df to link table
df2link(test, fun = sum)data.frame
data(otutab)
cbind(taxonomy, num = rowSums(otutab))[1:10, ] -> test
df2link(test)
#> $links
#> from to weight
#> 1 k__Bacteria p__Actinobacteria 54986
#> 2 k__Bacteria p__Bacteroidetes 16484
#> 3 k__Bacteria p__Proteobacteria 74430
#> 4 p__Actinobacteria c__Actinobacteria 54986
#> 5 p__Bacteroidetes c__Flavobacteriia 16484
#> 6 p__Proteobacteria c__Alphaproteobacteria 7789
#> 7 p__Proteobacteria c__Betaproteobacteria 36154
#> 8 p__Proteobacteria c__Gammaproteobacteria 30487
#> 9 c__Actinobacteria o__Actinomycetales 54986
#> 10 c__Alphaproteobacteria o__Rhizobiales 7789
#> 11 c__Betaproteobacteria o__Burkholderiales 36154
#> 12 c__Flavobacteriia o__Flavobacteriales 16484
#> 13 c__Gammaproteobacteria o__Pseudomonadales 30487
#> 14 o__Actinomycetales f__Micromonosporaceae 8518
#> 15 o__Actinomycetales f__Pseudonocardiaceae 9508
#> 16 o__Actinomycetales f__Streptomycetaceae 10813
#> 17 o__Actinomycetales f__Thermomonosporaceae 26147
#> 18 o__Burkholderiales f__Comamonadaceae 25217
#> 19 o__Burkholderiales f__un_o__Burkholderiales 10937
#> 20 o__Flavobacteriales f__Flavobacteriaceae 16484
#> 21 o__Pseudomonadales f__Pseudomonadaceae 30487
#> 22 o__Rhizobiales f__Rhizobiaceae 7789
#> 23 f__Comamonadaceae g__Pelomonas 25217
#> 24 f__Flavobacteriaceae g__Flavobacterium 16484
#> 25 f__Micromonosporaceae g__Actinoplanes 8518
#> 26 f__Pseudomonadaceae g__Rhizobacter 30487
#> 27 f__Pseudonocardiaceae g__Lentzea 9508
#> 28 f__Rhizobiaceae g__Rhizobium 7789
#> 29 f__Streptomycetaceae g__Streptomyces 10813
#> 30 f__Thermomonosporaceae g__un_f__Thermomonosporaceae 26147
#> 31 f__un_o__Burkholderiales g__un_o__Burkholderiales 10937
#> 32 g__Actinoplanes s__un_g__Actinoplanes 8518
#> 33 g__Flavobacterium s__Flavobacterium_terrae 16484
#> 34 g__Lentzea s__Lentzea_flaviverrucosa 9508
#> 35 g__Pelomonas s__Pelomonas_puraquae 25217
#> 36 g__Rhizobacter s__Rhizobacter_bergeniae 16592
#> 37 g__Rhizobacter s__un_g__Rhizobacter 13895
#> 38 g__Rhizobium s__un_g__Rhizobium 7789
#> 39 g__Streptomyces s__un_g__Streptomyces 10813
#> 40 g__un_f__Thermomonosporaceae s__un_f__Thermomonosporaceae 26147
#> 41 g__un_o__Burkholderiales s__un_o__Burkholderiales 10937
#>
#> $nodes
#> name level weight
#> 1 k__Bacteria Kingdom 145900
#> 2 p__Actinobacteria Phylum 54986
#> 3 p__Bacteroidetes Phylum 16484
#> 4 p__Proteobacteria Phylum 74430
#> 5 c__Actinobacteria Class 54986
#> 6 c__Alphaproteobacteria Class 7789
#> 7 c__Betaproteobacteria Class 36154
#> 8 c__Flavobacteriia Class 16484
#> 9 c__Gammaproteobacteria Class 30487
#> 10 o__Actinomycetales Order 54986
#> 11 o__Burkholderiales Order 36154
#> 12 o__Flavobacteriales Order 16484
#> 13 o__Pseudomonadales Order 30487
#> 14 o__Rhizobiales Order 7789
#> 15 f__Comamonadaceae Family 25217
#> 16 f__Flavobacteriaceae Family 16484
#> 17 f__Micromonosporaceae Family 8518
#> 18 f__Pseudomonadaceae Family 30487
#> 19 f__Pseudonocardiaceae Family 9508
#> 20 f__Rhizobiaceae Family 7789
#> 21 f__Streptomycetaceae Family 10813
#> 22 f__Thermomonosporaceae Family 26147
#> 23 f__un_o__Burkholderiales Family 10937
#> 24 g__Actinoplanes Genus 8518
#> 25 g__Flavobacterium Genus 16484
#> 26 g__Lentzea Genus 9508
#> 27 g__Pelomonas Genus 25217
#> 28 g__Rhizobacter Genus 30487
#> 29 g__Rhizobium Genus 7789
#> 30 g__Streptomyces Genus 10813
#> 31 g__un_f__Thermomonosporaceae Genus 26147
#> 32 g__un_o__Burkholderiales Genus 10937
#> 33 s__Flavobacterium_terrae Species 16484
#> 34 s__Lentzea_flaviverrucosa Species 9508
#> 35 s__Pelomonas_puraquae Species 25217
#> 36 s__Rhizobacter_bergeniae Species 16592
#> 37 s__un_f__Thermomonosporaceae Species 26147
#> 38 s__un_g__Actinoplanes Species 8518
#> 39 s__un_g__Rhizobacter Species 13895
#> 40 s__un_g__Rhizobium Species 7789
#> 41 s__un_g__Streptomyces Species 10813
#> 42 s__un_o__Burkholderiales Species 10937
#>