R/SummaryFigures_WithAttributes.R
In R-Burke/SiteSummaryTool: Ecological Site Summaries using Assessment, Inventory, and Monitoring (AIM) and Landscape Monitoring Framework (LMF) data
Defines functions
SummaryFigures_WithAttributes
## Prep species
SummaryFigures_WithAttributes <- function(SpeciesList, Species_plots_ecosite, EcologicalSiteId,
SummaryVar, Interactive, Attributed_Pks, EcoSitePlots){
#Prep
SpeciesList <- SpeciesList %>% dplyr::select(Species, ScientificName, CommonName,
Family, SpeciesState,
SynonymOf, UpdatedSpeciesCode) %>%
dplyr::mutate(link = paste("https://plants.sc.egov.usda.gov/core/profile?symbol=", Species, sep = ""))
#Merge with species list so we can hover for scientific name
Species_plots_ecosite_attributed <- merge(Species_plots_ecosite, Attributed_Pks, by = "PrimaryKey", all = TRUE) %>%
unique()
EcoSitePlots_Attributed <- merge(EcoSitePlots, Attributed_Pks, by = "PrimaryKey", all = TRUE)
#Unhardcode last 3 columns in selection
Species_plots_ecosite_attributed <- merge(Species_plots_ecosite_attributed , SpeciesList , by = c("Species" , "SpeciesState")) %>%
dplyr::select(Species, ScientificName, CommonName, PrimaryKey,
PlotID, AH_SpeciesCover,
AH_SpeciesCover_n, Hgt_Species_Avg,
Hgt_Species_Avg_n, GrowthHabit, GrowthHabitSub, Duration,
Noxious, SG_Group, link,
ALLOT_NAME, ALLOT_NO) %>%
dplyr::mutate_if(is.numeric, round , digits = 2)
#Get Noxious versus Non in Standard Format
Species_plots_ecosite_attributed$Noxious <- gsub("YES" , "Yes", Species_plots_ecosite_attributed$Noxious)
Species_plots_ecosite_attributed$Noxious <- gsub("NO", "No", Species_plots_ecosite_attributed$Noxious)
#Ignoring NAs- make disclosure as this may overestimate cover
#For summarizing across all plots
Species_cover_summary <- Species_plots_ecosite_attributed %>% filter(!is.na(AH_SpeciesCover)) %>%
mutate(Tally = 1) %>%
group_by(Species , GrowthHabit , GrowthHabitSub ,
Duration , Noxious , ScientificName ,
CommonName , SG_Group, link) %>%
summarize(AveragePercentCover = mean(AH_SpeciesCover) ,
StandardDeviation = sd(AH_SpeciesCover),
MinCover = min(AH_SpeciesCover) ,
MaxCover = max(AH_SpeciesCover) , n = sum(Tally)) %>%
mutate_if(is.numeric, round , digits = 2) %>%
dplyr::select(Species, ScientificName,
AveragePercentCover, StandardDeviation,
MinCover, MaxCover, n, GrowthHabit,
GrowthHabitSub, Duration,
Noxious, CommonName, SG_Group, link)
##Setting color palette for plot
NoxNonPal_Fill <- c("grey75" , "#D55E00")
NoxNonPal_Dot <- c("grey33" , "#993300")
## Setting color for attribute title
## FIgure out how to not hardcode ALLOT_NAME and instead use attribute_title
Attribute_Fill <- scales::seq_gradient_pal("#009966", "#E69F00", "Lab")(seq(0,1, length.out = length(unique(Species_plots_ecosite_attributed$ALLOT_NAME))))
#Remove NAs for plotting
Species_plots_ecosite_attributed <- Species_plots_ecosite_attributed %>% filter(!is.na(AH_SpeciesCover))
if(SummaryVar == "GrowthHabitSub"){
if(Interactive){
Plots <- lapply(X = split(Species_plots_ecosite_attributed, Species_plots_ecosite_attributed[["GrowthHabitSub"]] ,
drop = TRUE),
FUN = function(Species_plots_ecosite_attributed){
current_plot <- ggplot2::ggplot(Species_plots_ecosite_attributed ,
aes(x = GrowthHabitSub,
y = AH_SpeciesCover,
text = paste("Primary Key: " , PrimaryKey ,
"Plot ID: " , PlotID , "Species: " ,
ScientificName , "Code: " , Species ,
"Percent Cover: " , AH_SpeciesCover ,
"Noxious: " , Noxious ,
"Allotment: ", ALLOT_NAME,
sep = "<br>"))) +
geom_boxplot(width = .6 , outlier.shape = NA) +
geom_jitter(width = .2 , size = 2 , shape = 21) +
theme_light() +
scale_y_continuous(limits = c(0 , 100)) +
