#Load Data
CrowCreek <- read.csv("~/Dropbox/p/crow creek/CrowCreek.csv",h=TRUE,stringsAsFactors = F)
food <- read.csv("~/Dropbox/p/crow creek/CrowCreekFood.csv",h=TRUE,stringsAsFactors = F)
#Require Packages
require(tidyverse)## Loading required package: tidyverse## Loading tidyverse: ggplot2
## Loading tidyverse: tibble
## Loading tidyverse: tidyr
## Loading tidyverse: readr
## Loading tidyverse: purrr
## Loading tidyverse: dplyr## Conflicts with tidy packages ----------------------------------------------## filter(): dplyr, stats
## lag(): dplyr, stats#Splitout genus only
for(i in 1:dim(CrowCreek)[1]){
CrowCreek[i,"Genus"]<-strsplit(CrowCreek[i,2]," ")[[1]][1]}
#Merge in food data
food$isFood<-"yes"
CrowCreek<-merge(CrowCreek,food,by=c("Study","Species"),all.x=T)
CrowCreek[is.na(CrowCreek$isFood),"isFood"]<-"no"Write a function to count up number of unique taxa to each of the 7 regions:
vennsections<-function(){
a<-setdiff(Asp,union(Bsp,Csp)) #species unique to a
b<-setdiff(Bsp,union(Asp,Csp)) #species unique to a
c<-setdiff(Csp,union(Bsp,Asp)) #species unique to a
ab<-setdiff(intersect(Asp,Bsp),Csp) #species shared by AB but not C
ac<-setdiff(intersect(Asp,Csp),Bsp) #species shared by AC but not B
bc<-setdiff(intersect(Bsp,Csp),Asp) #species shared by BC but not A
abc<-intersect(intersect(Asp,Bsp),Csp) #species shared by all 3 studies
#doublecheck
if(length(Asp)==length(a)+length(ab)+length(ac)+length(abc)&length(Bsp)==length(b)+length(ab)+length(bc)+length(abc)&length(Csp)==length(c)+length(bc)+length(ac)+length(abc)){
regionnames<-c("a","b","c","ab","ac","bc","abc")
lengths<-c(length(a),length(b),length(c),length(ab),length(ac),length(bc),length(abc))
identities<-c(paste(a, sep="", collapse=", "),paste(b, sep="", collapse=", "),paste(c, sep="", collapse=", "),paste(ab, sep="", collapse=", "),paste(ac, sep="", collapse=", "),paste(bc, sep="", collapse=", "),paste(abc, sep="", collapse=", "))
data.frame(regionnames,lengths,identities)}
}Asp <- CrowCreek[CrowCreek$Study=="A"&CrowCreek$TaxonType=="species","Species"]
Bsp <- CrowCreek[CrowCreek$Study=="B"&CrowCreek$TaxonType=="species","Species"]
Csp <- CrowCreek[CrowCreek$Study=="C"&CrowCreek$TaxonType=="species","Species"]
vennsections()## regionnames lengths
## 1 a 27
## 2 b 40
## 3 c 74
## 4 ab 15
## 5 ac 4
## 6 bc 21
## 7 abc 19
## identities
## 1 Achillea millefolium, Citrullus lanatus, Cucumis melo, Cucurbita pepo, Daucus carota, Echinocystis lobata, Hydrastis canadensis, Lemna minor, Lewisia rediviva, Ligusticum porteri, Lonicera tatarica, Malus domestica, Matricaria chamomilla, Mentha piperita, Mentha spicata, Morus alba, Nepeta cataria, Opuntia macrorhiza, Portulaca oleracea, Ribes odoratum, Rumex hymenosepalus, Rumex maritimus, Salix eriocephala, Solanum lycopersicum, Taraxacum officinale, Thuja occidentalis, Verbascum thapsus
## 2 Acer saccharinum, Allium canadense, Artemisia dracunculus, Betula papyrifera, Callirhoe involucrata, Celtis occidentalis, Corylus americana, Cucurbita