Re: [R-sig-eco] ecodist (MRM) error message

2011-03-15 Thread Sarah Goslee 
Alfredo,

I'd be happy to try to help, but need rather more information.
What version of R, ecodist? What OS?

What do your data look like - str() is very helpful in this regard,
or possibly summary(as.vector(Dx)) and summary(as.vector(Dy)).
What are Dx and Dy? How were the dissimilarities calculated?

Can you provide a reproducible example so that I can see the error
for myself?

With only what you have provided here, there's nothing I or anyone else
can do to assist you.

Sarah

On Mon, Mar 14, 2011 at 6:08 PM, Alfredo Tello alfredote...@gmail.com wrote:
 Hi Everyone,

 MRM is returning what seems to be a matrix singularity error:

 Error in solve.default(XX) :
  system is computationally singular: reciprocal condition number =
 1.88323e-86

 when running MRM(Dy~exp(Dx)).

 I would appreciate it if anyone could help me around this.

 Thanks,

 A

-- 
Sarah Goslee
http://www.functionaldiversity.org

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Re: [R-sig-eco] ecodist (MRM) error message

2011-03-15 Thread Alfredo Tello 
Hi Sarah,

Thanks for your reply. I've solved the problem (or at least gotten around
it). Dy is a Bray-Curtis dissimilarity matrix and Dx a euclidean matrix
representing an environmental gradient. I was running MRM as:
MRM(Dy~exp(Dx)). If I run MRM(log(Dy)~Dx) I don't get the error message.
Should have thought about it before. I have provided the information you
asked for below in case this is something you might want to check (I'd be
interested in hearing back if you do). Thanks for your good disposition to
help!

R v.2.11.1
ecodist v.1.2.2
OS MacOSX v.10.6.6

summary(as.vector(Dx)):
Min. 1st Qu.  MedianMean 3rd Qu.Max. 
   0.003.00   21.00   34.61   69.00  100.00 
summary(as.vector(Dy)):
Min. 1st Qu.  MedianMean 3rd Qu.Max. 
0.04222 0.11010 0.13800 0.14760 0.17480 0.33970 

X-rep(c(100,31,3,10,1,0),c(4,4,4,4,4,4))
Dx-vegdist(X,euclidean)

