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Functions to combine and adjust the outputs of the fourthcorner and randtest.rlq functions created using permutational models 2 and 4 (sequential approach).

Usage

combine.randtest.rlq(obj1, obj2, ...)
combine.4thcorner(four1,four2)
p.adjust.4thcorner(x, p.adjust.method.G = p.adjust.methods,
p.adjust.method.D = p.adjust.methods, p.adjust.D = c("global",
"levels"))

Arguments

four1

an object of the class 4thcorner created with modeltype = 2 (or 4)

four2

an object of the class 4thcorner created with modeltype = 4 (or 2)

obj1

an object created with randtest.rlq and modeltype = 2 (or 4)

obj2

an object created with randtest.rlq and modeltype = 4 (or 2)

x

an object of the class 4thcorner

p.adjust.method.G

a string indicating a method for multiple adjustment used for output tabG, see p.adjust.methods for possible choices

p.adjust.method.D

a string indicating a method for multiple adjustment used for output tabD/tabD2, see p.adjust.methods for possible choices

p.adjust.D

a string indicating if multiple adjustment for tabD/tabD2 should be done globally or only between levels of a factor ("levels", as in the original paper of Legendre et al. 1997)

...

further arguments passed to or from other methods

Details

The functions combines the outputs of two objects (created by fourthcorner and randtest.rlq functions) as described in Dray and Legendre (2008) and ter Braak et al (2012).

Value

The functions return objects of the same class than their argument. They simply create a new object where pvalues are equal to the maximum of pvalues of the two arguments.

References

Dray, S. and Legendre, P. (2008) Testing the species traits-environment relationships: the fourth-corner problem revisited. Ecology, 89, 3400–3412.

ter Braak, C., Cormont, A., and Dray, S. (2012) Improved testing of species traits-environment relationships in the fourth corner problem. Ecology, 93, 1525–1526.

