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present.qmd
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---
title: "Present"
---
```{r include=FALSE, echo=FALSE, message=FALSE, warning=FALSE}
library(tidyverse)
library("png")
library("patchwork")
```
LANDFIRE's [Existing Vegetation Type, Cover and Height](https://landfire.gov/vegetation.php){target="blank"} datasets describe vegetation conditions.
- Existing Vegetation Type (EVT) - represents the current distribution of the terrestrial ecological systems classification, developed by NatureServe for the western hemisphere, through 2020.
- Existing Vegetation Cover (EVC) - represents the vertically projected percent cover of the live canopy layer for a 30-m cell.
- Existing Vegetation Height (EVH) - represents the average height of the dominant vegetation for a 30-m cell.
[Read more about LANDFIRE Vegetation Products](https://landfire.gov/vegetation.php){target="blank"}
## Most Prevalent Existing Vegetation Types
<br>
{width=100%}
<br>
```{r evt chart, echo=FALSE, message=FALSE, warning=FALSE, fig.width=10, fig.height=10}
evtname <- read.csv(file = "data/evt_aoi_attributes.csv") %>%
group_by(EVT_NAME) %>%
summarize(ACRES = sum(ACRES),
REL_PERCENT = sum(REL_PERCENT)) %>%
arrange(desc(REL_PERCENT)) %>%
top_n(n = 10, wt = REL_PERCENT)
# plot
evtChart <-
ggplot(data = evtname, aes(x = EVT_NAME, y = REL_PERCENT)) +
geom_bar(stat = "identity") +
labs(
title = "Top 10 Existing Vegetation Types",
subtitle = "Represents dominant vegetation systems ca2020",
caption = "\nData from landfire.gov.",
x = "",
y = "Percent of landscape") +
scale_x_discrete(limits = rev(evtname$EVT_NAME),
labels = function(x) str_wrap(x, width = 18)) +
coord_flip() +
theme_bw(base_size = 14)
evtChart
```
<br>
## Existing Vegetation Cover
<br>
{width=100%}
<br>
```{r evc chart, echo=FALSE, message=FALSE, warning=FALSE, fig.width=10, fig.height=10}
evcname <- read.csv("data/evc_aoi_attributes.csv")
# create "type" column based on conditions
evcname <- evcname %>% mutate(type = if_else(VALUE %in% 11, "Open Water",
if_else(VALUE %in% 12, "Snow / Ice",
if_else(VALUE %in% c(13:25), "Developed",
if_else(VALUE %in% 31, "Barren",
if_else(VALUE %in% c(60:70), "Agriculture",
if_else(VALUE %in% 32, "Quarries",
if_else(VALUE %in% 100, "Sparse Vegetation",
if_else(VALUE %in% c(101:199), "Tree",
if_else(VALUE %in% c(201:299), "Shrub",
if_else(VALUE %in% c(301:399), "Herb",
"Other")))))))))))
# create reverse substr() function
revSubstr <- function(x, start, stop) {
x <- strsplit(x, "")
sapply(x,
function(x) paste(rev(rev(x)[start:stop]), collapse = ""),
USE.NAMES = FALSE) }
# create cover column based on 2nd and 3rd to last values of classname
# if "Other" type, make 0
evcname <- evcname %>% mutate(cover = as.numeric(if_else(VALUE > 100,
revSubstr(evcname$CLASSNAMES, start = 2, stop = 3),
"0")))
# create bin breaks for grouping
breaks <- seq(0, 100, 10)
# create intervals for grouping and summarize
# also create factor order for "type"
evcgroup <- evcname %>%
mutate(interval = cut(cover,
breaks,
include.lowest = TRUE,
right = T,
labels = c("0-9", "10-19", "20-29", "30-39", "40-49", "50-59", "60-69", "70-79",
"80-89", "90-100")),
type = factor(type, levels = c("Tree", "Shrub", "Herb", "Open Water", "Snow / Ice", "Developed", "Agriculture", "Sparse Vegetation", "Barren", "Quarries", "Other"))) %>%
group_by(type, interval) %>%
summarize(Freq = sum(Freq),
ACRES = sum(ACRES),
REL_PERCENT = sum(REL_PERCENT))
# add label and legend names based on condition
evcgroup <- evcgroup %>% mutate(label = if_else(type %in% c("Tree", "Shrub", "Herb"),
paste0(type, " Cover = ", interval, "%"), as.character(type)),
legend = if_else(type %in% c("Tree", "Shrub", "Herb", "Open Water"),
type, as.factor("Other")))
# turn current label order to factors
evclabel.list <- evcgroup$label
evcgroup <- evcgroup %>% mutate(label = fct_rev(factor(label, evclabel.list)))
# create factor level colors for legend (original from Myles)
## cols <- c("Tree" = "#196F3D", "Shrub" = "#229954", "Herb" = "#52BE80", "Open Water" = "#7FB3D5",
## "Other" = "#808B96")
# join in custom cols column to color bars by specific label
evc_group_cols <- read.csv("data/evc_group_cols.csv")