as.numeric(Dy)
  [1] 0.06700782 0.08376230 0.09909706 0.12461558 0.14438454 0.06081251
  [7] 0.07148765 0.12363789 0.11589077 0.17594412 0.23683629 0.20668179
 [13] 0.13095731 0.16297324 0.13696261 0.14601568 0.20881977 0.14832791
 [19] 0.17773578 0.17901283 0.25579823 0.33966925 0.19422022 0.08303545
 [25] 0.07909383 0.14990078 0.15595243 0.09204931 0.08683072 0.11779759
 [31] 0.12444775 0.16406134 0.25084616 0.22665500 0.15704370 0.16780219
 [37] 0.14767869 0.14192482 0.22739584 0.15541371 0.13306881 0.17721980
 [43] 0.26714896 0.28449197 0.20127940 0.08083726 0.10962154 0.11345836
 [49] 0.07954765 0.06127723 0.14011358 0.12030707 0.14353869 0.20578010
 [55] 0.18541670 0.13782273 0.11022268 0.11764977 0.14781207 0.18777078
 [61] 0.11485322 0.14577802 0.15492318 0.22155020 0.31315450 0.15588707
 [67] 0.14414003 0.14247672 0.10155890 0.08317417 0.14763451 0.14792530
 [73] 0.14875964 0.20888002 0.17465407 0.13602950 0.13308165 0.12874080
 [79] 0.15034760 0.18140344 0.10823317 0.11705517 0.16173102 0.21262619
 [85] 0.27832472 0.15928755 0.06876770 0.13076783 0.09455192 0.17209052
 [91] 0.14840100 0.12422850 0.19023886 0.16950682 0.18101891 0.15449655
 [97] 0.15209334 0.16504904 0.19194634 0.13262124 0.16472254 0.17541841
[103] 0.23131761 0.31423360 0.14329032 0.11754625 0.09363360 0.18596449
[109] 0.14963883 0.14267731 0.19752469 0.18053717 0.16634437 0.14120062
[115] 0.14349948 0.17639152 0.19656690 0.14510724 0.16015122 0.17586870
[121] 0.22992404 0.26821391 0.14866853 0.06778119 0.10217397 0.08147583
[127] 0.13426895 0.17988601 0.17827445 0.08544477 0.12235510 0.10401747
[133] 0.10498380 0.18320970 0.11387430 0.14546688 0.14947183 0.19424262
[139] 0.30280431 0.14408871 0.12761382 0.11501332 0.11369858 0.18716134
[145] 0.16889755 0.12830243 0.12314921 0.10082947 0.12568844 0.16733396
[151] 0.09694770 0.11431960 0.14356895 0.21846974 0.30084684 0.13508708
[157] 0.04222194 0.09948040 0.21147397 0.17194458 0.12665215 0.13520422
[163] 0.13895700 0.08458339 0.19295051 0.14138126 0.13299794 0.14416027
[169] 0.23637788 0.29302635 0.17505158 0.07860891 0.19118050 0.15639354
[175] 0.11852640 0.11506420 0.12073787 0.07966940 0.18364503 0.13145598
[181] 0.14392055 0.15298438 0.21619575 0.29808153 0.15443375 0.11906375
[187] 0.12847290 0.12501444 0.10072444 0.10618654 0.06222056 0.14916935
[193] 0.08697711 0.10846572 0.14039835 0.16833996 0.28827410 0.09394061
[199] 0.12784852 0.13242015 0.11873356 0.12215396 0.14279656 0.11375601
[205] 0.12055113 0.13534332 0.12662213 0.07651950 0.26956270 0.07759475
[211] 0.14816469 0.09668246 0.12734489 0.12874116 0.07493926 0.11475184
[217] 0.13662820 0.09040167 0.11918906 0.25222106 0.09877668 0.11503860
[223] 0.09299715 0.09932252 0.15445820 0.09835570 0.13162197 0.12087659
[229] 0.15259950 0.30820412 0.12573894 0.05650551 0.09907881 0.12120693
[235] 0.08287615 0.10787729 0.07209802 0.14482351 0.26734141 0.08675368
[241] 0.10114104 0.12447440 0.07961229 0.08423764 0.08955118 0.16254741
[247] 0.28158102 0.08205883 0.13811524 0.07944738 0.12494488 0.12517100
[253] 0.16335532 0.28385888 0.11370302 0.10488326 0.11913666 0.10728133
[259] 0.10919732 0.22440659 0.11069469 0.07939423 0.09213015 0.12276458
[265] 0.27271430 0.06930216 0.07808054 0.15932098 0.22047097 0.10176994
[271] 0.12213696 0.23325491 0.09323771 0.22493665 0.08676381 0.25084021

MRM(Dy~exp(Dx))
Error in solve.default(XX) : 
  system is computationally singular: reciprocal condition number =
1.88323e-86

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Re: [R-sig-eco] ecodist (MRM) error message

2011-03-15 Thread Alfredo Tello 
Sarah,

I don't think I've got the programming skills at the moment to contribute a
patch, but I'll keep it mind for the future. Thanks for the log()
reminder. It could definitely be tragic to confuse bases.

Best wishes,

A

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[R-sig-eco] ecodist (MRM) error message

2011-03-14 Thread Alfredo Tello 
Hi Everyone,

MRM is returning what seems to be a matrix singularity error: 

Error in solve.default(XX) : 
  system is computationally singular: reciprocal condition number =
1.88323e-86

when running MRM(Dy~exp(Dx)). 

I would appreciate it if anyone could help me around this.

Thanks,

A

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http://r-sig-ecology.471788.n2.nabble.com/ecodist-MRM-error-message-tp6170910p6170910.html
Sent from the r-sig-ecology mailing list archive at Nabble.com.

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