SummaryFigures_Height: SummaryFigures_Height

In R-Burke/SiteSummaryTool: Ecological Site Summaries using Assessment, Inventory, and Monitoring (AIM) and Landscape Monitoring Framework (LMF) data

Description

Returns a static or interactive (plotly-friendly) ggplot boxplot summarizing species heights across your ecological site(s) based on summary variables (Growth habit, individual species, or sagebrush.)

Usage

SummaryFigures_Height(Species_plots_ecosite, EcologicalSiteId, SummaryVar, GroupBy, Interactive)

Arguments

Species_plots_ecosite	Combined AIM and LMF species indicator, subset to your ecological site(s). Returned output from Combine_AIM_LMF_Species and SubsetEcologicalSite_Species.
EcologicalSiteId	Full ecological site id, list of ecological sites, or object
SummaryVar	"Height""
GroupBy	c("Species", "GrowthHabit", "Sagebrush")
Interactive	logical. If TRUE, boxplot aesthetics will be set up for interactive plotly::ggplotly object. If FALSE, will return static box plot.

Details

If GroupBy == "Species", returns a list of plots that must be called on- boxplots are broken up by GrowthHabitSub, with individual species within each group as faceting row. Y values are height in cm. See example for how to call on plot. If GroupBy == "GrowthHabit", returns a boxplot. X values are growth habit, Y values are height in cm. If GroupBy == "Sagebrush", returns a boxplot. X values are sagebrush species, Y values are height in cm.

Author(s)

Rachel Burke, ecologist/analyst @ Jornada

Examples

# If SummaryVar == "Height", GroupBy == "GrowthHabit", Interactive == TRUE:

plotly::ggplotly(SummaryFigures_Height(Species_plots_ecosite,
                  EcologicalSiteId, SummaryVar = "Height",
                  GroupBy = "GrowthHabit", Interactive = TRUE),
                  tooltip = "text")

# If SummaryVar == "Height", GroupBy == "GrowthHabit", Interactive == FALSE:

SummaryFigures_Height(Species_plots_ecosite, EcologicalSiteId,
                      SummaryVar = "Height", GroupBy = "GrowthHabit",
                      Interactive = FALSE)

# If SummaryVar == "Height", GroupBy == "Species", Interactive == TRUE:

Plots <- SummaryFigures_Height(Species_plots_ecosite,
                               EcologicalSiteId,
                               SummaryVar = "Height",
                               GroupBy = "Species",
                               Interactive = TRUE)

plotly::ggplotly((Plots[["Graminoid.Annual"]]), tooltip = "text")

# If SummaryVar == "Height", GroupBy == "Species", Interactive == FALSE:

Plots <- SummaryFigures_Height(Species_plots_ecosite,
                               EcologicalSiteId,
                               SummaryVar = "Height",
                               GroupBy = "Species",
                               Interactive = FALSE)

Plots[["Graminoid.Annual"]]

