I have two data matrices (predictor matrix and response matrix) on which I am running PLS. My question is 'How does their relationship differ between clean and polluted sites?'
I can observe this on plot, but would like ellipses around each group - clean and polluted.
my code is:
data[complete.cases(data),]-> trans
my_pls2=plsreg2(trans[,-c(1:11)], trans[,-c(1:4,12:35)], comps=3, crosval = TRUE)
blok<-as.numeric(trans[,3]) ####column 3 is STATUS (CLEAN and POLLUTED)
col.status<-c("blue", "red")
palette(col.status)
plot(my_pls2, what="observations", where=c("u","u"), show.names = FALSE, main="Map of observation_(u,u)_transplant", col.points = blok, pch=19)
ordiellipse(my_pls2,trans[,3],conf=0.99) # puts elipse on pca graph based on pca file created and according to the file 3rd column
But then I am getting an error:
Error in scores.default(ord, display = display, ...) : Can't find scores
The packages that I am using are plsdepot and vegan.
dput(data)
site ind STATUS BLOK E1 E2 E3 E4 E5 E6 E7 Li Rb Mo Ag Cd Sn Sb Pb Bi U Al Ti V Cr Mn Fe Co Ni Cu Zn Sr Ba As Se
A A1 C N 73.858 78.044 24.59 22.57 0.85 16.92 3.4 1.522 5.949 0.987 0.025 0.721 0.069 0.025 0.737 0.01 0.099 619.5 32.4 3.229 1.438 9.19 425.3 0.753 1.492 4.759 107.7 33.3 3.46 24 3.672
A A2 C N 66.848 68.608 40.984 20.52 0.58 17.1 1.62 1.522 5.949 0.987 0.025 0.721 0.069 0.025 0.737 0.01 0.099 619.5 32.4 3.229 1.438 9.19 425.3 0.753 1.492 4.759 107.7 33.3 3.46 24 3.672
A A3 C N 66.718 32.434 99.666 14.96 0.08 22.21 4 1.522 5.949 0.987 0.025 0.721 0.069 0.025 0.737 0.01 0.099 619.5 32.4 3.229 1.438 9.19 425.3 0.753 1.492 4.759 107.7 33.3 3.46 24 3.672
A A4 C N 103.134 74.44 34.946 27.61 1.48 16.39 2.42 1.522 5.949 0.987 0.025 0.721 0.069 0.025 0.737 0.01 0.099 619.5 32.4 3.229 1.438 9.19 425.3 0.753 1.492 4.759 107.7 33.3 3.46 24 3.672
A A5 C N 69.078 44.9 54.358 29.72 2.14 12.76 1.21 1.522 5.949 0.987 0.025 0.721 0.069 0.025 0.737 0.01 0.099 619.5 32.4 3.229 1.438 9.19 425.3 0.753 1.492 4.759 107.7 33.3 3.46 24 3.672
A A6 C N 53.236 51.874 40.706 22.67 1.85 15.92 7.76 1.522 5.949 0.987 0.025 0.721 0.069 0.025 0.737 0.01 0.099 619.5 32.4 3.229 1.438 9.19 425.3 0.753 1.492 4.759 107.7 33.3 3.46 24 3.672
A A7 C N 70.044 47.672 40.706 31.53 0.1 16.1 1.58 1.522 5.949 0.987 0.025 0.721 0.069 0.025 0.737 0.01 0.099 619.5 32.4 3.229 1.438 9.19 425.3 0.753 1.492 4.759 107.7 33.3 3.46 24 3.672
A A8 C N 68.328 44.174 36.238 27.98 0.91 23.21 9.02 1.522 5.949 0.987 0.025 0.721 0.069 0.025 0.737 0.01 0.099 619.5 32.4 3.229 1.438 9.19 425.3 0.753 1.492 4.759 107.7 33.3 3.46 24 3.672
A A9 C N 120.928 47.576 34.946 26.19 0.83 15.39 3.47 1.522 5.949 0.987 0.025 0.721 0.069 0.025 0.737 0.01 0.099 619.5 32.4 3.229 1.438 9.19 425.3 0.753 1.492 4.759 107.7 33.3 3.46 24 3.672
A A10 C N 79.588 56.958 66.444 20.64 0.49 11.76 3.83 1.522 5.949 0.987 0.025 0.721 0.069 0.025 0.737 0.01 0.099 619.5 32.4 3.229 1.438 9.19 425.3 0.753 1.492 4.759 107.7 33.3 3.46 24 3.672
B B1 P N 151.374 81.816 47.812 20.73 0.18 15.68 9.04 1.204 5.974 1.252 0.07 0.642 0.45 0.065 8.411 0.026 0.112 184.6 13.1 18.127 2.484 5.15 235 0.441 1.126 16.208 176.9 65.9 11.16 23.79 3.215
B B2 P N 146.716 155.784 67.864 67.25 2.73 15.8 2.51 1.204 5.974 1.252 0.07 0.642 0.45 0.065 8.411 0.026 0.112 184.6 13.1 18.127 2.484 5.15 235 0.441 1.126 16.208 176.9 65.9 11.16 23.79 3.215
B B3 P N 165.122 36.742 63.35 27.86 0.68 16.4 10.64 1.204 5.974 1.252 0.07 0.642 0.45 0.065 8.411 0.026 0.112 184.6 13.1 18.127 2.484 5.15 235 0.441 1.126 16.208 176.9 65.9 11.16 23.79 3.215
B B4 P N 115.256 55.78 93.304 52.85 1.63 15.98 2.61 1.204 5.974 1.252 0.07 0.642 0.45 0.065 8.411 0.026 0.112 184.6 13.1 18.127 2.484 5.15 235 0.441 1.126 16.208 176.9 65.9 11.16 23.79 3.215
B B5 P N 185.064 44.9 104.488 44.77 2.3 22.02 1.42 1.204 5.974 1.252 0.07 0.642 0.45 0.065 8.411 0.026 0.112 184.6 13.1 18.127 2.484 5.15 235 0.441 1.126 16.208 176.9 65.9 11.16 23.79 3.215
B B6 P N 83.362 72.99 156.73 29.58 0.67 14.68 1.42 1.204 5.974 1.252 0.07 0.642 0.45 0.065 8.411 0.026 0.112 184.6 13.1 18.127 2.484 5.15 235 0.441 1.126 16.208 176.9 65.9 11.16 23.79 3.215
B B7 P N 49.506 35.008 81.74 32.98 0.19 16.9 1.39 1.204 5.974 1.252 0.07 0.642 0.45 0.065 8.411 0.026 0.112 184.6 13.1 18.127 2.484 5.15 235 0.441 1.126 16.208 176.9 65.9 11.16 23.79 3.215
B B8 P N 99.64 100.57 54.494 32.19 2.25 17.3 2.89 1.204 5.974 1.252 0.07 0.642 0.45 0.065 8.411 0.026 0.112 184.6 13.1 18.127 2.484 5.15 235 0.441 1.126 16.208 176.9 65.9 11.16 23.79 3.215
B B9 P N 179.53 52.368 72.77 39.15 2 14.98 8.7 1.204 5.974 1.252 0.07 0.642 0.45 0.065 8.411 0.026 0.112 184.6 13.1 18.127 2.484 5.15 235 0.441 1.126 16.208 176.9 65.9 11.16 23.79 3.215
B B10 P N 152.89 37.102 66.632 32.73 2.39 22.9 3.94 1.204 5.974 1.252 0.07 0.642 0.45 0.065 8.411 0.026 0.112 184.6 13.1 18.127 2.484 5.15 235 0.441 1.126 16.208 176.9 65.9 11.16 23.79 3.215
C C1 C M 60.25 62.024 34.686 33.51 0.49 19.69 4.39 1.366 6.739 7.213 0.04 0.875 0.057 0.022 0.962 0.014 0.139 408.4 22.6 2.543 1.255 17.32 284.5 0.71 1.779 5.244 64.2 36.1 6.68 32.39 5.301