theme(axis.text.y = element_blank() , axis.ticks.y = element_blank() ,
axis.title.y = element_blank() , axis.title.x = element_blank() ,
axis.line.y = element_blank()) + theme(panel.grid.major.y = element_blank() ,
axis.title.y = element_blank()) +
ggtitle(paste0("Percent Cover by Functional Group: " ,
Species_plots_ecosite_attributed$GrowthHabitSub,
toString(EcologicalSiteId), sep = " ")) +
coord_flip() + facet_grid(cols = vars(GrowthHabitSub) ,
rows = vars(Duration) ,
switch = "y" ,
scales = "free" , drop = TRUE)
return(current_plot)
}
)
}
if(!Interactive){
Plots <- lapply(X = split(Species_plots_ecosite_attributed, Species_plots_ecosite_attributed[["GrowthHabitSub"]] , drop = TRUE),
FUN = function(Species_plots_ecosite_attributed){
current_plot <- ggplot2::ggplot(Species_plots_ecosite_attributed , aes(x = GrowthHabitSub , y = AH_SpeciesCover)) +
geom_boxplot(width = .6 , outlier.shape = NA) +
geom_jitter(width = .2 , size = 2, aes(color = ALLOT_NAME, shape = Noxious)) +
scale_color_manual(values = Attribute_Fill, na.value="#000000") +
labs(y = "Percent Cover",
caption = paste("Percent cover in: ", toString(EcologicalSiteId))) +
scale_y_continuous(limits = c(0 , 100)) +
theme_light() +
theme(axis.text.y = element_blank() , axis.ticks.y = element_blank() ,
axis.line.y = element_blank()) + theme(panel.grid.major.y = element_blank() ,
axis.title.y = element_blank()) +
ggtitle(paste("Percent Cover by Functional Group:",
Species_plots_ecosite_attributed$GrowthHabitSub,
toString(EcologicalSiteId), sep = " ")) +
coord_flip() + facet_grid(cols = vars(GrowthHabitSub) ,
rows = vars(Duration) , switch = "y" ,
scales = "free" , drop = TRUE)
return(current_plot)
})
}
}
if(SummaryVar == "Noxious"){
if(Interactive){
Plots <- Species_plots_ecosite_attributed %>% group_by(Noxious) %>%
filter(!is.na(Noxious)) %>% filter(!is.na(AH_SpeciesCover)) %>%
ggplot2::ggplot((aes(x = Noxious , y = AH_SpeciesCover ,
text = paste("Primary Key : " , PrimaryKey,
"Plot ID: " , PlotID ,
"Species: " , ScientificName,
"Code: " , Species,
"Percent Cover: " , AH_SpeciesCover,
"Noxious: " , Noxious ,
"Allotment: ", ALLOT_NAME,
sep = "<br>")))) +
geom_boxplot(width = .6 , outlier.shape = NA) +
geom_jitter(width = .15 , size = 2 , shape = 21) +
theme_light() +
scale_y_continuous(limits = c(0 , 100)) +
labs(y = "Percent Cover") +
ggtitle(paste("Percent Cover, Noxious vs. Non-Noxious Species: " ,
toString(EcologicalSiteId))) +
theme(axis.title.y = element_blank() , axis.text.y = element_blank() ,
axis.ticks.y = element_blank() , axis.line.y = element_blank() ,
axis.title.x = element_blank()) +
theme(panel.grid.major.y = element_blank() , legend.position = "none") +
coord_flip() +
facet_grid(rows = vars(Noxious) , switch = "y" , scales = "free" ,
drop = TRUE)
return(Plots)
}
if(!Interactive){
Plots <- Species_plots_ecosite_attributed %>% group_by(Noxious) %>%
filter(!is.na(Noxious)) %>% filter(!is.na(AH_SpeciesCover)) %>%
ggplot2::ggplot((aes(x = Noxious , y = AH_SpeciesCover))) +
geom_boxplot(width = .6 , outlier.shape = NA) +
geom_jitter(width = .15 , size = 2 , aes(color = ALLOT_NAME, shape = Noxious)) +
scale_color_manual(values = Attribute_Fill, na.value="#000000") +
theme_light() +
scale_y_continuous(limits = c(0 , 100)) +
labs(y = "Percent Cover") +
ggtitle(paste("Percent Cover, Noxious vs. Non-Noxious Species: " ,
toString(EcologicalSiteId))) +
theme(axis.title.y = element_blank() , axis.text.y = element_blank() ,
axis.ticks.y = element_blank() ,
axis.line.y = element_blank() ,
panel.grid.major.y = element_blank()) +
coord_flip() +
facet_grid(rows = vars(Noxious) ,
switch = "y" , scales = "free" , drop = TRUE)
}}
if(SummaryVar == "Species"){
