Redundancy Analysis (RDA)
21/jun/2018
This file explains the procedure followed by Ernesto Igartua to perform redundancy analysis on genetic features of the genotypes (probability of belonging to each one of the four germplasm groups), explained by geographic and agro-climatic features of the locations of collection of the genotypes. This uses library vegan.
library(vegan)Input of environmental, geographic, genetic data
#Input data, (Q matrix, all geographic and agro-climatic variables for all accessions)
SBCC <- read.table("RDA/RDA_complete.tsv", header = TRUE)
#Probabilities derived from structure, 4 populations or germplasm groups
Cluster <- SBCC[,c("Q1","Q2","Q3","Q4")]
#Dummy variables
Dummies <- SBCC[,6:17]
#All explanatory variables, environmental, geographic, dummies
EnvGeoDum<-SBCC[,6:ncol(SBCC)]
#Just geographic variables
Geo <- SBCC[,c("altitude","utmx","utmy")]
#Just environmental variables, all, non-standardized
Env <- SBCC[,21:ncol(SBCC)]
head(SBCC) structure_cluster Q1 Q2 Q3 Q4 dummy_01 dummy_02
SBCC001 1 0.525 0.000 0.449 0.025 1.1319747 0.9428862
SBCC002 1 0.790 0.001 0.120 0.090 0.9170711 1.1143330
SBCC003 3 0.075 0.000 0.767 0.158 1.0191159 1.0413141
SBCC004 1 0.526 0.126 0.149 0.199 1.0668731 1.0424424
SBCC005 3 0.026 0.001 0.805 0.168 0.9339675 0.9611360
SBCC006 3 0.040 0.000 0.880 0.080 1.0643861 1.0118885
dummy_03 dummy_04 dummy_05 dummy_06 dummy_07 dummy_08
SBCC001 0.9517142 0.9672275 0.9582126 0.9624485 1.0230726 0.9751187
SBCC002 1.0708767 1.0701706 1.0953819 1.0844107 0.9313422 0.9940330
SBCC003 1.0017011 1.0582434 1.0069600 0.9374063 1.0025110 1.0312523
SBCC004 0.9286685 1.0242339 0.9740021 0.9672581 0.9665652 0.9782558
SBCC005 0.9243257 1.0511030 1.0400764 0.9597972 0.9874042 0.9924280
SBCC006 1.0906860 0.7611184 1.1753876 0.9487512 0.9578449 0.7389713
dummy_09 dummy_10 dummy_11 dummy_12 altitude utmx utmy
SBCC001 0.9767225 1.0010688 0.9460738 1.0757837 482 502732 4723800
SBCC002 1.0349442 0.9778595 0.9645447 1.0799071 540 527235 4744210
SBCC003 0.9880549 0.9848837 1.0249680 0.9795045 685 487315 4498070
SBCC004 0.9860799 1.0216805 1.0403354 0.9700889 821 355768 4547580
SBCC005 1.0179045 1.0233084 0.9506567 1.0640068 564 253330 4370640
SBCC006 0.9925718 1.1401919 0.9582850 1.0342159 40 796705 4522510
tamp_aut tamp_spr tamp_win tamp_01 tamp_02 tamp_03 tamp_04
SBCC001 10.364702 11.22652 7.522248 7.107619 8.698300 10.69802 11.11819
SBCC002 10.280801 10.93643 7.801900 7.521173 8.912690 10.59006 10.74763
SBCC003 12.587445 13.37007 10.303525 10.091963 11.632977 13.30806 12.97233
SBCC004 12.255573 13.10919 9.308032 8.798272 10.901658 12.82562 12.83884
SBCC005 11.045733 11.91527 8.836782 8.770574 9.651395 11.14923 11.62650
SBCC006 9.800245 11.03953 8.993074 8.765983 9.800018 10.91975 11.02245
tamp_05 tamp_06 tamp_11 tamp_12 et0_annual bal_01
SBCC001 11.87548 13.05807 7.966463 6.894517 1010.2940 16.030180
SBCC002 11.51205 12.39278 8.039158 7.183892 946.3984 47.748058
SBCC003 13.78787 15.66418 10.393627 9.311220 1190.0853 6.483904
SBCC004 13.65312 15.80469 9.666140 8.316976 1148.9209 9.759199
SBCC005 13.01388 14.95655 9.010626 8.086374 1259.1362 33.579746
SBCC006 11.15042 11.40402 8.710864 8.401956 1260.8562 -10.490158
bal_02 bal_03 bal_04 bal_05 bal_06 bal_11
SBCC001 -1.316006 -32.214577 -29.431923 -58.54840 -89.56256 25.93165
SBCC002 25.985321 -3.201065 -2.130508 -37.13115 -75.67059 55.65340
SBCC003 -9.479664 -53.222786 -46.435722 -81.24417 -142.64290 14.04456
SBCC004 -11.491652 -50.191227 -52.717690 -71.78388 -131.76453 12.48698
SBCC005 8.480724 -39.913464 -41.957478 -95.43474 -158.01036 50.24101
SBCC006 -27.532696 -57.258400 -61.561779 -82.42670 -136.89633 6.09193
bal_12 bal_anual bal_aut bal_spr bal_win frost_aut
SBCC001 27.409134 -464.7049 -50.56499 -120.19489 42.12331 2.490913391
SBCC002 55.101673 -166.6375 16.09494 -42.46272 128.83505 3.796501875
SBCC003 22.602428 -760.8821 -87.75922 -180.90268 19.60667 7.147752762
SBCC004 21.202555 -708.5820 -88.64977 -174.69278 19.47010 8.131834030
SBCC005 62.567299 -663.6476 -37.54980 -177.30568 104.62777 0.667363703
SBCC006 -2.529942 -720.7607 -42.82809 -201.24689 -40.55279 -0.001111744
frost_spr frost_win frost_01 frost_02 frost_03 frost_04
SBCC001 4.0943942 20.566034 7.961690 6.9437447 3.2569995 0.7383289
SBCC002 7.6530123 28.027317 10.767150 9.7420244 5.7339659 1.7506678
SBCC003 9.2015142 41.317066 16.401331 12.9830036 6.7514234 2.1746197
SBCC004 10.4518528 42.434082 16.882498 13.5875559 7.6643286 2.5782735
SBCC005 0.9431090 10.128152 4.589581 2.6760125 0.7927416 0.1466327
SBCC006 -0.3576986 3.148009 1.524418 0.6490459 -0.1877015 -0.1478900
frost_05 frost_06 frost_11 frost_12 et0_01 et0_11
SBCC001 0.05954794 -0.003065024 2.43061352 6.377321 29.66736 36.13636
SBCC002 0.13989802 0.002800880 3.50943160 8.434424 28.54635 34.80265
SBCC003 0.27114588 0.003286499 6.39535952 13.283036 28.12958 35.62622
SBCC004 0.20164837 -0.088716581 7.50490761 13.373107 25.88338 34.13942
SBCC005 0.01972251 0.000000000 0.64865631 3.190523 29.41825 38.15626
SBCC006 -0.02196008 0.000000000 0.03640607 1.085427 48.19383 54.19547
et0_12 et0_02 et0_03 et0_04 et0_05 et0_06 pcp_01
SBCC001 27.92051 41.65010 71.82702 86.00639 116.9779 134.7142 45.69754
SBCC002 27.34063 39.78799 68.48199 81.39371 110.1499 124.6810 76.29441
SBCC003 25.50862 41.85015 76.75745 98.66719 136.3115 170.5163 34.61349
SBCC004 23.85222 40.46392 74.91299 95.76203 133.5958 164.9551 35.64258
SBCC005 26.26012 43.16258 79.39007 105.76667 148.8481 182.6243 62.99799
SBCC006 46.46136 60.25217 91.03366 113.90443 140.7850 161.6706 37.70367
pcp_02 pcp_03 pcp_04 pcp_05 pcp_06 pcp_11 pcp_12
SBCC001 40.33409 39.61244 56.57446 58.42951 45.15160 62.06801 55.32965
SBCC002 65.77332 65.28093 79.26321 73.01875 49.01046 90.45605 82.44231
SBCC003 32.37049 23.53466 52.23147 55.06734 27.87337 49.67078 48.11105
SBCC004 28.97227 24.72176 43.04434 61.81192 33.19058 46.62639 45.05477