foetidissima, Dalea aurea, Fragaria virginiana, Fraxinus pennslyvanica, Gentiana saponaria, Gymnocladus dioicus, Hedeoma hispida, Helianthus annuus, Lagenaria siceraria, Lilium philadephicum, Linum lewisii, Mentha canadensis, Mentzelia nuda, Mirabilis nyctaginea, Nelumbo lutea, Opuntia humifusa, Panax quinquefolius, Phaseolus vulgaris, Pinus contorta subsp. murrayana, Pulsatilla patens, Quercus rubra, Ribes missouriense, Rubus strigosus, Sambucus nigra, Silphium laciniatum, Symphoricarpos orbiculatus, Ulmus americana, Ulmus thomasii, Verbena hastata, Viburnum lentago, Viburnum opulus, Vitis cinerea, Zizania aquatica
## 3 Allium drummondii, Ambrosia artemisiifolia, Ambrosia trifida, Amorpha fruticosa, Antennaria parvifolia, Arctostaphylos uva-ursi, Argemone polyanthemos, Artemisia cana, Artemisia tridentata, Asclepias pumila, Asclepias stenophylla, Asclepias verticillata, Asclepias viridiflora, Astragalus canadensis, Astragalus gracilis, Astragalus racemosus, Bouteloua gracilis, Calamovilfa longifolia, Chamaesyce geyeri, Cicuta maculata, Clematis ligusticifolia, Conium maculatum, Coreopsis tinctoria, Crataegus chrysocarpa, Croton texensis, Dalea purpurea var. purpurea, Dalea villosa var. villosa, Delphinium carolinianum, Dichanthelium oligosanthes, Equisetum hyemale, Eriogonum annuum, Euphorbia marginata, Fragaria vesca, Fraxinus pennsylvanica, Fritillaria atropurpurea, Gaura coccinea, Gutierrezia sarothrae, Hedeoma drummondii, Hesperostipa spartea, Heuchera richardsonii, Hymenopappus tenuifolius, Lepidium densiflorum, Liatris punctata, Lithospermum caroliniense, Lomatium orientale, Lygodesmia juncea, Mirabilis linearis, Nuphar lutea, Oenothera biennis, Onosmodium molle, Ostrya virginiana, Oxytropis lambertii, Pascopyrum smithii, Pediomelum cuspidatum, Penstemon angustifolius, Penstemon gracilis, Persicaria amphibia, Pycnanthemum virginianum, Quercus velutina, Rhus aromatica, Ribes americanum, Ribes aureum, Rosa woodsii, Rumex altissimus, Rumex venosus, Schizachyrium scoparium, Sium suave, Solanum triflorum, Solidago rigida, Tilia americana, Toxicodendron rydbergii, Tradescantia bracteata, Xanthium strumarium, Zigadenus venenosus
## 4 Acer negundo, Apios americana, Artemisia frigida, Cornus amomum, Juniperus virginiana, Lomatium foeniculaceum, Melilotus albus, Melilotus officinalis, Nicotiana quadrivalvis, Pediomelum esculentum, Quercus macrocarpa, Rosa arkansana, Rumex crispus, Ulmus rubra, Zea mays
## 5 Artemisia campestris, Asclepias speciosa, Ipomoea leptophylla, Pediomelum argophyllum
## 6 Agastache foeniculum, Astragalus crassicarpus, Carya ovata, Ceanothus herbaceus, Celastrus scandens, Dyssodia papposa, Grindelia squarrosa, Helianthus tuberosus, Humulus lupulus, Juglans nigra, Physalis heterophylla, Prunus pumila var. besseyi, Psoralidium tenuiflorum, Ratibida columnifera, Rubus occidentalis, Sagittaria latifolia, Schoenoplectus tabernaemontani, Sphaeralcea coccinea, Symphoricarpos occidentalis, Thalictrum dasycarpum, Urtica dioica
## 7 