[R-sig-eco] trasformation of matrix for iNEXT extrapolation interpolation of Hill's numbers

[Law, Jason]

I'm not sure what your data looks like. But the reshape package can be used to easily create matrix or array data from a 'long' format. Combining that with split would make it relatively to create matrices.

library(iNEXT)
library(reshape2)
data(ciliates)
# Maybe your data is in long format like this:
df <- melt(ciliates, varnames = c('species', 'sample'), value.name = 'count') 
# Then this will work
df.list <- lapply(split(df, df$L1), function(x) acast(x, species ~ sample, value.var='count')) 

# If your data is just one wide (sorted) matrix, then you just need lapply and the column indices
mat <- acast(df, species ~ L1 + sample, value.var='count')
df.list <- lapply(list(c(1,17), c(18,36), c(37,51)), function(i) mat[,i[1]:i[2]])

Regards,

Jason

-----Original Message-----
From: R-sig-ecology <r-sig-ecology-bounces using r-project.org> On Behalf Of Irene Adamo
Sent: Thursday, June 20, 2019 07:28
To: r-sig-ecology using r-project.org
Subject: [R-sig-eco] trasformation of matrix for iNEXT extrapolation interpolation of Hill's numbers

Hi all,

I am working with iNEXT package for diversity analyses however, I would like to use a incidence_raw data type which in iNEXT is a list of matrices like this:

data(ciliates)
head(ciliates)

$SouthernNamibDesert
                                                     x9 x17 x19 x20 x21 x22
x23 x24
Acaryophrya.collaris                                  0   0   0   0   0   0
  0   0
Actinobolina.multinucleata.n..sp.                     0   0   0   0   0   0
  0   0
Afroamphisiella.multinucleata.n..sp.                  0   0   0   0   0   0
  0   0
Afrothrix.multinucleata.n..sp.                        0   1   0   0   0   0
  0   0
Amphisiella.binucleata.multicirrata.n..ssp.           0   0   0   0   0   0
  0   0
Amphisiella.elegans.n..sp.                            0   0   0   0   0   0
  1   0
Amphisiella.longiseries.n..sp.                        0   0   0   0   0   0
  0   0
Amphisiella.magnigranulosa                            0   0   0   0   0   0
  0   1
Amphisiella.multinucleata.n..sp.                      0   0   0   0   0   0
  0   0
Amphisiella.namibiensis.n..sp.                        0   0   0   0   0   0
  0   0
Amphisiella.polycirrata                               0   0   0   0   0   0
  0   0
Amphisiella.procera.n..sp.                            1   0   0   0   0   0
  0   0

do you know how can I create anlist with four matrices like the one they have in example data?

thanks a lot for any help!

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