## The function is currently defined as
function (Species_plots_ecosite, EcologicalSiteId, SummaryVar,
    GroupBy, Interactive)
{
    NoxNonPal_Fill <- c("grey75", "#D55E00")
    NoxNonPal_Dot <- c("grey33", "#993300")
    HgtPrep <- Species_plots_ecosite %>% filter(!is.na(Hgt_Species_Avg)) %>%
        filter(!is.na(GrowthHabitSub))
    if (SummaryVar == "Height" & GroupBy == "Species") {
        if (Interactive) {
            Plots <- lapply(X = split(HgtPrep, list(HgtPrep$GrowthHabitSub,
                HgtPrep$Duration), drop = TRUE), FUN = function(HgtPrep) {
                current_plot <- ggplot(HgtPrep, aes(x = Species,
                  y = Hgt_Species_Avg, text = paste("Plot Id: ",
                    PlotID, "PrimaryKey: ", PrimaryKey, "Species: ",
                    Species, "Average Height: ", Hgt_Species_Avg,
                    "Average Height , n: ", Hgt_Species_Avg_n,
                    sep = "<br>"))) + geom_boxplot(width = 0.6,
                  outlier.shape = NA) + geom_jitter(width = 0.15,
                  shape = 21) + scale_y_continuous(limits = c(0,
                  100)) + theme_light() + coord_flip() + theme(axis.text.y = element_blank(),
                  axis.ticks.y = element_blank(), axis.line.y = element_blank()) +
                  facet_grid(rows = vars(Species), switch = "y",
                    scales = "free_y", drop = TRUE)
                return(current_plot)
            })
        }
        if (!Interactive) {
            Plots <- lapply(X = split(HgtPrep, list(HgtPrep$GrowthHabitSub,
                HgtPrep$Duration), drop = TRUE), FUN = function(HgtPrep) {
                current_plot <- ggplot(HgtPrep, aes(x = Species,
                  y = Hgt_Species_Avg)) + geom_boxplot(width = 0.6,
                  outlier.shape = NA) + geom_jitter(width = 0.15,
                  size = 1, aes(color = Noxious)) + scale_color_manual(values = NoxNonPal_Dot) +
                  scale_y_continuous(limits = c(0, 100)) + theme_light() +
                  labs(x = "Species", y = "Average Height, cm",
                    caption = paste("Species height in: ", toString(EcologicalSiteId),
                      sep = "")) + theme(axis.text.y = element_blank(),
                  axis.ticks.y = element_blank(), axis.line.y = element_blank()) +
                  coord_flip() + facet_grid(rows = vars(Species),
                  switch = "y", scales = "free_y", drop = TRUE)
                return(current_plot)
            })
        }
    }
    if (SummaryVar == "Height" & GroupBy == "GrowthHabit") {
        if (Interactive) {
            Plots <- ggplot(HgtPrep, aes(x = GrowthHabit, y = Hgt_Species_Avg,
                text = paste("Plot Id: ", PlotID, "PrimaryKey: ",
                  PrimaryKey, "Species: ", Species, "Average Height (cm): ",
                  Hgt_Species_Avg, "Average Height , n: ", Hgt_Species_Avg_n,
                  sep = "<br>"))) + geom_boxplot() + geom_jitter(width = 0.1,
                shape = 21) + theme_light() + theme(axis.ticks.y = element_blank(),
                axis.line.y = element_blank(), axis.title.y = element_blank(),
                axis.title.x = element_blank(), axis.text.y = element_blank()) +
                coord_flip() + facet_grid(rows = vars(GrowthHabitSub),
                switch = "y", scales = "free_y", drop = TRUE)
        }
        if (!Interactive) {
            Plots <- ggplot(HgtPrep, aes(x = GrowthHabit, y = Hgt_Species_Avg)) +
                geom_boxplot() + geom_jitter(width = 0.2, aes(text = PlotID)) +
                labs(x = "Growth Habit", y = "Average Height, cm",
                  caption = paste("Species height in: ", toString(EcologicalSiteId),
                    sep = "")) + theme_light() + theme(axis.text.y = element_blank(),
                axis.ticks.y = element_blank(), axis.line.y = element_blank()) +
                coord_flip() + facet_grid(rows = vars(GrowthHabitSub),
                switch = "y", scales = "free_y", drop = TRUE)
        }
    }
    if (SummaryVar == "Height" & GroupBy == "Sagebrush") {
        Sagebrush <- HgtPrep %>% subset(SG_Group == "Sagebrush")
        if (nrow(Sagebrush) < 1) {
            Plots <- NULL
        }
        else {
            if (Interactive) {
                Plots <- ggplot(Sagebrush, aes(x = Species, y = Hgt_Species_Avg,
                  text = paste("Plot Id: ", PlotID, "PrimaryKey: ",
                    PrimaryKey, "Species: ", Species, "Average Height (cm): ",
                    Hgt_Species_Avg, "Average Height , n: ",
                    Hgt_Species_Avg_n, sep = "<br>"))) + geom_boxplot() +
                  geom_jitter(width = 0.1, shape = 21) + theme_light() +
                  theme(axis.ticks.y = element_blank(), axis.line.y = element_blank(),
                    axis.title.y = element_blank(), axis.title.x = element_blank(),
                    axis.text.y = element_blank()) + facet_grid(rows = vars(Species),
                  scales = "free_y", drop = TRUE) + coord_flip()
            }
            if (!Interactive) {
                Plots <- ggplot(Sagebrush, aes(x = Species, y = Hgt_Species_Avg)) +
                  geom_boxplot() + geom_jitter(width = 0.1, shape = 21) +
                  theme_light() + theme(axis.ticks.y = element_blank(),
                  axis.line.y = element_blank()) + labs(x = "Species",
                  y = "Average Height, cm", caption = paste("Species height in: ",
                    toString(EcologicalSiteId), sep = "")) +
                  coord_flip()
            }
        }
    }
    return(Plots)
  }

R-Burke/SiteSummaryTool documentation built on Oct. 15, 2020, 8:21 p.m.