Author

Stéphane Dray stephane.dray@univ-lyon1.fr

Examples

data(aravo)
four2 <- fourthcorner(aravo$env, aravo$spe, aravo$traits, nrepet=99,modeltype=2)
four4 <- fourthcorner(aravo$env, aravo$spe, aravo$traits, nrepet=99,modeltype=4)
four.comb <- combine.4thcorner(four2,four4)
## or directly :
## four.comb <- fourthcorner(aravo$env, aravo$spe, aravo$traits, nrepet=99,modeltype=6)
summary(four.comb)
#> Fourth-corner Statistics
#> ------------------------
#> Permutation method  Comb. 2 and 4  ( 99  permutations)
#> 
#> Adjustment method for multiple comparisons:   holm 
#>               Test Stat           Obs     Std.Obs     Alter Pvalue Pvalue.adj  
#> 1  Aspect / Height    r  -0.045735104 -1.16056804 two-sided   0.28       1.00  
#> 2   Slope / Height    r   0.094917344  2.10616338 two-sided   0.03       1.00  
#> 3    Form / Height    F  15.219879474  2.61169655   greater   0.03       1.00  
#> 4   PhysD / Height    r   0.113164322  1.95670623 two-sided   0.04       1.00  
#> 5   ZoogD / Height    F  15.227717714  2.15749663   greater   0.04       1.00  
#> 6    Snow / Height    r  -0.271739531 -5.94003192 two-sided   0.01       0.48  
#> 7  Aspect / Spread    r  -0.044170141 -1.50519083 two-sided   0.14       1.00  
#> 8   Slope / Spread    r  -0.017325425 -0.58484575 two-sided   0.60       1.00  
#> 9    Form / Spread    F   5.548173196  0.15996975   greater   0.31       1.00  
#> 10  PhysD / Spread    r  -0.051680330 -0.70770496 two-sided   0.52       1.00  
#> 11  ZoogD / Spread    F   0.120114487 -1.09483273   greater   0.97       1.00  
#> 12   Snow / Spread    r   0.065634673  0.61870811 two-sided   0.54       1.00  
#> 13  Aspect / Angle    r  -0.090837201 -1.78670739 two-sided   0.08       1.00  
#> 14   Slope / Angle    r   0.100281966  2.18691561 two-sided   0.03       1.00  
#> 15    Form / Angle    F  30.664664234  7.65142303   greater   0.01       0.48  
#> 16   PhysD / Angle    r   0.221380084  4.18396355 two-sided   0.01       0.48  
#> 17   ZoogD / Angle    F  28.051040522  3.40460234   greater   0.03       1.00  
#> 18    Snow / Angle    r  -0.269613756 -2.84488459 two-sided   0.02       0.72  
#> 19   Aspect / Area    r   0.031237858  0.68772978 two-sided   0.47       1.00  
#> 20    Slope / Area    r  -0.003864605 -0.06761600 two-sided   0.91       1.00  
#> 21     Form / Area    F  13.609309880  1.99637785   greater   0.04       1.00  
#> 22    PhysD / Area    r  -0.134371361 -2.12848630 two-sided   0.03       1.00  
#> 23    ZoogD / Area    F  49.672266332 12.49633111   greater   0.01       0.48  
#> 24     Snow / Area    r  -0.024574466 -0.64262951 two-sided   0.51       1.00  
#> 25  Aspect / Thick    r  -0.058466142 -1.84179759 two-sided   0.08       1.00  
#> 26   Slope / Thick    r   0.074151819  1.69103722 two-sided   0.13       1.00  
#> 27    Form / Thick    F  14.204346501  2.39286926   greater   0.04       1.00  
#> 28   PhysD / Thick    r   0.143161734  2.55814626 two-sided   0.03       1.00  
#> 29   ZoogD / Thick    F   2.825887968  0.21135429   greater   0.29       1.00  
#> 30    Snow / Thick    r  -0.154660144 -1.69220168 two-sided   0.09       1.00  
#> 31    Aspect / SLA    r  -0.007694551 -0.12131481 two-sided   0.90       1.00  
#> 32     Slope / SLA    r  -0.235864886 -4.18124897 two-sided   0.01       0.48  
#> 33      Form / SLA    F 100.787472071 13.95082688   greater   0.01       0.48  
#> 34     PhysD / SLA    r  -0.275524984 -4.33405203 two-sided   0.01       0.48  
#> 35     ZoogD / SLA    F   0.984301951 -0.93596671   greater   0.86       1.00  
#> 36      Snow / SLA    r   0.481181824  7.82597644 two-sided   0.01       0.48  
#> 37 Aspect / N_mass    r  -0.061575524 -1.14795000 two-sided   0.33       1.00  
#> 38  Slope / N_mass    r  -0.201308154 -3.73690796 two-sided   0.01       0.48  
#> 39   Form / N_mass    F  70.042280400 10.93881391   greater   0.01       0.48  
#> 40  PhysD / N_mass    r  -0.212434381 -3.83482413 two-sided   0.01       0.48  
#> 41  ZoogD / N_mass    F  10.300092724  0.61495960   greater   0.23       1.00  
#> 42   Snow / N_mass    r   0.429271163  7.47210139 two-sided   0.01       0.48  
#> 43   Aspect / Seed    r   0.011598435  0.49474310 two-sided   0.68       1.00  
#> 44    Slope / Seed    r   0.077073974  1.72751152 two-sided   0.11       1.00  
#> 45     Form / Seed    F   5.561841954 -0.02385651   greater   0.46       1.00  
#> 46    PhysD / Seed    r   0.078156305  1.42319208 two-sided   0.16       1.00  
#> 47    ZoogD / Seed    F   3.369068338  1.39648268   greater   0.11       1.00  
#> 48     Snow / Seed    r  -0.177640721 -1.83548235 two-sided   0.08       1.00  
#> 
#> ---
#> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 
plot(four.comb, stat = "G")