The document discusses using random forest algorithms to model and map soil organic carbon. It provides instructions on fitting a random forest regression model in R using sample soil data, assessing model performance, and using the model to predict and map soil organic carbon across a study area. Key steps include randomly splitting the data into training and testing sets, fitting a random forest model with 1000 trees, calculating error metrics like RMSE to evaluate the model, using the model to predict SOC for the testing data, plotting predicted vs observed values, and finally using the fitted model to predict and plot a soil organic carbon map for the study area.

1. GSP - Asian Soil
Partnership
Training Workshop on
Soil Organic Carbon
Mapping
Bangkok, Thailand,
24-29 April 2017
Yusuf YIGINI, PhD - FAO, Land and Water Division (CBL)

2. DAY 5 – 28 April 2017
TIME TOPIC INSTRUCTORS
8:30 - 10:30 Exploratory Data Analysis
Hands-on: Basic Spatial Operations
Dr. Yusuf Yigini, FAO
Dr. Ate Poortinga
Dr. Lucrezia Caon, FAO
10:30 - 11:00 COFFEE BREAK
11:00 - 13:00 Linear Models
Hands-on: Linear Models
13:00 - 14:00 LUNCH
14:00 - 16:00 Modelling Soil Properties
R - Spatial Multiple Linear Regression
R - Random Forests
16:00- 16:30 COFFEE BREAK
16:30 - 17:30 Hands-on

3. Random Forest

4. Random Forest
An increasingly popular data mining algorithm in
DSM and soil sciences, and even in applied sciences
in general is the Random Forests model. This
algorithm is provided in the randomForest package
and can be used for both regression and
classification.

5. Random Forest
Random Forests are a boosted decision tree model.
Fitting a Random Forest model in R is relatively
straightforward. It is better consulting the rhelp
files regarding the randomForest package and the
functions.

6. Random Forest
We will use the randomForest() function and a couple of
extractor functions to tease out some of the model fitting
diagnostics. We will use the sample() function to
randomly split the data into two parts: training and
testing.
> DSM_table2 <- read.csv("DSM_table2.csv")
> training <- sample(nrow(DSM_table2), 0.7 * nrow(DSM_table2))
> modelF <- randomForest(Value ~ dem + twi + slp + tmpd + tmpn, data =
DSM_table2[training, ],importance = TRUE, ntree = 1000)

7. Random Forest
The print function is to quickly assess the model fit.
print(modelF)
Call:
randomForest(formula = Value ~ dem + twi + slp + tmpd + tmpn,
data = DSM_table2[training, ], importance = TRUE, ntree = 1000)
Type of random forest: regression
Number of trees: 1000
No. of variables tried at each split: 1
Mean of squared residuals: 1.801046
% Var explained: 59.35

8. Random Forest
Generally, we confront this question by comparing
observed values with their predictions. Some of the more
common “quality” measures are the root mean square
error (RMSE), bias, and the R2 value
> Predicted <- predict(modelF, newdata =
DSM_table2[-training, ])
> RMSE <- sqrt(mean((DSM_table2$Value[-training] - Predicted)^2))
> RMSE
[1] 1.249491
> lm <- lm(Predicted~ DSM_table2$Value[-training])
> summary(lm)[["r.squared"]]
[1] 0.6079515
> bias <- mean(Predicted) - mean(DSM_table2$Value[-training])
> bias
[1] 0.01450241

9. Random Forest
plot(DSM_table2$Value[-training],Predicted)
abline(a=0,b=1,lty=2, col="red")
abline(lm, col="blue")

10. Random Forest
plot(DSM_table2$Value[-training],Predicted)
abline(a=0,b=1,lty=2, col="red")
abline(lm, col="blue")
regression on predicted and observed values - blue
1:1 comparison - red

11. Final Steps - Random Forest
Covs <- list.files(path = "C:/mc/covs", pattern = ".tif$",full.names
= TRUE)
covStack <- stack(Covs)
MapSoc <- predict(covStack, modelF, "SOCMAPofMAcedonia", format =
"GTiff", datatype = "FLT4S", overwrite = TRUE)
plot(MapSoc, main = "Random Forest model predicted 0-30cm SOC Map of
Macedonia %")

12. Final Steps - Random Forest
Covs <- list.files(path = "C:/mc/covs", pattern = ".tif$",full.names
= TRUE)
covStack <- stack(Covs)
MapSoc <- predict(covStack, modelF, "SOCMAPofMAcedonia", format =
"GTiff", datatype = "FLT4S", overwrite = TRUE)
plot(MapSoc, main = "Random Forest model predicted 0-30cm SOC Map of
Macedonia %")
Random Forest model predicted 0-30cm SOC Map

13. Exercise
Produce and plot the Soil Organic Carbon Map
Using your Multiple Linear Regression Model.
And share it here, https://goo.gl/jKxHfN