PercentCover <- Species_plots_ecosite_attributed %>% subset(AH_SpeciesCover > 0.000000)
if(Interactive){
Plots <-lapply(X = split(PercentCover, list(PercentCover$GrowthHabitSub , PercentCover$Duration) , drop = TRUE),
FUN = function(PercentCover){
current_plot <- ggplot2::ggplot(PercentCover , aes(x = Species , y = AH_SpeciesCover,
text = paste("PrimaryKey: ", PrimaryKey ,
"Plot ID: " , PlotID , "Species: " ,
ScientificName , "Code: " , Species ,
"Percent Cover: " , AH_SpeciesCover , "Noxious: " ,
Noxious ,
"Allotment: ", ALLOT_NAME,
sep = "<br>"))) +
geom_boxplot(width = .6 , outlier.shape = NA) +
geom_jitter(width = .15 , size = 1, shape = 21) +
scale_y_continuous(limits = c(0 , 100)) +
theme_light() +
labs(y = "Percent Cover") +
ggtitle(paste("Percent Cover by Species, " ,
PercentCover$GrowthHabitSub,
PercentCover$Duration ,
toString(EcologicalSiteId))) +
theme(axis.title.y = element_blank() ,
axis.text.y = element_blank(),
axis.ticks.y = element_blank(),
axis.title.x = element_blank())+
theme(panel.grid.major.y = element_blank() ,
axis.title.y = element_blank()) +
coord_flip() + facet_grid(rows = vars(Species),
scales = "free" , switch = "y", drop = TRUE)
return(current_plot)
})
}
if(!Interactive){
Plots <- lapply(X = split(PercentCover, list(PercentCover$GrowthHabitSub ,
PercentCover$Duration) ,
drop = TRUE),
FUN = function(PercentCover){
current_plot <- ggplot2::ggplot(PercentCover , aes(x = Species , y = AH_SpeciesCover)) +
geom_boxplot(width = .6 , outlier.shape = NA) +
geom_jitter(width = .15 , size = 1 , aes(color = ALLOT_NAME, shape = Noxious)) +
scale_color_manual(values = Attribute_Fill, na.value="#000000") +
scale_y_continuous(limits = c(0 , 100)) +
theme_light() +
labs(y = "Percent Cover") +
ggtitle(paste("Percent Cover by Species, " ,
PercentCover$GrowthHabitSub ,
PercentCover$Duration ,
toString(EcologicalSiteId))) +
theme(axis.title.y = element_blank()) +
coord_flip() + facet_grid(cols = vars(GrowthHabitSub) , rows = vars(Duration) ,
switch = "y" , scales = "free" , drop = TRUE)
return(current_plot)
})
}
}
if(SummaryVar == "GroundCover"){
#Prep
#BareSoilCover
#TotalFoliarCover
#FH_TotalLitterCover
#FH_RockCover
Ground_Cover_Tall <- EcoSitePlots_Attributed %>%
dplyr::select(PlotID, PrimaryKey, BareSoilCover ,
TotalFoliarCover , FH_TotalLitterCover ,
FH_RockCover, ALLOT_NAME, ALLOT_NO) %>%
gather(key = Indicator , value = Percent,
BareSoilCover:FH_RockCover) %>% mutate(Tally = 1)
if(Interactive){
Plots <- Ground_Cover_Tall %>% mutate_if(is.numeric , round , digits = 2) %>%
ggplot2::ggplot((aes(x = Indicator , y = Percent ,
text = paste("PlotID: " , PlotID ,
"PrimaryKey: " , PrimaryKey ,
"Indicator: " , Indicator ,
"Percent Cover: " , Percent ,
"Allotment: ", ALLOT_NAME,
sep = "<br>" )))) +
geom_boxplot(width = .6 , outlier.shape = NA) +
geom_jitter(width = .15 , shape = 21) +
theme_light() +
scale_y_continuous(limits = c(0 , 100)) +
labs(y = "Ground Cover (%)" , x = "Indicator") +
theme(axis.text.y = element_blank() ,
axis.ticks.y = element_blank() ,
axis.line.y = element_blank() ,
axis.title.x = element_blank() ,
axis.title.y = element_blank()) +
coord_flip() + facet_grid(rows = vars(Indicator) ,
switch = "y" ,
scales = "free_y" , drop = TRUE)
}
if(!Interactive){
Plots <- Ground_Cover_Tall %>% mutate_if(is.numeric , round , digits = 2) %>%
ggplot2::ggplot((aes(x = Indicator , y = Percent))) +
geom_boxplot(width = .6 , outlier.shape = NA) +
geom_jitter(width = .15, aes(color = ALLOT_NAME)) +
theme_light() +
scale_color_manual(values = Attribute_Fill, na.value="#000000") +
scale_y_continuous(limits = c(0 , 100)) +
labs(y = "Ground Cover (%)" , x = "Indicator") +
