rand.hp: Randomization Test for Hierarchical Partitioning

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/hier.part.R

Description

Randomizes elements in each column in xcan and recalculates hier.part num.reps times

Usage

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 rand.hp(y, xcan, family = "gaussian", gof = "RMSPE",
                    num.reps = 100)

Arguments

y

a vector containing the dependent variables

xcan

a dataframe containing the n independent variables

family

family argument of glm

gof

Goodness-of-fit measure. Currently "RMSPE", Root-mean-square 'Prediction' error, "NLL", Negative log Likelihood or "Rsqu", R-squared

num.reps

Number of repeated randomizations

Details

This function is a randomization routine for the hier.part function which returns a matrix of I values (the independent contribution towards explained variance in a multivariate dataset) for all values from num.reps randomizations. For each randomization, the values in each variable (i.e each column of xcan) are randomized independently, and hier.part is run on the randomized xcan. As well as the randomized I matrix, the function returns a summary table listing the observed I values, the 95th and 99th percentile values of I for the randomized dataset.

Value

a list containing

Irands

matrix of num.reps + 1 rows of I values for each dependent variable. The first row contains the observed I values and the remaining num.reps rows contains the I values returned for each randomization.

Iprobs

data.frame of observed I values for each variable, Z-scores for the generated distribution of randomized Is and an indication of statistical significance. Z-scores are cacluated as (observed - mean(randomizations))/sd(randomizations), and statistical significance (*) is based on upper 0.95 confidence limit (Z >= 1.65).

Author(s)

Chris Walsh [email protected].

References

Hatt, B. E., Fletcher, T. D., Walsh, C. J. and Taylor, S. L. 2004 The influence of urban density and drainage infrastructure on the concentrations and loads of pollutants in small streams. Environmental Management 34, 112–124.

Mac Nally, R. 2000 Regression and model building in conservation biology, biogeography and ecology: the distinction between and reconciliation of 'predictive' and 'explanatory' models. Biodiversity and Conservation 9, 655–671.

Mac Nally, R. 2002 Multiple regression and inference in conservation biology and ecology: further comments on identifying important predictor variables. Biodiversity and Conservation 11, 1397–1401.

Walsh, C. J., Papas, P. J., Crowther, D., Sim, P. T., and Yoo, J. 2004 Stormwater drainage pipes as a threat to a stream-dwelling amphipod of conservation significance, Austrogammarus australis, in southeastern Australia. Biodiversity and Conservation 13, 781–793.

See Also

hier.part, partition

Examples

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    #linear regression of log(electrical conductivity) in streams
    #against four independent variables describing catchment
    #characteristics (from Hatt et al. 2004).

    data(urbanwq)
    env <- urbanwq[,2:5]
    rand.hp(urbanwq$lec, env, fam = "gaussian", gof = "Rsqu")$Iprobs

    #logistic regression of an amphipod species occurrence in
    #streams against four independent variables describing
    #catchment characteristics (from Walsh et al. 2004).

    data(amphipod)
    env1 <- amphipod[,2:5]
    rand.hp(amphipod$australis, env1, fam = "binomial",
    gof = "logLik")$Iprobs

Example output

Loading required package: gtools

Please wait: running 100 randomizations 
           Obs Z.score sig95
fimp      0.24    1.94     *
sconn     0.46    3.03     *
sdensep   0.01   -0.65      
unsealden 0.14    0.88      

Please wait: running 100 randomizations 
        Obs Z.score sig95
fimp   2.74    2.69     *
fconn  7.54    9.75     *
densep 1.10    0.50      
unseal 2.13    2.02     *

hier.part documentation built on May 29, 2017, 7:12 p.m.