Main /
Hierarchical Partitioning
Summary
- Ctenophorus fordi - spinifex and bare are significant.
- Ctenotus atlas - spinifex and bare ground are significant.
- Ctenotus schomburgkii - clay is significant.
- Lerista distinguenda - spinifex is significant.
- Lerista edwardsae - no single factor significant. Melaleuca then bare are the highest.
- Menetia greyii - Bare ground significant.
- Nephrurus stellatus - Bare ground is significant.
- Pogona sp. - Melaleuca is significant.
Joint was not very high for any species.
Spinifex, bare ground, and leaf litter varied significantly (P < 0.05) between the five site treatments (Connected, Isolated, ParkDune, ParkSwale, Roadside).
When looking at Conn (Connected, Disconnected) and Setting (Park, Dune), Setting was significant for spinifex. Nothing else was significant at P<0.05.
Using LME
Reptiles
- Cten ford - setting
- Cten atla - setting
- Cten scho - setting
- Leri dist - setting
- Mene grey - setting, dune, site:dune
- Neph stel - dune
- Pogo sp - NONE
- NumSpec - setting, site:conn (log+1)
- Sum - setting (log+1)
Vegetation
- Spinifex - setting, setting:dune - significantly higher in park. Park swale > Park dunes. Farm dune > Farm swale (no spinifex in farm swales)
- Melaleuca - setting:dune- farm dune > park dune, park swale > farm swale
- Eucalyptus - site:setting - farm dunes < farm swales, park dunes > swale
- Bare - dune - higher in dune
- Leaf - dune, setting:dune, site:setting:dune
- Other - site:setting, setting:dune, site:setting:dune
- Clay - dune - higher in swale
- Canopy - dune, site:setting - Hincks farm > Pinks farm, Pinks park > Hinks park
- NumSpec -setting, site:conn, Hincks connected > Pinks connected, Pinks isolated > Hincks isolated
- Sum - setting - more animals in park
- which veg things are different between park and reserve?
Code
# Test the five site treatments on continuous vegetation data
for (name in c(attributes(env)$names)) {
envvar <- epdata[[name]]
print(name)
a <- aov(envvar ~ TreatCode, data=epdata)
print(summary(a))
}
# LME tests of species counts vs formal structure
# nb - is it meaningful to log+1 transform number of species? Either way, same parameters were significant.
for (name in c(attributes(lotsacritters)$names,"NumSpec","Sum")) {
species<-epdata[[name]]
print(name)
mod<-lme(log(1+species) ~ Site + Setting + Dune + Conn
+ Site:Setting + Site:Dune + Site:Conn
+ Setting:Dune + Setting:Dune:Site,
random = ~1|Block,
data=epdata,
method="ML")
print(anova(mod))
}
# LME tests of veg data vs formal structure
for (name in c(attributes(env)$names, "NumSpec", "Sum")) {
veg<-epdata[[name]]
print(name)
mod<-lme(veg ~ Site + Setting + Dune + Conn
+ Site:Setting + Site:Dune + Site:Conn
+ Setting:Dune + Setting:Dune:Site,
random = ~1|Block,
data=epdata,
method="ML")
print(anova(mod))
}
Ctenophorus fordi
$IJ
I J Total
Spinifex 0.282519609 0.053795696 0.336315305
Melaleuca 0.004119899 0.000889869 0.005009768
Eucalyptus 0.017213825 0.005975337 0.023189162
Bare 0.108952403 0.018625901 0.127578304
Leaf 0.055508647 -0.010063317 0.045445331
Other 0.031691511 -0.029826892 0.001864619
Clay 0.007497372 0.001082470 0.008579842
Canopy 0.029493098 -0.016444191 0.013048907
$I.perc
I
Spinifex 52.6110840 0.027 *
Melaleuca 0.7672117 0.839
Eucalyptus 3.2055758 0.485
Bare 20.2892255 0.070 .
Leaf 10.3368758 0.199
Other 5.9016249 0.305
Clay 1.3961681 0.739
Canopy 5.4922342 0.384
Setting 24.5132084 0.013 Spinifex 35.5790558 0.029 Melaleuca 0.6008803 0.877 Eucalyptus 4.0676255 0.345 Bare 16.4034445 0.071 Leaf 8.6495974 0.221 Other 3.2757966 0.536 Clay 0.9567297 0.806 Canopy 5.9536618 0.331
Including condition and setting:
$IJ
I J Total
Setting 0.0789431157 0.1773859982 0.256329114
Condition 0.0294446182 0.1019102599 0.131354878
Spinifex 0.1163063281 0.2200089766 0.336315305
Melaleuca -0.0004874122 0.0054971803 0.005009768
Eucalyptus 0.0082522630 0.0149368991 0.023189162
Bare 0.0449315548 0.0826467493 0.127578304
Leaf 0.0148009251 0.0306444055 0.045445331
Other 0.0024835818 -0.0006189629 0.001864619
Clay 0.0013572105 0.0072226311 0.008579842
Canopy 0.0344263895 -0.0213774821 0.013048907
$I.perc
I
Setting 23.8889597 0.002 **
Condition 8.9102298 0.164
Spinifex 35.1954336 0.025 *
Melaleuca -0.1474957 1.000
Eucalyptus 2.4972156 0.523
Bare 13.5967284 0.100
Leaf 4.4789048 0.374
Other 0.7515562 0.913
Clay 0.4107052 0.910
Canopy 10.4177625 0.322
Ctenotus atlas
$IJ
I J Total
Spinifex 0.13468950 0.045250568 1.799401e-01
Melaleuca 0.05499363 0.021555405 7.654904e-02
Eucalyptus 0.05818458 -0.001471621 5.671296e-02
Bare 0.10872661 0.043340162 1.520668e-01
Leaf 0.01142134 -0.011330472 9.086391e-05
Other 0.03047367 -0.014637202 1.583647e-02
Clay 0.00592294 -0.001512726 4.410214e-03
Canopy 0.01291559 0.018413198 3.132879e-02
$I.perc
I
Spinifex 32.274264 0.028 *
Melaleuca 13.177561 0.200
Eucalyptus 13.942175 0.154
Bare 26.053044 0.068 .
