Title: MSH species clade breakdown
Name: Tammy L. Elliott
Date: April 16, 2016
R version 3.2
Taxonomic levels - temporal comparison (683 species)
####number of orders
length(levels(sp.numbers$Order))
## [1] 41
####number of families
length(levels(sp.numbers$Family))
## [1] 99
#number of species/family
(sp.family<-ddply(sp.numbers,.(Family), summarize, freq=length(Family)))
## Family freq
## 1 Adoxaceae 6
## 2 Alismataceae 2
## 3 Amaranthaceae 4
## 4 Amaryllidaceae 2
## 5 Anacardiaceae 2
## 6 Apiaceae 10
## 7 Apocynaceae 2
## 8 Aquifoliaceae 1
## 9 Araceae 1
## 10 Araliaceae 6
## 11 Aristolochiaceae 1
## 12 Asparagaceae 4
## 13 Aspleniaceae 2
## 14 Asteraceae 72
## 15 Athyriaceae 1
## 16 Balsaminaceae 2
## 17 Berberidaceae 2
## 18 Betulaceae 7
## 19 Boraginaceae 5
## 20 Brassicaceae 18
## 21 Campanulaceae 4
## 22 Cannabaceae 1
## 23 Caprifoliaceae 10
## 24 Caryophyllaceae 13
## 25 Celastraceae 2
## 26 Colchicaceae 3
## 27 Convolvulaceae 1
## 28 Cornaceae 4
## 29 Cupressaceae 2
## 30 Cyperaceae 71
## 31 Dennstaedtiaceae 2
## 32 Diplaziopsidaceae 1
## 33 Dryopteridaceae 10
## 34 Equisetaceae 6
## 35 Ericaceae 14
## 36 Euphorbiaceae 4
## 37 Fabaceae 15
## 38 Fagaceae 4
## 39 Geraniaceae 1
## 40 Grossulariaceae 7
## 41 Hamamelidaceae 1
## 42 Hydrangeaceae 1
## 43 Hypericaceae 5
## 44 Iridaceae 2
## 45 Isoetaceae 2
## 46 Juglandaceae 3
## 47 Juncaceae 6
## 48 Lamiaceae 11
## 49 Liliaceae 4
## 50 Lycopodiaceae 8
## 51 Lythraceae 1
## 52 Malvaceae 2
## 53 Melanthiaceae 3
## 54 Menyanthaceae 1
## 55 Molluginaceae 1
## 56 Montiaceae 1
## 57 Myricaceae 1
## 58 Nymphaeaceae 1
## 59 Oleaceae 3
## 60 Onagraceae 9
## 61 Ophioglossaceae 5
## 62 Orchidaceae 16
## 63 Orobanchaceae 3
## 64 Osmundaceae 3
## 65 Oxalidaceae 2
## 66 Papaveraceae 5
## 67 Penthoraceae 1
## 68 Phrymaceae 1
## 69 Phytolaccaceae 1
## 70 Pinaceae 7
## 71 Plantaginaceae 13
## 72 Poaceae 68
## 73 Polemoniaceae 1
## 74 Polygonaceae 12
## 75 Polypodiaceae 1
## 76 Portulacaceae 1
## 77 Primulaceae 9
## 78 Pteridaceae 1
## 79 Ranunculaceae 21
## 80 Rosaceae 44
## 81 Rubiaceae 9
## 82 Salicaceae 14
## 83 Sapindaceae 5
## 84 Saxifragaceae 5
## 85 Scrophulariaceae 3
## 86 Selaginellaceae 1
## 87 Solanaceae 3
## 88 Staphyleaceae 1
## 89 Taxaceae 1
## 90 Thelypteridaceae 4
## 91 Thymelaeaceae 1
## 92 Typhaceae 3
## 93 Ulmaceae 2
## 94 Urticaceae 3
## 95 Verbenaceae 1
## 96 Violaceae 10
## 97 Vitaceae 3
## 98 Woodsiaceae 7
## 99 Xanthorrhoeaceae 1
#number of families and species per order
(order.sp.family<-with(sp.numbers,aggregate(cbind(Family,Species) ~ Order,FUN=function(x){length(unique(x))})))
