JoeModel_Run_Batch: Batch Joe Model Run

In mattjbayly/JoeModelCE: Joe Model for Cumulative Effects

Batch Joe Model Run

Description

Batch version of JoeModel_Run across scenarios input file.

Usage

JoeModel_Run_Batch(scenarios = NA, dose = NA, sr_wb_dat = NA, MC_sims = 10)

Arguments

scenarios	dataframe. Custom scenarios dataframe with columns Scenario (scenario ID), Stressor (stressor name), Metric (either Mean or SD) and Multiplier (a numeric multiplier).
dose	dataframe. Stressor magnitude file exported from StressorMagnitudeWorkbook().
sr_wb_dat	list object. Stressor response workbook returned from StressorResponseWorkbook().
MC_sims	numeric. set number of Monte Carlo simulations for the Joe Model. set number of Monte Carlo simulations for the Joe model.

Details

Runs the Joe Model for cumulative system capacity across multiple scenarios. See vignette for custom input file format.

Examples

## Not run: 
library(JoeModelCE)
library(dplyr)
library(ggplot2)

# Import stressor-magnitude workbook
filename_rm <- system.file("extdata", "stressor_magnitude_unc_ARTR.xlsx", package = "JoeModelCE")
stressor_magnitude <- StressorMagnitudeWorkbook(filename = filename_rm, 
scenario_worksheet = "natural_unc")

# Import stressor-response workbook
filename_sr <- system.file("extdata", "stressor_response_fixed_ARTR.xlsx", package = "JoeModelCE")
stressor_response <- StressorResponseWorkbook(filename = filename_sr)

# Import the custom scenarios workbook
filename_batch <- system.file("extdata", "scenario_batch_joe.xlsx", package = "JoeModelCE")
scenarios <- readxl::read_excel(filename_batch)


# Run the Joe Model with batch scenarios
exp_dat <- JoeModel_Run_Batch(scenarios = scenarios, dose = stressor_magnitude,
 sr_wb_dat = stressor_response, MC_sims = 3)

#-----------------------------------------------------
# Plot result for single HUC - filter by name or ID
hub_sub <- exp_dat[exp_dat$HUC == 1701010204, ]
plot_title <- paste0("Watershed Name - ", 1701010204)

# Add mean and error bars (SD)
hub_sb <- hub_sub %>%
  group_by(Scenario) %>%
  summarise(
    mean = mean(CE, na.rm = TRUE),
    sd = sd(CE, na.rm = TRUE)
  )

hub_sb$lower <- hub_sb$mean - hub_sb$sd
hub_sb$upper <- hub_sb$mean + hub_sb$sd

ggplot(hub_sb, aes(x = mean, y = Scenario, xmin = lower, xmax = upper)) +
  geom_rect(aes(xmin = 0, xmax = 0.2, ymin = -Inf, ymax = Inf),
    fill = "pink", alpha = 0.02
  ) +
  geom_rect(aes(xmin = 0.2, xmax = 0.5, ymin = -Inf, ymax = Inf),
    fill = "orange", alpha = 0.02
  ) +
  geom_rect(aes(xmin = 0.5, xmax = 0.75, ymin = -Inf, ymax = Inf),
    fill = "yellow", alpha = 0.02
  ) +
  geom_rect(aes(xmin = 0.75, xmax = 1, ymin = -Inf, ymax = Inf),
    fill = "green", alpha = 0.02
  ) +
  geom_point() +
  geom_errorbarh(height = .2) +
  ggtitle(plot_title) +
  xlab("System Capacity (0 - 1)") +
  ylab("Recovery Scenario") +
  theme_bw()

#-----------------------------------------------------
# Plot result for single scenario
sen_sub <- exp_dat[exp_dat$Scenario == "scenario_1", ]
plot_title <- paste0("Scenario 1 ...")

# Add mean and error bars (SD)
sen_sb <- sen_sub %>%
  group_by(HUC) %>%
  summarise(
    mean = mean(CE, na.rm = TRUE),
    sd = sd(CE, na.rm = TRUE)
  )

sen_sb$lower <- sen_sb$mean - sen_sb$sd
sen_sb$upper <- sen_sb$mean + sen_sb$sd

sen_sb$HUC <- as.character(sen_sb$HUC)

ggplot(sen_sb, aes(x = mean, y = HUC, xmin = lower, xmax = upper)) +
  geom_rect(aes(xmin = 0, xmax = 0.2, ymin = -Inf, ymax = Inf),
    fill = "pink", alpha = 0.02
  ) +
  geom_rect(aes(xmin = 0.2, xmax = 0.5, ymin = -Inf, ymax = Inf),
    fill = "orange", alpha = 0.02
  ) +
  geom_rect(aes(xmin = 0.5, xmax = 0.75, ymin = -Inf, ymax = Inf),
    fill = "yellow", alpha = 0.02
  ) +
  geom_rect(aes(xmin = 0.75, xmax = 1, ymin = -Inf, ymax = Inf),
    fill = "green", alpha = 0.02
  ) +
  geom_point() +
  geom_errorbarh(height = .2) +
  ggtitle(plot_title) +
  xlab("System Capacity (0 - 1)") +
  ylab("Recovery Scenario") +
  theme_bw()

## End(Not run)

mattjbayly/JoeModelCE documentation built on Nov. 14, 2023, 5:34 p.m.