[Analogue-commits] r351 - in pkg: R inst tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Jul 25 18:55:27 CEST 2013
Author: gsimpson
Date: 2013-07-25 18:55:27 +0200 (Thu, 25 Jul 2013)
New Revision: 351
Modified:
pkg/R/chooseTaxa.R
pkg/inst/ChangeLog
pkg/tests/Examples/analogue-Ex.Rout.save
Log:
fix warning, and dropping of empty dimensions
Modified: pkg/R/chooseTaxa.R
===================================================================
--- pkg/R/chooseTaxa.R 2013-07-21 22:50:59 UTC (rev 350)
+++ pkg/R/chooseTaxa.R 2013-07-25 16:55:27 UTC (rev 351)
@@ -9,7 +9,7 @@
type <- "AND"
type <- match.arg(type)
## issue a warning if any values in object are NA
- if(any(is.na(object)))
+ if(!na.rm && any(is.na(object)))
warning("'NA's present in data; results may not be what you expect.\nConsider using 'na.rm = TRUE'.")
occ.want <- colSums(object > 0, na.rm = na.rm) >= n.occ
abun.want <- apply(object, 2, max, na.rm = na.rm) >= max.abun
@@ -21,7 +21,7 @@
if(value) {
rname <- rownames(object)
cname <- colnames(object)
- object <- object[, want]
+ object <- object[, want, drop = FALSE]
rownames(object) <- rname
colnames(object) <- cname[want]
} else {
Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog 2013-07-21 22:50:59 UTC (rev 350)
+++ pkg/inst/ChangeLog 2013-07-25 16:55:27 UTC (rev 351)
@@ -43,6 +43,13 @@
argument `scaling`. This makes the `lines` method more broadly
useful.
+ * chooseTaxa: would drop empty dimensions if conditions resulted
+ in just a single taxon being selected. Reported by Michael
+ Burstert.
+
+ The warning about `NA`s was also being issued even if
+ `na.rm = TRUE` was used. Now fixed.
+
* Streamlined some of the documentation to avoid runnning the same
code many times.
Modified: pkg/tests/Examples/analogue-Ex.Rout.save
===================================================================
--- pkg/tests/Examples/analogue-Ex.Rout.save 2013-07-21 22:50:59 UTC (rev 350)
+++ pkg/tests/Examples/analogue-Ex.Rout.save 2013-07-25 16:55:27 UTC (rev 351)
@@ -6022,6 +6022,454 @@
>
>
> cleanEx()
+> nameEx("residuals.prcurve")
+> ### * residuals.prcurve
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: residuals.prcurve
+> ### Title: Residuals of a principal curve fit.
+> ### Aliases: residuals.prcurve resid.prcurve
+> ### Keywords: methods
+>
+> ### ** Examples
+>
+> ## Load Abernethy Forest data set
+> data(abernethy)
+>
+> ## Remove the Depth and Age variables
+> abernethy2 <- abernethy[, -(37:38)]
+>
+> ## Fit the principal curve, preserving the data in the smooth.spline
+> ## smooth functions fitted via keep.data = TRUE
+> aber.pc <- prcurve(abernethy2, method = "ca", keep.data = TRUE)
+>
+> ## default "distance" residuals
+> resid(aber.pc)
+ 1 2 3 4 5 6 7 8
+14.264852 3.339616 4.534670 7.343308 1.395606 2.276634 1.497317 5.424320
+ 9 10 11 12 13 14 15 16
+ 2.571996 2.803516 3.041763 4.775465 1.715575 2.382978 4.218761 4.606372
+ 17 18 19 20 21 22 23 24