## Order Family Species
## 1 Alismatales 2 3
## 2 Apiales 2 16
## 3 Aquifoliales 1 1
## 4 Asparagales 5 25
## 5 Asterales 3 77
## 6 Boraginales 1 5
## 7 Brassicales 1 18
## 8 Caryophyllales 7 33
## 9 Celastrales 1 2
## 10 Cornales 2 5
## 11 Crossosomatales 1 1
## 12 Cupressales 2 3
## 13 Dipsacales 2 16
## 14 Equisetales 1 6
## 15 Ericales 4 26
## 16 Fabales 1 15
## 17 Fagales 4 15
## 18 Gentianales 2 11
## 19 Geraniales 1 1
## 20 Isoetales 1 2
## 21 Lamiales 7 35
## 22 Liliales 3 10
## 23 Lycopodiales 1 8
## 24 Malpighiales 4 33
## 25 Malvales 2 3
## 26 Myrtales 2 10
## 27 Nymphaeales 1 1
## 28 Ophioglossales 1 5
## 29 Osmundales 1 3
## 30 Oxiladales 1 2
## 31 Pinales 1 7
## 32 Piperales 1 1
## 33 Poales 4 148
## 34 Polypodiales 9 29
## 35 Ranunculales 3 28
## 36 Rosales 4 50
## 37 Sapindales 2 7
## 38 Saxifragales 4 14
## 39 Selaginellales 1 1
## 40 Solanales 2 4
## 41 Vitales 1 3
Change in number of species per family
species.change <- merge(order.sp.family.nf, order.sp.family.additions,by.x = "Family",by.y = "Family",all = TRUE)
species.change[is.na(species.change)] <- 0
colnames(species.change)<-c("Family", "Not found", "Added")
species.change
## Family Not found Added
## 1 Adoxaceae 1 2
## 2 Amaranthaceae 1 1
## 3 Amaryllidaceae 1 0
## 4 Anacardiaceae 0 1
## 5 Apiaceae 1 2
## 6 Aspleniaceae 1 1
## 7 Asteraceae 5 20
## 8 Berberidaceae 1 0
## 9 Boraginaceae 2 2
## 10 Brassicaceae 2 8
## 11 Campanulaceae 1 1
## 12 Cannabaceae 0 1
## 13 Caprifoliaceae 2 4
## 14 Caryophyllaceae 1 7
## 15 Celastraceae 0 1
## 16 Colchicaceae 0 1
## 17 Convolvulaceae 0 1
## 18 Cornaceae 1 0
## 19 Cupressaceae 1 0
## 20 Cyperaceae 2 32
## 21 Dryopteridaceae 0 4
## 22 Equisetaceae 0 2
## 23 Ericaceae 8 0
## 24 Euphorbiaceae 0 3
## 25 Fabaceae 0 8
## 26 Fagaceae 0 1
## 27 Grossulariaceae 0 2
## 28 Hydrangeaceae 0 1
## 29 Hypericaceae 2 1
## 30 Iridaceae 0 1
## 31 Isoetaceae 2 0
## 32 Juncaceae 0 4
## 33 Lamiaceae 0 4
## 34 Lycopodiaceae 2 2
## 35 Molluginaceae 1 0
## 36 Oleaceae 0 1
## 37 Onagraceae 2 1
## 38 Ophioglossaceae 1 0
## 39 Orchidaceae 10 1
## 40 Orobanchaceae 0 1
## 41 Phytolaccaceae 0 1
## 42 Pinaceae 0 2
## 43 Plantaginaceae 0 5
## 44 Poaceae 2 32
## 45 Polemoniaceae 0 1
## 46 Polygonaceae 1 3
## 47 Primulaceae 2 3
## 48 Ranunculaceae 3 3
## 49 Rosaceae 8 10
## 50 Rubiaceae 0 3
## 51 Salicaceae 0 5
## 52 Sapindaceae 0 1
## 53 Solanaceae 0 2
## 54 Staphyleaceae 1 0
## 55 Taxaceae 1 0
## 56 Typhaceae 0 1
## 57 Urticaceae 0 1
## 58 Violaceae 1 1
## 59 Vitaceae 0 1
## 60 Xanthorrhoeaceae 0 1