03-requireddata.Rmd

# Required data

In this section you will find the instructions on how to download and read the soil dataset used in our paper.

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You can download the file ['SoilNIRSaoPaulo.rds'](https://github.com/l-ramirez-lopez/VNIR_spectroscopy_for_robust_soil_mapping/raw/master/SoilNIRSaoPaulo.rds), alternatively you can visit to the [GitHub repository of the paper](https://github.com/l-ramirez-lopez/VNIR_spectroscopy_for_robust_soil_mapping) where the file resides.

This `rds` file contains a `data.frame` with 910 rows (samples) and the following variables: 

* Nr: An arbitrary sample number.
* ID: A `factor` indicating the sample IDs. The first character is a letter which indicates the depth layer at which the sample was collected (A: 0-20 cm and B: 80-100 cm).  
* POINT_X: The X (geographical) coordinate. 
* POINT_Y: The Y (geographical) coordinate.
* Sand: The percentage of sand contnet in the soil sample. 
* Silt: The percentage of silt contnet in the soil sample. 
* Clay: The percentage of clay contnet in the soil sample. 
* Ca: The exchangeable Calcium content in the sample ($mmol_{c}$ $kg^{−1}$). 
* set: A `factor` indicating whether the sample is used for model's validation or if it can be used to calibrate models. 
* spc: A set of 307 variables representing the wavelengths from 502 nm to 2338 nm in steps of 6 nm. 

Further information on this dataset can be found in [our paper](https://onlinelibrary.wiley.com/doi/epdf/10.1111/ejss.12752)

We recommend to create a local folder (e.g. "./myworkingdirectory"). If you downloaded the file to this local folder then:
``` r
workingd <- "/myworkingdirectory"
setwd(workingd)
data <- readRDS("SoilNIRSaoPaulo.rds")
```

Alternatively, you can also read the file directly from the [GitHub repository of the paper](https://github.com/l-ramirez-lopez/VNIR_spectroscopy_for_robust_soil_mapping):

```{r, eval = TRUE}
nirfile <- file("https://github.com/l-ramirez-lopez/VNIR_spectroscopy_for_robust_soil_mapping/raw/master/SoilNIRSaoPaulo.rds")
data <- readRDS(nirfile)
names(data)
```

Plot the spectra of the loaded data..
```{r, eval = TRUE, fig.cap = "Spectra in the SoilNIRSaoPaulo dataset"}
obg <- par()$bg 
par(bg = rgb(0.11, 0.12, 0.17))
tcol <- rgb(0.6,0.6,0.6,0.8)
scol <- rgb(0, 1, 0, 0.2)
matplot(x = as.numeric(colnames(data$spc)),
        y = t(data$spc),
        type = "l",
        lty = 1,
        col = scol,
        xlab = "wavelength (nm)",
        ylab = "Absorbance", 
        col.axis = tcol, 
        col.lab = tcol)
grid(lty = 1, col = tcol)

## reset the background color of your plots 
## to the original color
par(bg = obg)
```


In addition you also need a `R` object of class (`SpatialPolygonsDataFrame` of the package `sp`) which contains the polygon of the study area. You can also download the file (polygon.rds) containing this object by clicking [here](https://github.com/l-ramirez-lopez/VNIR_spectroscopy_for_robust_soil_mapping/raw/master/polygon.rds).