SBCC005 51.64331 39.47660 63.80919 53.41341 24.61393 88.39727 88.82742
SBCC006 32.71947 33.77526 52.34266 58.35835 24.77428 60.28740 43.93142
pcp_aut pcp_spr pcp_win pfrost_01 et0_aut et0_spr et0_win
SBCC001 148.1554 153.3053 134.5255 98.84942 200.3169 274.8113 99.23798
SBCC002 208.9885 218.7869 218.1904 105.17625 191.6563 260.0256 95.67498
SBCC003 132.6123 129.4659 110.0076 103.54833 221.6234 311.7361 95.48835
SBCC004 128.8849 132.1367 108.3039 114.89696 215.6340 304.2708 90.19952
SBCC005 198.2723 156.8794 198.4585 67.82032 236.6400 334.0049 98.84095
SBCC006 208.1822 144.4620 108.4269 44.19824 250.6436 345.7231 154.90735
tmax_01 tmax_02 tmax_03 tmax_04 tmax_05 tmax_06 tmax_11
SBCC001 8.927575 10.89837 14.66975 16.35761 20.39333 24.66487 12.90131
SBCC002 8.587955 10.23787 13.67565 15.29750 19.22715 23.06756 12.35011
SBCC003 9.779446 11.95809 16.09264 17.70301 22.14308 28.44434 13.75328
SBCC004 8.300636 11.01292 15.00842 16.71203 21.03377 27.14706 12.42673
SBCC005 11.547831 13.50394 17.50837 19.16188 23.73140 30.31623 15.63577
SBCC006 13.837197 15.42218 18.58848 20.71064 24.24916 28.56415 17.66535
tmax_12 tmax_aut tmax_spr tmax_win tmed_01 tmed_02 tmed_03
SBCC001 9.401919 8.927575 10.89837 16.35761 5.530060 6.556567 9.298419
SBCC002 9.012092 8.587955 10.23787 15.29750 4.800714 5.706694 8.373159
SBCC003 10.219626 9.779446 11.95809 17.70301 4.661055 6.117057 9.456995
SBCC004 8.848109 8.300636 11.01292 16.71203 3.862065 5.515276 8.611197
SBCC005 11.986932 11.547831 13.50394 19.16188 7.284565 8.746998 11.906110
SBCC006 14.226012 13.837197 15.42218 20.71064 9.502035 10.567306 13.126157
tmed_04 tmed_05 tmed_06 tmed_11 tmed_12 tmed_aut tmed_spr
SBCC001 10.803855 14.47743 18.15925 8.966720 6.132750 5.530060 6.556567
SBCC002 9.961397 13.55722 16.96390 8.247371 5.414033 4.800714 5.706694
SBCC003 11.223665 15.24478 20.62258 8.499343 5.437186 4.661055 6.117057
SBCC004 10.320453 14.20157 19.22267 7.544904 4.637295 3.862065 5.515276
SBCC005 13.299864 17.15576 22.76584 11.226816 8.096213 7.284565 8.746998
SBCC006 15.172699 18.65013 22.85452 13.365388 10.075735 9.502035 10.567306
tmed_win tmin_01 tmin_02 tmin_03 tmin_04 tmin_05
SBCC001 10.803855 2.1221862 2.27165627 3.939585 5.196490 8.503592
SBCC002 9.961397 1.1433396 1.29185939 3.052116 4.536126 7.762789
SBCC003 11.223665 -0.4103809 0.27906990 2.807721 4.770380 8.405106
SBCC004 10.320453 -0.4996339 0.05272181 2.196594 3.934825 7.427178
SBCC005 13.299864 2.9576321 3.97515321 6.352129 7.485093 10.642312
SBCC006 15.172699 5.0448809 5.64280748 7.679469 9.670547 13.045450
tmin_06 tmin_11 tmin_12 tmin_aut tmin_spr tmin_win
SBCC001 11.60855 5.088486 2.8539019 2.1221862 2.27165627 5.196490
SBCC002 10.84273 4.269669 1.9435205 1.1433396 1.29185939 4.536126
SBCC003 12.85773 3.243410 0.7150939 -0.4103809 0.27906990 4.770380
SBCC004 11.32423 2.735377 0.5392753 -0.4996339 0.05272181 3.934825
SBCC005 15.15131 6.809390 4.1508422 2.9576321 3.97515321 7.485093
SBCC006 17.10206 8.993849 5.7970200 5.0448809 5.64280748 9.670547
verna_d_01 verna_d_02 verna_d_03 verna_d_04 verna_01 verna_02
SBCC001 15.42000 28.64593 42.45234 56.53029 44.96055 65.64942
SBCC002 14.98455 28.54227 43.24152 58.23542 43.75400 63.23307
SBCC003 16.96500 32.26210 48.10253 64.19965 40.33420 58.34750
SBCC004 15.62109 29.92539 45.36249 61.82481 41.19423 59.56752
SBCC005 17.82721 32.13572 46.17304 59.72951 42.82933 63.18630
SBCC006 23.13376 40.22333 56.71679 73.33250 34.72694 52.11789
verna_03 verna_04 verna_05 verna_06 verna_11 verna_12
SBCC001 84.25145 102.06100 115.84116 122.62193 71.38354 22.94700
SBCC002 81.33349 99.96902 115.66930 124.58776 75.20112 22.75618
SBCC003 74.70019 90.34036 102.79706 108.69465 63.80278 20.46584
SBCC004 76.77201 93.97660 108.13731 115.59081 69.87321 21.31396
SBCC005 79.77531 93.03412 102.05942 105.21869 56.54910 20.49502
SBCC006 66.31318 76.29522 81.29912 82.12591 42.19517 15.92693#Input data for a third redundancy analysis. Input of set of variables chosen by cluster analysis, 17 agro-climatic, plus 3 geographic and 12 dummies; they are already standardized
#Input data, (Q matrix, all geographic and agro-climatic variables for all accessions)
SBCCc<- read.table("RDA/RDA3.tsv", header = TRUE)
#All variables, geographical, dummies, environmental, all standardized
Allc<-SBCCc[,c("dummy_01","dummy_02","dummy_03","dummy_04","dummy_05","dummy_06","dummy_07",
"dummy_08","dummy_09","dummy_10","dummy_11","dummy_12","lon","lat","alt",
"verna_30d","verna_jan_feb","verna_mar_apr","pfrost_01","pcp_aut","pcp_win",
"pcp_mar_apr","pcp_may_jun","frost_jan_feb","frost_apr_may","tamp_win",
"tamp_spr","et0_spr","bal_aut","bal_win","bal_jun","bal_mar_apr_may")]
#Just dummies
Dummyc<-SBCCc[,c("dummy_01","dummy_02","dummy_03","dummy_04","dummy_05","dummy_06","dummy_07",
"dummy_08","dummy_09","dummy_10","dummy_11","dummy_12")]
#Just geographic
Geoc<-SBCCc[,c("lon","lat","alt")]
#Just environmental (agro-climatic)
Envc<-SBCCc[,c("verna_30d","verna_jan_feb","verna_mar_apr","pfrost_01","pcp_aut","pcp_win",
"pcp_mar_apr","pcp_may_jun","frost_jan_feb","frost_apr_may","tamp_win",
"tamp_spr","et0_spr","bal_aut","bal_win","bal_jun","bal_mar_apr_may")]
#Just probabilities derived from structure, 4 populations or germplasm groups
Clusterc <- SBCCc[,c("Q1","Q2","Q3","Q4")]Standardization of variables
#Standardization of variables
scaled.EnvGeoDum<-scale(EnvGeoDum)
scaledEnvGeoDum.df<-as.data.frame(scaled.EnvGeoDum)
scaled.env<-scale(Env)
scaledenv.df <- as.data.frame(scaled.env)
scaled.geo<-scale(Geo)
scaledgeo.df <- as.data.frame(scaled.geo)First redundancy analysis with just environmental (agroclimatic) variables. Then selection of most significant variables is done with step-wise regression, and a second, reduced, redundancy analysis is performed, with just the variables selected in multiple regression with default settings, until the first dummy variable was entered into the model.
