Antonio Punzon
2006-Dec-05 15:35 UTC
[R] Cummulative Variance in Correspondence Analysis (ADE4)
Hi all: How can I calculate the cumulative variance (or variance for each component) in correspondence analysis? If were possible in ADE4 package Thank you -- Antonio Punzón Merino O__---- Instituto Español de Oceanografía c/ /'_ --- Centro Oceanográfico de Santander (*) \(*) -- Promontorio de San Martín S/N ~~~~~~~~~~ 39004-Santander; Spain PO BOX: 240 Tlf: +34 942 29 10 60 Fax: +34 942 27 50 72 e-mail: antonio.punzon@st.ieo.es web: www.ieo.es <www.ieo.es> web: www.sap-ieo.wikispaces.com <www.sap-ieo.wikispaces.com> ________________________________________ La información contenida en este e-mail y sus ficheros adjuntos es totalmente confidencial y no debería ser usado si no fuera usted alguno de los destinatarios. Si ha recibido este e-mail por error, por favor avise al remitente y bórrelo de su buzón o de cualquier otro medio de almacenamiento. This email is confidential and should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage mechanism. [[alternative HTML version deleted]]
Stéphane Dray
2006-Dec-05 16:22 UTC
[R] Cummulative Variance in Correspondence Analysis (ADE4)
Dear Antonio, if you have questions on the ade4 package, please send email to adelist (http://listes.univ-lyon1.fr/wws/info/adelist). The total inertia (variance) of CA is equal to the sum of all eigenvalues : > data(rpjdl) > rpjdl.coa <- dudi.coa(rpjdl$fau, scannf = FALSE, nf = 4) > sum(rpjdl.coa$eig) [1] 4.468333 This is equal to the chi2 stat divided by the number of individuals: > chisq.test(rpjdl$fau)$statistic/sum(rpjdl$fau) X-squared 4.468333 One can obtain the inertia associated to i-th axis by dividing the i-th eigenvalue by the total inertia. Here are percentages: > round(rpjdl.coa$eig/sum(rpjdl.coa$eig)*100,2) [1] 16.86 6.56 5.13 4.58 3.52 3.39 3.37 3.12 2.87 2.72 2.63 2.56 [13] 2.49 2.43 2.34 2.21 2.09 2.00 1.86 1.76 1.61 1.48 1.45 1.43 [25] 1.38 1.26 1.23 1.15 1.14 1.08 1.07 1.01 0.94 0.92 0.89 0.83 [37] 0.77 0.71 0.65 0.61 0.59 0.49 0.47 0.46 0.38 0.36 0.35 0.32 [49] 0.29 0.19 The cumulative inertia is obtained by : > round(cumsum(rpjdl.coa$eig)/sum(rpjdl.coa$eig)*100,2) [1] 16.86 23.41 28.55 33.13 36.65 40.03 43.41 46.53 49.39 52.11 [11] 54.75 57.31 59.79 62.23 64.57 66.78 68.87 70.87 72.73 74.49 [21] 76.10 77.58 79.02 80.45 81.83 83.09 84.32 85.47 86.61 87.69 [31] 88.76 89.77 90.71 91.63 92.53 93.36 94.13 94.84 95.49 96.10 [41] 96.69 97.19 97.66 98.12 98.49 98.85 99.20 99.52 99.81 100.00 Antonio Punzon wrote:> Hi all: > How can I calculate the cumulative variance (or variance for each component) > in correspondence analysis? > If were possible in ADE4 package > Thank you > > > > -- Antonio Punz?n Merino > O__---- Instituto Espa?ol de Oceanograf?a > c/ /'_ --- Centro Oceanogr?fico de Santander > (*) \(*) -- Promontorio de San Mart?n S/N > ~~~~~~~~~~ 39004-Santander; Spain > PO BOX: 240 > Tlf: +34 942 29 10 60 > Fax: +34 942 27 50 72 > e-mail: antonio.punzon at st.ieo.es > web: www.ieo.es <www.ieo.es> > web: www.sap-ieo.wikispaces.com <www.sap-ieo.wikispaces.com> > ________________________________________ > > > > La informaci?n contenida en este e-mail y sus ficheros adjuntos es totalmente confidencial y no deber?a ser usado si no fuera usted alguno de los destinatarios. Si ha recibido este e-mail por error, por favor avise al remitente y b?rrelo de su buz?n o de cualquier otro medio de almacenamiento. This email is confidential and should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage mechanism. > [[alternative HTML version deleted]] > > > ------------------------------------------------------------------------ > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >-- St?phane DRAY (dray at biomserv.univ-lyon1.fr ) Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - Lyon I 43, Bd du 11 Novembre 1918, 69622 Villeurbanne Cedex, France Tel: 33 4 72 43 27 57 Fax: 33 4 72 43 13 88 http://biomserv.univ-lyon1.fr/~dray/