fao-sid / soc-mapping-cookbook Goto Github PK

I uploaded the image 3 times but it has not been replaced. It's still the old image!

Figure 1.1: Proposed graphical workflow for producing a SOC map from data preparation to final result publishing

was there on 1st edition!

"The validation plot shows the regression line between observed and predicted of a
model that uses 75% (black line) and the regression lines of 10 model realizations,
each with a different random combination of data for training and validating the
models." - there is no picture of this plot

I'm checking continuity of the codes in the cookbook.
The cookbook has a code (optional) for rasterizing a soil map. Then the code for overlaying covariates (mandatory) refers to previously rasterized soil map. So, we need a soil map. The cookbook refers to a file "MK_soilmap_simple.shp".
@midraed do you have this file?
? Do we keep soil map as a part of covariate stack in the (main) example or we leave it out?

Can we remove the chapter 12. I think it's not needed anymore since we have done with the data collection.

On page 126, wrong AVE values did not change in the table although the formula in the code changed.

using RMSE corr ratio

Section 6.3.7 Technical steps - Using quantile regression forest...
Step 3 is empty. The corresponding section of a code is set 'eval=false'

\index{Soil Information System (SIS)!global} - not working

topsoils <- topsoils[, c("ID", "X", "Y", "OC_percent", "BLD",
"OCSKGM", "meaERROR")] - should be "SOC" instead of "OC_percent"

profiles <- profiles[, c("ID", "X", "Y", "SOC", "BLD",
"OCSKGM", "meaERROR")] - should be "id" instead of "ID"

one more paragraph and a workflow

1. Validation code in Chapter 12 is only for Random Forest which is not interesting. I think it would be better to copy there the codes from Chapter 7.5

2. In Chapter 7.5 the code
   dat <- extract(x = OCSKGM_RK, y = dat, sp = TRUE) will not work, because raster OCSKGM_RK is in metric coordinate system with which it was created in Chapter 6. We either need to reproject it in Chapter 7 before extracting values, or in Chapter 6 before writing a .tiff file.

3. In Chapter 7.5. the formulas for amount of variance explained are wrong. E.g.:
   AVE_GM <- 1 - sum(dat$PE_GM^2, na.rm=TRUE) /
   sum( (dat$MKD_OCSKGM_GM - mean(dat$OCSKGM, na.rm = TRUE))^2,
   na.rm = TRUE)
   should be:
   AVE_GM <- 1 - sum(dat$PE_GM^2, na.rm=TRUE) /
   sum( (dat$OCSKGM - mean(dat$OCSKGM, na.rm = TRUE))^2,
   na.rm = TRUE)
   Same error also for AVE_RK, AVE_rf, AVE_svm

Chapter 12 code for Quantile Regression Forest uses column OCSKGMlog instead of OCSKGM. This column is created in Chapter 4, but never in Chapter 12, therefore the code in Chapter 12 doesn't work. We need either to change the code in Chapter 12 QuantileRF (e.g. by using log(OCSKGM) instead of OCSKGMlog), or add the creation of OCSKGMlog column to Chapter 12 data preparation scripts.

@USDA_2018 and @united1975soil
Author = {United States Department of Agriculture. Soil Conservation Service} is transformed to “of Agriculture. Soil Conservation Service, U. S. D.” probably because of bibtex naming rules.

good job