Removed yieldprediction from CI_report_dashboard_planet.Rmd edited online with Bitbucket
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Martin Folkerts
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@ -275,103 +275,3 @@ print(" PRINT")
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```
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```
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# Yield prediction
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The below table shows estimates of the biomass if you would harvest them now.
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```{r message=FALSE, warning=FALSE, include=FALSE}
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#CI_quadrant <- readRDS(here(cumulative_CI_vals_dir,"All_pivots_Cumulative_CI_quadrant_year_v2.rds"))
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CI_quadrant <- readRDS(here(cumulative_CI_vals_dir,"All_pivots_Cumulative_CI_quadrant_year_v2.rds")) %>%
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group_by(model) %>% # Group by model or other relevant columns
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fill(field, sub_field, .direction = "downup") %>% # Fill down then up within each group
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ungroup()
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if (all(is.na(CI_quadrant$tonnage_ha))) {
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log_message("Lacking historic harvest data, please provide for yield prediction calculation")
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knitr::knit_exit() # Exit the chunk if tonnage_ha is empty
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}
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harvesting_data <- harvesting_data %>% rename(season = year)
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CI_and_yield <- left_join(CI_quadrant , harvesting_data, by = c("field", "sub_field", "season")) %>% #filter(!is.na(tonnage_ha)) %>%
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group_by(sub_field, season) %>% slice(which.max(DOY)) %>%
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dplyr::select(field, sub_field, tonnage_ha, cumulative_CI, DOY, season, sub_area) %>%
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mutate(CI_per_day = cumulative_CI/ DOY)
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predictors <- c( "cumulative_CI" , "DOY" ,"CI_per_day" )
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response <- "tonnage_ha"
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# CI_and_yield_test <- as.data.frame(CI_and_yield_test)
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CI_and_yield_test <- CI_and_yield %>% as.data.frame() %>% filter(!is.na(tonnage_ha))
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CI_and_yield_validation <- CI_and_yield_test
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prediction_yields <- CI_and_yield %>% as.data.frame() %>% filter(is.na(tonnage_ha))
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ctrl <- trainControl(method="cv",
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savePredictions = TRUE,
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allowParallel= TRUE,
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number = 5,
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verboseIter = TRUE)
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set.seed(202)
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model_ffs_rf <- ffs( CI_and_yield_test[,predictors],
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CI_and_yield_test[,response],
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method="rf" ,
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trControl=ctrl,
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importance=TRUE,
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withinSE = TRUE,
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tuneLength = 5,
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na.rm = TRUE
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)
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# Function to prepare predictions
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prepare_predictions <- function(predictions, newdata) {
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return(predictions %>%
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as.data.frame() %>%
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rename(predicted_Tcha = ".") %>%
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mutate(sub_field = newdata$sub_field,
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field = newdata$field,
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Age_days = newdata$DOY,
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total_CI = round(newdata$cumulative_CI, 0),
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predicted_Tcha = round(predicted_Tcha, 0),
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season = newdata$season) %>%
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dplyr::select(field, sub_field, Age_days, total_CI, predicted_Tcha, season) %>%
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left_join(., newdata, by = c("field", "sub_field", "season")))
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}
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# Predict yields for the validation dataset
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pred_ffs_rf <- prepare_predictions(predict(model_ffs_rf, newdata = CI_and_yield_validation), CI_and_yield_validation)
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# Predict yields for the current season
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pred_rf_current_season <- prepare_predictions(predict(model_ffs_rf, newdata = prediction_yields), prediction_yields) %>%
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filter(Age_days > 300) %>%
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mutate(CI_per_day = round(total_CI / Age_days, 1))
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```
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```{r yield_plaatjes, echo=FALSE }
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if (all(is.na(CI_quadrant$tonnage_ha))) {
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log_message("Lacking historic harvest data, please provide for yield prediction calculation")
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knitr::knit_exit() # Exit the chunk if tonnage_ha is empty
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}
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ggplot(pred_ffs_rf, aes(y = predicted_Tcha, x = tonnage_ha)) +
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geom_point(size = 2, alpha = 0.6) + # Adjust point size and transparency
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geom_abline(intercept = 0, slope = 1, linetype = "dashed", color = "red") + # Reference line
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scale_x_continuous(limits = c(0, 200)) +
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scale_y_continuous(limits = c(0, 200)) +
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labs(title = "Model Performance: \nPredicted vs Actual Tonnage/ha",
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x = "Actual tonnage/ha (Tcha)",
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y = "Predicted tonnage/ha (Tcha)") +
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theme_minimal()
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ggplot(pred_rf_current_season, aes(x = Age_days, y = predicted_Tcha)) +
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geom_point(size = 2, alpha = 0.6) + # Adjust point size and transparency
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labs(title = "Predicted Yields for Fields Over 300 Days \nOld Yet to Be Harvested",
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x = "Age (days)",
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y = "Predicted tonnage/ha (Tcha)") +
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# facet_wrap(~sub_area) +
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scale_y_continuous(limits = c(0, 200)) + # Optional: Set limits for y-axis
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theme_minimal()
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knitr::kable(pred_rf_current_season,
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digits = 0,
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caption = "Predicted Tonnage/ha for Fields Over 300 Days Old")
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```
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