evcgroup <- left_join(evcgroup, evc_group_cols, by = "label")
evcgroup$label <- factor(evcgroup$label, levels = rev(evcgroup$label))
# plot
evcChart <-
ggplot(data = evcgroup, aes(x = label, y = REL_PERCENT, fill = colors)) +
geom_bar(stat = "identity") +
labs(
title = "Existing Vegetation Cover",
subtitle = "Represents canopy cover per dominant lifeform, ca 2020",
caption = "\nData from landfire.gov.",
x = "",
y = "Percent of landscape") +
scale_fill_identity() +
coord_flip() +
theme_bw(base_size = 12)+
theme(legend.position = "none")
evcChart
```
<br>
## Existing Vegetation Height
<br>
{width=100%}
<br>
```{r evh chart, echo=FALSE, message=FALSE, warning=FALSE, fig.width=10, fig.height=10}
# load evh attribute table
evhname <- read.csv(file = "data/evh_aoi_attributes.csv")
# create "type" column based on conditions
evhname <- evhname %>% mutate(type = if_else(VALUE %in% 11, "Open Water",
if_else(VALUE %in% 12, "Snow / Ice",
if_else(VALUE %in% c(13:25), "Developed",
if_else(VALUE %in% 31, "Barren",
if_else(VALUE %in% c(60:70), "Agriculture",
if_else(VALUE %in% 32, "Quarries",
if_else(VALUE %in% 100, "Sparse Vegetation",
if_else(VALUE %in% c(101:199), "Tree",
if_else(VALUE %in% c(201:299), "Shrub",
if_else(VALUE %in% c(301:399), "Herb",
"Other"))))))))))) %>%
mutate(height_m = if_else(type %in% "Tree", (VALUE -100),
if_else(type %in% "Shrub", ((VALUE - 200) / 10),
if_else(type %in% "Herb", ((VALUE - 300) / 10), 0))) %>%
as.character() %>% as.numeric())
# create bin breaks for grouping
breaks <- c(0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100)
# create intervals for grouping and summarize
# also create factor order for "type"
evhgroup <- evhname %>%
mutate(interval = cut(height_m,
breaks,
include.lowest = TRUE,
right = F,
labels = c("0", "0.1-0.2", "0.2-0.3", "0.3-0.4" ,"0.4-0.5", "0.5-0.6", "0.6-0.7", "0.7-0.8", "0.8-0.9", "0.9-1.0", "1-5", "5-10", "10-15", "15-20", "20-25", "25-30", "30-35", "35-40", "40-45", "45-50", "50-55", "55-60", "60-65", "65-70", "70-75", "75-80", "80-85", "85-90", "90-95", "95-100")),
type = factor(type, levels = c("Tree", "Shrub", "Herb", "Open Water", "Snow / Ice", "Developed", "Agriculture", "Sparse Vegetation", "Barren", "Quarries", "Other"))) %>%
group_by(type, interval) %>%
summarise(VALUE = sum(VALUE),
ACRES = sum(ACRES),
REL_PERCENT = sum(REL_PERCENT))
# add label and legend names based on condition
evhgroup <- evhgroup %>% mutate(label = if_else(type %in% c("Tree", "Shrub", "Herb"),
paste0(type, " Height = ", interval, " m"), as.character(type)),
legend = if_else(type %in% c("Tree", "Shrub", "Herb", "Open Water"),
type, as.factor("Other")))
# turn current label order to factors
evhlabel.list <- evhgroup$label
evhgroup <- evhgroup %>% mutate(label = fct_rev(factor(label, evhlabel.list)))
# create factor level colors for legend
##cols <- c("Tree" = "#196F3D", "Shrub" = "#229954", "Herb" = "#52BE80", "Open Water" = "#7FB3D5","Other" = "#808B96")
# join in custom cols column to color bars by specific label
evh_group_cols <- read.csv("data/evh_group_cols.csv")
evhgroup <- left_join(evhgroup, evh_group_cols, by = "label")
evhgroup$label <- factor(evhgroup$label, levels = rev(evhgroup$label))
# plot
evhChart <-
ggplot(data = evhgroup, aes(x = label, y = REL_PERCENT, fill = colors)) +
geom_bar(stat = "identity") +
labs(
title = "Existing Vegetation Height",
subtitle = "Represents canopy height of dominant lifeform ca2020",
caption = "\nData from landfire.gov.",
x = "",
y = "Percent of landscape") +
scale_fill_identity() +
coord_flip() +
theme_bw(base_size = 12)+
theme(legend.position = "none")
evhChart
# plot with original color scheme
# evhChart <-
# ggplot(data = evhgroup, aes(x = label, y = REL_PERCENT, fill = legend)) +
# geom_bar(stat = "identity") +
# labs(
# title = "Existing Vegetation Height",
# subtitle = "landscape_name",
# caption = "\nData from landfire.gov.",
# x = "",
# y = "Percent of landscape") +
# scale_fill_manual(values = cols, name = "") +
# coord_flip() +
# theme_bw()
#
# evhChart
```
<br>