Morfometrické parametry
Robert Hruban
12 prosince 2018
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Cíl statistické analýzy
Cílem statistické analýzy je vyhodnotit morfologické vlastnosti terénu, které jsou vytvořeny na základě digitálního modelu terénu.
Příprava dílčích morfometrických parametrů proběhla v počítačovém programu SAGA. Jako podkladový digitální model terénu byl použit DMT 4. generace s rozlišením 10 m. Ten byl pro účely analýz přesamplován na rozlišení 20 (případně 30m).Hodnoty dílčích morfometrických parametrů byly přeneseny z podkladových rastrů na body sítě NIL2 (celkem 7772 bodů)
V rámci statistické analýzy budou zhodnoceny dálčí morfometrické paramtery, jejich vzájemné vztahy a jejich příapdný vztah k vegetaci.
Statistická analýza
Vytvoření pracovního prostředí, načtení knihoven, načtení dat
Vytvoření pracovního adresáře
Data k řešení analýzy jsou uloženy v následujícím adresáři.
setwd("D:/Doct/R")Načtení požadovaných knihoven
library(tidyverse)
library(stringr)
library(vegan)
library(ade4)
library(gclus)
library(ape)
library(ggplot2)
library(foreign)Import funkcí
Pro řešení vícerozměrných analýz jsou načteny následující podpůrné funkce.
source ("cleanplot.pca.R")
source("evplot.R")Načtení dat
Data - morfometrické veličiny
library(foreign)
data_morfo <- read.dbf("data/f_p_nfi2_MORFO_final_R_pro_vege.dbf")
# doplnění nul do prázdných položek
data_morfo[is.na(data_morfo)] <- 0Data - vegetace
# library(foreign)
# data_vege <- read.dbf("data/f_p_nfi2_VEGE_finish_R.dbf")
library(readxl)
data_vege_100 <- read_excel("data/vystup_t_plants_layer_500_R_upr.xlsx", sheet="vystup_100")
# doplnění nul do prázdných položek
#data_vege[is.na(data_vege)] <- 0
# data_vegeExploratorní analýza
Výpis proměnných
# str(data_morfo)
# head(data_morfo)
# str(data_vege)
# head(data_vege)Statistická charakteristika proměnných
# summary(data_morfo)Korelace proměnných
# pouze morfologické proměnné (odstranění 1. sloupce /GID/)
data_morfo_only <- data_morfo[,-1:-2]
# korelace morfologických proměnných
cor(data_morfo_only)## aspect slope TPI Convexity
## aspect 1.000000e+00 0.125876144 8.205589e-05 0.233047050
## slope 1.258761e-01 1.000000000 2.858188e-02 0.548832906
## TPI 8.205589e-05 0.028581879 1.000000e+00 0.158369893
## Convexity 2.330470e-01 0.548832906 1.583699e-01 1.000000000
## wetnes_ind -1.896817e-01 -0.583755815 -4.051594e-01 -0.648772681
## Gradient 1.215172e-01 0.423971849 7.356557e-02 0.208377772
## surface_ar 6.164078e-02 0.921019637 3.200670e-02 0.385918969
## terrain_ru 8.224598e-04 0.022415213 9.617244e-01 0.178134366
## Converge_1 -1.391626e-02 -0.008953974 5.755929e-01 0.105469395
## Diurnal.An 1.942485e-01 0.028039980 4.432072e-02 0.010350909
## Gradient.D 5.732842e-02 0.304115393 -2.644304e-01 0.291684306
## Mass.Balan -1.513519e-03 0.057765921 7.659216e-01 0.123671869
## Melton.Rug 6.717280e-02 0.577829594 -2.494984e-01 0.300663187
## MRRTF -2.039299e-01 -0.460498528 8.553497e-02 -0.506305237
## MRVBF -2.210954e-01 -0.539728035 -9.441797e-02 -0.796131737
## Negative.O -1.081494e-01 -0.818104600 -4.029381e-01 -0.651387801
## Positive.O -1.010287e-01 -0.835333102 3.455029e-01 -0.400928253
## Protection 9.062978e-02 0.758591193 -3.279758e-01 0.372364895
## Terrain.Ru 1.144925e-01 0.988766231 2.009181e-02 0.535638549
## Texture 7.101991e-02 0.544883242 3.976512e-04 0.355292156
## Valley.Dep 3.699246e-02 0.373623506 -2.231344e-01 0.001910672
## Vector.Ter 4.871829e-02 0.315481452 -1.210013e-01 0.164422334
## WI.values -1.042152e-01 -0.622617980 -3.719410e-01 -0.490810685
## Zabaged10m 7.265039e-02 0.130950056 6.232458e-02 0.294709583
## Downslope -4.303131e-02 -0.370063733 6.674699e-01 -0.051584569
## wetnes_ind Gradient surface_ar terrain_ru Converge_1
## aspect -0.18968171 0.12151716 0.061640779 0.0008224598 -0.013916256
## slope -0.58375582 0.42397185 0.921019637 0.0224152127 -0.008953974
## TPI -0.40515938 0.07356557 0.032006699 0.9617244267 0.575592934
## Convexity -0.64877268 0.20837777 0.385918969 0.1781343661 0.105469395
## wetnes_ind 1.00000000 -0.24056509 -0.447191656 -0.4227506745 -0.465298458
## Gradient -0.24056509 1.00000000 0.462545823 0.0413230715 0.012949712
## surface_ar -0.44719166 0.46254582 1.000000000 0.0230167252 -0.004364528
## terrain_ru -0.42275067 0.04132307 0.023016725 1.0000000000 0.580055206
## Converge_1 -0.46529846 0.01294971 -0.004364528 0.5800552062 1.000000000
## Diurnal.An -0.02405374 0.02472475 0.040965125 0.0406511952 0.008514879
## Gradient.D -0.18931347 -0.06238209 0.211008834 -0.2668563385 -0.102919903
## Mass.Balan -0.34532866 0.10844289 0.060306149 0.7423948242 0.542483881
## Melton.Rug -0.16444890 0.19204497 0.498958482 -0.2633998927 -0.153616028
## MRRTF 0.22382742 -0.12258769 -0.289687425 0.0954845460 0.260100753
## MRVBF 0.67740809 -0.12497727 -0.346344689 -0.1004086064 -0.174000675
## Negative.O 0.69166252 -0.33287024 -0.739108499 -0.4103856929 -0.248536750
## Positive.O 0.28958723 -0.35293783 -0.766608383 0.3623827266 0.249935043
## Protection -0.25561474 0.32115109 0.691294760 -0.3435254939 -0.233600447
## Terrain.Ru -0.56604933 0.42238255 0.927948245 0.0155154785 -0.009310314
## Texture -0.33368297 0.26575755 0.503928929 -0.0217662611 -0.027254461
## Valley.Dep 0.05345789 0.18812823 0.354738314 -0.2489879963 -0.158724679
## Vector.Ter -0.09282864 0.19498371 0.322010471 -0.1401150458 -0.126909544
## WI.values 0.75583914 -0.25331923 -0.508100983 -0.3900940681 -0.360306023
## Zabaged10m -0.13097971 -0.01745011 0.062172185 0.0749824182 0.041002516
## Downslope -0.09673424 -0.19654358 -0.368412522 0.7180766950 0.464123905
## Diurnal.An Gradient.D Mass.Balan Melton.Rug MRRTF
## aspect 0.194248481 0.057328421 -0.001513519 0.06717280 -0.203929924
## slope 0.028039980 0.304115393 0.057765921 0.57782959 -0.460498528
## TPI 0.044320724 -0.264430378 0.765921639 -0.24949836 0.085534967
## Convexity 0.010350909 0.291684306 0.123671869 0.30066319 -0.506305237
## wetnes_ind -0.024053743 -0.189313470 -0.345328661 -0.16444890 0.223827423
## Gradient 0.024724749 -0.062382090 0.108442890 0.19204497 -0.122587686
## surface_ar 0.040965125 0.211008834 0.060306149 0.49895848 -0.289687425
## terrain_ru 0.040651195 -0.266856338 0.742394824 -0.26339989 0.095484546
## Converge_1 0.008514879 -0.102919903 0.542483881 -0.15361603 0.260100753
## Diurnal.An 1.000000000 -0.003157676 -0.001589078 -0.02292389 0.009459594
## Gradient.D -0.003157676 1.000000000 -0.235448262 0.26465191 -0.312034303
## Mass.Balan -0.001589078 -0.235448262 1.000000000 -0.20906017 0.071261749
## Melton.Rug -0.022923894 0.264651915 -0.209060171 1.00000000 -0.352307319
## MRRTF 0.009459594 -0.312034303 0.071261749 -0.35230732 1.000000000
## MRVBF 0.008824647 -0.376987180 -0.107163896 -0.33508994 0.470902240
## Negative.O -0.044189730 -0.133291107 -0.370104557 -0.36457282 0.332942091
## Positive.O -0.011481961 -0.332673713 0.267157568 -0.62312438 0.457004354
## Protection 0.003289107 0.301740276 -0.250449843 0.56949916 -0.423595295
## Terrain.Ru 0.027939915 0.303187685 0.055326855 0.57624441 -0.445856988
## Texture 0.039832888 0.118609530 0.018781367 0.17433127 -0.233064467
## Valley.Dep 0.054303604 0.102504652 -0.137154944 0.47618096 -0.203561909
## Vector.Ter 0.070445527 0.039342792 -0.115639004 0.04054049 -0.133035523
## WI.values -0.027254357 -0.123139310 -0.371445429 -0.11416691 0.211636276
## Zabaged10m -0.009989047 0.105597886 0.041005038 0.23953767 -0.175871137
## Downslope -0.006533720 -0.238509887 0.488529010 -0.27168247 0.219595068
## MRVBF Negative.O Positive.O Protection Terrain.Ru
## aspect -0.221095368 -0.10814943 -0.10102875 0.090629777 0.114492495
## slope -0.539728035 -0.81810460 -0.83533310 0.758591193 0.988766231
## TPI -0.094417974 -0.40293810 0.34550287 -0.327975772 0.020091807
## Convexity -0.796131737 -0.65138780 -0.40092825 0.372364895 0.535638549
## wetnes_ind 0.677408086 0.69166252 0.28958723 -0.255614736 -0.566049331
## Gradient -0.124977269 -0.33287024 -0.35293783 0.321151094 0.422382551
## surface_ar -0.346344689 -0.73910850 -0.76660838 0.691294760 0.927948245
## terrain_ru -0.100408606 -0.41038569 0.36238273 -0.343525494 0.015515478
## Converge_1 -0.174000675 -0.24853675 0.24993504 -0.233600447 -0.009310314
## Diurnal.An 0.008824647 -0.04418973 -0.01148196 0.003289107 0.027939915
## Gradient.D -0.376987180 -0.13329111 -0.33267371 0.301740276 0.303187685
## Mass.Balan -0.107163896 -0.37010456 0.26715757 -0.250449843 0.055326855
## Melton.Rug -0.335089943 -0.36457282 -0.62312438 0.569499157 0.576244410
## MRRTF 0.470902240 0.33294209 0.45700435 -0.423595295 -0.445856988
## MRVBF 1.000000000 0.55394909 0.42458964 -0.391408824 -0.525857509
## Negative.O 0.553949086 1.00000000 0.54131961 -0.509129367 -0.818951691
## Positive.O 0.424589639 0.54131961 1.00000000 -0.916147068 -0.842925801
## Protection -0.391408824 -0.50912937 -0.91614707 1.000000000 0.764784598
## Terrain.Ru -0.525857509 -0.81895169 -0.84292580 0.764784598 1.000000000
## Texture -0.292455718 -0.52193667 -0.59880189 0.551443218 0.553719433
## Valley.Dep -0.046167338 -0.13701641 -0.62005301 0.541703078 0.374471565
## Vector.Ter -0.148397751 -0.23070368 -0.41024942 0.379281922 0.328908344
## WI.values 0.482991239 0.71718496 0.37482606 -0.335035676 -0.620243047
## Zabaged10m -0.259865516 -0.23410481 -0.04277026 0.002839166 0.121774359
## Downslope 0.101067714 0.02518580 0.64882352 -0.598290819 -0.379459983
## Texture Valley.Dep Vector.Ter WI.values
## aspect 0.0710199143 0.036992456 0.04871829 -0.1042151905
## slope 0.5448832424 0.373623506 0.31548145 -0.6226179802
## TPI 0.0003976512 -0.223134409 -0.12100126 -0.3719409949
## Convexity 0.3552921564 0.001910672 0.16442233 -0.4908106846
## wetnes_ind -0.3336829671 0.053457889 -0.09282864 0.7558391398
## Gradient 0.2657575514 0.188128230 0.19498371 -0.2533192334
## surface_ar 0.5039289292 0.354738314 0.32201047 -0.5081009826
## terrain_ru -0.0217662611 -0.248987996 -0.14011505 -0.3900940681
## Converge_1 -0.0272544610 -0.158724679 -0.12690954 -0.3603060229
## Diurnal.An 0.0398328879 0.054303604 0.07044553 -0.0272543567
## Gradient.D 0.1186095297 0.102504652 0.03934279 -0.1231393096
## Mass.Balan 0.0187813670 -0.137154944 -0.11563900 -0.3714454290
## Melton.Rug 0.1743312712 0.476180957 0.04054049 -0.1141669132
## MRRTF -0.2330644674 -0.203561909 -0.13303552 0.2116362760
## MRVBF -0.2924557175 -0.046167338 -0.14839775 0.4829912395
## Negative.O -0.5219366670 -0.137016406 -0.23070368 0.7171849563
## Positive.O -0.5988018909 -0.620053013 -0.41024942 0.3748260639
## Protection 0.5514432179 0.541703078 0.37928192 -0.3350356764
## Terrain.Ru 0.5537194335 0.374471565 0.32890834 -0.6202430473
## Texture 1.0000000000 0.280153301 0.49944972 -0.4322253701
## Valley.Dep 0.2801533014 1.000000000 0.19048504 -0.0319432060
## Vector.Ter 0.4994497223 0.190485044 1.00000000 -0.1606502557
## WI.values -0.4322253701 -0.031943206 -0.16065026 1.0000000000
## Zabaged10m -0.1546788039 0.016876401 -0.11973386 -0.0259758116
## Downslope -0.5087144886 -0.340814221 -0.45892650 -0.0002991106
## Zabaged10m Downslope
## aspect 0.072650386 -0.0430313057
## slope 0.130950056 -0.3700637326
## TPI 0.062324580 0.6674699299
## Convexity 0.294709583 -0.0515845690
## wetnes_ind -0.130979713 -0.0967342424
## Gradient -0.017450113 -0.1965435836
## surface_ar 0.062172185 -0.3684125222
## terrain_ru 0.074982418 0.7180766950
## Converge_1 0.041002516 0.4641239049
## Diurnal.An -0.009989047 -0.0065337196
## Gradient.D 0.105597886 -0.2385098871
## Mass.Balan 0.041005038 0.4885290099
## Melton.Rug 0.239537671 -0.2716824742
## MRRTF -0.175871137 0.2195950680
## MRVBF -0.259865516 0.1010677138
## Negative.O -0.234104813 0.0251858042
## Positive.O -0.042770264 0.6488235154
## Protection 0.002839166 -0.5982908189
## Terrain.Ru 0.121774359 -0.3794599829
## Texture -0.154678804 -0.5087144886
## Valley.Dep 0.016876401 -0.3408142212
## Vector.Ter -0.119733860 -0.4589264977
## WI.values -0.025975812 -0.0002991106
## Zabaged10m 1.000000000 0.1750684280
## Downslope 0.175068428 1.0000000000# export dat do xlsx
write.table(cor(data_morfo_only), "data/cor_data_morfo_only.xls", sep="\t")
Korelace morfologických proměnných
Statistická analýza morfologických proměnných
K analýze morfologických a vegetačních dat v prostředí R je využita knihovna vegan.
PCA
PCA_morfo <- prcomp(data_morfo_only, scale = TRUE)
PCA_morfo## Standard deviations (1, .., p=25):
## [1] 2.8773946 2.2211947 1.3948477 1.1825441 1.0916921 0.9705817 0.9225614
## [8] 0.8908693 0.8635031 0.7786783 0.7596701 0.6872969 0.6383886 0.6034255
## [15] 0.5701413 0.5350209 0.4639280 0.4296388 0.3809871 0.3556654 0.2963380
## [22] 0.2177178 0.1789929 0.1758845 0.1010590
##
## Rotation (n x k) = (25 x 25):
## PC1 PC2 PC3 PC4 PC5
## aspect 0.0645932619 -0.02226040 0.16642755 -0.26008461 -0.602945829
## slope 0.3316690395 -0.02625619 -0.04617505 0.11343152 0.015854328
## TPI -0.0140267051 -0.40977924 -0.11966302 0.07595412 -0.064997035
## Convexity 0.2293593882 -0.13766673 0.31106174 -0.20529798 0.010045666
## wetnes_ind -0.2113492069 0.26543859 -0.10012618 0.17066299 -0.092017778
## Gradient 0.1511559188 -0.02624286 -0.23789857 0.10038372 -0.215794031
## surface_ar 0.2962644589 -0.01091934 -0.17397233 0.17481682 0.002998328
## terrain_ru -0.0175615931 -0.41727239 -0.09595467 0.07131409 -0.053047960
## Converge_1 -0.0097019193 -0.32393902 -0.06369978 0.01629361 0.102871629
## Diurnal.An 0.0129636228 -0.01234069 -0.04899540 -0.15784308 -0.647439131
## Gradient.D 0.1258120967 0.09455740 0.34007340 -0.12631450 0.213040029
## Mass.Balan 0.0005903641 -0.36007439 -0.14646818 0.09404774 -0.032144552
## Melton.Rug 0.2066300546 0.11770522 0.16658551 0.41449691 -0.060119268
## MRRTF -0.1856869408 -0.04421709 -0.29557678 0.05791262 0.099964738
## MRVBF -0.2253275338 0.11637295 -0.34698944 0.20971339 -0.079198666
## Negative.O -0.2794878263 0.20921751 0.03644206 -0.06107876 -0.016094688
## Positive.O -0.3086811724 -0.16697865 0.06823130 -0.08470160 -0.005332409
## Protection 0.2871253951 0.16106732 -0.07056400 0.06652512 0.019882067
## Terrain.Ru 0.3313230336 -0.02166582 -0.06083112 0.11421587 0.023319561
## Texture 0.2252580606 0.02157365 -0.27579140 -0.28428284 0.074795119
## Valley.Dep 0.1482564842 0.16203057 -0.14472776 0.35702765 -0.186596408
## Vector.Ter 0.1400630906 0.09046688 -0.27742446 -0.36149015 -0.011595981
## WI.values -0.2184622449 0.23046453 0.07654758 0.13583256 -0.120940870
## Zabaged10m 0.0493183548 -0.06793323 0.39854202 0.30279478 -0.131213658
## Downslope -0.1589765829 -0.32066806 0.14348339 0.22389847 -0.065921985
## PC6 PC7 PC8 PC9
## aspect -0.1114478170 0.356598062 0.296863038 -0.26559427
## slope 0.0315442301 0.047962984 -0.052514160 0.13918197
## TPI -0.0720806093 -0.174075537 0.120771464 0.08848810
## Convexity -0.1762198952 -0.056758212 -0.056584989 -0.03986608
## wetnes_ind -0.1370682387 -0.206517092 0.041383564 0.10436263
## Gradient -0.3600376395 0.517219605 -0.219267422 0.11043186
## surface_ar 0.0454277973 0.093785785 -0.153252512 0.17890438
## terrain_ru -0.0588696641 -0.168346774 0.100975971 0.09364256
## Converge_1 0.3457526170 0.163191325 0.008133131 -0.43855053
## Diurnal.An 0.5103392918 -0.242375166 -0.277283533 0.27900056
## Gradient.D 0.4122833162 0.042533033 0.087593605 0.20591938
## Mass.Balan -0.0748655367 -0.103519982 0.189114829 0.01236824
## Melton.Rug 0.0929751967 0.035723124 0.057021721 -0.10393864
## MRRTF 0.3352462943 0.261388707 -0.375767419 -0.34896964
## MRVBF 0.0008136563 -0.003225197 -0.028539156 0.17088033
## Negative.O 0.0352045260 0.099672141 0.119919622 -0.07377850
## Positive.O -0.0476389958 0.030258802 -0.066209793 0.05969387
## Protection 0.0422452713 -0.021061917 0.089452631 -0.04268415
## Terrain.Ru 0.0386689491 0.041266480 -0.062044917 0.13736903
## Texture -0.0400796099 -0.212650291 0.078324827 -0.12685571
## Valley.Dep 0.1513456063 -0.210173652 0.413972014 -0.35731520
## Vector.Ter -0.1819627725 -0.374951473 -0.203801874 -0.28452690
## WI.values -0.1371971914 -0.113632672 -0.014139657 -0.04291321
## Zabaged10m -0.1901888828 -0.252876287 -0.534746539 -0.31826649
## Downslope 0.0194061498 -0.048594220 0.079905163 0.06887217
## PC10 PC11 PC12 PC13 PC14
## aspect -0.327909049 0.35014065 -0.042498233 0.0597428505 -0.01226533
## slope -0.130093533 0.08415819 -0.072037437 -0.0705606611 -0.04360281
## TPI 0.052779401 0.11254725 -0.078026140 0.1403988018 0.13496875
## Convexity 0.111786648 -0.26902612 -0.044692087 0.2491965155 0.16160726
## wetnes_ind 0.022185445 0.16406987 0.004338255 0.1632394706 -0.15366123
## Gradient 0.595860148 -0.02880990 0.089279081 0.0450124387 0.09675492
## surface_ar -0.150446169 0.19614732 -0.131511262 -0.0003163832 -0.09089963
## terrain_ru -0.001709667 0.09306909 -0.099505168 0.1077374144 0.23337563
## Converge_1 0.199265425 -0.04613507 -0.066422293 -0.1085339234 -0.35354142
## Diurnal.An 0.124159699 -0.23695430 0.036851916 -0.0064687308 -0.06766596
## Gradient.D 0.390133380 0.60807165 0.047620080 0.1601652127 0.08604406
## Mass.Balan 0.131619753 0.12993353 0.183934073 0.0245737031 -0.57992423
## Melton.Rug -0.046759213 -0.18126306 -0.404877499 0.3298370145 -0.20512890
## MRRTF -0.153435512 0.07806794 -0.044000098 0.3302490043 0.25511022
## MRVBF -0.172728628 0.27539186 0.114111782 -0.0416226683 0.06278024
## Negative.O 0.185856417 -0.04266780 -0.010593778 -0.1420498843 -0.02321816
## Positive.O 0.027212147 0.03108476 -0.047263625 0.0627490672 -0.06027840
## Protection -0.046961529 -0.07248775 0.013260382 -0.0440625014 0.05212859
## Terrain.Ru -0.134890012 0.09661051 -0.076481496 -0.0616681843 -0.05522896
## Texture -0.048645439 -0.02288852 0.394160259 0.5483164106 0.02104525
## Valley.Dep 0.270012032 -0.03242785 0.179598952 -0.1491532361 0.31567856
## Vector.Ter 0.187404153 0.26341495 -0.516989872 -0.2316050737 0.01273176
## WI.values 0.185454353 0.06016821 -0.270031974 0.4421536633 -0.17588093
## Zabaged10m -0.033688380 0.24113648 0.367122364 -0.0982241025 -0.01741453
## Downslope 0.016476849 0.02421669 -0.240865589 -0.0121091605 0.36344572
## PC15 PC16 PC17 PC18
## aspect 1.462646e-03 -0.013971043 0.03538363 -0.001725837
## slope -2.991303e-02 -0.069873034 -0.15229485 -0.023542836
## TPI 5.506066e-02 -0.022425688 -0.11345592 0.256145296
## Convexity -1.799453e-01 -0.138487768 0.16156144 -0.604023786
## wetnes_ind -2.693373e-02 -0.141597175 0.40009637 -0.156298669
## Gradient 8.847689e-02 0.078170870 0.07219294 0.062252305
## surface_ar -6.373348e-02 -0.264790749 -0.27003301 -0.170157757
## terrain_ru 7.121535e-02 -0.045661850 -0.06404033 0.161709407
## Converge_1 4.406692e-01 -0.337065841 0.09071195 -0.156732165
## Diurnal.An -4.538524e-03 0.009273515 0.02300132 0.020365555
## Gradient.D 4.489587e-05 0.092464162 0.07362627 -0.004605102
## Mass.Balan -4.880171e-01 0.185766038 0.14866518 -0.049578789
## Melton.Rug 2.019788e-01 0.549075064 0.05972992 0.034306750
## MRRTF -4.327455e-01 0.063784357 0.07893736 0.024957711
## MRVBF 3.428878e-01 0.086956972 0.15052415 -0.427607841
## Negative.O 1.548000e-02 0.062782530 -0.18176234 0.148246614
## Positive.O 3.078978e-02 0.130928448 -0.09213538 -0.087790241
## Protection -4.685835e-02 -0.300575788 0.59966996 0.411342183
## Terrain.Ru -3.045139e-02 -0.076168896 -0.11217379 -0.035969451
## Texture 3.321718e-01 0.089531956 -0.07209742 0.062430765
## Valley.Dep -1.824099e-01 0.003251644 -0.22482214 -0.205661396
## Vector.Ter -3.907353e-03 0.177437117 0.06189701 -0.035836798
## WI.values -5.841359e-02 -0.496801628 -0.27773461 0.103565300
## Zabaged10m 9.176161e-02 0.022388662 -0.02054802 0.113407580
## Downslope 9.070495e-02 -0.054358110 0.27329349 -0.047182420
## PC19 PC20 PC21 PC22
## aspect 0.031359277 -0.006341312 0.005555135 -0.0008362025
## slope 0.037089550 0.082208286 -0.010599763 -0.2903857699
## TPI 0.100984566 -0.430272966 -0.082556696 -0.0882098034
## Convexity -0.076808232 -0.238546130 -0.249730466 -0.0620906694
## wetnes_ind 0.684830333 -0.022702923 -0.021059957 -0.0367449738
## Gradient 0.040735938 0.037561727 0.063853319 -0.0025161938
## surface_ar 0.109750438 0.093679252 -0.340772796 0.5254225818
## terrain_ru 0.089942517 -0.222050170 -0.081196686 -0.0127366272
## Converge_1 0.110450462 -0.049005208 0.018466913 -0.0432383817
## Diurnal.An -0.011261235 0.013372119 -0.014938227 -0.0114023449
## Gradient.D -0.029457365 -0.050292119 0.027780887 0.0117445638
## Mass.Balan -0.216741413 0.145507901 -0.102510431 -0.0526511980
## Melton.Rug -0.007128688 -0.097961064 -0.062307162 0.0583268016
## MRRTF 0.044308742 -0.041185310 -0.037034190 -0.0878825889
## MRVBF -0.461851235 -0.213958054 -0.079665218 -0.1202307859
## Negative.O 0.024795242 -0.001366452 -0.821394776 -0.1489496209
## Positive.O -0.026993614 -0.012931249 0.085712699 0.6139075406
## Protection -0.294671101 -0.154303950 -0.149502294 