theme(axis.text.y = element_blank() ,
axis.ticks.y = element_blank() ,
axis.line.y = element_blank()) +
coord_flip() + facet_grid(rows = vars(Indicator) ,
switch = "y" ,
scales = "free_y" , drop = TRUE)
}
}
if(SummaryVar == "Gap"){
Gap <- EcoSitePlots_Attributed %>% dplyr::select(PlotID , PrimaryKey ,
GapCover_25_50 , GapCover_51_100 ,
GapCover_101_200 , GapCover_200_plus ,
GapCover_25_plus, ALLOT_NAME, ALLOT_NO) %>%
gather(key = Gap_Class_cm ,
value = Percent , GapCover_25_50:GapCover_25_plus) %>%
mutate_if(is.numeric , round, digits = 2)
#Plot prep
if(Interactive){
Plots <- ggplot2::ggplot(data = Gap , aes(x = Gap_Class_cm , y = Percent ,
text = paste("PlotID: " , PlotID ,
"PrimaryKey: ", PrimaryKey ,
"Gap Class (cm): " , Gap_Class_cm,
"Percent Cover: " , Percent ,
"Allotment: ", ALLOT_NAME,
sep = "<br>"))) +
geom_boxplot() + coord_flip() +
geom_jitter(width = 0.1 , shape = 21) +
theme_light() +
theme(axis.title.x = element_blank() ,
axis.text.y = element_blank() ,
axis.ticks.y = element_blank() ,
axis.title.y = element_blank() ,
axis.line.y = element_blank(),
panel.grid.major.y = element_blank()) +
facet_grid(rows = vars(Gap_Class_cm) , switch = "y" ,
scales = "free_y" , drop = TRUE)
}
if(!Interactive){
Plots <- ggplot2::ggplot(data = Gap , aes(x = Gap_Class_cm , y = Percent)) +
labs(y = "Percent Cover" , x = "Gap Size Class (cm)",
caption = paste("Percent cover of canopy gap in: ",
toString(EcologicalSiteId))) +
geom_boxplot() +
coord_flip() +
geom_jitter(width = 0.1, aes(color = ALLOT_NAME)) +
theme_light() +
scale_color_manual(values = Attribute_Fill, na.value="#000000") +
theme(axis.text.y = element_blank() ,
axis.ticks.y = element_blank() ,
axis.line.y = element_blank(),
panel.grid.major.y = element_blank()) +
facet_grid(rows = vars(Gap_Class_cm) , switch = "y" ,
scales = "free_y" , drop = TRUE)
}
}
if(SummaryVar == "SoilStability"){
soil_labels <- c("SoilStability_All" = "All" , "SoilStability_Protected" = "Protected" ,
"SoilStability_Unprotected" = "Unprotected")
SoilStability <- EcoSitePlots_Attributed %>% dplyr::select(PlotID , PrimaryKey ,
SoilStability_All ,
SoilStability_Protected ,
SoilStability_Unprotected,
ALLOT_NAME,
ALLOT_NO) %>%
gather(key = Veg , value = Rating ,
SoilStability_All:SoilStability_Unprotected) %>%
mutate_if(is.numeric, round, digits = 2)
if(Interactive){
Plots <- ggplot2::ggplot(data = SoilStability ,
aes(x = Veg , y = Rating ,
text = paste("Primary Key: " , PrimaryKey,
"Plot ID: " , PlotID ,
"Rating: " , Rating ,
"Allotment: ", ALLOT_NAME,
sep = "<br>"))) +
geom_boxplot() +
coord_flip() +
geom_jitter(width = 0.1 , shape = 21) +
theme_light() +
theme(axis.text.y = element_blank() ,
axis.ticks.y = element_blank() ,
axis.line.y = element_blank(),
panel.grid.major.y = element_blank(),
axis.title = element_blank()) +
facet_grid(rows = vars(Veg) , switch = "y" ,
scales = "free_y" , drop = TRUE ,
labeller = as_labeller(soil_labels))
}
if(!Interactive){
Plots <- ggplot2::ggplot(data = SoilStability ,
aes(x = Veg , y = Rating)) +
labs(x = "Vegetation cover class" ,
y = "Soil Stability Rating",
caption = paste("Soil stability ratings in: ",
toString(EcologicalSiteId))) +
geom_boxplot() + coord_flip() + geom_jitter(width = 0.1, aes(color = ALLOT_NAME)) +
theme_light() +
scale_color_manual(values = Attribute_Fill, na.value="#000000") +
theme(axis.text.y = element_blank() ,
axis.ticks.y = element_blank() ,
axis.line.y = element_blank(),
panel.grid.major.y = element_blank()) +
facet_grid(rows = vars(Veg) ,
switch = "y" ,
scales = "free_y" ,
drop = TRUE ,
labeller = as_labeller(soil_labels))
}
}
return(Plots)
}
R-Burke/SiteSummaryTool documentation built on Oct. 15, 2020, 8:21 p.m.
