In emf-creaf/medfatereports: Medfate Evaluation Reports

n_sites <- length(params$codes)
n_confs <- length(params$confs)
n_rows <- n_sites*n_confs
df <- data.frame(Site = rep(NA, n_rows), 
                 Mode = rep(NA, n_rows),
                 Path = rep(NA, n_rows))
df$SiteData = vector("list", n_rows)
df$InputObject = vector("list", n_rows)
df$Result = vector("list", n_rows)
cnt <- 0
for(i in 1:n_sites) {
  site <- params$codes[i]
  for(j in 1:n_confs) {
    conf <- params$confs[j]
    cnt <- cnt+1
    df$Site[cnt] <- site
    df$Mode[cnt] <- conf
    df$Path[cnt] <- file.path('Output', packageVersion('medfate')[[1]], params$model, conf, site)
    file_name_input <- file.path(df$Path[cnt],
                       paste0('simulation_input.rds'))
    file_name_output <- file.path(df$Path[cnt],
                       paste0('simulation_result.rds'))
    df$InputObject[[cnt]] = readRDS(file_name_input)
    df$Result[[cnt]] = readRDS(file_name_output)
    df$SiteData[[cnt]] <- medfatereports::load_list(site)
  }
}

Soil moisture

df_eval <-NULL
for(i in 1:n_rows) {
  eval_REW <- "SWC" %in% names(df$SiteData[[i]]$measuredData)
  if(eval_REW) {
    v<-medfate::evaluation_stats(df$Result[[i]], df$SiteData[[i]]$measuredData, type= "REW")
    if(is.null(df)) df_eval <- v
    else df_eval <- cbind(df_eval, v)
  }
}
if(!is.null(df)) {
  df_all <- cbind(df[,c("Site", "Mode")], as.data.frame(t(df_eval)))
  row.names(df_all)<- NULL
  knitr::kable(df_all)
}

Plant transpiration

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

Leaf water potentials

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