In diazrenata/scads: What the Package Does (One Line, Title Case)

knitr::opts_chunk$set(echo = FALSE)

Miscellaneous Abundance

Elita Baldridge's community abundance dataset.

library(dplyr)
library(ggplot2)

ma <- MATSS::import_retriever_data("community-abundance-misc")

names(ma)
head(ma$community_abundance_misc_main)

ma_totals <- ma$community_abundance_misc_main %>%
  group_by(site_id) %>%
  summarize(nspp = n(),
            nind = sum(abundance)) %>%
  ungroup()


ma_plot <- ggplot(data = ma_totals, aes(x = nspp, y = nind)) +
  geom_point(alpha = .5) +
  theme_bw() +
  ggtitle("S and N for Misc Abund Dataset")

ma_plot

ma_small <- ma_totals %>%
  filter(nspp <= 100,
         nind <= 40000)

ma_small_plot <- ggplot(data = ma_small, aes(x = nspp, y = nind)) +
  geom_point(alpha = .5) +
  theme_bw() +
  ggtitle("S and N for Misc Abund Dataset - only small communities")

ma_small_plot

MCDB

Mammal community database

mcdb <- MATSS::import_retriever_data("mammal-community-db")

mcdb_totals <- mcdb$mammal_community_db_communities %>%
  filter(presence_only == 0) %>%
  group_by(site_id) %>%
  summarize(nspp = n(),
            nind = sum(abundance)) %>%
  ungroup()

mcdb_plot <- ggplot(data = mcdb_totals, aes(x = nspp, y = nind)) +
  geom_point(alpha = .5) +
  theme_bw() +
  ggtitle("S and N for MCDB")

mcdb_plot

Gentry forest transects

gentry <- MATSS::import_retriever_data("gentry-forest-transects")

gentry_totals <- gentry$gentry_forest_transects_counts %>%
  group_by(site_code, line) %>%
  summarize(nspp = n(),
            nind = sum(count)) %>%
  ungroup()


gentry_plot <- ggplot(data = gentry_totals, aes(x = nspp, y = nind)) +
  geom_point(alpha = .5) +
  theme_bw() +
  ggtitle("S and N for Gentry")

gentry_plot