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Defines functions SummaryFigures_WithAttributes
## Prep species
SummaryFigures_WithAttributes <- function(SpeciesList, Species_plots_ecosite, EcologicalSiteId,
SummaryVar, Interactive, Attributed_Pks, EcoSitePlots){
#Prep
SpeciesList <- SpeciesList %>% dplyr::select(Species, ScientificName, CommonName,
Family, SpeciesState,
SynonymOf, UpdatedSpeciesCode) %>%
dplyr::mutate(link = paste("https://plants.sc.egov.usda.gov/core/profile?symbol=", Species, sep = ""))
#Merge with species list so we can hover for scientific name
Species_plots_ecosite_attributed <- merge(Species_plots_ecosite, Attributed_Pks, by = "PrimaryKey", all = TRUE) %>%
unique()
EcoSitePlots_Attributed <- merge(EcoSitePlots, Attributed_Pks, by = "PrimaryKey", all = TRUE)
#Unhardcode last 3 columns in selection
Species_plots_ecosite_attributed <- merge(Species_plots_ecosite_attributed , SpeciesList , by = c("Species" , "SpeciesState")) %>%
dplyr::select(Species, ScientificName, CommonName, PrimaryKey,
PlotID, AH_SpeciesCover,
AH_SpeciesCover_n, Hgt_Species_Avg,
Hgt_Species_Avg_n, GrowthHabit, GrowthHabitSub, Duration,
Noxious, SG_Group, link,
ALLOT_NAME, ALLOT_NO) %>%
dplyr::mutate_if(is.numeric, round , digits = 2)
#Get Noxious versus Non in Standard Format
Species_plots_ecosite_attributed$Noxious <- gsub("YES" , "Yes", Species_plots_ecosite_attributed$Noxious)
Species_plots_ecosite_attributed$Noxious <- gsub("NO", "No", Species_plots_ecosite_attributed$Noxious)
#Ignoring NAs- make disclosure as this may overestimate cover
#For summarizing across all plots
Species_cover_summary <- Species_plots_ecosite_attributed %>% filter(!is.na(AH_SpeciesCover)) %>%
mutate(Tally = 1) %>%
group_by(Species , GrowthHabit , GrowthHabitSub ,
Duration , Noxious , ScientificName ,
CommonName , SG_Group, link) %>%
summarize(AveragePercentCover = mean(AH_SpeciesCover) ,
StandardDeviation = sd(AH_SpeciesCover),
MinCover = min(AH_SpeciesCover) ,
MaxCover = max(AH_SpeciesCover) , n = sum(Tally)) %>%
mutate_if(is.numeric, round , digits = 2) %>%
dplyr::select(Species, ScientificName,
AveragePercentCover, StandardDeviation,
MinCover, MaxCover, n, GrowthHabit,
GrowthHabitSub, Duration,
Noxious, CommonName, SG_Group, link)
##Setting color palette for plot
NoxNonPal_Fill <- c("grey75" , "#D55E00")
NoxNonPal_Dot <- c("grey33" , "#993300")
## Setting color for attribute title
## FIgure out how to not hardcode ALLOT_NAME and instead use attribute_title
Attribute_Fill <- scales::seq_gradient_pal("#009966", "#E69F00", "Lab")(seq(0,1, length.out = length(unique(Species_plots_ecosite_attributed$ALLOT_NAME))))
#Remove NAs for plotting
Species_plots_ecosite_attributed <- Species_plots_ecosite_attributed %>% filter(!is.na(AH_SpeciesCover))
if(SummaryVar == "GrowthHabitSub"){
if(Interactive){
Plots <- lapply(X = split(Species_plots_ecosite_attributed, Species_plots_ecosite_attributed[["GrowthHabitSub"]] ,
drop = TRUE),
FUN = function(Species_plots_ecosite_attributed){
current_plot <- ggplot2::ggplot(Species_plots_ecosite_attributed ,
aes(x = GrowthHabitSub,
y = AH_SpeciesCover,
text = paste("Primary Key: " , PrimaryKey ,
"Plot ID: " , PlotID , "Species: " ,
ScientificName , "Code: " , Species ,
"Percent Cover: " , AH_SpeciesCover ,
"Noxious: " , Noxious ,
"Allotment: ", ALLOT_NAME,
sep = "<br>"))) +
geom_boxplot(width = .6 , outlier.shape = NA) +
geom_jitter(width = .2 , size = 2 , shape = 21) +
theme_light() +
scale_y_continuous(limits = c(0 , 100)) +
theme(axis.text.y = element_blank() , axis.ticks.y = element_blank() ,
axis.title.y = element_blank() , axis.title.x = element_blank() ,
