Plant survey exploration

require(dplyr)

plants <- read.csv('C:/Users/tuh09869/Google Drive/Megalopolis Ecology/data/PWD_plant_list_surveys_soft_sites.csv')
plants$binomial <- paste(plants$Genus, plants$Species, sep=' ')
approvedHerb <- read.csv('C:/Users/tuh09869/Google Drive/Megalopolis Ecology/data/GSI_Landscape_Guidebook_Plant_list_herbaceous.csv')
approvedTree <- read.csv('C:/Users/tuh09869/Google Drive/Megalopolis Ecology/data/GSI_Landscape_Guidebook_Plant_list_treesecsv.csv')
approvedHerb$binomial <- paste(approvedHerb$Genus, approvedHerb$Species, sep=' ')
approvedTree$binomial <- paste(approvedTree$Genus, approvedTree$Species, sep=' ')
approvedSpecies <- unique(c(approvedHerb$binomial, approvedTree$binomial))
addresses <- read.csv('C:/Users/tuh09869/Google Drive/Megalopolis Ecology/data/PWD SMP Addresses.csv')
plants <- left_join(plants, addresses, by='SMP.ID')

plants2 <- plants[! is.na(plants$SMP.Type),]

Overall, plants most used

plantFreq <- table(plants$binomial)
plantFreq <- as.data.frame(plantFreq)
plantFreq <- plantFreq[order(plantFreq$Freq),]
temporaryPlant <- plantFreq[plantFreq$Freq > 10,]
temporaryPlant2 <- data.frame(freq=temporaryPlant$Freq)
rownames(temporaryPlant2) <- temporaryPlant$Var1
par(mar=c(5.1,12,4.1,2.1))
barplot(t(as.matrix(temporaryPlant2)), beside=TRUE, horiz=T, las=1)

length(unique(plants$binomial)) # how many species in survey data

[1] 297

length(approvedSpecies) # how many species in 'approved' spreadsheet

[1] 626

By SMP type

rainGarden <- plants2[plants2$SMP.Type=='Rain Garden',]
length(unique(rainGarden$SMP.ID)) # number of rain gardens in survey data

[1] 65

plantFreq <- table(rainGarden$binomial)
plantFreq <- as.data.frame(plantFreq)
plantFreq <- plantFreq[order(plantFreq$Freq),]
temporaryPlant <- plantFreq[plantFreq$Freq > 10,]
temporaryPlant2 <- data.frame(freq=temporaryPlant$Freq)
rownames(temporaryPlant2) <- temporaryPlant$Var1
par(mar=c(5.1,12,4.1,2.1))
barplot(t(as.matrix(temporaryPlant2)), beside=TRUE, horiz=T, las=1)
planter <- plants2[plants2$SMP.Type=='Planter',]
length(unique(planter$SMP.ID)) # number of planters in survey data

[1] 48

plantFreq <- table(planter$binomial)
plantFreq <- as.data.frame(plantFreq)
plantFreq <- plantFreq[order(plantFreq$Freq),]
temporaryPlant <- plantFreq[plantFreq$Freq > 10,]
temporaryPlant2 <- data.frame(freq=temporaryPlant$Freq)
rownames(temporaryPlant2) <- temporaryPlant$Var1
par(mar=c(5.1,12,4.1,2.1))

barplot(t(as.matrix(temporaryPlant2)), beside=TRUE, horiz=T, las=1)
bumpout <- plants2[plants2$SMP.Type=='Bumpout',]
length(unique(bumpout$SMP.ID)) # number of bumpouts in survey data

[1] 22

plantFreq <- table(bumpout$binomial)
plantFreq <- as.data.frame(plantFreq)
plantFreq <- plantFreq[order(plantFreq$Freq),]
temporaryPlant <- plantFreq[plantFreq$Freq > 10,]
temporaryPlant2 <- data.frame(freq=temporaryPlant$Freq)
rownames(temporaryPlant2) <- temporaryPlant$Var1
par(mar=c(5.1,12,4.1,2.1))

barplot(t(as.matrix(temporaryPlant2)), beside=TRUE, horiz=T, las=1)
swale <- plants2[plants2$SMP.Type=='Swale',]
length(unique(swale$SMP.ID)) # number of swales in survey data

[1] 3

plantFreq <- table(swale$binomial)
plantFreq <- as.data.frame(plantFreq)
plantFreq <- plantFreq[order(plantFreq$Freq),]
# temporaryPlant <- plantFreq[plantFreq$Freq > 10,]
temporaryPlant <- plantFreq
temporaryPlant2 <- data.frame(freq=temporaryPlant$Freq)
rownames(temporaryPlant2) <- temporaryPlant$Var1
par(mar=c(5.1,12,4.1,2.1))

barplot(t(as.matrix(temporaryPlant2)), beside=TRUE, horiz=T, las=1)
basin <- plants2[plants2$SMP.Type=='Basin',]
length(unique(basin$SMP.ID)) # number of basins in survey data

[1] 1

plantFreq <- table(basin$binomial)
plantFreq <- as.data.frame(plantFreq)
plantFreq <- plantFreq[order(plantFreq$Freq),]
# temporaryPlant <- plantFreq[plantFreq$Freq > 10,]
temporaryPlant <- plantFreq
temporaryPlant2 <- data.frame(freq=temporaryPlant$Freq)
rownames(temporaryPlant2) <- temporaryPlant$Var1
par(mar=c(5.1,12,4.1,2.1))

barplot(t(as.matrix(temporaryPlant2)), beside=TRUE, horiz=T, las=1)

# Also data for green roofs?

SR by SMP

siteSR <- table(plants$SMP.ID)
siteSR <- as.data.frame(siteSR)
siteSR <- siteSR[order(siteSR$Freq),]
barplot(siteSR$Freq)

Tree trench and stormwater tree surveys

trees <- read.csv('C:/Users/tuh09869/Google Drive/Megalopolis Ecology/data/PWD_plant_list_surveys_tree_trenches.csv')
treeFreq <- table(trees$SPECIES)
treeFreq <- as.data.frame(treeFreq)
treeFreq <- treeFreq[order(treeFreq$Freq),]
temporaryPlant <- treeFreq[treeFreq$Freq > 10,]
temporaryPlant <- temporaryPlant[temporaryPlant$Freq < 100,]
temporaryPlant2 <- data.frame(freq=temporaryPlant$Freq)
rownames(temporaryPlant2) <- temporaryPlant$Var1
par(mar=c(5.1,12,4.1,2.1))
barplot(t(as.matrix(temporaryPlant2)), beside=TRUE, horiz=T, las=1)