uncertainty.R
In ConFluxPro: Soil Gas Analysis and Flux Modeling

## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----setup--------------------------------------------------------------------
library(ConFluxPro)

## ----load base_dat------------------------------------------------------------
data("base_dat", package = "ConFluxPro")
mod_pf <- pro_flux(base_dat)

## ----bootstrap-gasdata--------------------------------------------------------
set.seed(42) # to get exactly same result every time 
mod_pf_bs_gasdata <- 
  bootstrap_error(mod_pf, 
                  n_samples = 25, 
                  sample_from = "gasdata")

## -----------------------------------------------------------------------------
## after bootstrapping
mod_pf_bs_gasdata %>%
  filter(prof_id == 1) %>%
  efflux()

## originial model
mod_pf %>%
  filter(prof_id == 1) %>%
  efflux()

## -----------------------------------------------------------------------------
mod_pf_bs_gasdata %>%
  filter(prof_id == 1) %>%
  production()

## -----------------------------------------------------------------------------
library(dplyr)
soilphys <- cfp_soilphys(base_dat)

set.seed(42)
soilphys_replicate_TPS <-
soilphys %>%
  # get base TPS info
  select(site, upper, lower, TPS) %>%
  distinct() %>%
  rename(TPS_mean = TPS) %>%
  # repeat each row 3 times 
  cross_join(data.frame(replicate_id = 1:3)) %>%
  # generate new, random TPS values
  mutate(TPS = rnorm(n(), TPS_mean, 0.01)) %>%
  # join with rest of dataset
  left_join(soilphys %>% select(!TPS),
            by = c("site", "upper", "lower"),
            relationship = "many-to-many") %>%
  # recaluclate DS and c_air
  complete_soilphys(DSD0_formula = "a*AFPS^b", quiet = TRUE) %>%
  cfp_soilphys(id_cols = c("site", "Date", "replicate_id"))


## -----------------------------------------------------------------------------
replicate_dat <- 
  cfp_dat(cfp_gasdata(base_dat),
          soilphys_replicate_TPS,
          cfp_layers_map(base_dat))

mod_pf_replicate <-
  cfp_pfmod(replicate_dat)


## -----------------------------------------------------------------------------
set.seed(42)
mod_pf_bs_soilphys <- 
  bootstrap_error(mod_pf_replicate, 
                  n_samples = 25, 
                  sample_from = "soilphys",
                  rep_cols = "replicate_id")

## -----------------------------------------------------------------------------
## boostrapping from soilphys
mod_pf_bs_soilphys %>%
  filter(prof_id < 10) %>%
  efflux()

## boostrapping from gasdata
mod_pf_bs_gasdata %>%
  filter(prof_id < 10) %>%
  efflux()

## -----------------------------------------------------------------------------
set.seed(42)
mod_pf_bs_both <- 
  bootstrap_error(mod_pf_replicate, 
                  n_samples = 25, 
                  sample_from = "both",
                  rep_cols = "replicate_id")
mod_pf_bs_both %>%
  filter(prof_id < 10) %>%
  efflux()