axis.line.y = element_blank()) + theme(panel.grid.major.y = element_blank() ,
axis.title.y = element_blank()) +
ggtitle(paste0("Percent Cover by Functional Group: " ,
Species_plots_ecosite_attributed$GrowthHabitSub,
toString(EcologicalSiteId), sep = " ")) +
coord_flip() + facet_grid(cols = vars(GrowthHabitSub) ,
rows = vars(Duration) ,
switch = "y" ,
scales = "free" , drop = TRUE)
return(current_plot)
}
)
}
if(!Interactive){
Plots <- lapply(X = split(Species_plots_ecosite_attributed, Species_plots_ecosite_attributed[["GrowthHabitSub"]] , drop = TRUE),
FUN = function(Species_plots_ecosite_attributed){
current_plot <- ggplot2::ggplot(Species_plots_ecosite_attributed , aes(x = GrowthHabitSub , y = AH_SpeciesCover)) +
geom_boxplot(width = .6 , outlier.shape = NA) +
geom_jitter(width = .2 , size = 2, aes(color = ALLOT_NAME, shape = Noxious)) +
scale_color_manual(values = Attribute_Fill, na.value="#000000") +
labs(y = "Percent Cover",
caption = paste("Percent cover in: ", toString(EcologicalSiteId))) +
scale_y_continuous(limits = c(0 , 100)) +
theme_light() +
theme(axis.text.y = element_blank() , axis.ticks.y = element_blank() ,
axis.line.y = element_blank()) + theme(panel.grid.major.y = element_blank() ,
axis.title.y = element_blank()) +
ggtitle(paste("Percent Cover by Functional Group:",
Species_plots_ecosite_attributed$GrowthHabitSub,
toString(EcologicalSiteId), sep = " ")) +
coord_flip() + facet_grid(cols = vars(GrowthHabitSub) ,
rows = vars(Duration) , switch = "y" ,
scales = "free" , drop = TRUE)
return(current_plot)
})
}
}
if(SummaryVar == "Noxious"){
if(Interactive){
Plots <- Species_plots_ecosite_attributed %>% group_by(Noxious) %>%
filter(!is.na(Noxious)) %>% filter(!is.na(AH_SpeciesCover)) %>%
ggplot2::ggplot((aes(x = Noxious , y = AH_SpeciesCover ,
text = paste("Primary Key : " , PrimaryKey,
"Plot ID: " , PlotID ,
"Species: " , ScientificName,
"Code: " , Species,
"Percent Cover: " , AH_SpeciesCover,
"Noxious: " , Noxious ,
"Allotment: ", ALLOT_NAME,
sep = "<br>")))) +
geom_boxplot(width = .6 , outlier.shape = NA) +
geom_jitter(width = .15 , size = 2 , shape = 21) +
theme_light() +
scale_y_continuous(limits = c(0 , 100)) +
labs(y = "Percent Cover") +
ggtitle(paste("Percent Cover, Noxious vs. Non-Noxious Species: " ,
toString(EcologicalSiteId))) +
theme(axis.title.y = element_blank() , axis.text.y = element_blank() ,
axis.ticks.y = element_blank() , axis.line.y = element_blank() ,
axis.title.x = element_blank()) +
theme(panel.grid.major.y = element_blank() , legend.position = "none") +
coord_flip() +
facet_grid(rows = vars(Noxious) , switch = "y" , scales = "free" ,
drop = TRUE)
return(Plots)
}
if(!Interactive){
Plots <- Species_plots_ecosite_attributed %>% group_by(Noxious) %>%
filter(!is.na(Noxious)) %>% filter(!is.na(AH_SpeciesCover)) %>%
ggplot2::ggplot((aes(x = Noxious , y = AH_SpeciesCover))) +
geom_boxplot(width = .6 , outlier.shape = NA) +
geom_jitter(width = .15 , size = 2 , aes(color = ALLOT_NAME, shape = Noxious)) +
scale_color_manual(values = Attribute_Fill, na.value="#000000") +
theme_light() +
scale_y_continuous(limits = c(0 , 100)) +
labs(y = "Percent Cover") +
ggtitle(paste("Percent Cover, Noxious vs. Non-Noxious Species: " ,
toString(EcologicalSiteId))) +
theme(axis.title.y = element_blank() , axis.text.y = element_blank() ,
axis.ticks.y = element_blank() ,
axis.line.y = element_blank() ,
panel.grid.major.y = element_blank()) +
coord_flip() +
facet_grid(rows = vars(Noxious) ,
switch = "y" , scales = "free" , drop = TRUE)
}}
if(SummaryVar == "Species"){
PercentCover <- Species_plots_ecosite_attributed %>% subset(AH_SpeciesCover > 0.000000)