Leaf 2.736778 0.716
Other 7.302094 0.396
Clay 1.419253 0.781
Canopy 3.094831 0.700
Setting 35.1161831 0.016 Spinifex 15.3046099 0.111 Melaleuca 9.4886690 0.195 Eucalyptus 14.1790256 0.116 Bare 17.4852104 0.084 Leaf 2.5040231 0.659 Other 3.1871242 0.573 Clay 0.5524115 0.931 Canopy 2.1827433 0.765
Including condition and setting:
$IJ
I J Total
Setting 0.0850725881 0.202765652 2.878382e-01
Condition 0.0810476061 0.209020368 2.900680e-01
Spinifex 0.0460075757 0.133932491 1.799401e-01
Melaleuca 0.0225981500 0.053950890 7.654904e-02
Eucalyptus 0.0385725802 0.018140381 5.671296e-02
Bare 0.0479264148 0.104140361 1.520668e-01
Leaf 0.0046114950 -0.004520631 9.086391e-05
Other 0.0064443959 0.009392075 1.583647e-02
Clay -0.0003957471 0.004805961 4.410214e-03
Canopy 0.0136110270 0.017717763 3.132879e-02
$I.perc
I
Setting 24.6233146 0.012 *
Condition 23.4583283 0.019 *
Spinifex 13.3163812 0.094 .
Melaleuca 6.5407832 0.256
Eucalyptus 11.1644044 0.113
Bare 13.8717678 0.101
Leaf 1.3347459 0.733
Other 1.8652587 0.681
Clay -0.1145446 0.998
Canopy 3.9395604 0.711
Ctenotus schomburgkii
I J Total
Spinifex 0.007693853 -0.001357805 0.0063360479
Melaleuca 0.014093235 -0.013730399 0.0003628356
Eucalyptus 0.055730411 0.048853066 0.1045834775
Bare 0.050082097 0.031982205 0.0820643018
Leaf 0.031562937 0.065062025 0.0966249615
Other 0.075530605 -0.037602979 0.0379276263
Clay 0.119076878 0.048023720 0.1671005979
Canopy 0.040694868 0.033658265 0.0743531326
$I.perc
I
Spinifex 1.950453 0.717
Melaleuca 3.572748 0.580
Eucalyptus 14.128105 0.133
Bare 12.696212 0.206
Leaf 8.001457 0.380
Other 19.147612 0.095 .
Clay 30.186940 0.060 .
Canopy 10.316474 0.264
Including setting:
Setting 35.720563 0.001 Spinifex 3.911020 0.428 Melaleuca 2.059892 0.591 Eucalyptus 8.027591 0.210 Bare 8.117147 0.266 Leaf 5.678909 0.395 Other 8.083982 0.217 Clay 19.005655 0.075 Canopy 9.395242 0.244
Including condition and setting:
I J Total
Setting 0.0804953198 0.118082361 0.1985776805
Condition 0.0373524086 0.064407967 0.1017603761
Spinifex 0.0113189307 -0.004982883 0.0063360479
Melaleuca 0.0008819496 -0.000519114 0.0003628356
Eucalyptus 0.0293474992 0.075235978 0.1045834775
Bare 0.0215999924 0.060464309 0.0820643018
Leaf 0.0241960724 0.072428889 0.0966249615
Other 0.0148067348 0.023120892 0.0379276263
Clay 0.0727332909 0.094367307 0.1671005979
Canopy 0.0568532257 0.017499907 0.0743531326
$I.perc
I
Setting 23.0259371 0.001 ***
Condition 10.6847729 0.115
Spinifex 3.2378154 0.396
Melaleuca 0.2522844 0.959
Eucalyptus 8.3949436 0.149
Bare 6.1787451 0.258
Leaf 6.9213619 0.226
Other 4.2355126 0.302
Clay 20.8055845 0.050 *
Canopy 16.2630424 0.184
Lerista.distinguenda
$IJ
I J Total
Spinifex 0.158548186 0.034402921 1.929511e-01
Melaleuca 0.008878447 0.012691453 2.156990e-02
Eucalyptus 0.006565441 0.014601900 2.116734e-02
Bare 0.008518065 -0.002356438 6.161628e-03
Leaf 0.010665160 0.001849853 1.251501e-02
Other 0.006058410 -0.005992105 6.630434e-05
Clay 0.016264492 0.032209067 4.847356e-02
Canopy 0.033279092 0.030382187 6.366128e-02
$I.perc
I
Spinifex 63.730972 0.023
Melaleuca 3.568833 0.671
Eucalyptus 2.639084 0.841
Bare 3.423972 0.738
Leaf 4.287031 0.727
Other 2.435274 0.898
Clay 6.537772 0.543
Canopy 13.377062 0.351
Setting 54.174420 0.002 Spinifex 21.487833 0.087 Melaleuca 1.949073 0.696 Eucalyptus 2.998589 0.645 Bare 1.889921 0.742 Leaf 3.313789 0.657 Other 3.073721 0.708 Clay 5.127236 0.450 Canopy 5.985417 0.446
With condition and setting:
$IJ
I J Total
Setting 0.096030967 0.204872402 3.009034e-01
Condition 0.106655834 0.222735269 3.293911e-01
Spinifex 0.050400390 0.142550717 1.929511e-01
Melaleuca 0.003562767 0.018007133 2.156990e-02
Eucalyptus 0.009263527 0.011903814 2.116734e-02
Bare 0.002295763 0.003865865 6.161628e-03
Leaf 0.001554563 0.010960449 1.251501e-02
Other 0.001606906 -0.001540602 6.630434e-05
Clay 0.010656184 0.037817375 4.847356e-02
Canopy 0.018915523 0.044745756 6.366128e-02
$I.perc
I
Setting 31.9100797 0.011 *
Condition 35.4406109 0.001 ***
Spinifex 16.7475190 0.073 .
