phcfM R package

phcfM is an R package for modelling anthropogenic deforestation. It
was initially developed to obtain REDD+ baseline scenarios of
deforestation for the programme holistique de conservation des forêts
à Madagascar (from which the package is named after). It includes
two main functions:

1. demography(), to model the population growth with time in a
   hierarchical Bayesian framework using population census data and
   Gaussian linear mixed models.

2. deforestation(), to model the deforestation process in a
   hierarchical Bayesian framework using land-cover change data and
   Binomial logistic regression models with variable time-intervals
   between land-cover observations.

Code and manual

The last stable version of the phcfM R package (phcfM_1.3) is
officially available for several operating systems (Unix, Windows and
Mac OSX) on the Comprehensive R Archive Network (CRAN).

The source code and manual for the testing version (phcfM_1.3-1) is available here:

• Package source: phcfM_1.3-1.tar.gz
• Reference manual: phcfM_1.3-1.pdf

Example

A GRASS location (phcfM_SM) and two mapsets with geographical data
layers (PERMANENT and study_area_4) are available to illustrate the
use of the phcfM R package. Associated to the GRASS location, a
directory (./scripts) includes the data and the R/GRASS scripts used
for the demographic and deforestation models.

• GRASS location: phcfM_SM.zip
• ./scripts: scripts.zip

The following scheme illustrates the structure of the ./scripts folder.

./scripts
|-- 0_demography_SAs.R
|-- 1_deforestation_dataset_SA4.R
|-- 2_deforestation_model_SA4.R
|-- 3_deforestation_forecast_PS4.R
|-- data
|-- |-- 0_data_demography_SAs.txt
|-- |-- 1_data_deforestation_SA4.txt
|-- fragindex
|-- |-- recl.txt
|-- |-- r.forestfrag
|-- outputs
|-- |-- demography
|-- |-- forecast
|-- |-- model

Four scripts are available: 0_demography_SAs.R is a R script to
estimate the parameters of the demographic model using the function
demography() of the phcfM R package,
1_deforestation_dataset_SA4.R is a R/GRASS script to prepare the
data-set for the deforestation model from the geographic data layers
of the phcfM_SM GRASS location, 2_deforestation_model_SA4.R is a R
script to estimate the parameters of the deforestation model using the
function deforestation() of the phcfM R package and
3_deforestation_forecast_PS4.R is a R/GRASS script to forecast
deforestation and carbon dioxide emissions.

The ./scripts/data folder includes the population census data file
0_data_demography_SAs.txt used for the demographic model. Running
the 1_deforestation_dataset_SA4.R script generates the file
1_data_deforestation_SA4.txt (the data-set used for the
deforestation model) in the ./scripts/data folder. The
./scripts/fragindex folder includes the GRASS function
r.forestfrag to compute the forest fragmentation index. The
./scripts/outputs folder includes the outputs for the demographic
model, the deforestation model and the deforestation forecast.

Related publications

Vieilledent G., Grinand C., Vaudry R. 2013. Forecasting
deforestation and carbon emissions in tropical developing countries
facing demographic expansion: a case study in Madagascar. Ecology
and Evolution. 3:1702-1716. doi:
10.1002/ece3.550.

Contact

Ghislain Vieilledent
Cirad, UPR BSEF
Campus de Baillarguet
TA C-105/D
34398 Montpellier cedex 5
FRANCE

Skype: ghislain.vieilledent
Email: ghislain(dot)vieilledent(at)cirad(dot)fr
WWW: http://ghislain.vieilledent.free.fr