C C2 C M 22.088 124.372 70.17 49.88 0.68 18.65 3.48 1.366 6.739 7.213 0.04 0.875 0.057 0.022 0.962 0.014 0.139 408.4 22.6 2.543 1.255 17.32 284.5 0.71 1.779 5.244 64.2 36.1 6.68 32.39 5.301
C C3 C M 34.458 62.5 52.042 44.36 1.96 21.68 4.34 1.366 6.739 7.213 0.04 0.875 0.057 0.022 0.962 0.014 0.139 408.4 22.6 2.543 1.255 17.32 284.5 0.71 1.779 5.244 64.2 36.1 6.68 32.39 5.301
C C4 C M 33.456 70.816 61.326 49.87 2.57 18.98 2.59 1.366 6.739 7.213 0.04 0.875 0.057 0.022 0.962 0.014 0.139 408.4 22.6 2.543 1.255 17.32 284.5 0.71 1.779 5.244 64.2 36.1 6.68 32.39 5.301
C C5 C M 48.572 102.868 43.58 54.52 0.35 4.61 4.53 1.366 6.739 7.213 0.04 0.875 0.057 0.022 0.962 0.014 0.139 408.4 22.6 2.543 1.255 17.32 284.5 0.71 1.779 5.244 64.2 36.1 6.68 32.39 5.301
C C6 C M 62.214 55.654 34.686 38.58 0.71 19.1 2.59 1.366 6.739 7.213 0.04 0.875 0.057 0.022 0.962 0.014 0.139 408.4 22.6 2.543 1.255 17.32 284.5 0.71 1.779 5.244 64.2 36.1 6.68 32.39 5.301
C C7 C M 32.41 79.09 68.15 34.7 0.95 17.55 5.74 1.366 6.739 7.213 0.04 0.875 0.057 0.022 0.962 0.014 0.139 408.4 22.6 2.543 1.255 17.32 284.5 0.71 1.779 5.244 64.2 36.1 6.68 32.39 5.301
C C8 C M 33.574 90.35 52.042 56.13 3.96 22.68 8.24 1.366 6.739 7.213 0.04 0.875 0.057 0.022 0.962 0.014 0.139 408.4 22.6 2.543 1.255 17.32 284.5 0.71 1.779 5.244 64.2 36.1 6.68 32.39 5.301
C C9 C M 36.522 121.092 62.92 58.42 1.39 17.78 2.56 1.366 6.739 7.213 0.04 0.875 0.057 0.022 0.962 0.014 0.139 408.4 22.6 2.543 1.255 17.32 284.5 0.71 1.779 5.244 64.2 36.1 6.68 32.39 5.301
C C10 C M 31.608 70.058 43.58 32.02 0.89 5.52 2.66 1.366 6.739 7.213 0.04 0.875 0.057 0.022 0.962 0.014 0.139 408.4 22.6 2.543 1.255 17.32 284.5 0.71 1.779 5.244 64.2 36.1 6.68 32.39 5.301
D D1 P M 79.37 116.392 94.426 43.88 0.94 13.81 2.22 1.859 5.613 3.106 0.253 0.951 2.389 0.054 14.05 0.134 0.138 328.4 54.2 1.774 3.133 6.33 386.9 0.667 1.298 312.977 410.9 80.5 5.36 24.82 3.122
D D2 P M 132.234 88.232 71.56 49.76 0.36 9.51 2.68 1.859 5.613 3.106 0.253 0.951 2.389 0.054 14.05 0.134 0.138 328.4 54.2 1.774 3.133 6.33 386.9 0.667 1.298 312.977 410.9 80.5 5.36 24.82 3.122
D D3 P M 137.114 156.878 84.6 42.43 0.26 23.93 2.36 1.859 5.613 3.106 0.253 0.951 2.389 0.054 14.05 0.134 0.138 328.4 54.2 1.774 3.133 6.33 386.9 0.667 1.298 312.977 410.9 80.5 5.36 24.82 3.122
D D4 P M 161.826 132.916 59.922 41.64 0.34 6.96 2.68 1.859 5.613 3.106 0.253 0.951 2.389 0.054 14.05 0.134 0.138 328.4 54.2 1.774 3.133 6.33 386.9 0.667 1.298 312.977 410.9 80.5 5.36 24.82 3.122
D D5 P M 97.656 153.014 117.94 32.9 1.17 2.09 2.21 1.859 5.613 3.106 0.253 0.951 2.389 0.054 14.05 0.134 0.138 328.4 54.2 1.774 3.133 6.33 386.9 0.667 1.298 312.977 410.9 80.5 5.36 24.82 3.122
D D6 P M 100.3 155.406 65.88 35.97 0.42 14.81 1.85 1.859 5.613 3.106 0.253 0.951 2.389 0.054 14.05 0.134 0.138 328.4 54.2 1.774 3.133 6.33 386.9 0.667 1.298 312.977 410.9 80.5 5.36 24.82 3.122
D D7 P M 94.694 114.008 109.444 30.66 0.72 10.51 3.42 1.859 5.613 3.106 0.253 0.951 2.389 0.054 14.05 0.134 0.138 328.4 54.2 1.774 3.133 6.33 386.9 0.667 1.298 312.977 410.9 80.5 5.36 24.82 3.122
D D8 P M 175.182 153.594 49.322 30.97 0.72 22.93 2.9 1.859 5.613 3.106 0.253 0.951 2.389 0.054 14.05 0.134 0.138 328.4 54.2 1.774 3.133 6.33 386.9 0.667 1.298 312.977 410.9 80.5 5.36 24.82 3.122
D D9 P M 135.814 104.438 78.592 36.73 1.34 6.96 6.04 1.859 5.613 3.106 0.253 0.951 2.389 0.054 14.05 0.134 0.138 328.4 54.2 1.774 3.133 6.33 386.9 0.667 1.298 312.977 410.9 80.5 5.36 24.82 3.122
D D10 P M 70.534 141.234 106.052 36.33 0.97 1.09 2.93 1.859 5.613 3.106 0.253 0.951 2.389 0.054 14.05 0.134 0.138 328.4 54.2 1.774 3.133 6.33 386.9 0.667 1.298 312.977 410.9 80.5 5.36 24.82 3.122
E E1 C S 67.29 143.506 36.088 25.83 2.74 11.16 2.93 1.516 6.642 3.406 0.027 0.899 0.051 0.027 0.651 0.018 0.104 393.5 21.1 2.406 6.467 11.55 289.7 0.591 2.003 5.408 70.6 58.2 2.47 23.04 5.368
E E2 C S NA 75.094 44.758 28.71 0.33 15.77 5.72 1.516 6.642 3.406 0.027 0.899 0.051 0.027 0.651 0.018 0.104 393.5 21.1 2.406 6.467 11.55 289.7 0.591 2.003 5.408 70.6 58.2 2.47 23.04 5.368
E E3 C S 28.66 53.16 48.526 34.77 0.69 1.6 1.73 1.516 6.642 3.406 0.027 0.899 0.051 0.027 0.651 0.018 0.104 393.5 21.1 2.406 6.467 11.55 289.7 0.591 2.003 5.408 70.6 58.2 2.47 23.04 5.368
E E4 C S 72.53 108.82 48.634 37.05 1.53 16.77 6.37 1.516 6.642 3.406 0.027 0.899 0.051 0.027 0.651 0.018 0.104 393.5 21.1 2.406 6.467 11.55 289.7 0.591 2.003 5.408 70.6 58.2 2.47 23.04 5.368
E E5 C S 56.122 53.16 42.11 48.81 0.24 11.05 2.29 1.516 6.642 3.406 0.027 0.899 0.051 0.027 0.651 0.018 0.104 393.5 21.1 2.406 6.467 11.55 289.7 0.591 2.003 5.408 70.6 58.2 2.47 23.04 5.368
E E6 C S 79.63 98.662 35.928 26.18 0.78 12.16 3.39 1.516 6.642 3.406 0.027 0.899 0.051 0.027 0.651 0.018 0.104 393.5 21.1 2.406 6.467 11.55 289.7 0.591 2.003 5.408 70.6 58.2 2.47 23.04 5.368
E E7 C S 87.75 70.358 44.758 33.62 1.02 14.77 1.8 1.516 6.642 3.406 0.027 0.899 0.051 0.027 0.651 0.018 0.104 393.5 21.1 2.406 6.467 11.55 289.7 0.591 2.003 5.408 70.6 58.2 2.47 23.04 5.368