Melaleuca 1.1838701 0.782
Eucalyptus 3.0781724 0.524
Bare 0.7628579 0.837
Leaf 0.5165650 0.940
Other 0.5339581 0.963
Clay 3.5409376 0.455
Canopy 6.2854292 0.539
Lerista edwardsae
$IJ
I J Total
Spinifex 0.068770068 0.018098802 0.0868688705
Melaleuca 0.103633078 0.049848858 0.1534819356
Eucalyptus 0.005292995 -0.002890250 0.0024027450
Bare 0.079393097 -0.038382266 0.0410108306
Leaf 0.031066343 -0.030907214 0.0001591293
Other 0.045608649 0.036542347 0.0821509953
Clay 0.025790353 0.007842244 0.0336325966
Canopy 0.014295718 -0.011515882 0.0027798368
$I.perc
I
Spinifex 18.395082 0.134
Melaleuca 27.720475 0.064 .
Eucalyptus 1.415806 0.854
Bare 21.236601 0.109
Leaf 8.309835 0.370
Other 12.199709 0.221
Clay 6.898577 0.385
Canopy 3.823915 0.624
Spinifex 6.5606680 0.263 Melaleuca 16.4097518 0.069 Eucalyptus 0.8614492 0.893 Bare 11.3054938 0.133 Leaf 5.6088447 0.334 Other 9.7576900 0.151 Clay 2.9712002 0.528 Canopy 3.8089638 0.446 epdata...Site....epdata...Setting... 42.7159385 0.018 Setting 19.497802 0.080 Spinifex 9.019138 0.226 Melaleuca 20.983543 0.074 Eucalyptus 1.030877 0.889 Bare 18.035756 0.086 Leaf 7.809179 0.310 Other 13.829650 0.141 Clay 7.172307 0.310 Canopy 2.621747 0.702
Including condition and setting:
$IJ
I J Total
Setting 0.029225864 0.044476819 0.0737026824
Condition 0.113828312 0.147666909 0.2614952208
Spinifex 0.022806085 0.064062785 0.0868688705
Melaleuca 0.047618731 0.105863205 0.1534819356
Eucalyptus 0.003514044 -0.001111299 0.0024027450
Bare 0.045952736 -0.004941906 0.0410108306
Leaf 0.009335224 -0.009176095 0.0001591293
Other 0.036534017 0.045616979 0.0821509953
Clay 0.013559729 0.020072868 0.0336325966
Canopy 0.009580873 -0.006801036 0.0027798368
$I.perc
I
Setting 8.804148 0.209
Condition 34.290220 0.003 ***
Spinifex 6.870221 0.193
Melaleuca 14.344909 0.077
Eucalyptus 1.058588 0.768
Bare 13.843036 0.104
Leaf 2.812191 0.506
Other 11.005693 0.091
Clay 4.084802 0.398
Canopy 2.886191 0.785
Menetia greyii
$IJ
I J Total
Spinifex 0.10580019 -0.021682476 8.411771e-02
Melaleuca 0.05184491 0.007643409 5.948832e-02
Eucalyptus 0.01162429 -0.009358820 2.265469e-03
Bare 0.14144477 -0.079599815 6.184495e-02
Leaf 0.03173728 -0.031726563 1.071934e-05
Other 0.01392941 -0.011531731 2.397680e-03
Clay 0.05242940 0.015877986 6.830738e-02
Canopy 0.01223926 -0.002058008 1.018125e-02
$I.perc
I
Spinifex 25.127731 0.067 .
