Rock fragments

Warning: The name of the attribute in the database has changed in 2020. The \(`sosmW30s`\) variable is now \(`sosmW105s`\). Therefore, we have 2 ways for computing the RF.

Before 2020, the RF was computed in the following way:

\[RF_{30} = \frac{sosmW30s_{sp2}} {sosmW30s_{sp2}+sosmW30e_{sp2} }\]

After 2020, RF is computed using the weight of the coarse elements dried at 105°C:

\[RF_{105} = \frac{sosmW105s_{sp2}} {sosmW105s_{sp2}+sosmW30e_{sp2} }\]

Extract the soil data

As a first step, we load and prepare the data. They are extracted from the ICOS soil database located in the French soil information system (DONESOL), which contains all the data from all sites. These files came from a SQL query.

Then, I extract the data and the sampling year for the selected site.

Extract coordinates and site stratification details

To compute design-based estimates of soil properties, we rely on spatial stratification parameters derived from the ETC’s pre-sampling analysis.

Using the spcosa package and KMZ files (which contain spatial layers), we extract:

• \(idstratum\): Stratum identifier (ranging from 1 to 10).

• \(H\): Total number of strata.

• \(n_h\): Sample size (number of SP-I plots) per stratum.

• \(nSites\): Total sample size (sum of all SP-I plots across strata).

• \(stratumArea\): Area of each stratum (in pixels).

• \(a_h\): Relative area per stratum.

Note: For KML files, extraction from the KMZ archive is required—this can be done using Windows.

Extract the soil depth limits

Accurate soil depth limits are essential for BADM quality control by ETC-Soil. While some errors may evade automated checks during C portal submission, uncorrected depth values directly impact derived calculations (e.g., soil stock estimates).

Checking the soil organic carbon (SOC) content

Checking for negative and missing values in SOC content. If the table is not empty, it means that SOC content is negative or missing.

Negative and missing values of SOC content are imputed using the layer-specific averages.

The following graph shows the organic carbon content frequency \(SOC_{layer}\) distribution across soil layers, following imputation of missing values using the layer-specific averages.

Checking the total nitrogen (NT) content

Checking for negative and missing values in NT content.

Negative values are replaced with \(NA\) and the missing values of NT are imputed using the layer-specific averages.

The following graph shows the NT content frequency \(NT_{layer}\) distribution across soil layers, following imputation of missing values using the layer-specific averages.

Compute the soil inorganic carbon (SIC) content

Soil inorganic carbon (SIC; g.kg^-1) was calculated as the product of the result of the calcimetry analysis (CaCO₃; g.kg^-1 equivalent) multiplied by 0.12.

Checking for missing values in inorganic carbon content.

Note: Negative values of carbonates are not replaced with the mean because they represent the detection threshold of the laboratory analysis.

The following graph shows the \(SIC_{layer}\) content frequency distribution across soil layers

Compute residual water content using the wet-basis approach

We compute the residual water content (\(RW^l_{ik}\)) using the wet based approach as follow :

For mineral layers at SP-I level:

\[ RW^l_{ik} = \frac{SOSM\_WX30\_E^l_{ik} - SOSM\_WX105\_E^l_{ik}}{SOSM\_WX30\_E^l_{ik}} \]

For organic layers at SP-I level:

SOSM_W30_E is considered as a dry mass because residual water content is assumed to be negligible.

In order to check the data quality, missing and negative values of soil water mass at 30 and 105°C are listed in the two tables below:

If the table below is not empty, it means that either or both SOSM_WX30_E or SOSM_WX105_E are missing:

If the table below is not empty, it means that the residual water is negative, that is, SOSM_WX30_E < SOSM_WX105_E.

The negative values are replaced with \(NA\).

Negative values are replaced with \(NA\) and the missing values of \(RW^l_{ik}\) are imputed using the layer-specific averages.

The following graph shows the \(RW^l_{ik}\) frequency distribution across soil layers, following imputation of missing values using the layer-specific averages.

Compute the density and mass of soil fractions for SP-II plots

Bulk density

The map shows the bulk density per layer.

Rock fragments

The map shows the rock fragments per layer.