+ 5.301167 2.993025 9.986568 6.411143 3.234004 5.207111 6.458562 4.446028
+ 25 26 27 28 29 30 31 32
+ 4.648528 10.693325 8.145018 7.354527 6.058375 5.054151 4.866059 17.164061
+ 33 34 35 36 37 38 39 40
+13.632436 22.271686 6.458558 3.465228 6.082847 3.619209 6.032345 3.241343
+ 41 42 43 44 45 46 47 48
+ 5.045163 6.146788 14.719240 13.464204 12.087784 24.672399 14.475148 12.994268
+ 49
+19.998570
+>
+> ## residuals from the underlying smooth models, also illustrates
+> ## how to select specific types of residual from the individual
+> ## method using argument 'type'
+> resid(aber.pc, which = "smooths", type = "deviance")
+ Betula Pinus sylvestris Ulmus Quercus Alnus glutinosa
+ [1,] -2.3568160 0.129150193 -0.013915687 0.079415037 -0.026196824
+ [2,] -0.4075439 -2.492365530 -0.039673056 0.034621642 0.327227517
+ [3,] 3.1795872 0.429126767 -0.043901759 0.025847590 -0.261576556
+ [4,] 1.5921355 -0.106538689 0.298530963 -0.029896200 0.152575972
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+ [6,] -0.9362944 1.569895168 -0.069748608 -0.120315991 0.137792588
+ [7,] 0.2709890 1.124477590 -0.070619016 -0.132709233 -0.158319057
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+[49,] -2.730931e-05 2.558535e-06 2.280173e-06 3.954876e-07 -6.999858e-05
+ Epilobium-type Papilionaceae Anthyllis vulneraria Astragalus alpinus
+ [1,] -5.330066e-02 -1.123777e-01 2.831316e-02 2.293431e-01
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+ [5,] -4.824452e-02 7.923814e-01 -1.649058e-02 -2.889661e-01
+ [6,] -5.801477e-02 3.363865e-02 -3.994052e-02 4.283724e-01
+ [7,] -6.059746e-02 -2.642006e-01 -4.435915e-02 1.315752e+00
+ [8,] -2.524522e-01 -6.178048e-02 -2.565565e-01 -2.692691e-01
+ [9,] -2.853638e-01 -2.211951e-02 -2.881449e-01 -1.110511e-01
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+[18,] 1.425474e-02 -7.817446e-04 1.430619e-02 -2.252895e-03
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+[49,] 2.044005e-06 -4.988552e-07 2.033426e-06 -1.922349e-06
+ Ononis-type Rosaceae Rubiaceae Ranunculaceae Thalictrum
+ [1,] -1.372937e-01 1.654573e-01 0.0357345324 3.191122e-02 -1.116407e-02
+ [2,] -6.568944e-01 -7.469269e-02 0.0174694199 1.458846e-02 -5.813685e-02
+ [3,] -7.441653e-01 -6.492705e-02 0.0138457401 1.117886e-02 4.556740e-01
+ [4,] 1.416579e+00 -3.110089e-02 -0.0096995564 -1.067033e-02 -4.018084e-01
+ [5,] 5.397728e-01 -2.616427e-02 -0.0199977765 -2.008053e-02 -4.207849e-01
+ [6,] 4.601093e-01 -2.562087e-02 -0.0494985870 -4.668608e-02 -4.762187e-01
+ [7,] -4.974600e-01 -2.679256e-02 -0.0550754718 -5.166613e-02 7.742746e-01
+ [8,] 3.821056e-01 -1.655893e-01 -0.3322865847 -2.736133e-01 8.495744e-01
+ [9,] -2.966524e-01 8.600692e-01 0.6610923199 7.431614e-01 -4.640867e-01
+[10,] -2.616604e-01 -1.792077e-01 0.6177204870 -2.966642e-01 5.531244e-01
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+[21,] -1.217867e-03 5.544214e-03 0.1626063856 2.313855e-03 1.253402e-01
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+[41,] 6.360992e-06 8.919038e-02 0.0009122891 1.172453e-07 1.500910e-04