Melaleuca 12.313258 0.197
Eucalyptus 2.760789 0.647
Bare 33.593382 0.032 *
Leaf 7.537661 0.363
Other 3.308260 0.672
Clay 12.452074 0.192
Canopy 2.906845 0.728
Setting 11.482420 0.101 Aspect 9.678386 0.162 epdata...Setting....epdata...Dune... 27.852460 0.065 Spinifex 10.420934 0.147 Melaleuca 7.788696 0.298 Eucalyptus 2.000454 0.800 Bare 10.333203 0.201 Leaf 5.748670 0.421 Other 2.422753 0.799 Clay 9.524762 0.174 Canopy 2.747264 0.665
Including condition, setting:dune:
I J Total
Setting 0.02483714 0.079930614 1.047678e-01
Aspect 0.02462170 0.055591110 8.021281e-02
epdata...Setting....epdata...Dune... 0.06201528 0.196732414 2.587477e-01
Condition 0.04307311 0.122458698 1.655318e-01
Spinifex 0.02533964 0.058778074 8.411771e-02
Melaleuca 0.01986015 0.039628174 5.948832e-02
Eucalyptus 0.00837537 -0.006109900 2.265469e-03
Bare 0.02846058 0.033384377 6.184495e-02
Leaf 0.01369576 -0.013685042 1.071934e-05
Other 0.00802862 -0.005630940 2.397680e-03
Clay 0.01921285 0.049094533 6.830738e-02
Canopy 0.01269663 -0.002515378 1.018125e-02
$I.perc
I
Setting 8.558132 0.174
Aspect 8.483898 0.227
Setting:Dune 21.368604 0.102
Condition 14.841701 0.040 *
Spinifex 8.731278 0.238
Melaleuca 6.843210 0.322
Eucalyptus 2.885901 0.743
Bare 9.806660 0.192
Leaf 4.719148 0.519
Other 2.766421 0.715
Clay 6.620171 0.289
Canopy 4.374876 0.509
Nephrurus stellatus
$IJ
I J Total
Spinifex 0.018561305 0.001120501 0.019681807
Melaleuca 0.022830083 0.002005971 0.024836054
Eucalyptus 0.036956313 -0.031714796 0.005241517
Bare 0.161381675 -0.029211398 0.132170277
Leaf 0.033803446 0.059333287 0.093136733
Other 0.008584501 -0.001055600 0.007528901
Clay 0.064951205 0.053060102 0.118011306
Canopy 0.051488981 0.027776005 0.079264986
$I.perc
I
Spinifex 4.657121 0.474
Melaleuca 5.728178 0.453
Eucalyptus 9.272517 0.275
Bare 40.491440 0.023 *
Leaf 8.481447 0.349
Other 2.153893 0.817
Clay 16.296570 0.142
Canopy 12.918833 0.189
Aspect 24.530918 0.063 Spinifex 5.533636 0.474 Melaleuca 5.625037 0.434 Eucalyptus 8.265105 0.344 Bare 25.580785 0.074 Leaf 6.580042 0.434 Other 2.149101 0.828 Clay 11.654051 0.206 Canopy 10.081325 0.288
Including condition, dune:
$IJ
I J Total
Aspect 0.072870167 0.145123008 0.217993175
Condition 0.043846845 0.038774870 0.082621714
Spinifex 0.006880230 0.012801577 0.019681807
Melaleuca 0.006692614 0.018143440 0.024836054
Eucalyptus 0.003802960 0.001438557 0.005241517
Bare 0.059243901 0.072926376 0.132170277
Leaf 0.021304115 0.071832618 0.093136733
Other 0.003329119 0.004199783 0.007528901
Clay 0.033615470 0.084395836 0.118011306
Canopy 0.031333695 0.047931291 0.079264986
$I.perc
I
Aspect 25.756537 0.017 *
Condition 15.498014 0.090
Spinifex 2.431872 0.593
Melaleuca 2.365557 0.622
Eucalyptus 1.344186 0.776
Bare 20.940225 0.059
Leaf 7.530108 0.265
Other 1.176703 0.823
Clay 11.881654 0.135
Canopy 11.075142 0.345
Pogona sp.
$IJ
I J Total
Spinifex 0.004499951 0.004198701 0.008698652
Melaleuca 0.196274074 0.030004011 0.226278085
Eucalyptus 0.036317153 0.015002119 0.051319272
Bare 0.007197359 0.005920677 0.013118036
Leaf 0.015019426 0.003040418 0.018059844
Other 0.019036686 0.020284764 0.039321450
Clay 0.034212471 -0.015982038 0.018230433
Canopy 0.007506271 -0.007026771 0.000479500
$I.perc
I
Spinifex 1.405956 0.863
Melaleuca 61.323500 0.016 *
Eucalyptus 11.346863 0.329
Bare 2.248729 0.748
Leaf 4.692641 0.635
Other 5.947786 0.557
Clay 10.689280 0.341
Canopy 2.345245 0.864
Spinifex 1.405956 0.860 Melaleuca 61.323500 0.009 Eucalyptus 11.346863 0.288 Bare 2.248729 0.769 Leaf 4.692641 0.619 Other 5.947786 0.552 Clay 10.689280 0.334 Canopy 2.345245 0.848
Including condition:
I
Condition 7.312277 0.399
Spinifex 2.463616 0.732
Melaleuca 59.182230 0.005 ***
Eucalyptus 8.481841 0.332
Bare 1.592537 0.819
Leaf 4.160797 0.641
Other 5.963511 0.499
Clay 9.300349 0.315
Canopy 1.542842 0.941
NumSpec
$IJ
I J Total
Spinifex 0.022292769 0.001184860 0.023477629
Melaleuca 0.005981831 -0.003412719 0.002569112
Eucalyptus 0.005982440 -0.002009065 0.003973374
Bare 0.084434851 0.044125017 0.128559868
Leaf 0.012477617 -0.011453804 0.001023814
Other 0.041026452 0.021223510 0.062249961
Clay 0.079129974 -0.062584982 0.016544991
Canopy 0.093819398 -0.013990933 0.079828465
$I.perc
I
Spinifex 6.458951 0.481
Melaleuca 1.733134 0.791
Eucalyptus 1.733310 0.842
Bare 24.463565 0.108
Leaf 3.615178 0.709
Other 11.886718 0.272
Clay 22.926566 0.112
Canopy 27.182578 0.072 .