#Redundancy analysis, complete data set
SBCC_RDA<-rda(Cluster,scaledenv.df,scale=F)
#Stepwise selection of variables, complete data, environmental, geographic and dummy variables
RDA1<-rda(Cluster~1,scaledEnvGeoDum.df)
RDA2<-rda(Cluster~.,scaledEnvGeoDum.df)
step.forward<-ordistep(RDA1,scope=formula(RDA2), direction="forward",perm.max=200,pstep=999)
Start: Cluster ~ 1
Df AIC F Pr(>F)
+ pfrost_01 1 -141.52 26.8422 0.005 **
+ verna_11 1 -139.86 24.8929 0.005 **
+ tmin_11 1 -139.64 24.6281 0.005 **
+ tmed_01 1 -139.62 24.6034 0.005 **
+ tmed_aut 1 -139.62 24.6034 0.005 **
+ tmax_01 1 -139.43 24.3899 0.005 **
+ tmax_aut 1 -139.43 24.3899 0.005 **
+ tmed_11 1 -139.43 24.3824 0.005 **
+ tmin_04 1 -139.24 24.1609 0.005 **
+ tmin_win 1 -139.24 24.1609 0.005 **
+ tmin_05 1 -139.03 23.9229 0.005 **
+ tmax_12 1 -139.02 23.9061 0.005 **
+ tmin_03 1 -139.02 23.9061 0.005 **
+ tmed_12 1 -138.98 23.8604 0.005 **
+ tmin_02 1 -138.81 23.6691 0.005 **
+ tmin_spr 1 -138.81 23.6691 0.005 **
+ verna_06 1 -138.49 23.2954 0.005 **
+ tmed_02 1 -138.18 22.9363 0.005 **
+ tmed_spr 1 -138.18 22.9363 0.005 **
+ tmax_11 1 -138.17 22.9215 0.005 **
+ tmin_01 1 -138.14 22.8857 0.005 **
+ tmin_aut 1 -138.14 22.8857 0.005 **
+ tmin_12 1 -137.81 22.5080 0.005 **
+ frost_01 1 -137.49 22.1402 0.005 **
+ verna_05 1 -136.69 21.2237 0.005 **
+ frost_win 1 -136.64 21.1682 0.005 **
+ tmed_03 1 -136.43 20.9243 0.005 **
+ tmed_04 1 -136.28 20.7551 0.005 **
+ tmed_win 1 -136.28 20.7551 0.005 **
+ tmin_06 1 -136.00 20.4371 0.005 **
+ tmax_02 1 -135.97 20.4019 0.005 **
+ tmax_spr 1 -135.97 20.4019 0.005 **
+ frost_12 1 -135.85 20.2602 0.005 **
+ frost_02 1 -135.83 20.2375 0.005 **
+ frost_11 1 -135.17 19.4953 0.005 **
+ tmed_05 1 -134.87 19.1504 0.005 **
+ verna_12 1 -134.85 19.1322 0.005 **
+ frost_aut 1 -133.92 18.0808 0.005 **
+ verna_04 1 -133.27 17.3548 0.005 **
+ verna_d_01 1 -132.81 16.8499 0.005 **
+ verna_d_02 1 -131.97 15.9190 0.005 **
+ tmax_04 1 -131.95 15.8997 0.005 **
+ tmax_win 1 -131.95 15.8997 0.005 **
+ frost_03 1 -131.86 15.7927 0.005 **
+ tmax_03 1 -131.76 15.6882 0.005 **
+ altitude 1 -131.62 15.5306 0.005 **
+ verna_d_03 1 -131.34 15.2239 0.005 **
+ et0_01 1 -130.99 14.8386 0.005 **
+ verna_01 1 -130.99 14.8355 0.005 **
+ et0_11 1 -130.67 14.4918 0.005 **
+ et0_win 1 -130.29 14.0723 0.005 **
+ tmed_06 1 -130.16 13.9351 0.005 **
+ frost_spr 1 -129.95 13.7023 0.005 **
+ et0_02 1 -129.90 13.6467 0.005 **
+ tmax_05 1 -129.80 13.5372 0.005 **
+ verna_d_04 1 -129.51 13.2273 0.005 **
+ verna_03 1 -129.43 13.1375 0.005 **
+ utmy 1 -129.02 12.6923 0.005 **
+ verna_02 1 -128.35 11.9703 0.005 **
+ et0_12 1 -128.20 11.8127 0.005 **
+ et0_aut 1 -127.19 10.7320 0.005 **
+ frost_04 1 -127.13 10.6653 0.005 **
+ tamp_06 1 -126.53 10.0348 0.005 **
+ bal_05 1 -125.90 9.3663 0.005 **
+ et0_03 1 -125.81 9.2720 0.005 **
+ et0_spr 1 -125.77 9.2294 0.005 **
+ et0_05 1 -125.53 8.9778 0.005 **
+ et0_04 1 -125.46 8.9030 0.005 **
+ et0_annual 1 -124.77 8.1809 0.005 **
+ tmax_06 1 -124.64 8.0452 0.005 **
+ tamp_aut 1 -124.29 7.6819 0.005 **
+ frost_05 1 -123.90 7.2724 0.005 **
+ pcp_05 1 -123.73 7.0945 0.005 **
+ pcp_06 1 -123.63 6.9894 0.005 **
+ et0_06 1 -122.93 6.2673 0.005 **
+ dummy_10 1 -121.91 5.2160 0.005 **
+ utmx 1 -121.87 5.1802 0.005 **
+ bal_06 1 -124.30 7.6874 0.010 **
+ bal_spr 1 -120.75 4.0371 0.010 **
+ tamp_spr 1 -120.49 3.7734 0.010 **
+ dummy_02 1 -121.62 4.9222 0.015 *
+ pcp_03 1 -121.46 4.7636 0.015 *
+ tamp_05 1 -120.92 4.2076 0.015 *
+ tamp_03 1 -120.52 3.8071 0.015 *
+ bal_04 1 -119.71 2.9817 0.020 *
+ tamp_01 1 -120.45 3.7277 0.035 *
+ pcp_aut 1 -119.90 3.1780 0.040 *
+ pcp_02 1 -120.03 3.3083 0.045 *
+ tamp_04 1 -119.50 2.7727 0.055 .
+ dummy_06 1 -119.24 2.5110 0.055 .
+ dummy_03 1 -119.73 3.0052 0.060 .
+ pcp_11 1 -120.02 3.2993 0.065 .
+ dummy_01 1 -119.40 2.6742 0.065 .
+ pcp_01 1 -119.37 2.6412 0.065 .
+ tamp_12 1 -119.19 2.4656 0.090 .
+ pcp_12 1 -118.61 1.8763 0.115
+ pcp_win 1 -119.30 2.5750 0.120
+ dummy_11 1 -118.71 1.9834 0.125
+ dummy_07 1 -118.48 1.7556 0.175
+ bal_anual 1 -118.59 1.8613 0.185
+ dummy_04 1 -118.38 1.6522 0.185
+ tamp_11 1 -118.18 1.4554 0.210
+ tamp_02 1 -118.27 1.5389 0.225
+ tamp_win 1 -118.16 1.4297 0.265
+ bal_11 1 -117.81 1.0886 0.325
+ bal_12 1 -117.79 1.0680 0.340
+ dummy_05 1 -117.77 1.0413 0.350
+ dummy_09 1 -117.72 0.9961 0.365
+ frost_06 1 -117.66 0.9381 0.370
+ pcp_spr 1 -117.64 0.9178 0.370
+ bal_aut 1 -117.50 0.7761 0.460
+ bal_win 1 -117.49 0.7635 0.475
+ bal_01 1 -117.31 0.5843 0.580
+ bal_02 1 -117.22 0.5044 0.580
+ dummy_08 1 -117.28 0.5638 0.590
+ dummy_12 1 -117.22 0.5029 0.625
+ bal_03 1 -117.10 0.3822 0.750
+ pcp_04 1 -117.06 0.3365 0.785
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Step: Cluster ~ pfrost_01
Df AIC F Pr(>F)
+ bal_06 1 -150.59 11.2799 0.005 **
+ utmx 1 -148.65 9.2380 0.005 **
+ pcp_06 1 -148.18 8.7443 0.005 **
+ tmed_02 1 -147.93 8.4901 0.005 **
+ tmed_spr 1 -147.93 8.4901 0.005 **
+ et0_06 1 -147.61 8.1531 0.005 **
+ tmed_03 1 -147.30 7.8293 0.005 **
+ tmed_06 1 -147.19 7.7154 0.005 **
+ tmax_06 1 -146.99 7.5077 0.005 **
+ bal_05 1 -146.98 7.5019 0.005 **
+ et0_05 1 -145.92 6.4125 0.005 **
+ tmed_11 1 -145.75 6.2381 0.005 **
+ et0_12 1 -145.51 5.9955 0.005 **
+ dummy_02 1 -145.35 5.8280 0.005 **
+ bal_spr 1 -145.31 5.7887 0.005 **
+ bal_anual 1 -145.13 5.6018 0.005 **
+ et0_annual 1 -144.84 5.3017 0.005 **
+ tmax_03 1 -144.50 4.9607 0.005 **
+ tmin_06 1 -144.29 4.7497 0.005 **
+ tmin_04 1 -144.28 4.7417 0.005 **
+ tamp_06 1 -144.22 4.6787 0.005 **
+ et0_win 1 -144.11 4.5677 0.005 **
+ tmed_win 1 -144.06 4.5177 0.005 **
+ dummy_10 1 -144.62 5.0808 0.010 **
+ tmax_spr 1 -144.58 5.0399 0.010 **
+ tmax_11 1 -144.41 4.8702 0.010 **
+ et0_01 1 -144.39 4.8542 0.010 **
+ tmin_win 1 -144.28 4.7417 0.010 **
+ tmin_03 1 -144.17 4.6275 0.010 **
+ et0_04 1 -144.12 4.5770 0.010 **
+ tmed_04 1 -144.06 4.5177 0.010 **
+ bal_03 1 -143.69 4.1384 0.010 **
+ bal_aut 1 -143.45 3.8965 0.010 **
+ dummy_11 1 -143.40 3.8507 0.010 **
+ pcp_05 1 -144.03 4.4843 0.015 *
+ pcp_spr 1 -143.92 4.3756 0.015 *
+ frost_03 1 -143.65 4.1044 0.015 *
+ bal_04 1 -143.48 3.9261 0.015 *
+ tmax_05 1 -143.16 3.6128 0.015 *
+ tmax_02 1 -144.58 5.0399 0.020 *
+ pcp_03 1 -144.40 4.8611 0.020 *
+ tamp_aut 1 -143.44 3.8944 0.020 *
+ frost_04 1 -143.14 3.5906 0.020 *
+ tmax_win 1 -143.14 3.5879 0.020 *
+ utmy 1 -142.96 3.4093 0.020 *
+ frost_spr 1 -143.53 3.9765 0.025 *
+ et0_spr 1 -143.92 4.3713 0.030 *
+ tmed_aut 1 -142.58 3.0295 0.030 *
+ tmax_aut 1 -142.40 2.8460 0.030 *
+ tmed_12 1 -143.94 4.3945 0.035 *
+ tmax_04 1 -143.14 3.5879 0.035 *
+ tmed_05 1 -142.98 3.4243 0.035 *
+ et0_11 1 -142.96 3.4037 0.035 *
+ pcp_aut 1 -142.76 3.2050 0.035 *
+ dummy_06 1 -142.98 3.4236 0.040 *
+ tmax_12 1 -142.90 3.3505 0.045 *
+ tmed_01 1 -142.58 3.0295 0.050 *
+ et0_aut 1 -142.57 3.0213 0.050 *
+ tamp_05 1 -142.21 2.6585 0.050 *
+ dummy_01 1 -142.03 2.4789 0.060 .
+ verna_02 1 -141.94 2.3868 0.065 .
+ tmax_01 1 -142.40 2.8460 0.070 .
+ frost_02 1 -142.07 2.5154 0.070 .
+ verna_01 1 -141.86 2.3094 0.070 .
+ verna_d_04 1 -142.04 2.4895 0.080 .
+ tmin_02 1 -141.63 2.0824 0.080 .
+ verna_03 1 -141.74 2.1922 0.100 .
+ frost_05 1 -142.22 2.6678 0.105
+ pcp_04 1 -141.84 2.2928 0.110
+ tmin_05 1 -141.40 1.8498 0.120
+ tamp_spr 1 -141.69 2.1382 0.125
+ tmin_spr 1 -141.63 2.0824 0.130
+ et0_02 1 -141.76 2.2119 0.140
+ verna_04 1 -141.32 1.7739 0.140
+ tmin_12 1 -141.43 1.8815 0.150
+ tamp_11 1 -141.36 1.8087 0.150
+ verna_d_03 1 -141.43 1.8768 0.160
+ tamp_03 1 -141.31 1.7605 0.205
+ verna_11 1 -141.03 1.4908 0.210
+ tamp_01 1 -140.92 1.3746 0.215
+ tamp_04 1 -141.24 1.6964 0.225
+ pcp_11 1 -140.96 1.4131 0.240
+ verna_05 1 -140.93 1.3844 0.240
+ verna_12 1 -140.84 1.3004 0.240
+ dummy_07 1 -141.10 1.5578 0.250
+ tamp_02 1 -140.79 1.2515 0.255
+ dummy_05 1 -140.90 1.3582 0.260
+ pcp_02 1 -140.80 1.2582 0.275
+ frost_aut 1 -140.82 1.2742 0.305
+ dummy_08 1 -140.90 1.3530 0.315
+ dummy_12 1 -140.72 1.1807 0.315
+ tamp_win 1 -140.72 1.1834 0.350
+ frost_06 1 -140.47 0.9301 0.360
+ bal_11 1 -140.65 1.1096 0.380
+ tamp_12 1 -140.54 1.0053 0.380
+ frost_12 1 -140.51 0.9779 0.395
+ frost_win 1 -140.47 0.9383 0.410
+ verna_d_02 1 -140.44 0.9069 0.425
+ tmin_11 1 -140.51 0.9751 0.430
+ pcp_01 1 -140.35 0.8156 0.435
+ bal_02 1 -140.47 0.9300 0.440
+ verna_06 1 -140.53 0.9966 0.450
+ frost_11 1 -140.45 0.9127 0.450
+ pcp_win 1 -140.36 0.8281 0.460
+ bal_12 1 -140.36 0.8212 0.470
+ bal_win 1 -140.24 0.7097 0.470
+ et0_03 1 -140.37 0.8345 0.475
+ altitude 1 -140.32 0.7823 0.525
+ dummy_03 1 -140.24 0.7033 0.555
+ dummy_09 1 -140.19 0.6533 0.570
+ verna_d_01 1 -140.10 0.5736 0.600
+ pcp_12 1 -140.15 0.6217 0.645
+ bal_01 1 -140.07 0.5434 0.665
+ tmin_01 1 -140.00 0.4731 0.670
+ tmin_aut 1 -140.00 0.4731 0.685
+ dummy_04 1 -139.84 0.3187 0.790
+ frost_01 1 -139.69 0.1665 0.895
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Step: Cluster ~ pfrost_01 + bal_06
Df AIC F Pr(>F)
+ dummy_01 1 -152.01 3.3665 0.015 *
+ pcp_03 1 -151.03 2.3889 0.045 *
+ dummy_10 1 -151.39 2.7469 0.050 *
+ utmx 1 -151.19 2.5491 0.065 .
+ tmed_12 1 -151.43 2.7917 0.075 .
+ dummy_11 1 -151.25 2.6057 0.075 .
+ tmed_01 1 -150.88 2.2393 0.085 .
+ tmed_spr 1 -150.77 2.1325 0.085 .
+ tmin_12 1 -150.91 2.2765 0.090 .
+ tmed_11 1 -150.73 2.0990 0.095 .
+ dummy_02 1 -150.90 2.2670 0.100 .
+ tmin_aut 1 -150.62 1.9902 0.100 .
+ tmed_02 1 -150.77 2.1325 0.105
+ tmin_03 1 -150.62 1.9888 0.110
+ tmin_01 1 -150.62 1.9902 0.115
+ tmin_spr 1 -150.33 1.7048 0.130
+ bal_03 1 -150.69 2.0513 0.135
+ bal_05 1 -150.35 1.7193 0.135
+ tmed_aut 1 -150.88 2.2393 0.140
+ tmax_12 1 -150.47 1.8406 0.140
+ dummy_07 1 -150.51 1.8777 0.150
+ tamp_01 1 -150.27 1.6394 0.150
+ utmy 1 -150.83 2.1905 0.155
+ dummy_08 1 -150.51 1.8828 0.165
+ tmin_02 1 -150.33 1.7048 0.195
+ tamp_12 1 -149.98 1.3546 0.205
+ tmax_01 1 -150.13 1.5108 0.210
+ tmax_aut 1 -150.13 1.5108 0.215
+ pcp_spr 1 -150.20 1.5760 0.225
+ bal_aut 1 -150.13 1.5024 0.230
+ pcp_aut 1 -150.15 1.5211 0.235
+ verna_11 1 -149.85 1.2306 0.250
+ bal_spr 1 -150.11 1.4889 0.255
+ tmin_11 1 -150.14 1.5136 0.260
+ pcp_02 1 -149.76 1.1408 0.265
+ bal_04 1 -149.79 1.1750 0.295
+ tamp_win 1 -149.69 1.0782 0.315
+ pcp_04 1 -149.60 0.9873 0.320
+ bal_anual 1 -149.83 1.2132 0.325
+ tmin_04 1 -149.69 1.0704 0.335
+ bal_02 1 -149.63 1.0122 0.340
+ tmax_11 1 -149.75 1.1324 0.350
+ tmin_win 1 -149.69 1.0704 0.405
+ pcp_05 1 -149.65 1.0376 0.405
+ pcp_11 1 -149.67 1.0569 0.415
+ bal_11 1 -149.66 1.0493 0.415
+ frost_03 1 -149.48 0.8657 0.435
+ verna_06 1 -149.54 0.9333 0.445
+ verna_05 1 -149.47 0.8650 0.455
+ verna_d_01 1 -149.42 0.8114 0.455
+ tamp_05 1 -149.40 0.7951 0.455
+ tmin_06 1 -149.50 0.8927 0.460
+ tamp_11 1 -149.42 0.8132 0.460
+ frost_spr 1 -149.38 0.7710 0.470
+ et0_11 1 -149.41 0.7966 0.480
+ altitude 1 -149.36 0.7511 0.480
+ frost_05 1 -149.31 0.7051 0.480
+ dummy_09 1 -149.35 0.7387 0.485
+ pcp_win 1 -149.48 0.8686 0.505
+ dummy_06 1 -149.45 0.8370 0.505
+ frost_02 1 -149.31 0.7075 0.520
+ verna_04 1 -149.39 0.7834 0.530
+ et0_aut 1 -149.27 0.6602 0.530
+ tmax_spr 1 -149.24 0.6339 0.530
+ verna_03 1 -149.31 0.7078 0.540
+ frost_04 1 -149.26 0.6547 0.540
+ pcp_12 1 -149.27 0.6669 0.555
+ bal_win 1 -149.36 0.7490 0.560
+ et0_12 1 -149.31 0.7041 0.565
+ bal_12 1 -149.27 0.6640 0.575
+ tmax_05 1 -149.14 0.5415 0.585
+ verna_12 1 -149.20 0.5995 0.590
+ verna_01 1 -149.22 0.6195 0.600
+ verna_02 1 -149.27 0.6648 0.605
+ pcp_01 1 -149.29 0.6863 0.610
+ et0_01 1 -149.12 0.5194 0.615
+ et0_03 1 -149.24 0.6392 0.620
+ tmax_02 1 -149.24 0.6339 0.620
+ tmed_06 1 -149.21 0.6040 0.620
+ bal_01 1 -149.23 0.6259 0.625
+ tamp_04 1 -149.20 0.5932 0.630
+ tamp_spr 1 -149.20 0.5982 0.635
+ et0_02 1 -149.18 0.5752 0.635
+ tamp_03 1 -149.09 0.4905 0.650
+ et0_win 1 -149.21 0.6037 0.655
+ verna_d_04 1 -149.11 0.5050 0.665
+ tamp_02 1 -149.09 0.4919 0.675
+ tmed_05 1 -149.02 0.4207 0.680
+ frost_win 1 -149.02 0.4189 0.685
+ et0_04 1 -149.06 0.4624 0.695
+ frost_06 1 -149.06 0.4546 0.695
+ tmed_03 1 -149.03 0.4357 0.720
+ frost_aut 1 -149.02 0.4249 0.730
+ dummy_03 1 -149.07 0.4721 0.740
+ frost_12 1 -149.02 0.4228 0.740
+ tamp_06 1 -148.99 0.3918 0.745
+ verna_d_03 1 -148.99 0.3928 0.750
+ tmin_05 1 -148.96 0.3631 0.750
+ dummy_04 1 -148.91 0.3117 0.750
+ verna_d_02 1 -149.00 0.4042 0.765
+ frost_11 1 -148.98 0.3781 0.765
+ et0_annual 1 -148.90 0.3016 0.775
+ pcp_06 1 -148.86 0.2675 0.805
+ dummy_12 1 -148.94 0.3385 0.810
+ et0_spr 1 -148.91 0.3159 0.820
+ et0_06 1 -148.86 0.2675 0.825
+ tmax_06 1 -148.85 0.2592 0.840
+ frost_01 1 -148.82 0.2311 0.865
+ et0_05 1 -148.82 0.2250 0.910
+ tmax_win 1 -148.75 0.1583 0.930
+ dummy_05 1 -148.74 0.1471 0.930
+ tmax_04 1 -148.75 0.1583 0.940
+ tmed_win 1 -148.70 0.1066 0.950
+ tamp_aut 1 -148.67 0.0777 0.950
+ tmed_04 1 -148.70 0.1066 0.955
+ tmax_03 1 -148.64 0.0551 0.990
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Step: Cluster ~ pfrost_01 + bal_06 + dummy_01
Df AIC F Pr(>F)
+ tmed_12 1 -152.85 2.7628 0.035 *
+ utmy 1 -152.63 2.5461 0.050 *
+ tmed_aut 1 -152.30 2.2210 0.060 .
+ tmed_spr 1 -152.29 2.2093 0.060 .
+ pcp_03 1 -152.78 2.6942 0.065 .
+ dummy_11 1 -152.49 2.4105 0.065 .
+ utmx 1 -152.65 2.5639 0.070 .
+ dummy_10 1 -152.49 2.4099 0.085 .
+ tmed_11 1 -152.22 2.1382 0.085 .
+ tmed_01 1 -152.30 2.2210 0.090 .
+ bal_03 1 -152.66 2.5726 0.095 .
+ tmed_02 1 -152.29 2.2093 0.100 .
+ dummy_02 1 -152.09 2.0122 0.130
+ bal_aut 1 -152.01 1.9340 0.135
+ tmin_03 1 -151.96 1.8903 0.145
+ tmax_12 1 -151.93 1.8595 0.150
+ pcp_aut 1 -151.88 1.8117 0.160
+ tmin_12 1 -151.87 1.7979 0.165
+ dummy_07 1 -151.75 1.6786 0.165
+ pcp_spr 1 -151.67 1.6088 0.170
+ bal_05 1 -151.89 1.8220 0.175
+ bal_spr 1 -151.98 1.9066 0.195
+ bal_anual 1 -151.61 1.5474 0.195
+ tmin_aut 1 -151.49 1.4266 0.205
+ pcp_02 1 -151.53 1.4728 0.210
+ tmin_01 1 -151.49 1.4266 0.215
+ tmax_aut 1 -151.56 1.5015 0.220
+ tmax_01 1 -151.56 1.5015 0.240
+ tmin_spr 1 -151.52 1.4584 0.250
+ tmin_02 1 -151.52 1.4584 0.255
+ dummy_09 1 -151.15 1.1006 0.260
+ bal_04 1 -151.37 1.3146 0.265
+ bal_02 1 -151.35 1.2964 0.280
+ pcp_11 1 -151.32 1.2641 0.290
+ tmin_11 1 -151.35 1.2929 0.295
+ pcp_05 1 -151.11 1.0605 0.315
+ pcp_win 1 -151.16 1.1056 0.330
+ tmin_win 1 -151.13 1.0805 0.330
+ et0_aut 1 -151.09 1.0438 0.330
+ dummy_08 1 -151.07 1.0259 0.345
+ altitude 1 -151.25 1.1992 0.350
+ bal_11 1 -151.28 1.2259 0.355
+ verna_11 1 -151.06 1.0133 0.360
+ tamp_01 1 -151.12 1.0724 0.375
+ tmax_11 1 -151.05 1.0013 0.385
+ pcp_04 1 -150.96 0.9175 0.385
+ tmin_04 1 -151.13 1.0805 0.390
+ tmin_06 1 -150.98 0.9372 0.400
+ bal_win 1 -150.96 0.9153 0.415
+ et0_04 1 -151.06 1.0147 0.420
+ pcp_01 1 -150.94 0.8968 0.435
+ frost_03 1 -150.90 0.8599 0.435
+ et0_03 1 -151.06 1.0088 0.440
+ pcp_12 1 -150.86 0.8188 0.480
+ frost_spr 1 -150.83 0.7855 0.485
+ frost_05 1 -150.83 0.7894 0.490
+ frost_02 1 -150.78 0.7449 0.490
+ frost_04 1 -150.73 0.6962 0.495
+ verna_06 1 -150.83 0.7933 0.520
+ verna_05 1 -150.80 0.7585 0.520
+ et0_spr 1 -150.79 0.7470 0.520
+ verna_04 1 -150.73 0.6934 0.530
+ bal_12 1 -150.81 0.7727 0.540
+ dummy_06 1 -150.75 0.7110 0.540
+ tamp_12 1 -150.85 0.8069 0.545
+ et0_11 1 -150.76 0.7235 0.550
+ bal_01 1 -150.82 0.7752 0.555
+ verna_d_01 1 -150.84 0.8003 0.560
+ verna_03 1 -150.66 0.6245 0.565
+ et0_02 1 -150.66 0.6245 0.575
+ et0_12 1 -150.63 0.5963 0.580
+ verna_12 1 -150.61 0.5796 0.580
+ et0_win 1 -150.59 0.5599 0.600
+ verna_01 1 -150.58 0.5501 0.605
+ tmed_03 1 -150.58 0.5446 0.605
+ et0_annual 1 -150.51 0.4840 0.605
+ verna_02 1 -150.62 0.5877 0.650
+ tmax_02 1 -150.65 0.6106 0.655
+ tmax_spr 1 -150.65 0.6106 0.655
+ tamp_05 1 -150.58 0.5443 0.655
+ tamp_win 1 -150.59 0.5574 0.660
+ frost_11 1 -150.51 0.4761 0.660
+ frost_06 1 -150.49 0.4633 0.660
+ tamp_spr 1 -150.49 0.4568 0.665
+ tamp_03 1 -150.43 0.4035 0.670
+ frost_aut 1 -150.51 0.4773 0.680
+ verna_d_02 1 -150.45 0.4225 0.695
+ tamp_06 1 -150.48 0.4488 0.700
+ dummy_03 1 -150.51 0.4837 0.705
+ frost_win 1 -150.47 0.4397 0.710
+ verna_d_04 1 -150.49 0.4630 0.730
+ tamp_04 1 -150.49 0.4594 0.730
+ dummy_04 1 -150.38 0.3531 0.730
+ tmed_06 1 -150.46 0.4328 0.735
+ et0_01 1 -150.48 0.4503 0.750
+ tmin_05 1 -150.33 0.3095 0.755
+ frost_12 1 -150.43 0.3977 0.765
+ et0_05 1 -150.34 0.3116 0.780
+ verna_d_03 1 -150.41 0.3815 0.805
+ dummy_12 1 -150.29 0.2713 0.825
+ tamp_11 1 -150.32 0.2940 0.835
+ frost_01 1 -150.29 0.2700 0.840
+ tamp_02 1 -150.19 0.1761 0.905
+ pcp_06 1 -150.13 0.1143 0.930
+ tmax_05 1 -150.16 0.1381 0.935
+ dummy_05 1 -150.15 0.1351 0.940
+ et0_06 1 -150.13 0.1143 0.945
+ tmed_05 1 -150.10 0.0857 0.960
+ tamp_aut 1 -150.11 0.0944 0.970
+ tmax_04 1 -150.05 0.0369 0.975
+ tmax_03 1 -150.07 0.0599 0.985
+ tmax_06 1 -150.06 0.0457 0.990
+ tmed_win 1 -150.05 0.0381 0.990
+ tmed_04 1 -150.05 0.0381 0.995
+ tmax_win 1 -150.05 0.0369 1.000
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Step: Cluster ~ pfrost_01 + bal_06 + dummy_01 + tmed_12
Df AIC F Pr(>F)
+ utmy 1 -154.80 3.8283 0.025 *
+ pcp_03 1 -153.97 3.0080 0.040 *
+ bal_03 1 -153.92 2.9635 0.040 *
+ dummy_11 1 -153.40 2.4610 0.070 .
