pca - RDA analysis in R gives error "attempt to set an attribute on NULL" -
i'm running analysis in r vegan
package. it's simple in way want summary extract values. keeps telling me error message. why?
i have dataset
feed.raw1 =structure(c(0l, 0l, 2l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 5l, 0l, 2l, 0l, 0l, 0l, 0l, 0l, 0l, 2l, 0l, 7l, 11l, 3l, 1l, 0l, 1l, 0l, 0l, 0l, 0l, 0l, 0l, 1l, 2l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 3l, 0l, 5l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 2l, 0l, 0l, 8l, 7l, 5l, 1l, 0l, 0l, 1l, 0l, 0l, 0l, 0l, 0l, 10l, 5l, 0l, 0l, 1l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 1l, 5l, 0l, 0l, 8l, 9l, 0l, 0l, 5l, 0l, 0l, 0l, 1l, 0l, 0l, 0l, 1l, 0l, 0l, 0l, 1l, 0l, 0l, 0l, 15l, 0l, 51l, 10l, 0l, 0l, 0l, 0l, 2l, 0l, 0l, 0l, 0l, 2l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 1l, 3l, 0l, 1l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 45l, 203l, 17l, 54l, 4l, 1l, 0l, 0l, 0l, 0l, 10l, 9l, 0l, 0l, 0l, 2l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 12l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 2l, 0l, 22l, 206l, 9l, 16l, 1l, 1l, 6l, 6l, 0l, 0l, 4l, 5l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 7l, 0l, 0l, 3l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 2l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 12l, 3l, 1l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 23l, 4l, 1l, 2l, 0l, 2l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 76l, 0l, 96l, 0l, 1l, 0l, 0l, 0l, 0l, 0l, 11l, 0l, 3l, 1l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 270l, 144l, 7l, 8l, 15l, 6l, 6l, 2l, 6l, 1l, 25l, 5l, 0l, 1l, 1l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 14l, 2l, 1l, 0l, 0l, 0l, 0l, 0l, 3l, 0l, 0l, 0l, 3l, 2l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 2l, 1l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 2l, 1l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l, 2l, 7l, 0l, 0l, 0l, 0l, 0l, 0l, 14l, 1l, 0l, 0l, 0l, 0l, 0l, 1l, 0l, 0l, 1l, 0l, 0l, 0l, 0l, 0l), .dim = c(12l, 32l), .dimnames = list(c("a", "b", "c", "d", "e", "f", "g", "h", "i", "j", "k", "l"), c("a", "b", "c", "d", "e", "f", "g", "h", "i", "j", "k", "l", "m", "n", "o", "p", "q", "r", "s", "t", "u", "v", "w", "x", "y", "z", "a1", "b1", "c1", "d1", "e1", "f1")))
and i'm running analysis:
library(vegan) feed_raw.hel = decostand(feed.raw1, method = "pa") pca.feed=vegan::rda(feed_raw.hel, scale=false) head(summary(pca.feed))
it gives me error:
canonical correspondence analysis class: rda cca call: rda(x = feed_raw.hel, scale = false) total inertia: 0 eigenvalues: error in names(vec) <- paste("ax", 1:length(vec), sep = "") : attempt set attribute on null
no error found (see comments in op):
> library(vegan) > feed_raw.hel = decostand(feed.raw1, method = "pa") > > pca.feed=vegan::rda(feed_raw.hel, scale=false) > head(summary(pca.feed)) call: rda(x = feed_raw.hel, scale = false) partitioning of variance: inertia proportion total 5.394 1 unconstrained 5.394 1 eigenvalues, , contribution variance importance of components: pc1 pc2 pc3 pc4 pc5 pc6 pc7 eigenvalue 2.0696 0.7676 0.6639 0.5502 0.41578 0.31941 0.22209 proportion explained 0.3837 0.1423 0.1231 0.1020 0.07708 0.05922 0.04117 cumulative proportion 0.3837 0.5260 0.6491 0.7511 0.82817 0.88739 0.92856 pc8 pc9 pc10 pc11 eigenvalue 0.15383 0.11310 0.07857 0.03984 proportion explained 0.02852 0.02097 0.01457 0.00739 cumulative proportion 0.95708 0.97805 0.99261 1.00000 scaling 2 species , site scores * species scaled proportional eigenvalues * sites unscaled: weighted dispersion equal on dimensions * general scaling constant of scores: 2.775394 species scores pc1 pc2 pc3 pc4 pc5 pc6 -0.03289 -0.13245 0.18066 0.12616 -0.2028751 0.07257 b -0.19170 -0.26686 -0.20142 -0.16621 0.0739356 -0.16726 c -0.43542 -0.24013 -0.02194 0.16668 -0.0037653 0.18018 d -0.43702 0.08614 -0.05548 -0.06814 -0.0009418 -0.03947 e -0.24815 -0.06070 0.29795 0.18439 -0.0879021 -0.02246 f 0.08852 0.11597 -0.07947 0.02250 -0.0926734 -0.13060 .... site scores (weighted sums of species scores) pc1 pc2 pc3 pc4 pc5 pc6 -1.65813 0.55267 0.90341 0.4485 0.8856 -0.7321 b -1.70818 0.11084 -1.33080 -0.9734 -0.8929 0.4280 c -0.25333 -1.02024 1.39160 0.9718 -1.5627 0.5590 d -0.09478 -1.47685 -1.03494 1.1078 1.2228 -0.2536 e 0.26417 0.60502 0.71856 -0.6194 1.1614 1.2200 f 0.36048 -0.01608 -0.09826 -0.2709 0.3182 1.3866 ....
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