if(Interactive){
Plots <-lapply(X = split(PercentCover, list(PercentCover$GrowthHabitSub , PercentCover$Duration) , drop = TRUE),
FUN = function(PercentCover){
current_plot <- ggplot2::ggplot(PercentCover , aes(x = Species , y = AH_SpeciesCover,
text = paste("PrimaryKey: ", PrimaryKey ,
"Plot ID: " , PlotID , "Species: " ,
ScientificName , "Code: " , Species ,
"Percent Cover: " , AH_SpeciesCover , "Noxious: " ,
Noxious ,
"Allotment: ", ALLOT_NAME,
sep = "<br>"))) +
geom_boxplot(width = .6 , outlier.shape = NA) +
geom_jitter(width = .15 , size = 1, shape = 21) +
scale_y_continuous(limits = c(0 , 100)) +
theme_light() +
labs(y = "Percent Cover") +
ggtitle(paste("Percent Cover by Species, " ,
PercentCover$GrowthHabitSub,
PercentCover$Duration ,
toString(EcologicalSiteId))) +
theme(axis.title.y = element_blank() ,
axis.text.y = element_blank(),
axis.ticks.y = element_blank(),
axis.title.x = element_blank())+
theme(panel.grid.major.y = element_blank() ,
axis.title.y = element_blank()) +
coord_flip() + facet_grid(rows = vars(Species),
scales = "free" , switch = "y", drop = TRUE)
return(current_plot)
})
}
if(!Interactive){
Plots <- lapply(X = split(PercentCover, list(PercentCover$GrowthHabitSub ,
PercentCover$Duration) ,
drop = TRUE),
FUN = function(PercentCover){
current_plot <- ggplot2::ggplot(PercentCover , aes(x = Species , y = AH_SpeciesCover)) +
geom_boxplot(width = .6 , outlier.shape = NA) +
geom_jitter(width = .15 , size = 1 , aes(color = ALLOT_NAME, shape = Noxious)) +
scale_color_manual(values = Attribute_Fill, na.value="#000000") +
scale_y_continuous(limits = c(0 , 100)) +
theme_light() +
labs(y = "Percent Cover") +
ggtitle(paste("Percent Cover by Species, " ,
PercentCover$GrowthHabitSub ,
PercentCover$Duration ,
toString(EcologicalSiteId))) +
theme(axis.title.y = element_blank()) +
coord_flip() + facet_grid(cols = vars(GrowthHabitSub) , rows = vars(Duration) ,
switch = "y" , scales = "free" , drop = TRUE)
return(current_plot)
})
}
}
if(SummaryVar == "GroundCover"){
#Prep
#BareSoilCover
#TotalFoliarCover
#FH_TotalLitterCover
#FH_RockCover
Ground_Cover_Tall <- EcoSitePlots_Attributed %>%
dplyr::select(PlotID, PrimaryKey, BareSoilCover ,
TotalFoliarCover , FH_TotalLitterCover ,
FH_RockCover, ALLOT_NAME, ALLOT_NO) %>%
gather(key = Indicator , value = Percent,
BareSoilCover:FH_RockCover) %>% mutate(Tally = 1)
if(Interactive){
Plots <- Ground_Cover_Tall %>% mutate_if(is.numeric , round , digits = 2) %>%
ggplot2::ggplot((aes(x = Indicator , y = Percent ,
text = paste("PlotID: " , PlotID ,
"PrimaryKey: " , PrimaryKey ,
"Indicator: " , Indicator ,
"Percent Cover: " , Percent ,
"Allotment: ", ALLOT_NAME,
sep = "<br>" )))) +
geom_boxplot(width = .6 , outlier.shape = NA) +
geom_jitter(width = .15 , shape = 21) +
theme_light() +
scale_y_continuous(limits = c(0 , 100)) +
labs(y = "Ground Cover (%)" , x = "Indicator") +
theme(axis.text.y = element_blank() ,
axis.ticks.y = element_blank() ,
axis.line.y = element_blank() ,
axis.title.x = element_blank() ,
axis.title.y = element_blank()) +
coord_flip() + facet_grid(rows = vars(Indicator) ,
switch = "y" ,
scales = "free_y" , drop = TRUE)
}
if(!Interactive){
Plots <- Ground_Cover_Tall %>% mutate_if(is.numeric , round , digits = 2) %>%
ggplot2::ggplot((aes(x = Indicator , y = Percent))) +
geom_boxplot(width = .6 , outlier.shape = NA) +
geom_jitter(width = .15, aes(color = ALLOT_NAME)) +
theme_light() +
scale_color_manual(values = Attribute_Fill, na.value="#000000") +
scale_y_continuous(limits = c(0 , 100)) +
labs(y = "Ground Cover (%)" , x = "Indicator") +
theme(axis.text.y = element_blank() ,