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+[45,] -1.084208e-05 -4.971258e-02 -0.0010106282 1.751836e-05 -3.007482e-04
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+[49,] -2.980106e-06 -2.916819e-02 -0.0003697126 1.822958e-06 -7.507847e-05
+ Rumex acetosa-type Oxyria-type Parnassia palustris Saxifraga spp1
+ [1,] 2.426777e+00 1.851769e-02 2.504843e-02 5.199540e-02
+ [2,] 7.358972e-01 8.599773e-03 1.375980e-02 -3.266410e-01
+ [3,] -2.969326e+00 6.644267e-03 1.147960e-02 7.091831e-02
+ [4,] -3.313191e+00 -5.925327e-03 -3.792834e-03 3.312681e-01
+ [5,] 7.352067e-01 -1.135758e-02 -1.069145e-02 2.858254e-01
+ [6,] -8.442616e-01 -2.676180e-02 -3.097954e-02 -4.443279e-01
+ [7,] 1.269407e+00 -2.965169e-02 -3.488892e-02 -2.941500e-02
+ [8,] -1.175137e+01 -1.618425e-01 -2.675244e-01 -6.913929e-01
+ [9,] 1.130471e+01 -1.777625e-01 -3.277544e-01 1.357932e+00
+[10,] 1.084105e+01 8.219498e-01 -3.348532e-01 -7.208642e-01
+[11,] -6.230437e+00 -1.774463e-01 -3.419163e-01 -7.171662e-01
+[12,] 3.571385e+00 -1.762385e-01 1.553382e+00 1.188033e+00
+[13,] 4.413778e+00 -5.840849e-02 -1.463670e-01 -2.350281e-01
+[14,] -6.488385e+00 -3.535533e-02 -9.292240e-02 -1.421375e-01
+[15,] -2.671378e+00 -1.561605e-02 -4.566199e-02 -6.264411e-02
+[16,] -3.636150e+00 -2.340613e-03 -1.294173e-02 -9.209336e-03
+[17,] 4.121800e-01 1.359519e-03 -3.639963e-03 5.678642e-03
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+[19,] -2.267771e-01 7.102257e-03 1.604453e-02 2.863033e-02
+[20,] 5.572395e-01 4.997998e-03 1.150406e-02 2.014143e-02
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+[23,] 6.166727e-01 1.231557e-03 3.045601e-03 4.956825e-03
+[24,] 1.746760e-01 2.169622e-04 6.642281e-04 8.694676e-04
+[25,] -1.871573e-01 1.175255e-04 4.249800e-04 4.690540e-04
+[26,] 1.145552e-01 -2.143254e-04 -3.930204e-04 -8.666720e-04
+[27,] -6.871241e-02 -2.279172e-04 -4.276775e-04 -9.213459e-04
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+[35,] 2.683149e-02 -1.123990e-04 -2.822768e-04 -4.522608e-04
+[36,] -2.619057e-04 -4.286313e-05 -1.096512e-04 -1.724095e-04
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+[38,] 1.772313e-01 -1.182615e-05 -3.158434e-05 -4.752933e-05
+[39,] -1.464234e-02 -5.540762e-06 -1.566267e-05 -2.224279e-05
+[40,] -1.561463e-02 -1.266543e-06 -4.805398e-06 -5.048219e-06
+[41,] -1.584980e-02 2.320205e-08 -1.523404e-06 1.400701e-07
+[42,] -1.640559e-02 4.800451e-06 1.066467e-05 1.935670e-05
+[43,] -1.632776e-02 8.202316e-06 1.939106e-05 3.303940e-05
+[44,] -9.072600e-03 1.138474e-05 2.827182e-05 4.581829e-05
+[45,] -7.918169e-03 1.071432e-05 2.666891e-05 4.311836e-05
+[46,] -7.305807e-03 1.032456e-05 2.573113e-05 4.154884e-05
+[47,] -4.381939e-03 8.208252e-06 2.059927e-05 3.302805e-05
+[48,] -1.602903e-03 5.913067e-06 1.499449e-05 2.378819e-05
+[49,] 3.723101e-03 1.128893e-06 3.265048e-06 4.529640e-06
+ Saxifraga spp2 Sedum Urtica Veronica
