In emf-creaf/medfatereports: Medfate Evaluation Reports

out_path <- file.path(params$wd, 'Output', packageVersion('medfate')[[1]], params$model, params$conf, params$code)
if(params$save_plots) {
  out_evalplots <- file.path(out_path, 'EvaluationPlots')
  if (!dir.exists(out_evalplots)) {
    dir.create(out_evalplots, recursive = TRUE)
  }
}

eval_REW <- "SWC" %in% names(site_data$measuredData)

file_name_input <- file.path(out_path,
                       paste0('simulation_input.rds'))
file_name_output <- file.path(out_path,
                       paste0('simulation_result.rds'))
input_object <- readRDS(file_name_input)
control <- input_object$control
res <- readRDS(file_name_output)

Soil moisture

knitr::kable(as.data.frame(t(medfate::evaluation_stats(res, site_data$measuredData, type="REW"))))

p<-medfate::evaluation_plot(res, site_data$measuredData, type="REW")
if(params$save_plots) ggplot2::ggsave(filename = file.path(out_evalplots, paste0("REW_dynamics.png")),
                plot = p)
p

p<-medfate::evaluation_plot(res, site_data$measuredData, type="REW", plotType = "scatter")
if(params$save_plots) ggplot2::ggsave(filename = file.path(out_evalplots, paste0("REW_scatter.png")),
                plot = p)
p

Plant transpiration

cohNames <- row.names(input_object$cohorts)
df<-NULL
cohNamesOut <- character()
for(i in 1:length(cohNames)) {
  measured_var <- paste0("E_", cohNames[i])
  if(measured_var %in% names(site_data$measuredData)) {
      v<-medfate::evaluation_stats(res, site_data$measuredData, type= "E", cohort = cohNames[i])
      if(is.null(df)) df <- v
      else df <- cbind(df, v)
      cohNamesOut <-c(cohNamesOut, cohNames[i])
  }
}
if(!is.null(df)) {
  df <- as.data.frame(t(df), row.names = cohNamesOut)
  knitr::kable(df)
}

for(i in 1:length(cohNames)) {
  measured_var <- paste0("E_", cohNames[i])
  if(measured_var %in% names(site_data$measuredData)) {
    if(sum(is.na(site_data$measuredData[[measured_var]]))< nrow(site_data$measuredData)) {
      p<-medfate::evaluation_plot(res, site_data$measuredData, 
                                cohort = cohNames[i],
                                type="E", plotType = "dynamics")
      if(params$save_plots) ggplot2::ggsave(filename = file.path(out_evalplots,
                                         paste0(measured_var,"_dynamics.png")),
                    plot = p)
      print(p)
      p<-medfate::evaluation_plot(res, site_data$measuredData, 
                                cohort = cohNames[i],
                                type="E", plotType = "scatter")
      if(params$save_plots) ggplot2::ggsave(filename = file.path(out_evalplots,
                                         paste0(measured_var,"_scatter.png")),
                    plot = p)
      print(p)
    }
  }
}

Leaf water potential

cohNames <- row.names(input_object$cohorts)
df<-NULL
wpNamesOut <- character()
cohNamesOut <- character()
for(i in 1:length(cohNames)) {
  measured_var <- paste0("MD_", cohNames[i])
  if(measured_var %in% names(site_data$measuredData)) {
      v<-medfate::evaluation_stats(res, site_data$measuredData, type= "WP", cohort = cohNames[i])
      if(is.null(df)) df <- v
      else df <- rbind(df, v)
      wpNamesOut <-c(wpNamesOut, row.names(v))
      cohNamesOut <-c(cohNamesOut, rep(cohNames[i],2))
  }
}
if(!is.null(df)) {
  df <- data.frame(cohort = cohNamesOut, WP = wpNamesOut, df)
  df<- df[order(wpNamesOut),]
  knitr::kable(df, row.names = FALSE)

}

for(i in 1:length(cohNames)) {
  measured_out <- paste0("WP_", cohNames[i])
  measured_var <- paste0("MD_", cohNames[i])
  if(measured_var %in% names(site_data$measuredData)) {
    if(sum(is.na(site_data$measuredData[[measured_var]]))< nrow(site_data$measuredData)) {
      p<-medfate::evaluation_plot(res, site_data$measuredData, 
                                cohort = cohNames[i],
                                type="WP", plotType = "dynamics")
      if(params$save_plots) ggplot2::ggsave(filename = file.path(out_evalplots,
                                         paste0(measured_var,"_dynamics.png")),
                    plot = p)
      print(p)
      p<-medfate::evaluation_plot(res, site_data$measuredData, 
                                cohort = cohNames[i],
                                type="WP", plotType = "scatter")
      if(params$save_plots) ggplot2::ggsave(filename = file.path(out_evalplots,
                                         paste0(measured_out,"_scatter.png")),
                    plot = p)
      print(p)
    }
  }
}