Man pages for petrkeil/spasm
Species association measures for various data types

CA_brayBray-Curtis dissimilarity matrix
CA_chiChi-square distance matrix
CA_cov_corCovariance or correlation matrix calculated from community...
CA_hellHellinger distance matrix
CA_ruzAbundance-based Jaccard (a.k.a. Ruzicka) dissimilarity matrix
C_checkerNumber of checkerboard species pairs
C_comboNumber of unique species combinations
C_connNetwork connectance
C_forbesForbes' coefficient of association among species in a...
C_jaccPairwise Jaccard associations among species in a community...
C_matchSimple matching coefficient of Sokal & Michener (1958)
C_pearsPearson tetrachoric correaltions for binary data
C_ratioVariance ratio of Schluter (1984)
C_segThe classical 'C-score' seggregation metric of Stone &...
C_simPairwise Simpson aggregation among species in a community...
C_sorPairwise Sorensen associations among species in a community...
C_tog'Togetherness' metric of Stone & Roberts (1992), and its...
C_wWhittaker's index of overall association in a community...
data.AtmarAtmar & Patterson (1995) incidence matrices
data.HarvardOrwig, Foster & Ellison (2015) Harvard forest plot
data.UlrichUlrich & Gotelli (2010) abundance matrices
dist2listConversion of distance matrix to list
dpoint.MVNBivariate probablity density function in a 2D square
dpoint.MVN.imageFunciton that generates the MVN density as a pixel image
hubalekHubalek's indices calculated all at once
KDBivariate nearest neighbor distance function (D) and...
PCFrBivariate pair correlation function for a given distance r
PDFtexpTruncated exponential probability density function
plot.PMBivariate nearest neighbor distance function (D) and...
PM.multispecMulti-species P-M classfication of Wiegand et al. (2007)
ppp.to.commConversion of point pattern to community matrix Y
ppp.trimFunction that removes, from point pattern, species with N...
rpoint.MVNFunction that generates n points in a 2D space with a...
sim.comm.centeredFunction that simulates a "centered" community The simulation...
sim.comm.jitteredFunction that simulates a "jittered" community
sim.pairTwo point patterns with a given attraction or repulsion
spasmspasm
spasm-packageSpecies association measures for various data types
step_CA_ITOne realization of the IT algorithm of Ulrich & Gotelli...
step_CA_PoissonOne realization of the an algorithm that resamples each row...
step_CA_rowrandomOne realization of the an algorithm that resamples each row...
step_C_sim2One realization of the sim2 algorithm from EcoSimR
Z_scoreStandardized Z-score for a given null model algorithm and ISA...
petrkeil/spasm documentation built on June 14, 2019, 3:03 a.m.