+ dummy_10 1 -153.11 2.1780 0.105
+ utmx 1 -153.03 2.0972 0.120
+ tmin_06 1 -152.71 1.7817 0.125
+ pcp_05 1 -152.77 1.8439 0.145
+ bal_spr 1 -152.53 1.6085 0.205
+ pcp_aut 1 -152.42 1.5047 0.210
+ bal_05 1 -152.52 1.6011 0.225
+ et0_04 1 -152.34 1.4251 0.225
+ bal_aut 1 -152.54 1.6193 0.235
+ tmed_06 1 -152.24 1.3346 0.245
+ pcp_spr 1 -152.36 1.4453 0.270
+ dummy_07 1 -152.26 1.3541 0.270
+ pcp_02 1 -152.25 1.3398 0.270
+ tmax_01 1 -152.02 1.1211 0.275
+ pcp_11 1 -152.02 1.1188 0.275
+ bal_anual 1 -152.28 1.3736 0.280
+ dummy_02 1 -152.20 1.2901 0.290
+ bal_04 1 -151.97 1.0693 0.320
+ tamp_01 1 -152.08 1.1813 0.340
+ tmax_aut 1 -152.02 1.1211 0.350
+ dummy_08 1 -151.94 1.0477 0.350
+ altitude 1 -151.94 1.0442 0.355
+ et0_aut 1 -152.11 1.2090 0.370
+ bal_02 1 -152.01 1.1146 0.375
+ verna_11 1 -151.80 0.9125 0.375
+ verna_04 1 -151.85 0.9618 0.385
+ dummy_09 1 -151.86 0.9702 0.395
+ tamp_12 1 -151.80 0.9111 0.395
+ pcp_win 1 -151.80 0.9092 0.395
+ verna_05 1 -151.85 0.9575 0.405
+ frost_spr 1 -151.71 0.8258 0.410
+ et0_03 1 -151.84 0.9515 0.415
+ verna_03 1 -151.82 0.9293 0.415
+ tmin_aut 1 -151.75 0.8598 0.415
+ verna_02 1 -151.77 0.8764 0.425
+ verna_d_04 1 -151.72 0.8356 0.425
+ bal_11 1 -151.99 1.0944 0.430
+ frost_04 1 -151.79 0.8949 0.430
+ verna_06 1 -151.80 0.9096 0.435
+ et0_spr 1 -151.80 0.9128 0.440
+ tmin_01 1 -151.75 0.8598 0.450
+ frost_05 1 -151.78 0.8885 0.465
+ pcp_04 1 -151.70 0.8082 0.485
+ tmin_12 1 -151.67 0.7851 0.485
+ dummy_06 1 -151.61 0.7216 0.490
+ verna_01 1 -151.74 0.8542 0.495
+ pcp_06 1 -151.56 0.6776 0.500
+ frost_03 1 -151.60 0.7189 0.510
+ tmax_12 1 -151.62 0.7337 0.520
+ bal_win 1 -151.60 0.7130 0.530
+ et0_annual 1 -151.57 0.6912 0.545
+ verna_d_01 1 -151.44 0.5619 0.545
+ verna_12 1 -151.60 0.7165 0.555
+ pcp_01 1 -151.53 0.6499 0.590
+ et0_11 1 -151.62 0.7402 0.595
+ et0_06 1 -151.56 0.6776 0.595
+ tamp_win 1 -151.47 0.5903 0.595
+ tmin_05 1 -151.56 0.6732 0.600
+ bal_01 1 -151.41 0.5295 0.615
+ pcp_12 1 -151.55 0.6646 0.620
+ tmin_04 1 -151.44 0.5675 0.620
+ bal_12 1 -151.49 0.6103 0.625
+ verna_d_03 1 -151.48 0.5998 0.625
+ et0_12 1 -151.41 0.5347 0.635
+ tmin_win 1 -151.44 0.5675 0.640
+ frost_01 1 -151.44 0.5609 0.650
+ dummy_03 1 -151.37 0.4996 0.660
+ dummy_04 1 -151.37 0.4945 0.660
+ tmed_aut 1 -151.25 0.3762 0.660
+ frost_aut 1 -151.31 0.4399 0.675
+ frost_11 1 -151.38 0.5093 0.705
+ frost_12 1 -151.25 0.3814 0.705
+ tmax_06 1 -151.33 0.4600 0.720
+ et0_02 1 -151.32 0.4478 0.720
+ et0_05 1 -151.29 0.4168 0.740
+ tmed_01 1 -151.25 0.3762 0.755
+ frost_02 1 -151.22 0.3558 0.755
+ et0_win 1 -151.34 0.4680 0.760
+ verna_d_02 1 -151.21 0.3451 0.765
+ frost_win 1 -151.23 0.3618 0.775
+ tmax_11 1 -151.22 0.3524 0.780
+ dummy_12 1 -151.18 0.3137 0.785
+ tmin_03 1 -151.25 0.3835 0.790
+ frost_06 1 -151.21 0.3431 0.790
+ et0_01 1 -151.28 0.4133 0.795
+ tmed_11 1 -151.15 0.2817 0.805
+ tmed_05 1 -151.09 0.2232 0.820
+ tamp_11 1 -151.17 0.3051 0.850
+ tamp_06 1 -151.13 0.2616 0.885
+ tmax_spr 1 -151.02 0.1581 0.905
+ tmin_11 1 -151.03 0.1721 0.910
+ tmax_02 1 -151.02 0.1581 0.910
+ tamp_05 1 -151.04 0.1813 0.915
+ tmed_spr 1 -151.03 0.1709 0.920
+ tmed_02 1 -151.03 0.1709 0.935
+ tamp_03 1 -150.98 0.1230 0.935
+ tmed_03 1 -150.96 0.1042 0.940
+ tamp_02 1 -151.01 0.1520 0.945
+ tmed_win 1 -150.95 0.0924 0.945
+ tmin_02 1 -150.99 0.1311 0.950
+ tmin_spr 1 -150.99 0.1311 0.955
+ tamp_spr 1 -150.98 0.1201 0.955
+ tamp_aut 1 -150.94 0.0886 0.955
+ tamp_04 1 -150.97 0.1091 0.960
+ tmax_03 1 -150.91 0.0593 0.970
+ tmax_05 1 -150.90 0.0487 0.975
+ tmed_04 1 -150.95 0.0924 0.985
+ tmax_04 1 -150.87 0.0176 0.990
+ dummy_05 1 -150.88 0.0254 0.995
+ tmax_win 1 -150.87 0.0176 1.000
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Step: Cluster ~ pfrost_01 + bal_06 + dummy_01 + tmed_12 + utmy
Df AIC F Pr(>F)
+ dummy_10 1 -155.88 2.9514 0.035 *
+ altitude 1 -155.21 2.3071 0.055 .
+ tmin_06 1 -154.73 1.8449 0.125
+ utmx 1 -154.61 1.7223 0.135
+ pcp_05 1 -154.80 1.9074 0.145
+ dummy_11 1 -154.74 1.8552 0.170
+ pcp_03 1 -154.53 1.6481 0.175
+ bal_05 1 -154.50 1.6244 0.190
+ tmed_06 1 -154.36 1.4838 0.215
+ tmed_11 1 -154.14 1.2757 0.235
+ dummy_07 1 -154.24 1.3718 0.250
+ pcp_aut 1 -154.19 1.3242 0.260
+ tmed_05 1 -154.16 1.2993 0.260
+ dummy_04 1 -154.13 1.2671 0.260
+ tmed_04 1 -153.95 1.0941 0.270
+ bal_aut 1 -153.95 1.0908 0.275
+ pcp_spr 1 -154.04 1.1840 0.280
+ tmin_05 1 -154.22 1.3503 0.290
+ dummy_09 1 -154.12 1.2613 0.295
+ tmed_win 1 -153.95 1.0941 0.305
+ tmin_04 1 -153.91 1.0537 0.330
+ tmed_aut 1 -153.86 1.0111 0.355
+ bal_03 1 -154.00 1.1414 0.370
+ tmed_02 1 -153.83 0.9820 0.370
+ tmin_win 1 -153.91 1.0537 0.395
+ tmed_spr 1 -153.83 0.9820 0.400
+ tmed_01 1 -153.86 1.0111 0.405
+ tmax_05 1 -153.80 0.9537 0.415
+ dummy_02 1 -153.73 0.8865 0.455
+ dummy_06 1 -153.65 0.8072 0.465
+ frost_01 1 -153.69 0.8488 0.475
+ bal_spr 1 -153.62 0.7789 0.475
+ verna_d_01 1 -153.73 0.8807 0.480
+ verna_11 1 -153.61 0.7701 0.490
+ tmed_03 1 -153.66 0.8142 0.495
+ verna_06 1 -153.59 0.7510 0.495
+ tmax_04 1 -153.59 0.7482 0.495
+ tmax_win 1 -153.59 0.7482 0.500
+ et0_11 1 -153.52 0.6791 0.500
+ verna_03 1 -153.53 0.6896 0.505
+ et0_aut 1 -153.49 0.6584 0.505
+ verna_05 1 -153.62 0.7734 0.510
+ verna_04 1 -153.58 0.7440 0.510
+ et0_12 1 -153.60 0.7555 0.515
+ frost_05 1 -153.56 0.7185 0.515
+ frost_spr 1 -153.60 0.7629 0.520
+ tmax_02 1 -153.60 0.7558 0.525
+ tmax_spr 1 -153.60 0.7558 0.525
+ frost_03 1 -153.56 0.7240 0.530
+ frost_11 1 -153.53 0.6930 0.545
+ frost_04 1 -153.57 0.7337 0.555
+ pcp_04 1 -153.53 0.6883 0.555
+ et0_win 1 -153.47 0.6367 0.560
+ tmax_06 1 -153.40 0.5672 0.560
+ tmax_11 1 -153.54 0.6990 0.565
+ et0_02 1 -153.44 0.6101 0.565
+ bal_anual 1 -153.56 0.7187 0.580
+ pcp_11 1 -153.39 0.5603 0.580
+ et0_06 1 -153.43 0.5997 0.590
+ tmax_01 1 -153.43 0.5969 0.595
+ verna_02 1 -153.45 0.6167 0.610
+ verna_d_02 1 -153.39 0.5598 0.615
+ verna_01 1 -153.43 0.5990 0.625
+ verna_d_04 1 -153.39 0.5558 0.625
+ et0_01 1 -153.34 0.5104 0.625
+ frost_aut 1 -153.48 0.6432 0.630
+ tmax_aut 1 -153.43 0.5969 0.630
+ verna_12 1 -153.36 0.5298 0.640
+ frost_12 1 -153.35 0.5199 0.640
+ frost_win 1 -153.34 0.5145 0.645
+ bal_04 1 -153.38 0.5487 0.655
+ pcp_02 1 -153.38 0.5446 0.660
+ tmax_03 1 -153.35 0.5236 0.660
+ tmin_03 1 -153.28 0.4519 0.675
+ pcp_06 1 -153.43 0.5997 0.680
+ tamp_05 1 -153.35 0.5203 0.685
+ verna_d_03 1 -153.32 0.4923 0.690
+ et0_annual 1 -153.30 0.4767 0.700
+ tamp_02 1 -153.22 0.3992 0.700
+ dummy_03 1 -153.33 0.5024 0.705
+ bal_11 1 -153.28 0.4561 0.705
+ pcp_win 1 -153.20 0.3811 0.705
+ tamp_04 1 -153.28 0.4508 0.720
+ tamp_win 1 -153.22 0.3959 0.720
+ tamp_12 1 -153.22 0.3969 0.735
+ et0_03 1 -153.22 0.3953 0.740
+ frost_02 1 -153.23 0.4062 0.745
+ tamp_01 1 -153.26 0.4323 0.750
+ tamp_spr 1 -153.22 0.3934 0.760
+ bal_02 1 -153.15 0.3319 0.765
+ dummy_08 1 -153.16 0.3390 0.785
+ pcp_01 1 -153.14 0.3252 0.785
+ frost_06 1 -153.14 0.3256 0.790
+ tamp_03 1 -153.13 0.3123 0.805
+ et0_04 1 -153.17 0.3511 0.810
+ tamp_11 1 -153.13 0.3086 0.815
+ tmax_12 1 -153.12 0.3060 0.815
+ tmin_aut 1 -153.09 0.2715 0.815
+ tmin_12 1 -153.17 0.3506 0.820
+ tmin_01 1 -153.09 0.2715 0.825
+ dummy_12 1 -153.13 0.3153 0.840
+ tamp_06 1 -153.04 0.2310 0.840
+ bal_01 1 -153.04 0.2239 0.840
+ et0_spr 1 -153.10 0.2796 0.850
+ bal_win 1 -153.04 0.2271 0.860
+ et0_05 1 -153.03 0.2167 0.885
+ pcp_12 1 -153.03 0.2164 0.890
+ tmin_11 1 -152.97 0.1619 0.910
+ bal_12 1 -152.99 0.1742 0.935
+ tamp_aut 1 -152.87 0.0665 0.980
+ dummy_05 1 -152.85 0.0500 0.980
+ tmin_02 1 -152.85 0.0428 0.985
+ tmin_spr 1 -152.85 0.0428 0.990
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Step: Cluster ~ pfrost_01 + bal_06 + dummy_01 + tmed_12 + utmy + dummy_10
Df AIC F Pr(>F)
+ pcp_05 1 -156.10 2.1062 0.070 .