epdata...Site....epdata...Conn... 23.5950103 0.166 Setting 32.0841295 0.003 Spinifex 2.7284507 0.444 Melaleuca 1.2891081 0.611 Eucalyptus 1.0208294 0.716 Bare 13.6362620 0.063 Leaf 0.4136983 0.886 Other 5.7654162 0.236 Clay 3.0478780 0.416 Canopy 16.4192175 0.136
Including condition, setting, site:conn:
$IJ
I J Total
Site:Conn 0.07782809 0.1033055644 0.181133654
Setting 0.08386831 0.1922594215 0.276127728
Condition 0.09744256 0.1998319709 0.297274527
Spinifex 0.01986955 0.0036080802 0.023477629
Melaleuca 0.01494238 -0.0123732726 0.002569112
Eucalyptus 0.01752548 -0.0135521088 0.003973374
Bare 0.04621075 0.0823491225 0.128559868
Leaf 0.01327935 -0.0122555341 0.001023814
Other 0.02848004 0.0337699168 0.062249961
Clay 0.01643272 0.0001122722 0.016544991
Canopy 0.02230745 0.0575210137 0.079828465
$I.perc
I
Site:Conn 17.761400 0.092
Setting 19.139858 0.006 **
Condition 22.237681 0.002 **
Spinifex 4.534494 0.305
Melaleuca 3.410050 0.438
Eucalyptus 3.999547 0.368
Bare 10.545904 0.058
Leaf 3.030523 0.480
Other 6.499523 0.191
Clay 3.750164 0.339
Canopy 5.090856 0.280
Sum
$IJ
I J Total
Spinifex 0.020554995 0.005706324 0.0262613190
Melaleuca 0.005146626 -0.005016252 0.0001303742
Eucalyptus 0.008323711 0.005767381 0.0140910920
Bare 0.024068061 0.015561843 0.0396299037
Leaf 0.018385680 0.009908405 0.0282940853
Other 0.070021978 0.017306896 0.0873288740
Clay 0.009129871 0.010407720 0.0195375913
Canopy 0.068901978 0.061920175 0.1308221526
$I.perc
I
Spinifex 9.154558 0.464
Melaleuca 2.292148 0.822
Eucalyptus 3.707123 0.731
Bare 10.719169 0.432
Leaf 8.188413 0.585
Other 31.185620 0.120
Clay 4.066162 0.705
Canopy 30.686807 0.144
Setting 53.6825722 0.012 Spinifex 4.3199237 0.574 Melaleuca 0.9102594 0.896 Eucalyptus 1.7789326 0.833 Bare 5.2798853 0.483 Leaf 4.0610673 0.630 Other 12.3265543 0.260 Clay 1.7913453 0.786 Canopy 15.8494599 0.197
Including condition and setting:
$IJ
I J Total
Setting 0.082790194 0.184219843 0.2670100363
Condition 0.103363813 0.185953554 0.2893173669
Spinifex 0.008098196 0.018163123 0.0262613190
Melaleuca 0.002095943 -0.001965569 0.0001303742
Eucalyptus 0.006310573 0.007780519 0.0140910920
Bare 0.009794153 0.029835750 0.0396299037
Leaf 0.010328867 0.017965218 0.0282940853
Other 0.030083529 0.057245345 0.0873288740
Clay 0.002719269 0.016818322 0.0195375913
Canopy 0.044186903 0.086635250 0.1308221526
$I.perc
I
Setting 27.6177724 0.018 *
Condition 34.4808742 0.005 ***
Spinifex 2.7014567 0.586
Melaleuca 0.6991803 0.889
Eucalyptus 2.1051282 0.654
Bare 3.2672070 0.523
Leaf 3.4455808 0.499
Other 10.0354886 0.189
Clay 0.9071141 0.822
Canopy 14.7401977 0.247
RareSp
$IJ
I J Total
Spinifex 0.041990170 -0.0050859832 0.036904187
Melaleuca 0.022736797 0.0138569898 0.036593787
Eucalyptus 0.011464087 -0.0060269176 0.005437170
Bare 0.053109171 0.0089307065 0.062039877
Leaf 0.035077433 -0.0215004832 0.013576950
Other 0.060558287 0.0871025975 0.147660884
Clay 0.004586129 -0.0006186097 0.003967519
Canopy 0.076575567 -0.0057035333 0.070872033
$I.perc
I
Spinifex 13.717901 0.258
Melaleuca 7.427956 0.444
Eucalyptus 3.745239 0.639
Bare 17.350402 0.203