Acorus calamus, Amelanchier alnifolia, Amphicarpaea bracteata, Artemisia ludoviciana, Chenopodium album, Cornus stolonifera, Echinacea angustifolia, Glycyrrhiza lepidota, Hierochloe odorata, Mentha arvensis, Monarda fistulosa, Populus deltoides, Prunus americana, Prunus virginiana, Rhus glabra, Shepherdia argentea, Typha latifolia, Vitis riparia, Yucca glaucaAsp <- CrowCreek[CrowCreek$Study=="A"&CrowCreek$TaxonType=="species"|CrowCreek$TaxonType=="nonplant","Species"]
Bsp <- CrowCreek[CrowCreek$Study=="B"&CrowCreek$TaxonType=="species"|CrowCreek$TaxonType=="nonplant","Species"]
Csp <- CrowCreek[CrowCreek$Study=="C"&CrowCreek$TaxonType=="species"|CrowCreek$TaxonType=="nonplant","Species"]
vennsections()## regionnames lengths
## 1 a 27
## 2 b 40
## 3 c 74
## 4 ab 15
## 5 ac 4
## 6 bc 21
## 7 abc 26
## identities
## 1 Achillea millefolium, Citrullus lanatus, Cucumis melo, Cucurbita pepo, Daucus carota, Echinocystis lobata, Hydrastis canadensis, Lemna minor, Lewisia rediviva, Ligusticum porteri, Lonicera tatarica, Malus domestica, Matricaria chamomilla, Mentha piperita, Mentha spicata, Morus alba, Nepeta cataria, Opuntia macrorhiza, Portulaca oleracea, Ribes odoratum, Rumex hymenosepalus, Rumex maritimus, Salix eriocephala, Solanum lycopersicum, Taraxacum officinale, Thuja occidentalis, Verbascum thapsus
## 2 Acer saccharinum, Allium canadense, Artemisia dracunculus, Betula papyrifera, Callirhoe involucrata, Celtis occidentalis, Corylus americana, Cucurbita foetidissima, Dalea aurea, Fragaria virginiana, Fraxinus pennslyvanica, Gentiana saponaria, Gymnocladus dioicus, Hedeoma hispida, Helianthus annuus, Lagenaria siceraria, Lilium philadephicum, Linum lewisii, Mentha canadensis, Mentzelia nuda, Mirabilis nyctaginea, Nelumbo lutea, Opuntia humifusa, Panax quinquefolius, Phaseolus vulgaris, Pinus contorta subsp. murrayana, Pulsatilla patens, Quercus rubra, Ribes missouriense, Rubus strigosus, Sambucus nigra, Silphium laciniatum, Symphoricarpos orbiculatus, Ulmus americana, Ulmus thomasii, Verbena hastata, Viburnum lentago, Viburnum opulus, Vitis cinerea, Zizania aquatica
## 3 Allium drummondii, Ambrosia artemisiifolia, Ambrosia trifida, Amorpha fruticosa, Antennaria parvifolia, Arctostaphylos uva-ursi, Argemone polyanthemos, Artemisia cana, Artemisia tridentata, Asclepias pumila, Asclepias stenophylla, Asclepias verticillata, Asclepias viridiflora, Astragalus canadensis, Astragalus gracilis, Astragalus racemosus, Bouteloua gracilis, Calamovilfa longifolia, Chamaesyce geyeri, Cicuta maculata, Clematis ligusticifolia, Conium maculatum, Coreopsis tinctoria, Crataegus chrysocarpa, Croton texensis, Dalea purpurea var. purpurea, Dalea villosa var. villosa, Delphinium carolinianum, Dichanthelium oligosanthes, Equisetum hyemale, Eriogonum annuum, Euphorbia marginata, Fragaria vesca, Fraxinus pennsylvanica, Fritillaria atropurpurea, Gaura coccinea, Gutierrezia sarothrae, Hedeoma drummondii, Hesperostipa spartea, Heuchera richardsonii, Hymenopappus