mod9p1

library(vegan)

## Warning: package 'vegan' was built under R version 4.3.2

## Loading required package: permute

## Warning: package 'permute' was built under R version 4.3.2

## Loading required package: lattice

## This is vegan 2.6-4

dune.bio<-read.table("dune_bio.txt", sep="\t", header=T, row.names=1)
sum(dune.bio)

## [1] 685

colSums(dune.bio)

## Belper Empnig Junbuf Junart Airpra Elepal Rumace Viclat Brarut Ranfla Cirarv 
##     13      2     13     18      5     25     18      4     49     14      2 
## Hyprad Leoaut Potpal Poapra Calcus Tripra Trirep Antodo Salrep Achmil Poatri 
##      9     54      4     48     10      9     47     21     11     16     63 
## Chealb Elyrep Sagpro Plalan Agrsto Lolper Alogen Brohor 
##      1     26     20     26     48     58     36     15

colMeans(dune.bio)

## Belper Empnig Junbuf Junart Airpra Elepal Rumace Viclat Brarut Ranfla Cirarv 
##   0.65   0.10   0.65   0.90   0.25   1.25   0.90   0.20   2.45   0.70   0.10 
## Hyprad Leoaut Potpal Poapra Calcus Tripra Trirep Antodo Salrep Achmil Poatri 
##   0.45   2.70   0.20   2.40   0.50   0.45   2.35   1.05   0.55   0.80   3.15 
## Chealb Elyrep Sagpro Plalan Agrsto Lolper Alogen Brohor 
##   0.05   1.30   1.00   1.30   2.40   2.90   1.80   0.75

rowSums(dune.bio)

##  2 13  4 16  6  1  8  5 17 15 10 11  9 18  3 20 14 19 12  7 
## 42 33 45 33 48 18 40 43 15 23 43 32 42 27 40 31 24 31 35 40

rowMeans(dune.bio)

##         2        13         4        16         6         1         8         5 
## 1.4000000 1.1000000 1.5000000 1.1000000 1.6000000 0.6000000 1.3333333 1.4333333 
##        17        15        10        11         9        18         3        20 
## 0.5000000 0.7666667 1.4333333 1.0666667 1.4000000 0.9000000 1.3333333 1.0333333 
##        14        19        12         7 
## 0.8000000 1.0333333 1.1666667 1.3333333

median_sps_sites<-function(x){
  cat("The median number of individuals per sp is", apply(x, 2, median), "and for sites is", apply(x, 1, median))
}
median_sps_sites(dune.bio)

## The median number of individuals per sp is 0 0 0 0 0 0 0 0 2 0 0 0 2 0 3 0 0 2 0 0 0 4 0 0 0 0 1.5 2 0 0 and for sites is 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

dune.bio.relabu<-decostand(dune.bio, method = "total")
rowSums(dune.bio.relabu)

##  2 13  4 16  6  1  8  5 17 15 10 11  9 18  3 20 14 19 12  7 
##  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1

dune.bio.range<-decostand(dune.bio, method = "range")
dune.bio.stand<-decostand(dune.bio, method = "standardize")