Leaf 11.459557 0.345
Other 19.783977 0.169
Clay 1.498257 0.832
Canopy 25.016712 0.113
epdata...Site....epdata...Conn... 47.1985947 0.050 Spinifex 8.7879264 0.215 Melaleuca 2.6218967 0.572 Eucalyptus 1.2920455 0.810 Bare 10.0691191 0.189 Leaf 6.1883155 0.335 Other 9.5730578 0.179 Clay 0.9269207 0.865 Canopy 13.3421235 0.097
Including condition and site:conn:
$IJ
I J Total
Site:Conn 0.131022488 0.164548353 0.295570841
Condition 0.044971245 0.031116462 0.076087707
Spinifex 0.030803975 0.006100212 0.036904187
Melaleuca 0.012899747 0.023694040 0.036593787
Eucalyptus 0.006443976 -0.001006807 0.005437170
Bare 0.027196487 0.034843391 0.062039877
Leaf 0.006359432 0.007217519 0.013576950
Other 0.040996249 0.106664635 0.147660884
Clay 0.001041845 0.002925673 0.003967519
Canopy 0.054004761 0.016867272 0.070872033
$I.perc
I
Site:Conn 36.8309474 0.058
Condition 12.6415975 0.092
Spinifex 8.6591211 0.142
Melaleuca 3.6261707 0.406
Eucalyptus 1.8114276 0.622
Bare 7.6450415 0.196
Leaf 1.7876617 0.629
Other 11.5242102 0.102
Clay 0.2928669 0.883
Canopy 15.1809553 0.182
Site treatments on vegetation
Spinifex
Df Sum Sq Mean Sq F value Pr(>F) TreatCode 4 9.3370 2.3342 3.5866 0.01918 * Residuals 25 16.2704 0.6508
Using Conn + Setting:
Conn 1 0.0500 0.0500 0.0666 0.79834 Setting 1 5.2734 5.2734 7.0195 0.01331 * Residuals 27 20.2840 0.7513
Melaleuca
TreatCode 4 9.1362 2.2840 2.4184 0.07521 . Residuals 25 23.6112 0.9444
Using Conn + Setting:
Conn 1 0.020 0.020 0.0165 0.8987 Setting 1 0.005 0.005 0.0042 0.9487 Residuals 27 32.722 1.212
Eucalyptus
TreatCode 4 38.041 9.510 1.4681 0.2417 Residuals 25 161.947 6.478
Using Conn + Setting:
Conn 1 2.993 2.993 0.4102 0.5273 Setting 1 0.023 0.023 0.0032 0.9552 Residuals 27 196.973 7.295
Bare
TreatCode 4 51.596 12.899 3.7419 0.01612 * Residuals 25 86.181 3.447
Using Conn + Setting:
Conn 1 8.243 8.243 1.7896 0.1921 Setting 1 5.180 5.180 1.1247 0.2983 Residuals 27 124.354 4.606
Leaf
TreatCode 4 48.475 12.119 3.3267 0.02576 * Residuals 25 91.072 3.643
Using Conn + Setting:
Conn 1 3.153 3.153 0.636 0.4321 Setting 1 2.568 2.568 0.518 0.4779 Residuals 27 133.827 4.957
Other
TreatCode 4 3.2728 0.8182 1.6165 0.2013 Residuals 25 12.6542 0.5062
Using Conn + Setting:
Conn 1 0.6092 0.6092 1.1097 0.3015 Setting 1 0.4959 0.4959 0.9034 0.3503 Residuals 27 14.8219 0.5490
Clay
TreatCode 4 0.86667 0.21667 2.4074 0.07621 . Residuals 25 2.25000 0.09000
Using Conn + Setting:
Conn 1 0.00208 0.00208 0.0181 0.8939 Setting 1 0.01042 0.01042 0.0906 0.7657 Residuals 27 3.10417 0.11497
Canopy
TreatCode 4 29.880 7.470 2.3542 0.0813 . Residuals 25 79.325 3.173
Using Conn + Setting:
Conn 1 0.039 0.039 0.0102 0.9203 Setting 1 7.315 7.315 1.9392 0.1751 Residuals 27 101.851 3.772
LME tests
Spinifex
(this is the simplest model)
numDF denDF F-value p-value (Intercept) 1 16 17.531020 0.0007 Site 1 4 0.159401 0.7101 Setting 1 16 9.432623 0.0073 ** Dune 1 16 0.305526 0.5881 Conn 1 16 1.789425 0.1997 Site:Setting 1 16 0.257573 0.6187 Site:Dune 1 16 3.565201 0.0773 . Site:Conn 1 16 2.415924 0.1397 Setting:Dune 1 16 6.875744 0.0185 * Site:Setting:Dune 1 16 3.311502 0.0876 .