tenuifolius, Lepidium densiflorum, Liatris punctata, Lithospermum caroliniense, Lomatium orientale, Lygodesmia juncea, Mirabilis linearis, Nuphar lutea, Oenothera biennis, Onosmodium molle, Ostrya virginiana, Oxytropis lambertii, Pascopyrum smithii, Pediomelum cuspidatum, Penstemon angustifolius, Penstemon gracilis, Persicaria amphibia, Pycnanthemum virginianum, Quercus velutina, Rhus aromatica, Ribes americanum, Ribes aureum, Rosa woodsii, Rumex altissimus, Rumex venosus, Schizachyrium scoparium, Sium suave, Solanum triflorum, Solidago rigida, Tilia americana, Toxicodendron rydbergii, Tradescantia bracteata, Xanthium strumarium, Zigadenus venenosus
## 4 Acer negundo, Apios americana, Artemisia frigida, Cornus amomum, Juniperus virginiana, Lomatium foeniculaceum, Melilotus albus, Melilotus officinalis, Nicotiana quadrivalvis, Pediomelum esculentum, Quercus macrocarpa, Rosa arkansana, Rumex crispus, Ulmus rubra, Zea mays
## 5 Artemisia campestris, Asclepias speciosa, Ipomoea leptophylla, Pediomelum argophyllum
## 6 Agastache foeniculum, Astragalus crassicarpus, Carya ovata, Ceanothus herbaceus, Celastrus scandens, Dyssodia papposa, Grindelia squarrosa, Helianthus tuberosus, Humulus lupulus, Juglans nigra, Physalis heterophylla, Prunus pumila var. besseyi, Psoralidium tenuiflorum, Ratibida columnifera, Rubus occidentalis, Sagittaria latifolia, Schoenoplectus tabernaemontani, Sphaeralcea coccinea, Symphoricarpos occidentalis, Thalictrum dasycarpum, Urtica dioica
## 7 Acorus calamus, Amelanchier alnifolia, Amphicarpaea bracteata, Apiosporina morbosa, Artemisia ludoviciana, Chenopodium album, Cornus stolonifera, Echinacea angustifolia, Glycyrrhiza lepidota, Hierochloe odorata, Mentha arvensis, Monarda fistulosa, Morchella esculenta, Pleurotus ostreatus, Populus deltoides, Prunus americana, Prunus virginiana, Rhus glabra, Shepherdia argentea, Typha latifolia, Vitis riparia, Yucca glauca, Pleurotus ulmarius, Polystictus versicolor, Punctelia borreri, Usnea barbataAsp <- unique(CrowCreek[CrowCreek$Study=="A","Genus"])
Bsp <- unique(CrowCreek[CrowCreek$Study=="B","Genus"])
Csp <- unique(CrowCreek[CrowCreek$Study=="C","Genus"])
vennsections()## regionnames lengths
## 1 a 21
## 2 b 22
## 3 c 48
## 4 ab 11
## 5 ac 4
## 6 bc 25
## 7 abc 26
## identities
## 1 Achillea, Apiosporina, Citrullus, Cucumis, Daucus, Echinocystis, Hydrastis, Lemna, Lewisia, Ligusticum, Lonicera, Malus, Matricaria, Morchella, Nepeta, Poaceae, Portulaca, Taraxacum, Thuja, Vaccinium, Verbascum
## 2 Callirhoe, Celtis, Corylus, Gentiana, Gymnocladus, Lagenaria, Lilium, Linum, Mentzelia, Nelumbo, Panax, Phaseolus, Pinus, Polystictus, Pulsatilla, Punctelia, Sambucus, Silphium, Usnea, Verbena, Viburnum, Zizania
## 3 Ambrosia, Amorpha, Antennaria, Arctostaphylos, Argemone, Bouteloua, Calamovilfa, Chamaesyce, Cicuta, Clematis, Conium, Coreopsis, Crataegus, Croton, Cypripedium, Delphinium, Dichanthelium, Equisetum, Eriogonum, Euphorbia, Fritillaria, Gaura, Gutierrezia, Hesperostipa, Heuchera, Hymenopappus, Lepidium, Liatris, Lithospermum, Lygodesmia, Nuphar, Nymphaea, Oenothera, Onosmodium, Ostrya, Oxytropis, Pascopyrum, Penstemon, Persicaria, Pycnanthemum, Schizachyrium, Sium, Solidago, Tilia, Toxicodendron, Tradescantia, Xanthium, Zigadenus
