Rcentury: soil dynamics simulation with CENTURY and R

Downloading and setting up CENTURY

The goal of the Rcentury R package is to run the CENTURY soil dynamics simulation from R. Rcentury is NOT an implementation of CENTURY. Rather, it has been built as an interface in R to the actually CENTURY software, which must have been downloaded in advance and placed in a local folder. This guarantees that calculations are done via the actual CENTURY code.

We first need to download and install the CENTURY software locally. This must be done directly from the web site https://www.soilcarbonsolutionscenter.com (after filling out a consent form). Two zip-files are automatically downloaded, which must then be unzipped into a local folder of our choice. The uncompressed folders contain all the necessary files, plus several user manuals and examples. Any question related to CENTURY must be addressed directly to the creators of that software. See contact information on the https://www.soilcarbonsolutionscenter.com web page.

The CENTURY software can be used in stand-alone mode, to be run on a Windows command prompt. To do so, just follow the instructions in the accompanying documents (available after uncompressing). Additionally, a series of ASCII files must also be prepared in advance, which will then be read when CENTURY is executed. Those files include:

• A set of up to 11 option files with extension ‘.100’, containing a large set of parameters. The name of these files is fixed.
• A single site file, also with extension ‘.100’, containing site-specific parameters. The name of this file can be chosen at will.
• A weather file, with extension ‘.wth’, that includes monthly data for precipitation and minimum and maximum temperature for the site.
• A schedule file, with extension ‘.sch’, which specifies the timing for scheduling management actions and controlling crop growth throughout the simulation.

All these ASCII files, together with the executable ‘century_47.exe’ and ‘list100_47.exe’ programs, must be in the same folder. Notice that the CENTURY zip-files contain examples of those four types of ASCII input files plus the two ‘.exe’ programs. Therefore, the CENTURY example files can be used as starting templates to prepare our own parameter files. Those example files are located in three sub-folders that are created when unzipping the CENTURY downloaded files:

1. Grassland with grazing simulation ran for a site in Xilingol, Mongolia (sub-folder “/Century+Examples/Century Examples/1.soil_texture_ppt”).
2. Plant production for different grass types with different relative temperature growth curves (sub-folder “/Century+Examples/Century Examples/3.plant_production”).
3. Duke and Harvard forests (sub-folder “/Century+Examples/Century Examples/4.forest”).

In each of those folders we can also find the two executables ‘century_47.exe’ and ‘list100_47.exe’ that we will use in the simulations.

What is Rcentury for?

Editing, modifying and then saving on disk each of those input ASCII files individually is an extremely tedious and challenging task, particularly when our goal is to apply the CENTURY model to a large number of different sites, and/or under a variety of different climatic and land management scenarios. This manual process is also highly susceptible to errors, given the vast number of parameters that must be carefully tuned-up and adjusted.

Therefore, it is a significant improvement in workflow to be able to perform all these file operations from within a comprehensive software environment like R. As mentioned above, the goal of package Rcentury is thus to run CENTURY 4.7 from within R. That includes preparing all files (treatments, schedule, weather and site characteristic), and then read and load the result files into our R session as a data.frame.

Main functions in the Rcentury package

The ASCII files that are required by the CENTURY software can be read and write with functions that are provided with the Rcentury package:

• read_100/write_100: to read/write files with extension ‘.100’, save for site files.
• read_site/write_site: to read/write input site files (also extension ‘.100’).
• read_weather/write_weather: to read/write weather files (extension ‘.wth’).
• read_schedule/write_schedule: to read/write schedule files (extension ‘.sch’).
• read_lis: utility program to read binary ‘.bin’ files containing results from the simulation.

These functions allow us to first read the example files provided with the CENTURY software, change the parameters at will and then write the modified dataset on disk.

Once those files are available in the same directory where they two ‘.exe’ files are located, we can run CENTURY with the century_run.R function. Internally, century_run runs sequentially the following programs:

1. ‘century_47.exe’: it creates a binary file on disk with extension ‘.bin’.
2. ‘list100_47.exe’: it reads the ‘.bin’ file and builds an ASCII ASCII ‘.lis’ file containing a sequence of columns with results.
3. read_lis.R: it reads the ‘.lis’ ASCII file into the R session as a data.frame that can be manipulated and analysed.