424,6.658,12.013,5.953,12.407,12.851,10.765,20.959,3.931,10.914
+"oxidoreductase","bisonS","",806,1,19.947,3.124,9.061,14.65,11.452,18.187,4.314,13.49,11.356,25.295,5.852,5.8,11.266,5.416,12.556,11.038,9.881,18.677,3.615,8.648
+"oxidoreductase","bisonR","",475,1,22.105,3.225,7.754,14.065,10.305,18.667,4.465,11.215,8.371,26.863,5.724,5.175,12.221,6.28,13.528,9.419,9.385,16.613,3.928,7.92
+"oxidoreductase","bisonQ","",1035,1,23.552,3.589,9.329,12.511,9.813,18.391,4.726,12.643,6.772,25.654,6.181,5.646,12.47,7.604,14.17,10.739,11.202,16.961,3.759,7.238
+"oxidoreductase","bisonP","",850,1,22.975,3.327,8.98,12.325,9.489,18.242,4.535,12.387,6.978,24.821,6.075,5.562,11.731,7.2,13.728,10.288,10.844,16.789,3.656,7.287
+"transcription","bisonN","",470,1,14.906,1.715,7.691,15.449,6.238,11.498,3.517,10.353,10.294,20.883,3.806,4.687,7.421,5.911,13.249,9.309,7.534,13.715,1.577,5.204
+"transcription","bisonS","",603,1,15.464,1.758,7.756,14.028,5.72,11.604,3.265,9.735,9.128,20.101,3.746,4.164,7.806,5.97,13.882,9.066,7.743,13.542,1.751,4.703
+"transcription","bisonR","",509,1,19.521,1.497,8.234,16.656,5.639,12.878,4.271,8.835,7.53,24.713,3.658,3.731,10.358,7.585,17.475,8.623,8.77,13.697,2.035,5.297
+"transcription","bisonQ","",1127,1,20.441,2.002,9.895,14.476,5.851,12.53,4.808,10.532,6.184,23.698,4.239,4.801,10.147,9.392,17.06,10.815,10.209,13.877,2.163,4.996
+"transcription","bisonP","",1038,1,20.119,1.922,9.512,14.456,5.677,12.502,4.765,10.48,6.075,23.203,4.24,4.793,10.063,9.13,17.133,10.284,10.011,13.978,2.158,5.06
+"peptidase","bisonN","",472,1,18.053,1.303,11.561,18.903,10.434,19.576,4.138,14.803,16.225,25.225,4.816,7.538,11.153,6.343,14.155,13.032,10.485,19.22,3.021,9.672
+"peptidase","bisonS","",497,1,20.153,1.493,12.042,17.519,9.859,19.517,4.531,14.322,13.879,24.062,4.708,7.41,11.662,6.672,15.099,12.678,10.928,19.141,3.519,8.519
+"peptidase","bisonR","",612,1,27.964,1.722,12.894,19.021,9.912,22.132,5.479,12.719,8.954,30.214,4.993,7.725,15.943,9.861,20.652,12.475,13.515,20.033,4.533,9.088
+"peptidase","bisonQ","",1064,1,26.028,1.784,12.69,15.317,9.222,20.119,5.567,12.978,7.626,26.305,4.822,7.545,14.358,10.104,17.995,12.93,13.752,17.482,3.949,8.602
+"peptidase","bisonP","",990,1,25.312,1.856,12.346,15.217,8.714,19.308,5.467,12.647,6.953,25.637,4.778,7.121,14.083,9.651,18.093,12.07,13.104,17.332,3.829,8.007
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/chnosz -r 63