This worksheet provides guidance on how to prepare for the SEOSAW carbon dynamics workshop. The code chunks are all written in R.
This workshop assumes that you already know how to code in R.
In addition to a version of R, you should also have some kind of spreadsheet programme to visualise tabular data, and a web browser to download the workshop materials.
You can find this worksheet and other materials for the workshop in the Sharepoint folder.
If you don’t already have R installed on your computer, you should go to https://www.r-project.org/ and install the latest version for you operating system.
It is recommended to also install RStudio, which provides a user-friendly development environment for R code. Go to https://posit.co/downloads/ and install the latest version for your operating system.
The examples used in the workshop assume you are running a recent version of R. You must have R version 3.5.0 or above installed on your computer. You can check the version of R using:
R.Version()$version.string
## [1] "R version 4.2.3 (2023-03-15)"
We will use a number of different R packages during the workshop. You can
install packages using install.packages("<pkg>")
. You should have these
packages installed:
dplyr
ggplot2
taxize
lme4
ggeffects
data.table
remotes
Additionally, there are some packages which are not available on CRAN. These packages must be installed directly from their development repositories.
remotes::install_bitbucket("miombo/seosaw/seosawr/seosawr")
remotes::install_github("johngodlee/ProdVital")
remotes::install_github("umr-amap/BIOMASS")
The {seosawr}
package contains various functions used to clean and analyse
data from the SEOSAW dataset. In the SEOSAW office, we use the {seosawr}
package to check new data before it is assimilated into the database.
The {ProdVital}
package contains functions for estimating growth rates, rates
of productivity, loss, recruitment and mortality, using SEOSAW data.
The {BIOMASS}
package is used to calculate estimates of woody biomass, and is
very widely used. The BIOMASS package used to be on CRAN, but has since been
removed.
If you have trouble installing the {seosawr}
and {ProdVital}
packages,
anywhere the package is loaded (e.g. library(seosawr)
) you can instead load
the relevant functions from those packages from the R scipts in this
repository:
source("./rscripts/ProdVital_fn.R")
source("./rscripts/seosawr_fn.R")
The SEOSAW dataset is comprised of two main tables, “plots”, and “stems”. These
tables are linked by two columns plot_id
(ID of the plot) and census_date
(date of the census). The plots table contains one row per census per plot. The
stems table contains one row per measurement per stem.
Key columns in the stems table:
tree_id
- ID of treestem_id
- ID of stemstem_status
- Stem mortality status (“a” = alive, “r” = resprouting, “d” = dead)diam
- Stem diameter (cm)pom
- Height of the diameter measurement (m)agb
- Stem estimated above-ground woody biomassHere is an example of the stems stable:
Key columns in the plots table:
plot_area
- Area of plot (ha)min_diam_thresh
- Minimum stem diameter measured (cm)longitude_of_centre
, latitude_of_centre
- Lat-Lon coordinates of plot (decimal degrees)Here is an example of the plots table:
You can see more information about the columns in each of these tables by reading the “plot_columns.csv” and “stem_columns.csv” files in the Sharepoint folder.
For your data to be used in this workshop it must adhere to certain conditions. Unfortunately we don’t have time to clean and reformat new datasets.
Your data must: