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pgirmess (version 1.7.1)

Spatial Analysis and Data Mining for Field Ecologists

Description

Set of tools for reading, writing and transforming spatial and seasonal data, model selection and specific statistical tests for ecologists. It includes functions to interpolate regular positions of points between landmarks, to discretize polylines into regular point positions, link distant observations to points, read subsets of big rasters, compute zonal statistics or table of categories from raster within polygons or circular buffers. The package also provides miscellaneous functions for model selection, spatial statistics and inference on diversity indexes, 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

2,610

Version

1.7.1

License

GPL (>= 2)

Maintainer

Patrick Giraudoux

Last Published

December 10th, 2021

Functions in pgirmess (1.7.1)

TukeyHSDs

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

Draw line segments between pairs of points.
PermTest

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

Gives an index vector of the class category of each value of a numerical vector
QGIS2sp

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

Gives a correlation matrix and the probability of Ho for each correlation
date2winter

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

Computes the edge of a square from its diagonal
correlog

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

Confidence interval of percentages
dirSeg

Computes segment directions.
distNode

Computes the distances between each nodes of a polyline.
piankabioboot

Bootstrap Pianka's index
polycirc

Computes the polygon coordinates of a circle
distSeg

Computes distances between the top coordinates of segments.
dirProj

Computes new coordinates given bearings and distances.
difshannonbio

Empirical confidence interval of the bootstrap of the difference between two Shannon indices
ks.gof

Kolmogorof-Smirnov goodness of fit test to normal distribution
distNNeigh

Computes distances to the nearest neighbour
kruskalmc

Multiple comparison test after Kruskal-Wallis
findR

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

Multiple comparisons after Friedman test
pclig

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

Provide square polygons or their node coordinates along a segment
piankabio

Computes the Pianka's index of niche overlap
rmls

Select objects in the parent frame and remove them.
postxt

Computes coordinates defined from their relative position on x and y in the plotting region
polycirc2

Computes the polygon coordinates of a circle sector
permcont

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

Extract the contents of a SpatialPixelsDataFrame or a SpatialGridDataFrame of categorical values within various buffer sizes centred on spatial points
trans2pix

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

Boostrap Shannon's and equitability indices
shannonbio

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

Thin a track just keeping the points separated by a user defined minimal distance
trans2seg

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

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

Values of the partial chi-square in each cell of a contingency table
write.delim

Write a data.frame
print.mc

print method for objects of class 'mc'
preybiom

Jackal and Genet diet in Algeria
distTot

Computes the total length of a polyline.
expandpoly

Homothetia (size expansion) of a polygon
transLines2pix

Convert a SpatialLines or a SpatialLinesDataFrame object into SpatialPointsDataFrame with spatial points at regular distance along the lines
val4symb

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

Upload waypoints to Garmin GPS
siegelp179

Data on rats training
readVista

Download waypoints and tracks from a GPS
rwhatbufNum

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

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

Model selection according to information theoretic methods
rwhatbufCat2

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

Merge two SpatialPoints or SpatialPointsDataFrame objects, one modelling a track, the other observations
tabcont2categ

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

Write a data.frame that has Chinese characters
shannon

Computes Shannon's and equitability indices
writePRJ

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

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