## 4 Acer, Apios, Betula, Cucurbita, Juniperus, Melilotus, Nicotiana, Pleurotus, Salix, Ulmus, Zea
## 5 Asclepias, Ipomoea, Morus, Solanum
## 6 Agastache, Astragalus, Carya, Ceanothus, Celastrus, Dalea, Dyssodia, Fragaria, Fraxinus, Grindelia, Hedeoma, Helianthus, Humulus, Juglans, Mirabilis, Physalis, Psoralidium, Ratibida, Rubus, Sagittaria, Schoenoplectus, Sphaeralcea, Symphoricarpos, Thalictrum, Urtica
## 7 Acorus, Allium, Amelanchier, Amphicarpaea, Artemisia, Chenopodium, Cornus, Echinacea, Glycyrrhiza, Hierochloe, Lomatium, Mentha, Monarda, Opuntia, Pediomelum, Populus, Prunus, Quercus, Rhus, Ribes, Rosa, Rumex, Shepherdia, Typha, Vitis, YuccaCrowCreek <- subset(CrowCreek,isFood=="yes")Asp <- CrowCreek[CrowCreek$Study=="A"&CrowCreek$TaxonType=="species","Species"]
Bsp <- CrowCreek[CrowCreek$Study=="B"&CrowCreek$TaxonType=="species","Species"]
Csp <- CrowCreek[CrowCreek$Study=="C"&CrowCreek$TaxonType=="species","Species"]
vennsections()## regionnames lengths
## 1 a 18
## 2 b 23
## 3 c 20
## 4 ab 6
## 5 ac 0
## 6 bc 9
## 7 abc 6
## identities
## 1 Asclepias speciosa, Citrullus lanatus, Cucumis melo, Cucurbita pepo, Daucus carota, Echinocystis lobata, Lomatium foeniculaceum, Malus domestica, Mentha piperita, Morus alba, Opuntia macrorhiza, Populus deltoides, Portulaca oleracea, Ribes odoratum, Rumex hymenosepalus, Solanum lycopersicum, Taraxacum officinale, Yucca glauca
## 2 Acer saccharinum, Allium canadense, Celtis occidentalis, Corylus americana, Dyssodia papposa, Fragaria virginiana, Helianthus annuus, Linum lewisii, Mentha canadensis, Nelumbo lutea, Opuntia humifusa, Phaseolus vulgaris, Physalis heterophylla, Quercus macrocarpa, Quercus rubra, Ratibida columnifera, Ribes missouriense, Rubus strigosus, Sagittaria latifolia, Sambucus nigra, Viburnum lentago, Vitis cinerea, Zizania aquatica
## 3 Acorus calamus, Allium drummondii, Astragalus canadensis, Astragalus crassicarpus, Coreopsis tinctoria, Crataegus chrysocarpa, Dalea purpurea var. purpurea, Fragaria vesca, Hedeoma drummondii, Humulus lupulus, Liatris punctata, Lomatium orientale, Lygodesmia juncea, Monarda fistulosa, Nuphar lutea, Persicaria amphibia, Quercus velutina, Ribes americanum, Ribes aureum, Rosa woodsii
## 4 Acer negundo, Amphicarpaea bracteata, Apios americana, Pediomelum esculentum, Rosa arkansana, Zea mays
## 5
## 6 Agastache foeniculum, Carya ovata, Ceanothus herbaceus, Helianthus tuberosus, Juglans nigra, Mentha arvensis, Prunus pumila var. besseyi, Rubus occidentalis, Schoenoplectus tabernaemontani
## 7 Amelanchier alnifolia, Chenopodium album, Prunus americana, Prunus virginiana, Shepherdia argentea, Vitis ripariaAsp <- CrowCreek[CrowCreek$Study=="A"&CrowCreek$TaxonType=="species"|CrowCreek$TaxonType=="nonplant","Species"]
Bsp <- CrowCreek[CrowCreek$Study=="B"&CrowCreek$TaxonType=="species"|CrowCreek$TaxonType=="nonplant","Species"]