+ tmed_06 1 -155.78 1.8013 0.105
+ tmin_06 1 -155.97 1.9820 0.135
+ dummy_11 1 -155.87 1.8889 0.140
+ altitude 1 -155.45 1.4812 0.170
+ bal_05 1 -155.60 1.6278 0.180
+ pcp_03 1 -155.51 1.5467 0.200
+ tmin_05 1 -155.32 1.3649 0.245
+ dummy_04 1 -155.26 1.3024 0.265
+ pcp_aut 1 -155.23 1.2723 0.280
+ utmx 1 -155.21 1.2524 0.280
+ tmed_05 1 -155.16 1.2112 0.280
+ bal_aut 1 -155.08 1.1309 0.290
+ frost_01 1 -155.16 1.2100 0.295
+ dummy_03 1 -154.94 1.0023 0.310
+ bal_03 1 -155.19 1.2360 0.325
+ dummy_07 1 -155.06 1.1122 0.325
+ tmed_11 1 -155.12 1.1672 0.335
+ pcp_spr 1 -155.12 1.1702 0.340
+ tmin_win 1 -155.04 1.0966 0.340
+ frost_05 1 -154.88 0.9404 0.350
+ et0_06 1 -154.91 0.9736 0.370
+ tmed_01 1 -154.90 0.9660 0.370
+ tmin_04 1 -155.04 1.0966 0.395
+ pcp_06 1 -154.91 0.9736 0.405
+ tmed_aut 1 -154.90 0.9660 0.410
+ tmed_04 1 -154.82 0.8868 0.430
+ tmed_win 1 -154.82 0.8868 0.430
+ verna_d_01 1 -154.83 0.8987 0.435
+ frost_04 1 -154.87 0.9368 0.455
+ frost_11 1 -154.67 0.7436 0.460
+ tmax_06 1 -154.75 0.8215 0.475
+ bal_spr 1 -154.76 0.8273 0.480
+ frost_spr 1 -154.77 0.8427 0.490
+ dummy_09 1 -154.73 0.8057 0.490
+ bal_anual 1 -154.70 0.7740 0.490
+ tmax_05 1 -154.70 0.7708 0.500
+ tmed_spr 1 -154.57 0.6543 0.500
+ frost_aut 1 -154.57 0.6543 0.520
+ pcp_04 1 -154.62 0.6973 0.550
+ frost_03 1 -154.63 0.7076 0.560
+ tmed_02 1 -154.57 0.6543 0.565
+ frost_12 1 -154.60 0.6836 0.570
+ verna_05 1 -154.51 0.5917 0.575
+ tmed_03 1 -154.54 0.6242 0.580
+ verna_03 1 -154.48 0.5620 0.595
+ verna_01 1 -154.38 0.4673 0.610
+ frost_win 1 -154.56 0.6391 0.615
+ pcp_02 1 -154.49 0.5739 0.615
+ et0_annual 1 -154.46 0.5511 0.615
+ verna_d_02 1 -154.47 0.5571 0.625
+ verna_04 1 -154.52 0.6011 0.630
+ verna_11 1 -154.43 0.5160 0.635
+ et0_04 1 -154.42 0.5099 0.645
+ verna_06 1 -154.43 0.5166 0.650
+ bal_04 1 -154.48 0.5626 0.660
+ pcp_11 1 -154.49 0.5715 0.665
+ verna_d_03 1 -154.36 0.4516 0.675
+ verna_02 1 -154.40 0.4870 0.680
+ bal_11 1 -154.41 0.4985 0.685
+ verna_d_04 1 -154.36 0.4535 0.695
+ et0_aut 1 -154.42 0.5128 0.705
+ tmax_04 1 -154.38 0.4741 0.705
+ tmax_win 1 -154.38 0.4741 0.710
+ tmax_11 1 -154.36 0.4522 0.720
+ dummy_12 1 -154.36 0.4566 0.725
+ verna_12 1 -154.37 0.4660 0.730
+ tmin_03 1 -154.35 0.4430 0.730
+ dummy_02 1 -154.29 0.3909 0.740
+ dummy_06 1 -154.35 0.4463 0.760
+ frost_06 1 -154.25 0.3453 0.760
+ bal_02 1 -154.29 0.3901 0.770
+ tmin_01 1 -154.27 0.3680 0.775
+ tmin_11 1 -154.20 0.3002 0.775
+ tmin_12 1 -154.28 0.3738 0.780
+ frost_02 1 -154.25 0.3500 0.780
+ pcp_win 1 -154.28 0.3818 0.785
+ pcp_01 1 -154.22 0.3194 0.785
+ et0_spr 1 -154.19 0.2960 0.790
+ tmin_aut 1 -154.27 0.3680 0.795
+ et0_12 1 -154.19 0.2949 0.815
+ tmax_02 1 -154.18 0.2819 0.815
+ dummy_08 1 -154.24 0.3346 0.825
+ et0_05 1 -154.20 0.3048 0.825
+ tmax_01 1 -154.22 0.3168 0.830
+ et0_11 1 -154.22 0.3208 0.840
+ tmax_aut 1 -154.22 0.3168 0.840
+ bal_01 1 -154.14 0.2460 0.840
+ bal_win 1 -154.14 0.2486 0.845
+ tmax_spr 1 -154.18 0.2819 0.860
+ tamp_05 1 -154.12 0.2281 0.860
+ pcp_12 1 -154.11 0.2175 0.870
+ tamp_01 1 -154.09 0.2021 0.875
+ tamp_12 1 -154.06 0.1715 0.885
+ tmax_03 1 -154.11 0.2209 0.890
+ et0_win 1 -154.09 0.2007 0.900
+ bal_12 1 -154.07 0.1820 0.905
+ et0_02 1 -154.04 0.1531 0.905
+ tmax_12 1 -154.07 0.1814 0.910
+ et0_01 1 -154.05 0.1640 0.915
+ tamp_win 1 -154.07 0.1788 0.920
+ tamp_11 1 -154.06 0.1686 0.925
+ tamp_04 1 -154.02 0.1330 0.925
+ tamp_06 1 -154.05 0.1593 0.930
+ et0_03 1 -154.02 0.1285 0.930
+ tamp_02 1 -154.00 0.1163 0.930
+ tmin_spr 1 -154.00 0.1126 0.945
+ tmin_02 1 -154.00 0.1126 0.950
+ tamp_spr 1 -154.00 0.1085 0.960
+ dummy_05 1 -153.92 0.0362 0.975
+ tamp_aut 1 -153.96 0.0771 0.980
+ tamp_03 1 -153.91 0.0271 0.990
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1#Redundancy analysis, complete data reduced to env variables selected by forward selection, until first dummy variable entered in the model
SBCC_RDA_red<-rda(Cluster~pfrost_01+bal_06, data=scaledenv.df)Information on outcome of RDA. Variance inflation ratio informs on multicolinearity (values above 10 are too high). R-squared adjusted for the number of parameters indicates proportion of variation explained
#variance inflation ratio, above 10 indicates multicolinearity
vif.cca(SBCC_RDA) tamp_aut tamp_spr tamp_win tamp_01 tamp_02
4.295162e+02 3.540986e+04 9.302750e+03 8.268138e+03 2.999612e+04
tamp_03 tamp_04 tamp_05 tamp_06 tamp_11
2.295358e+05 1.211579e+05 8.338348e+04 1.130374e+04 5.594866e+03
tamp_12 et0_annual bal_01 bal_02 bal_03
2.970511e+03 1.277254e+04 7.150251e+02 4.111410e+02 8.940493e+12
bal_04 bal_05 bal_06 bal_11 bal_12
1.615430e+13 5.215773e+14 1.985650e+14 3.575522e+02 1.594152e+03
bal_anual bal_aut bal_spr bal_win frost_aut
6.925306e+03 5.317252e+03 1.243565e+14 NA 6.138931e+03
frost_spr frost_win frost_01 frost_02 frost_03
3.807555e+05 6.002322e+05 8.225854e+04 6.746602e+04 1.383191e+05
frost_04 frost_05 frost_06 frost_11 frost_12
3.887011e+04 3.963422e+03 5.927410e+01 5.502373e+03 5.826062e+04
et0_01 et0_11 et0_12 et0_02 et0_03
1.312442e+13 2.479961e+03 1.380325e+13 1.377879e+13 2.262344e+03
et0_04 et0_05 et0_06 pcp_01 pcp_02
2.463415e+03 1.481729e+14 7.257382e+13 NA NA
pcp_03 pcp_04 pcp_05 pcp_06 pcp_11
NA NA 1.500718e+14 4.477745e+13 NA
pcp_12 pcp_aut pcp_spr pcp_win pfrost_01
NA 3.930839e+03 5.580345e+03 3.565956e+03 3.426145e+02
et0_aut et0_spr et0_win tmax_01 tmax_02
3.435502e+03 NA 1.149129e+14 1.478811e+05 2.707371e+05
tmax_03 tmax_04 tmax_05 tmax_06 tmax_11
2.347263e+06 1.510571e+06 6.127409e+05 9.157733e+04 1.453267e+05
tmax_12 tmax_aut tmax_spr tmax_win tmed_01
8.881765e+04 NA NA NA 3.277640e+05
tmed_02 tmed_03 tmed_04 tmed_05 tmed_06
4.902122e+05 6.837286e+06 1.649220e+06 6.168732e+05 2.423067e+05
tmed_11 tmed_12 tmed_aut tmed_spr tmed_win
3.671119e+05 3.157238e+05 NA NA NA
tmin_01 tmin_02 tmin_03 tmin_04 tmin_05
1.057001e+05 3.031936e+05 2.969526e+06 4.684489e+05 5.013898e+05
tmin_06 tmin_11 tmin_12 tmin_aut tmin_spr
9.585096e+04 1.551695e+05 1.150441e+05 NA NA
tmin_win verna_d_01 verna_d_02 verna_d_03 verna_d_04
NA 1.047005e+03 1.039705e+03 1.265439e+03 6.242494e+02
verna_01 verna_02 verna_03 verna_04 verna_05
