pgirmess & pgirbric
functions for data handling and analysis in ecology
is a package of miscellaneous
developped in R for spatial analysis and model selection in ecology.
been used in
the course of on going research carried out at the Department
of the University of
Franche-Comté, as and when required, sometimes with several
contributors (mentioned in the documentation). The version under development can
The stable version and a pdf reference manual are can be downloaded on
package name comes from the acronym Patrick GIRaudoux MESS (the
reality and an indirect hommage to more essential packages, eg MASS,
etc.). We do the best we can to optimise each function and
pgir must be blamed for any misworking.
is a package with
functions not intended to be published on CRAN for some reasons (eg too
much device specific or still to improve or deprecated in other
packages, etc.). It can however be downloaded on GitHub. The
name is an
acronym of Patrick GIRaudoux BRIColage, the latter a French name for
'do-it-yourself' which may be another kind of mess, or for BRICk, some
functions seen as brick to build something more general later.
Same comments as above about misworkings.
Siegel & Castellan (1988)
am often asked which procedure is used for multiple comparisons in kruskalmc.
You'll find a citation of "Siegel and Castellan (1988) Non
parametric statistics for the behavioural sciences. MacGraw
Int., New York. pp 213-214"
pgirmess install on linux (e.g.
linux mint 14, 23.02.2013)
some versions of linux, I have got
reports of pgirmess "failing to install correctly". This is
generally not due to pgirmess (however see daily checks on CRAN) but
most often to a defective installation of gdal (on
pgirmess and rgdal depends on)
- in linux (synaptic or similar software), first install:
proj-devel lib & dependencies
- then, in R, install
libgdal1-dev lib & dependencies
pgirmess & dependencies (including rgdal)
under development: pgirmess
can also install directly the version under development from R with
only if package 'devtools' is not already installed
the latest changes
the package: pgirbric
can also install directly pgirbric from R with those commands:
# only if
'devtools' is not already installed
the latest change
Working prototypes of shell
scripts to run within GRASS 63 or
Those files must be copied into a folder
visible with PATH eg. under linux have a
folder in your home directory and add
to /usr/lib/grass/etc/Init.sh. To specify rights e.g. chmod a+x r.what.buff2
before running it may be necessary.
generates a text file of the frequency of each category of
a raster map
within various radius buffers computed on vector point sites. A
circular buffer is created around each point location of the vector
and the final output is text file of 4 columns: col 1 = radius, col 2 =
ID, col 3 = pixel category value, col 4 = pixel count
corresponding to this value. Category * is the null value.
permits to generate a text file of the frequency of each
a raster map
for areas covered by polygon vector objects. The output is a text file
of 3 columns: col 1 = polygon ID number, col 2 = category
value, col 3 = pixel count
corresponding to this category. Category * is the null value.
prototypes have their equivalent in R, package pgirmess
>= 1.4.5 with the functions rwhatbufCat, rwhatbufNum