inst/doc/diversity-hypothesis-testing.R

In breakaway: Species Richness Estimation and Modeling

## ---- include=FALSE-----------------------------------------------------------
# install.packages("remotes")
# remotes::install_github("adw96/breakaway")
if (requireNamespace('dplyr', quietly = TRUE)) {
  library(dplyr)
} else {
  message("'dplyr' is not installed!")
}
library(breakaway)
library(magrittr)
library(phyloseq)

## -----------------------------------------------------------------------------
data("soil_phylo")
soil_phylo %>% sample_data %>% head

## -----------------------------------------------------------------------------
subset_soil <- soil_phylo %>%
  subset_samples(Amdmt == 1) %>% # only biochar
  subset_samples(Day %in% c(0, 2))  # only Days 0 and 82

## -----------------------------------------------------------------------------
richness_soil <- subset_soil %>% breakaway
plot(richness_soil, physeq=subset_soil, color="Day", shape = "ID")

## -----------------------------------------------------------------------------
summary(richness_soil) %>% tibble::as_tibble()

## -----------------------------------------------------------------------------
meta <- subset_soil %>%
  sample_data %>%
  tibble::as_tibble() %>%
  dplyr::mutate("sample_names" = subset_soil %>% sample_names )

## -----------------------------------------------------------------------------
combined_richness <- meta %>%
  dplyr::left_join(summary(richness_soil),
            by = "sample_names")
# Old way (still works)
bt_day_fixed <- betta(chats = combined_richness$estimate,
                      ses = combined_richness$error,
                      X = model.matrix(~Day, data = combined_richness))
# Fancy new way -- thanks to Sarah Teichman for implementing!
bt_day_fixed <- betta(formula = estimate ~ Day, 
                      ses = error, data = combined_richness)
bt_day_fixed$table

## -----------------------------------------------------------------------------
# Old way (still works)
bt_day_fixed_id_random <- betta_random(chats = combined_richness$estimate,
                                       ses = combined_richness$error,
                                       X = model.matrix(~Day, data = combined_richness),
                                       groups=combined_richness$ID)
# Fancy new way 
bt_day_fixed_id_random <-
  betta_random(formula = estimate ~ Day | ID, 
               ses = error,  data = combined_richness)
bt_day_fixed_id_random$table

## -----------------------------------------------------------------------------
betta_lincom(fitted_betta = bt_day_fixed_id_random,
             linear_com = c(1,1),
             signif_cutoff = 0.05)

## -----------------------------------------------------------------------------
subset_soil_days_1_2 <- soil_phylo %>%
  subset_samples(Amdmt == 1) %>% # only biochar
  subset_samples(Day %in% c(0, 1, 2))  # Days 0, 12, and 82

## -----------------------------------------------------------------------------
meta_days_1_2 <- subset_soil_days_1_2 %>%
  sample_data %>%
  tibble::as_tibble() %>%
  dplyr::mutate("sample_names" = subset_soil_days_1_2 %>% sample_names )

## -----------------------------------------------------------------------------
richness_days_1_2 <- subset_soil_days_1_2 %>% 
  breakaway

combined_richness_days_1_2 <- meta_days_1_2 %>%
  dplyr::left_join(summary(richness_days_1_2),
            by = "sample_names")
combined_richness_days_1_2

## -----------------------------------------------------------------------------
bt_day_1_2_fixed_id_random <- betta_random(formula = estimate ~ Day | ID, 
               ses = error,  data = combined_richness_days_1_2)
bt_day_1_2_fixed_id_random$table

## -----------------------------------------------------------------------------
set.seed(345)
submodel_test <- test_submodel(bt_day_1_2_fixed_id_random,
                          submodel_formula = estimate~1,
                          method = "bootstrap",
                          nboot = 100)

submodel_test$pval