E E8 C S 76.722 33.79 48.526 44.37 0.32 2.6 3.4 1.516 6.642 3.406 0.027 0.899 0.051 0.027 0.651 0.018 0.104 393.5 21.1 2.406 6.467 11.55 289.7 0.591 2.003 5.408 70.6 58.2 2.47 23.04 5.368
E E9 C S 22.59 37.468 48.634 35.89 0.25 15.77 3.96 1.516 6.642 3.406 0.027 0.899 0.051 0.027 0.651 0.018 0.104 393.5 21.1 2.406 6.467 11.55 289.7 0.591 2.003 5.408 70.6 58.2 2.47 23.04 5.368
E E10 C S 56.59 40.78 42.11 19.6 0.25 12.05 2.42 1.516 6.642 3.406 0.027 0.899 0.051 0.027 0.651 0.018 0.104 393.5 21.1 2.406 6.467 11.55 289.7 0.591 2.003 5.408 70.6 58.2 2.47 23.04 5.368
F F1 P S 113.338 99.742 53.584 27.15 0.05 9.75 4.9 1.527 6.122 1.255 0.043 0.651 0.396 0.134 6.039 0.041 0.19 507.7 36.5 2.651 2.897 8.96 388.8 0.747 1.968 43.988 172.1 55.2 18.69 27.24 3.964
F F2 P S 32.006 158.122 50.918 47.87 0.19 2.53 4.79 1.527 6.122 1.255 0.043 0.651 0.396 0.134 6.039 0.041 0.19 507.7 36.5 2.651 2.897 8.96 388.8 0.747 1.968 43.988 172.1 55.2 18.69 27.24 3.964
F F3 P S 31.84 157.776 90.49 34.43 0.02 22.59 2.25 1.527 6.122 1.255 0.043 0.651 0.396 0.134 6.039 0.041 0.19 507.7 36.5 2.651 2.897 8.96 388.8 0.747 1.968 43.988 172.1 55.2 18.69 27.24 3.964
F F4 P S 36.362 86.126 70.18 32.314 0.02 26.35 6.7 1.527 6.122 1.255 0.043 0.651 0.396 0.134 6.039 0.041 0.19 507.7 36.5 2.651 2.897 8.96 388.8 0.747 1.968 43.988 172.1 55.2 18.69 27.24 3.964
F F5 P S 89.888 77.3 61.708 49.89 0.14 4.58 6.45 1.527 6.122 1.255 0.043 0.651 0.396 0.134 6.039 0.041 0.19 507.7 36.5 2.651 2.897 8.96 388.8 0.747 1.968 43.988 172.1 55.2 18.69 27.24 3.964
F F6 P S 57.914 68.176 89.308 32.05 0.03 8.75 6.05 1.527 6.122 1.255 0.043 0.651 0.396 0.134 6.039 0.041 0.19 507.7 36.5 2.651 2.897 8.96 388.8 0.747 1.968 43.988 172.1 55.2 18.69 27.24 3.964
F F7 P S 63.488 81.408 50.918 24.84 0.02 1.53 13.61 1.527 6.122 1.255 0.043 0.651 0.396 0.134 6.039 0.041 0.19 507.7 36.5 2.651 2.897 8.96 388.8 0.747 1.968 43.988 172.1 55.2 18.69 27.24 3.964
F F8 P S 65.04 69.306 88.642 28.68 0.31 23.59 6.45 1.527 6.122 1.255 0.043 0.651 0.396 0.134 6.039 0.041 0.19 507.7 36.5 2.651 2.897 8.96 388.8 0.747 1.968 43.988 172.1 55.2 18.69 27.24 3.964
F F9 P S 42.456 50.728 70.18 26.28 0.02 25.45 3.79 1.527 6.122 1.255 0.043 0.651 0.396 0.134 6.039 0.041 0.19 507.7 36.5 2.651 2.897 8.96 388.8 0.747 1.968 43.988 172.1 55.2 18.69 27.24 3.964
F F10 P S 42.644 73.532 64.778 32.35 0.02 5.58 11.07 1.527 6.122 1.255 0.043 0.651 0.396 0.134 6.039 0.041 0.19 507.7 36.5 2.651 2.897 8.96 388.8 0.747 1.968 43.988 172.1 55.2 18.69 27.24 3.964
