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pgirmess (version 1.6.9)

Spatial Analysis and Data Mining for Field Ecologists

Description

Set of tools for reading, writing and transforming spatial and seasonal data in ecology, model selection and specific statistical tests. It includes functions to discretize polylines into regular point intervals, link observations to those points, compute geographical coordinates at regular intervals between waypoints, read subsets of big rasters, compute zonal statistics or table of categories within polygons or circular buffers from raster. The package also provides miscellaneous functions for model selection, spatial statistics, geometries, writing data.frame with Chinese characters, and some other functions for field ecologists.

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Version

Install

install.packages('pgirmess')

Monthly Downloads

2,669

Version

1.6.9

License

GPL (>= 2)

Maintainer

Patrick Giraudoux

Last Published

March 12th, 2018

Functions in pgirmess (1.6.9)

Segments

Draw line segments between pairs of points.
dirSeg

Computes segment directions.
difshannonbio

Empirical confidence interval of the bootstrap of the difference between two Shannon indices
dirProj

Computes new coordinates given bearings and distances.
piankabio

Computes the Pianka's index of niche overlap
distNNeigh

Computes distances to the nearest neighbour
distSeg

Computes distances between the top coordinates of segments.
pave

Provide square polygons or their node coordinates along a segment
print.mc

print method for objects of class 'mc'
piankabioboot

Bootstrap Pianka's index
gps2gpx

Download waypoints or tracks from a GPS to a gpx file
readGDALbbox

Read a raster using rgdal within a user specified bounding box
postxt

Computes coordinates defined from their relative position on x and y in the plotting region
kruskalmc

Multiple comparison test after Kruskal-Wallis
polycirc

Computes the polygon coordinates of a circle
date2winter

Convert a POSIXt date into categories corresponding to a autumn/winter/spring sequence
diag2edge

Computes the edge of a square from its diagonal
pclig

Compute the percentage of each cell of a matrix or data.frame by row
permcont

Random permutation of a contingency table n row x 2 columns
shannonbioboot

Boostrap Shannon's and equitability indices
siegelp179

Data on rats training
rwhatbufCat2

Extract the contents of a raster file of categorical values within various buffer sizes centred on spatial points
rwhatbufCat

Extract the contents of a SpatialPixelsDataFrame or a SpatialGridDataFrame of categorical values within various buffer sizes centred on spatial points
distTot

Computes the total length of a polyline.
writecn.delim

Write a data.frame that has Chinese characters
tabcont2categ

Convert a contingency table (data.frame) into a presence/absence table of categories
expandpoly

Homothetia (size expansion) of a polygon
writePRJ

Write the projection file of a shapefile from a spatial object
polycirc2

Computes the polygon coordinates of a circle sector
thintrack

Thin a track just keeping the points separated by a user defined minimal distance
rwhatbufNum

Extract the contents of a SpatialPixelsDataFrame or a SpatialGridDataFrame of numerical values within various buffer sizes centred on spatial points
ks.gof

Kolmogorof-Smirnov goodness of fit test to normal distribution
preybiom

Jackal and Genet diet in Algeria
selMod

Model selection according to information theoretic methods
valchisq

Values of the partial chi-square in each cell of a contingency table
val4symb

Center a numerical vector on a parameter position and provides absolute values and colors according to negative and positive values
shannon

Computes Shannon's and equitability indices
shannonbio

Computes Shannon's and equitability indices from a data frame of dietary analysis (n, biomass,...)
mergeTrackObs

Merge two SpatialPoints or SpatialPointsDataFrame objects, one modelling a track, the other observations
readVista

Download waypoints and tracks from a GPS
rmls

Select objects in the parent frame and remove them.
transLines2pix

Convert a SpatialLines or a SpatialLinesDataFrame object into SpatialPointsDataFrame with spatial points at regular distance along the lines
trans2pix

Convert a transect coordinate file with some waypoints separated by NA into a matrix with intermediate coordinates replacing NA.
write.delim

Write a data.frame
writeGPX

Convert a data frame into a GPX file of waypoints or track
uploadGPS

Upload waypoints to Garmin GPS
trans2seg

Convert a transect coordinate file into a matrix with segment coordinates.
QGIS2sp

Changes a copied-to-clipboard QGIS attribute table into a sp Spatial object or a data.frame
TukeyHSDs

Simplify the list of a TukeyHSD object keeping the significant differences only.
findR

Computes the distance between the centroid and the most distant coordinate of a geographical coordinate set
classnum

Gives an index vector of the class category of each value of a numerical vector
friedmanmc

Multiple comparisons after Friedman test
pairsrp

Produces a matrix of scatterplot, regression coefficient and p(Ho)
distNode

Computes the distances between each nodes of a polyline.
cormat

Gives a correlation matrix and the probability of Ho for each correlation
CI

Confidence interval of percentages
PermTest

Permutation test for lm, lme and glm (binomial and Poisson) objects
correlog

Computes Moran's or Geary's coefficients on distance classes