Melaleuca
numDF denDF F-value p-value (Intercept) 1 16 23.785725 0.0002 Site 1 4 0.188107 0.6869 Setting 1 16 0.000052 0.9943 Dune 1 16 0.062714 0.8054 Conn 1 16 0.004043 0.9501 Site:Setting 1 16 0.643529 0.4342 Site:Dune 1 16 0.008394 0.9281 Site:Conn 1 16 0.683297 0.4206 Setting:Dune 1 16 8.522505 0.0100 * Site:Setting:Dune 1 16 0.674651 0.4235
Eucalyptus
numDF denDF F-value p-value (Intercept) 1 16 28.489203 0.0001 Site 1 4 1.247650 0.3266 Setting 1 16 0.054100 0.8190 Dune 1 16 2.489434 0.1342 Conn 1 16 0.007047 0.9341 Site:Setting 1 16 5.018700 0.0396 * Site:Dune 1 16 0.925821 0.3503 Site:Conn 1 16 0.001568 0.9689 Setting:Dune 1 16 3.862923 0.0670 Site:Setting:Dune 1 16 0.109604 0.7449
Bare
numDF denDF F-value p-value (Intercept) 1 16 95.20917 <.0001 Site 1 4 0.08328 0.7872 Setting 1 16 4.28296 0.0550 . Dune 1 16 16.38421 0.0009 *** Conn 1 16 0.23899 0.6316 Site:Setting 1 16 2.17917 0.1593 Site:Dune 1 16 0.82198 0.3781 Site:Conn 1 16 0.57622 0.4588 Setting:Dune 1 16 0.01863 0.8931 Site:Setting:Dune 1 16 0.10143 0.7542
Leaf
numDF denDF F-value p-value (Intercept) 1 16 179.04456 <.0001 Site 1 4 0.18962 0.6857 Setting 1 16 0.20546 0.6564 Dune 1 16 10.11734 0.0058 ** Conn 1 16 0.04448 0.8356 Site:Setting 1 16 3.42148 0.0829 , Site:Dune 1 16 0.00073 0.9787 Site:Conn 1 16 0.20058 0.6603 Setting:Dune 1 16 7.92401 0.0125 * Site:Setting:Dune 1 16 10.18328 0.0057 **
Other
numDF denDF F-value p-value (Intercept) 1 16 8.127317 0.0116 Site 1 4 0.174053 0.6980 Setting 1 16 4.036383 0.0617 . Dune 1 16 2.750591 0.1167 Conn 1 16 2.677369 0.1213 Site:Setting 1 16 11.108120 0.0042 ** Site:Dune 1 16 4.490934 0.0501 . Site:Conn 1 16 0.257868 0.6185 Setting:Dune 1 16 4.824904 0.0431 * Site:Setting:Dune 1 16 12.083409 0.0031 **
Clay
numDF denDF F-value p-value (Intercept) 1 16 10.521739 0.0051 Site 1 4 1.391304 0.3035 Setting 1 16 0.057971 0.8128 Dune 1 16 8.115942 0.0116 * Conn 1 16 0.760870 0.3960 Site:Setting 1 16 0.057971 0.8128 Site:Dune 1 16 0.041408 0.8413 Site:Conn 1 16 1.552795 0.2307 Setting:Dune 1 16 0.108696 0.7459 Site:Setting:Dune 1 16 0.434783 0.5190
Canopy
numDF denDF F-value p-value (Intercept) 1 16 60.24224 <.0001 Site 1 4 0.01210 0.9177 Setting 1 16 2.46862 0.1357 Dune 1 16 9.51481 0.0071 ** Conn 1 16 0.12082 0.7327 Site:Setting 1 16 5.87667 0.0276 * Site:Dune 1 16 0.06077 0.8084 Site:Conn 1 16 0.00032 0.9860 Setting:Dune 1 16 0.82124 0.3783 Site:Setting:Dune 1 16 0.13631 0.7168
NumSpec
numDF denDF F-value p-value (Intercept) 1 16 214.26613 <.0001 Site 1 4 0.00806 0.9328 Setting 1 16 10.97852 0.0044 ** Dune 1 16 0.02475 0.8770 Conn 1 16 0.48114 0.4979 Site:Setting 1 16 1.50936 0.2370 Site:Dune 1 16 0.00891 0.9260 Site:Conn 1 16 6.08257 0.0253 * Setting:Dune 1 16 0.37422 0.5493 Site:Setting:Dune 1 16 0.16632 0.6888
Sum
numDF denDF F-value p-value (Intercept) 1 16 149.31845 <.0001 Site 1 4 0.70851 0.4473 Setting 1 16 9.34625 0.0075 ** Dune 1 16 0.61018 0.4461 Conn 1 16 0.00376 0.9519 Site:Setting 1 16 0.85425 0.3691 Site:Dune 1 16 0.17692 0.6796 Site:Conn 1 16 3.25084 0.0903 . Setting:Dune 1 16 0.02633 0.8731 Site:Setting:Dune 1 16 0.02633 0.8731
LME - log+1 transformed, reptiles
Ctenophorus.fordi
numDF denDF F-value p-value (Intercept) 1 16 7.772721 0.0132 Site 1 4 0.744309 0.4369 Setting 1 16 22.816299 0.0002 *** Dune 1 16 2.366991 0.1435 Conn 1 16 0.394499 0.5388 Site:Setting 1 16 2.184868 0.1588 Site:Dune 1 16 2.366991 0.1435 Site:Conn 1 16 0.394499 0.5388 Setting:Dune 1 16 2.761490 0.1160 Site:Setting:Dune 1 16 2.761490 0.1160
Ctenotus.atlas
numDF denDF F-value p-value (Intercept) 1 16 18.289788 0.0006 Site 1 4 1.520751 0.2850 Setting 1 16 12.816642 0.0025 ** Dune 1 16 0.008929 0.9259 Conn 1 16 0.053576 0.8199 Site:Setting 1 16 2.812719 0.1129 Site:Dune 1 16 0.080363 0.7804 Site:Conn 1 16 0.857210 0.3683 Setting:Dune 1 16 3.375263 0.0848 . Site:Setting:Dune 1 16 0.000000 1.0000