Csp <- CrowCreek[CrowCreek$Study=="C"&CrowCreek$TaxonType=="species"|CrowCreek$TaxonType=="nonplant","Species"]
vennsections()## regionnames lengths
## 1 a 18
## 2 b 23
## 3 c 20
## 4 ab 6
## 5 ac 0
## 6 bc 9
## 7 abc 10
## identities
## 1 Asclepias speciosa, Citrullus lanatus, Cucumis melo, Cucurbita pepo, Daucus carota, Echinocystis lobata, Lomatium foeniculaceum, Malus domestica, Mentha piperita, Morus alba, Opuntia macrorhiza, Populus deltoides, Portulaca oleracea, Ribes odoratum, Rumex hymenosepalus, Solanum lycopersicum, Taraxacum officinale, Yucca glauca
## 2 Acer saccharinum, Allium canadense, Celtis occidentalis, Corylus americana, Dyssodia papposa, Fragaria virginiana, Helianthus annuus, Linum lewisii, Mentha canadensis, Nelumbo lutea, Opuntia humifusa, Phaseolus vulgaris, Physalis heterophylla, Quercus macrocarpa, Quercus rubra, Ratibida columnifera, Ribes missouriense, Rubus strigosus, Sagittaria latifolia, Sambucus nigra, Viburnum lentago, Vitis cinerea, Zizania aquatica
## 3 Acorus calamus, Allium drummondii, Astragalus canadensis, Astragalus crassicarpus, Coreopsis tinctoria, Crataegus chrysocarpa, Dalea purpurea var. purpurea, Fragaria vesca, Hedeoma drummondii, Humulus lupulus, Liatris punctata, Lomatium orientale, Lygodesmia juncea, Monarda fistulosa, Nuphar lutea, Persicaria amphibia, Quercus velutina, Ribes americanum, Ribes aureum, Rosa woodsii
## 4 Acer negundo, Amphicarpaea bracteata, Apios americana, Pediomelum esculentum, Rosa arkansana, Zea mays
## 5
## 6 Agastache foeniculum, Carya ovata, Ceanothus herbaceus, Helianthus tuberosus, Juglans nigra, Mentha arvensis, Prunus pumila var. besseyi, Rubus occidentalis, Schoenoplectus tabernaemontani
## 7 Amelanchier alnifolia, Chenopodium album, Morchella esculenta, Pleurotus ostreatus, Prunus americana, Prunus virginiana, Shepherdia argentea, Vitis riparia, Pleurotus ulmarius, Polystictus versicolorAsp <- unique(CrowCreek[CrowCreek$Study=="A","Genus"])
Bsp <- unique(CrowCreek[CrowCreek$Study=="B","Genus"])
Csp <- unique(CrowCreek[CrowCreek$Study=="C","Genus"])
vennsections()## regionnames lengths
## 1 a 15
## 2 b 13
## 3 c 14
## 4 ab 7
## 5 ac 2
## 6 bc 9
## 7 abc 9
## identities
## 1 Asclepias, Citrullus, Cucumis, Cucurbita, Daucus, Echinocystis, Malus, Morchella, Populus, Portulaca, Rumex, Solanum, Taraxacum, Vaccinium, Yucca
## 2 Celtis, Corylus, Dyssodia, Linum, Nelumbo, Phaseolus, Physalis, Polystictus, Ratibida, Sagittaria, Sambucus, Viburnum, Zizania
## 3 Acorus, Astragalus, Coreopsis, Crataegus, Cypripedium, Dalea, Hedeoma, Humulus, Liatris, Lygodesmia, Monarda, Nuphar, Nymphaea, Persicaria
## 4 Acer, Amphicarpaea, Apios, Opuntia, Pediomelum, Pleurotus, Zea
## 5 Lomatium, Morus
## 6 Agastache, Carya, Ceanothus, Fragaria, Helianthus, Juglans, Quercus, Rubus, Schoenoplectus
## 7 Allium, Amelanchier, Chenopodium, Mentha, Prunus, Ribes, Rosa, Shepherdia, Vitis