In mschmidty/AIMtools: Tools for working with AIM Data.

knitr::opts_chunk$set(echo = TRUE)

library(AIMtools)
library(magrittr)
?cover()

cover(agol_2019, type="detailed", by="line")%>%
  dplyr::filter(stringr::str_detect(symbol, "^AR"))%>%
  dplyr::filter(symbol != "ARPU9" & symbol != "ARCA14")%>%
  dplyr::mutate(sage_type = dplyr::case_when(
    symbol == "ARBI3" ~ "Bigelow sagebrush",
    symbol == "ARLU" ~ "White sagebrush",
    stringr::str_detect(symbol, "^ARTR") ~ "Big sagebrush",
    symbol == "ARNO4" ~ "Black sagebrush",
    stringr::str_detect(symbol, "^ARAR") ~ "Little sagebrush",
  ))

Test

library(tidyverse)
library(AIMtools)
library(arcgisbinding)
arc.check_product()
library(extrafont)
loadfonts()


theme_set(schmidtytheme::theme_schmidt()+
            theme(
              text=element_text(family="Public Sans"),
              title = element_text(family ="")
            ))


agol<-load_data()
agol_2019<-load_data(year=2019)
dima_2018<-readRDS("test_cache/DIMA_2018.rds")

sage<-rbind(
  sage_cover(agol, by="plot")%>%
    simplify_cover()%>%
    dplyr::mutate(year = 2020), 
  sage_cover(agol_2019, by="plot")%>%
    simplify_cover()%>%
    dplyr::mutate(year=2019)
  )

sage<-sage_cover(data, by="plot")

sage<-sage%>%
  dplyr::filter(sage_type=="Big sagebrush")%>%
  dplyr::mutate(strata = str_extract(PlotID, "^.."))%>%
  filter(!str_detect(PlotID, "^COC"))

sage%>%
  filter(strata%in%c("MS", "SS", "SD", "PJ"))%>%
  ggplot(aes(as.factor(year), cover_perc, fill=strata))+
  geom_boxplot()+
  facet_wrap(~strata)

sage%>%
  mutate(PlotID = fct_reorder(PlotID, cover_perc, ))%>%
  ggplot(aes(PlotID, cover_perc, color=strata, shape=as.factor(year)))+
  geom_point(size=3)+
  coord_flip()+
  scale_color_brewer(palette="Dark2")+
  scale_y_continuous(labels = scales::percent)+
  labs(title = "% Sage Cover by plot",
       subtitle="Years: 2019 and 2020",
       y="Sage % Cover")+
  theme(
    axis.line = element_line(size=1, color="#333333")
  )

DIMA cover

dima_cover(dima_2018, by="plot")%>%
  dplyr::filter(stringr::str_detect(symbol, "^AR"))%>%
  dplyr::filter(symbol != "ARPU9" & symbol != "ARCA14")%>%
  dplyr::mutate(sage_type = dplyr::case_when(
    symbol == "ARBI3" ~ "Bigelow sagebrush",
    symbol == "ARLU" ~ "White sagebrush",
    stringr::str_detect(symbol, "^ARTR") ~ "Big sagebrush",
    symbol == "ARNO4" ~ "Black sagebrush",
    stringr::str_detect(symbol, "^ARAR") ~ "Little sagebrush",
  ))

sage_all<-rbind(
  sage_cover(agol, by="plot")%>%
    simplify_cover(sage=TRUE)%>%
    dplyr::mutate(year = 2020), 
  sage_cover(agol_2019, by="plot")%>%
    simplify_cover(sage=TRUE)%>%
    dplyr::mutate(year=2019),
  dima_sage_cover(dima_2018, by="plot")%>%
    simplify_cover(sage=TRUE)%>%
    mutate(year=2018)
  )%>%
  dplyr::filter(sage_type=="Big sagebrush")%>%
  dplyr::mutate(strata = str_extract(PlotID, "^.."))%>%
  filter(!str_detect(PlotID, "^COC"))

sage_all%>%
  mutate(PlotID = fct_reorder(PlotID, cover_perc, ))%>%
  ggplot(aes(PlotID, cover_perc, color=strata, shape=as.factor(year)))+
  geom_point(size=3)+
  coord_flip()+
  scale_color_brewer(palette="Dark2")+
  scale_y_continuous(labels = scales::percent)+
  labs(title = "% Sage Cover by plot",
       subtitle="Years: 2018, 2019 and 2020",
       y="Sage % Cover",
       caption="Data: Tres Rios AIM Data | by Mike Schmidt")+
  theme(
    axis.line = element_line(size=1, color="#333333")
  )