Ctenotus.schomburgkii
numDF denDF F-value p-value (Intercept) 1 16 4.670527 0.0462 Site 1 4 0.401480 0.5607 Setting 1 16 11.801718 0.0034 ** Dune 1 16 0.128966 0.7242 Conn 1 16 0.021494 0.8853 Site:Setting 1 16 1.014480 0.3288 Site:Dune 1 16 0.724629 0.4072 Site:Conn 1 16 0.120771 0.7327 Setting:Dune 1 16 0.150460 0.7032 Site:Setting:Dune 1 16 0.845400 0.3715
Lerista.distinguenda
numDF denDF F-value p-value (Intercept) 1 16 14.291730 0.0016 Site 1 4 0.584284 0.4872 Setting 1 16 17.280960 0.0007 ** Dune 1 16 0.029640 0.8655 Conn 1 16 0.282932 0.6021 Site:Setting 1 16 2.397280 0.1411 Site:Dune 1 16 0.000009 0.9976 Site:Conn 1 16 2.457458 0.1365 Setting:Dune 1 16 0.001735 0.9673 Site:Setting:Dune 1 16 0.256437 0.6195
Lerista.edwardsae
numDF denDF F-value p-value (Intercept) 1 16 26.517125 0.0001 Site 1 4 6.378467 0.0650 . Setting 1 16 2.765171 0.1158 Dune 1 16 1.282132 0.2742 Conn 1 16 0.726683 0.4065 Site:Setting 1 16 4.252312 0.0558 . Site:Dune 1 16 2.736159 0.1176 Site:Conn 1 16 0.181254 0.6760 Setting:Dune 1 16 1.878315 0.1894 Site:Setting:Dune 1 16 0.195750 0.6641
Menetia.greyii
numDF denDF F-value p-value (Intercept) 1 16 20.488664 0.0003 Site 1 4 3.601449 0.1306 Setting 1 16 6.023564 0.0259 * Dune 1 16 8.690677 0.0094 ** Conn 1 16 3.077228 0.0985 . Site:Setting 1 16 0.094850 0.7621 Site:Dune 1 16 5.034130 0.0394 * Site:Conn 1 16 0.014135 0.9068 Setting:Dune 1 16 4.130300 0.0591 . Site:Setting:Dune 1 16 0.451971 0.5110
Nephrurus.stellatus
numDF denDF F-value p-value (Intercept) 1 16 40.59259 <.0001 Site 1 4 0.18498 0.6893 Setting 1 16 1.62388 0.2207 Dune 1 16 11.43736 0.0038 ** Conn 1 16 0.92919 0.3494 Site:Setting 1 16 0.26590 0.6131 Site:Dune 1 16 0.00549 0.9419 Site:Conn 1 16 1.01259 0.3293 Setting:Dune 1 16 0.02695 0.8716 Site:Setting:Dune 1 16 0.00064 0.9801
Pogona.sp
numDF denDF F-value p-value (Intercept) 1 16 8.128058 0.0116 Site 1 4 1.180501 0.3383 Setting 1 16 0.673725 0.4238 Dune 1 16 0.105763 0.7492 Conn 1 16 0.004713 0.9461 Site:Setting 1 16 0.148068 0.7055 Site:Dune 1 16 0.481232 0.4978 Site:Conn 1 16 0.943386 0.3459 Setting:Dune 1 16 1.892551 0.1879 Site:Setting:Dune 1 16 0.075702 0.7867
NumSpec
numDF denDF F-value p-value (Intercept) 1 16 594.6073 <.0001 Site 1 4 0.1203 0.7462 Setting 1 16 9.7247 0.0066 ** Dune 1 16 0.0595 0.8103 Conn 1 16 0.0855 0.7738 Site:Setting 1 16 1.6931 0.2116 Site:Dune 1 16 0.0052 0.9436 Site:Conn 1 16 6.4133 0.0222 * Setting:Dune 1 16 0.5176 0.4822 Site:Setting:Dune 1 16 0.0048 0.9459
Sum
numDF denDF F-value p-value (Intercept) 1 16 590.3910 <.0001 Site 1 4 1.4137 0.3002 Setting 1 16 8.0847 0.0117 * Dune 1 16 0.3693 0.5519 Conn 1 16 0.2642 0.6143 Site:Setting 1 16 1.1607 0.2973 Site:Dune 1 16 0.3376 0.5693 Site:Conn 1 16 2.7901 0.1143 Setting:Dune 1 16 0.1216 0.7318 Site:Setting:Dune 1 16 0.4175 0.5274
Condition
Simplified model
mod9<-lme(Condition ~ Setting, random = ~1|Block, data=epdata, method="ML")
numDF denDF F-value p-value
(Intercept) 1 23 234.44723 <.0001
Setting 1 23 36.29065 <.0001 ***
Notes culled from paper
The conservation park setting was also significant, as C. fordi was not found in farmland (24%, P = 0.002).
Nephrurus stellatus aspect (26%, P = 0.017) – more in dunes
Ctenotus atlas populations were explained by setting (25%, P = 0.012) and condition (23%, P = 0.019). More in cons parks Only appeared in sites with good condition
Lerista distinguenda setting (31%, P = 0.011) – more in park Condition (35%, P = 0.001) – more in better condition
Lerista edwardsae? Condition (35%, P = 0.003) – more in worse sites
Condition
Menetia greyii condition (15%, P = 0.040) - more in worse condition
NumSpec – Setting (19%, P = 0.006) – more in park Condition (22%, P = 0.002) – more in better condition
Sum – Setting (28%, P = 0.018) – more in park Condition (34%, P = 0.005) – more in better
RareSp – nothing