2.278741e+04 7.347226e+04 1.243496e+05 2.592596e+05 3.564866e+05
verna_06 verna_11 verna_12
1.865621e+05 1.192771e+04 4.405101e+03 vif.cca(SBCC_RDA_red)pfrost_01 bal_06
1.972673 1.972673 #R-squared, raw and adjusted, explained by rda
RsquareAdj(SBCC_RDA_red)$r.squared
[1] 0.2348693
$adj.r.squared
[1] 0.2231879RsquareAdj(SBCC_RDA)$r.squared
[1] 0.7827899
$adj.r.squared
[1] 0.3853415Plots of both redundancy analyses, scaling=0 chosen, as it results in good visualization of the plot; see help of the package for other scaling options
#Triplot of rda results, check scaling options in help file
plot(SBCC_RDA,type="text", scaling=0)
plot(SBCC_RDA_red,type="text", scaling=0)
Third redundancy analysis with just 17 chosen environmental (agroclimatic) variables.
#Redundancy analysis, complete data set
SBCCc_RDA<-rda(Clusterc,Envc,scale=F)Information on outcome of RDA. Variance inflation ratio informs on multicollinearity (values above 10 are too high). R-squared adjusted for the number of parameters indicates proportion of variation explained
#variance inflation ratio, above 10 indicates multicolinearity
vif.cca(SBCCc_RDA) verna_30d verna_jan_feb verna_mar_apr pfrost_01
742.997516 99.174744 489.132365 44.955736
pcp_aut pcp_win pcp_mar_apr pcp_may_jun
229.443398 258.416685 251.925945 209.041842
frost_jan_feb frost_apr_may tamp_win tamp_spr
24.344763 12.073368 6.939531 11.120701
et0_spr bal_aut bal_win bal_jun
619.553508 310.071210 249.272417 139.253122
bal_mar_apr_may
1425.818277 #R-squared, raw and adjusted, explained by rda
RsquareAdj(SBCCc_RDA)$r.squared
[1] 0.3735195
$adj.r.squared
[1] 0.2817077Plot of redundancy analyses, scaling=0 chosen, as it results in good visualization of the plot; see help of the package for other scaling options
#Triplot of rda results, check scaling options in help file
plot(SBCCc_RDA,type="text", scaling=0)
Variance of distribution of germplasm groups explained by #1 full model (all agro-climatic variables); #2 geographic variables, after agro-climatic variables are taken into account; #3 agro-climatic variables are taken into account. Significance calculated.
#Variance explained by different fractions of variables
#1
anova(SBCCc_RDA)Permutation test for rda under reduced model
Permutation: free
Number of permutations: 999
Model: rda(X = Clusterc, Y = Envc, scale = F)
Df Variance F Pr(>F)
Model 17 0.15287 4.0683 0.001 ***
Residual 116 0.25640
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1#2
anova.cca(rda(Clusterc,Geoc,Envc),step=1000)Permutation test for rda under reduced model
Permutation: free
Number of permutations: 999
Model: rda(X = Clusterc, Y = Geoc, Z = Envc)
Df Variance F Pr(>F)
Model 3 0.003595 0.5356 0.841
Residual 113 0.252810 #3
anova.cca(rda(Clusterc,Envc,Geoc),step=1000)Permutation test for rda under reduced model
Permutation: free
Number of permutations: 999
Model: rda(X = Clusterc, Y = Envc, Z = Geoc)
Df Variance F Pr(>F)
Model 17 0.06711 1.7645 0.008 **
Residual 113 0.25281
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Percentage of variation of distribution of germplasm groups explained by environmental (agro-climatic) variables alone (fraction a), geographic variables alone (fraction c), environmental and geographic simultaneously (fraction b). Self-explanatory plot
# Variation partitioning
spe.part <- varpart(Clusterc, Envc, Geoc)
spe.part
Partition of variance in RDA
Call: varpart(Y = Clusterc, X = Envc, Geoc)
Explanatory tables:
X1: Envc
X2: Geoc
No. of explanatory tables: 2
Total variation (SS): 54.434
Variance: 0.40928
No. of observations: 134
Partition table:
Df R.squared Adj.R.squared Testable
[a+b] = X1 17 0.37352 0.28171 TRUE
[b+c] = X2 3 0.21833 0.20029 TRUE
[a+b+c] = X1+X2 20 0.38230 0.27298 TRUE
Individual fractions
[a] = X1|X2 17 0.07268 TRUE
[b] 0 0.20902 FALSE
[c] = X2|X1 3 -0.00873 TRUE
[d] = Residuals 0.72702 FALSE
---
Use function 'rda' to test significance of fractions of interestplot(spe.part, digits=2)
Test of variance explained by different sets of variables
# Test of fractions [a+b], only environmental variables
anova.cca(rda(Clusterc, Envc), step=1000)Permutation test for rda under reduced model
Permutation: free
Number of permutations: 999
Model: rda(X = Clusterc, Y = Envc)
Df Variance F Pr(>F)
Model 17 0.15287 4.0683 0.001 ***
Residual 116 0.25640
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1# Test of fractions [b+c], only geographic variables
anova.cca(rda(Clusterc, Geoc), step=1000)Permutation test for rda under reduced model
Permutation: free
Number of permutations: 999
Model: rda(X = Clusterc, Y = Geoc)
Df Variance F Pr(>F)
Model 3 0.08936 12.104 0.001 ***
Residual 130 0.31992
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1# Test of fractions [a+b+c], union of environmental and geographic
env.pars <- cbind(Envc, Geoc)
anova.cca(rda(Clusterc, env.pars), step=1000)Permutation test for rda under reduced model
Permutation: free
Number of permutations: 999
Model: rda(X = Clusterc, Y = env.pars)
Df Variance F Pr(>F)
Model 20 0.15647 3.4969 0.001 ***
Residual 113 0.25281
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1#Test of fraction [a], environmental variables, excluding variation shared with geographic
anova.cca(rda(Clusterc, Envc, Geoc), step=1000)Permutation test for rda under reduced model
Permutation: free
Number of permutations: 999
Model: rda(X = Clusterc, Y = Envc, Z = Geoc)
Df Variance F Pr(>F)
Model 17 0.06711 1.7645 0.005 **
Residual 113 0.25281
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1#Test of fraction [c], geographic variables, excluding variation shared with environmental (b)
anova.cca(rda(Clusterc, Geoc, Envc), step=1000)Permutation test for rda under reduced model
Permutation: free
Number of permutations: 999
Model: rda(X = Clusterc, Y = Geoc, Z = Envc)
Df Variance F Pr(>F)
Model 3 0.003595 0.5356 0.831
Residual 113 0.252810 Export results, files stored in directory RDA:
Scores<-scores(SBCCc_RDA)
Summaries<-summary(SBCCc_RDA)
write.table(Scores$sites,'RDA/scores_genotypes.txt', sep='\t')
write.table(Summaries$biplot,'RDA/scores_env.txt', sep='\t')
write.table(Scores$species,'RDA/scores_germplasmgroups.txt', sep='\t')