+ [1,] -4.475967e-02 -1.536234e-03 1.563617e-01 1.560104e-01
+ [2,] -5.859376e-02 -3.392649e-01 -9.684482e-02 8.098336e-02
+ [3,] 3.496461e-01 -3.971910e-01 -8.919475e-02 6.597204e-02
+ [4,] -6.914392e-02 5.847736e-02 -6.377708e-02 -3.298724e-02
+ [5,] -7.506157e-02 6.668903e-01 -5.996042e-02 -7.695110e-02
+ [6,] -9.947818e-02 -5.563766e-01 2.435235e-01 -2.045296e-01
+ [7,] -1.049991e-01 8.017602e-01 -5.623522e-02 -2.288780e-01
+ [8,] -4.817282e-01 4.895166e-01 3.430241e-01 -1.558441e+00
+ [9,] -5.595670e-01 -2.586787e-01 -1.885371e-01 -1.847755e+00
+[10,] 4.336650e-01 -2.317867e-01 -2.017115e-01 1.122912e+00
+[11,] 6.883410e-01 -2.024520e-01 -2.186508e-01 -1.903603e+00
+[12,] 3.761852e-01 -1.788861e-01 -2.346457e-01 5.701164e+00
+[13,] -2.170931e-01 3.877211e-02 8.201077e-01 -7.622344e-01
+[14,] -1.351060e-01 3.722462e-02 2.698059e-01 -4.787337e-01
+[15,] -6.362354e-02 3.146732e-02 -2.108221e-02 -2.299768e-01
+[16,] -1.474885e-02 2.498679e-02 -4.517688e-01 -5.892500e-02
+[17,] -9.709263e-04 2.271451e-02 -8.732805e-02 -1.051961e-02
+[18,] 2.951273e-02 5.462627e-03 -8.385884e-02 1.012932e-01
+[19,] 2.489902e-02 4.285782e-03 -6.769569e-02 8.565379e-02
+[20,] 1.770419e-02 2.250300e-03 -5.255625e-02 6.113132e-02
+[21,] 5.188563e-03 -5.651022e-03 -5.466446e-02 1.814041e-02
+[22,] 4.799094e-03 -6.189107e-03 -5.536375e-02 1.679495e-02
+[23,] 4.542768e-03 -6.567785e-03 -5.584583e-02 1.590913e-02
+[24,] 9.094491e-04 -1.578650e-02 2.988217e-01 3.314791e-03
+[25,] 5.483528e-04 -1.750613e-02 2.895610e-01 2.056970e-03
+[26,] -6.734541e-04 -2.697973e-02 -4.983517e-02 -2.219195e-03
+[27,] -7.244826e-04 -2.761364e-02 -4.891744e-02 -2.398963e-03
+[28,] -1.085519e-03 -3.341175e-02 -4.004162e-02 -3.676754e-03
+[29,] -1.236263e-03 -3.691340e-02 -3.430089e-02 -4.215311e-03
+[30,] -1.303098e-03 -3.878150e-02 -3.106463e-02 -4.455798e-03
+[31,] -1.316619e-03 1.408154e-01 -3.034033e-02 -4.504621e-03
+[32,] -1.338105e-03 -3.984151e-02 -2.913245e-02 -4.582349e-03
+[33,] -1.418688e-03 1.575206e-01 -2.372515e-02 -4.876032e-03
+[34,] -1.490144e-03 -4.543301e-02 -6.291086e-03 -5.167730e-03
+[35,] -4.182901e-04 -1.308288e-02 5.777574e-03 -1.469275e-03
+[36,] -1.612285e-04 -5.078440e-03 3.043595e-03 -5.683485e-04
+[37,] -5.017694e-05 -1.603294e-03 1.469012e-03 -1.781707e-04
+[38,] -4.562158e-05 -1.460438e-03 1.397435e-03 -1.621483e-04
+[39,] -2.211384e-05 -7.227530e-04 1.017091e-03 -7.943783e-05
+[40,] -6.102226e-06 -2.197669e-04 7.458173e-04 -2.307180e-05
+[41,] -1.265754e-06 -6.773203e-05 6.615246e-04 -6.040046e-06
+[42,] 1.667558e-05 4.968112e-04 3.361091e-04 5.717230e-05
+[43,] 2.949198e-05 9.009269e-04 8.456444e-05 1.023753e-04
+[44,] 4.209481e-05 1.310915e-03 -4.512920e-04 1.475391e-04
+[45,] 3.966891e-05 1.236477e-03 -4.506672e-04 1.390993e-04
+[46,] 3.825352e-05 1.192939e-03 -4.478434e-04 1.341691e-04
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/analogue -r 351
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