BlueCarbon

BlueCarbon is a collection of functions with the main focus to help "blue carbon" scientists

Installation

Please note that the devtools, tidyverse, aomisc, drc package are necessary, and must be available prior to the installation of 'BlueCarbon'.

install.packages("tidyverse")  # only the first time
install.packages("drc")  # only the first time

install.packages("devtools") # only the first time
devtools::install_github("OnofriAndreaPG/aomisc")

library("aomisc")
library("tidyverse")
library("drc")

Install the BlueCarbon package (and the vignettes):

# You can install (and update) the BlueCarbon package from GitHub

devtools::install_github("costavale/BlueCarbon", build_vignettes = TRUE)

Expected data format

To use the functions collected here, you need to provide 2 data.frame:

1. Sediment core properties
2. Sediment sample properties

The data is expected to follow tidy data format, with one observation per row and one variable per column.

1. Sediment core properties

In particular, for each core core_ID (one row per each core) the following information need to be provided :

1. sampler_length, total length of the sampler
2. sampler_diameter, internal diameter of the sampler
3. internal_distance, distance between sampler top and core surface
4. external_distance, distance between sampler top and sediment surface

2. Sediment sample properties

1. Core_ID, Important use the same identification code in both data.frames as this column is the key to identify the core from which a sample is originated.
2. sample_ID, identification code used to identify each sample
3. depth, sampling depth in cm of each sample
4. weight, weight in g of each sample
5. LOI, value of each sample
6. Corg, value of each sample
7. other variables (optional)

Contents

The following functions are presented:

1. bc_compaction (WORKING)
2. bc_depth_correction (WORK IN PROGRESS)
3. bc_decomp (OLD VERSION - NOT WORKING)
4. bc_stock (WORK IN PROGRESS)

1. bc_compaction

The user provides the core_data data.frame and the function calculates compaction rates (in percentage) adding a column in the data.frame.
The function uses four arguments

bc_compaction(
  core_data,
  sampler_lenght,
  internal_distance,
  external_distance)

Arguments

• core_data data.frame with core properties
• sampler_lenght name of the column with the length of the sampler,
• internal_distance name of the column with the distance between sampler top and core surface,
• external_distance name of the column with the distance between sampler top and sediment surface

Output

compaction rates, percentage of compression in the core

2. bc_depth_correction

The user provides the core_data data.frame and the sample_data sample data.frame and the function calculates corrected sample depth and sample volume to account for compaction (linear or exponential methods).

The user can specify if the sample volume is estimated from a half of the core or in another way.

The function returns the sample data.frame modified with the addition of the estimated parameters.

bc_depth_correction(
  core_data,
  sample_data,
  sampler_lenght,
  sampler_diameter,
  internal_distance,
  external_distance,
  method)

Arguments

• core_data data.frame with core properties,
• sample_data data.frame with sample properties,
• sampler_length name of the column with the length of the sampler,
• sampler_diameter name of the column with the diameter of the sampler,
• internal_distance name of the column with the distance between sampler top and core surface,
• external_distance name of the column with the distance between sampler top and sediment surface
• method used to estimate the decompressed depth of each section, "linear" or "exp". Default is "linear"

Output

corrected sample depth, sample depth corrected taking into account the compaction rate sample volume, volume of each sample corrected for the compaction rate

3. bc_decomp (OLD VERSION - NOT WORKING...)

Suggestions:
Break down in 2 functions:  

1. Correct sample depth and sample volume to account for compaction (linear and exponential methods). Currently done in `bc_decomp`
        - User provides the core data.frame from `1` and another data.frame with the sample data. User can specify if the sample volume is estimated from a half of the core or if the sample volume was measured in another way.

2. Estimate carbon content from LOI, using pre-measured values. Currently done in `bc_decomp`
        - User can provide some measurements of carbon content and organic matter. The OC content of samples where OC was NOT measured is then added (when OC was measured, that value is maintained). Also allows the user to provide more data that just the one being analyzed (if you are analyzing cores from one area but have more samples with measured OC contents and wnat to use them in your model)

2.1 Add dry bulk density and carbon concentation (g cm3)

bc_decomp uses six arguments

bc_decomp(data, tube_lenght, core_in, core_out, diameter, method = "linear)

Arguments

• data data.frame with the following columns "ID" "cm" "weight" "LOI" "c_org"
• tube_length length in cm of the sampler,
• core_in length in cm of the part of the sampler left outside of the sediment (from the inside of the sampler),
• core_outlength in cm of the part of the sampler left outside of the sediment (from the outside of the sampler),
• diameter in cm of the sampler
• method used to estimate the decompressed depth of each section, "linear" or "exp". Default is "linear"

Output

The output is a data.frame that use the same "ID" of the data provided. For each row, the following information are calculated:

cm_deco, decompressed depth of each section expressed in cm
sect_h, height of each section expressed in cm
volume, volume of each section expressed in cm³
density, density of each section expressed in g/cm³
c_org_est, estimation of organic carbon concentration based on the linear relationship between LOI and c_org data provided
c_org_density, density of organic carbon concentration expressed in g/cm³
c_org_dens_sect, density of organic carbon concentration of each section expressed in g/cm²

4. bc_stock (Work In Progress)

bc_stock calculates carbon stock

bc_stock(data, depth = 1)

Arguments

• data data.frame with the following columns "ID", "cm_deco", "c_org_dens_sect"
• depth used to standardize the amount of carbon stored. Default is 1 m

Code of Conduct

Please note that the BlueCarbon project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.