axis.ticks.y = element_blank() ,
axis.line.y = element_blank()) +
coord_flip() + facet_grid(rows = vars(Indicator) ,
switch = "y" ,
scales = "free_y" , drop = TRUE)
}
}
if(SummaryVar == "Gap"){
Gap <- EcoSitePlots_Attributed %>% dplyr::select(PlotID , PrimaryKey ,
GapCover_25_50 , GapCover_51_100 ,
GapCover_101_200 , GapCover_200_plus ,
GapCover_25_plus, ALLOT_NAME, ALLOT_NO) %>%
gather(key = Gap_Class_cm ,
value = Percent , GapCover_25_50:GapCover_25_plus) %>%
mutate_if(is.numeric , round, digits = 2)
#Plot prep
if(Interactive){
Plots <- ggplot2::ggplot(data = Gap , aes(x = Gap_Class_cm , y = Percent ,
text = paste("PlotID: " , PlotID ,
"PrimaryKey: ", PrimaryKey ,
"Gap Class (cm): " , Gap_Class_cm,
"Percent Cover: " , Percent ,
"Allotment: ", ALLOT_NAME,
sep = "<br>"))) +
geom_boxplot() + coord_flip() +
geom_jitter(width = 0.1 , shape = 21) +
theme_light() +
theme(axis.title.x = element_blank() ,
axis.text.y = element_blank() ,
axis.ticks.y = element_blank() ,
axis.title.y = element_blank() ,
axis.line.y = element_blank(),
panel.grid.major.y = element_blank()) +
facet_grid(rows = vars(Gap_Class_cm) , switch = "y" ,
scales = "free_y" , drop = TRUE)
}
if(!Interactive){
Plots <- ggplot2::ggplot(data = Gap , aes(x = Gap_Class_cm , y = Percent)) +
labs(y = "Percent Cover" , x = "Gap Size Class (cm)",
caption = paste("Percent cover of canopy gap in: ",
toString(EcologicalSiteId))) +
geom_boxplot() +
coord_flip() +
geom_jitter(width = 0.1, aes(color = ALLOT_NAME)) +
theme_light() +
scale_color_manual(values = Attribute_Fill, na.value="#000000") +
theme(axis.text.y = element_blank() ,
axis.ticks.y = element_blank() ,
axis.line.y = element_blank(),
panel.grid.major.y = element_blank()) +
facet_grid(rows = vars(Gap_Class_cm) , switch = "y" ,
scales = "free_y" , drop = TRUE)
}
}
if(SummaryVar == "SoilStability"){
soil_labels <- c("SoilStability_All" = "All" , "SoilStability_Protected" = "Protected" ,
"SoilStability_Unprotected" = "Unprotected")
SoilStability <- EcoSitePlots_Attributed %>% dplyr::select(PlotID , PrimaryKey ,
SoilStability_All ,
SoilStability_Protected ,
SoilStability_Unprotected,
ALLOT_NAME,
ALLOT_NO) %>%
gather(key = Veg , value = Rating ,
SoilStability_All:SoilStability_Unprotected) %>%
mutate_if(is.numeric, round, digits = 2)
if(Interactive){
Plots <- ggplot2::ggplot(data = SoilStability ,
aes(x = Veg , y = Rating ,
text = paste("Primary Key: " , PrimaryKey,
"Plot ID: " , PlotID ,
"Rating: " , Rating ,
"Allotment: ", ALLOT_NAME,
sep = "<br>"))) +
geom_boxplot() +
coord_flip() +
geom_jitter(width = 0.1 , shape = 21) +
theme_light() +
theme(axis.text.y = element_blank() ,
axis.ticks.y = element_blank() ,
axis.line.y = element_blank(),
panel.grid.major.y = element_blank(),
axis.title = element_blank()) +
facet_grid(rows = vars(Veg) , switch = "y" ,
scales = "free_y" , drop = TRUE ,
labeller = as_labeller(soil_labels))
}
if(!Interactive){
Plots <- ggplot2::ggplot(data = SoilStability ,
aes(x = Veg , y = Rating)) +
labs(x = "Vegetation cover class" ,
y = "Soil Stability Rating",
caption = paste("Soil stability ratings in: ",
toString(EcologicalSiteId))) +
geom_boxplot() + coord_flip() + geom_jitter(width = 0.1, aes(color = ALLOT_NAME)) +
theme_light() +
scale_color_manual(values = Attribute_Fill, na.value="#000000") +
theme(axis.text.y = element_blank() ,
axis.ticks.y = element_blank() ,
axis.line.y = element_blank(),
panel.grid.major.y = element_blank()) +
facet_grid(rows = vars(Veg) ,
switch = "y" ,
scales = "free_y" ,
drop = TRUE ,
labeller = as_labeller(soil_labels))
}
}
return(Plots)
}
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