0.2582144854
## Terrain.Ru 0.071898740 0.095873017 -0.001358997 -0.3042725544
## Texture 0.011480385 0.325815473 -0.134187632 0.0393914460
## Valley.Dep 0.024207099 -0.004651935 0.117508505 0.1466183185
## Vector.Ter -0.051851042 0.055551626 -0.002012114 0.0102479241
## WI.values -0.335800114 0.063484467 0.139813553 -0.1131123745
## Zabaged10m -0.025046283 -0.016916464 -0.102422301 0.0041892708
## Downslope -0.071596947 0.679007422 -0.117242898 -0.0408720603
## PC23 PC24 PC25
## aspect -0.0052965615 -0.002869300 -0.0018090991
## slope 0.4148025644 0.285305638 0.6610592283
## TPI -0.3429769090 0.528715384 -0.0326938202
## Convexity 0.0396269580 0.046055837 -0.0078854933
## wetnes_ind 0.0809224196 0.041211823 0.0263693225
## Gradient 0.0116964880 -0.015848720 -0.0011398263
## surface_ar -0.3023272601 -0.130134188 0.0292096374
## terrain_ru 0.3796211945 -0.653038685 0.0304754620
## Converge_1 0.0308713373 0.006620290 0.0084767651
## Diurnal.An -0.0006897044 -0.003996325 0.0007993823
## Gradient.D -0.0102607850 -0.025489096 0.0066447984
## Mass.Balan -0.0175410164 -0.052478194 0.0100684356
## Melton.Rug -0.0177829921 -0.046606182 0.0044091094
## MRRTF 0.0397253823 0.029612784 0.0061997568
## MRVBF 0.0075162055 0.007137107 -0.0008286818
## Negative.O 0.1552019629 0.055184122 -0.0280276342
## Positive.O 0.5365441853 0.359161373 -0.0777442255
## Protection 0.1654945029 0.093634218 -0.0173033085
## Terrain.Ru 0.3211269799 0.155824265 -0.7425378111
## Texture 0.0414355331 0.053848289 -0.0031003948
## Valley.Dep 0.0871843330 0.064854175 -0.0211792120
## Vector.Ter -0.0001755383 0.010030241 0.0067905752
## WI.values 0.0395958322 -0.014500308 -0.0091289238
## Zabaged10m 0.0139085385 -0.001266239 -0.0040673689
## Downslope -0.0981485311 0.111870340 0.0039360159# summary(PCA)
plot(PCA_morfo, type = "l")
biplot(PCA_morfo, scale = 0)
str(PCA_morfo)## List of 5
## $ sdev : num [1:25] 2.88 2.22 1.39 1.18 1.09 ...
## $ rotation: num [1:25, 1:25] 0.0646 0.3317 -0.014 0.2294 -0.2113 ...
## ..- attr(*, "dimnames")=List of 2
## .. ..$ : chr [1:25] "aspect" "slope" "TPI" "Convexity" ...
## .. ..$ : chr [1:25] "PC1" "PC2" "PC3" "PC4" ...
## $ center : Named num [1:25] 3.0408 8.8174 0.0356 39.6389 7.5568 ...
## ..- attr(*, "names")= chr [1:25] "aspect" "slope" "TPI" "Convexity" ...
## $ scale : Named num [1:25] 1.86 6.76 1.3 7.39 1.9 ...
## ..- attr(*, "names")= chr [1:25] "aspect" "slope" "TPI" "Convexity" ...
## $ x : num [1:7013, 1:25] 1.209 4.211 -1.887 0.226 -0.639 ...
## ..- attr(*, "dimnames")=List of 2
## .. ..$ : NULL
## .. ..$ : chr [1:25] "PC1" "PC2" "PC3" "PC4" ...
## - attr(*, "class")= chr "prcomp"PCA2_morfo <- cbind(data_morfo, PCA_morfo$x[,1:2])
head(PCA2_morfo)## PID PNAME aspect slope TPI Convexity
## 1 283360 2012_2_2_9_29 0.5541134 15.290102 0.7345990 43.97727
## 2 279179 2015_2_4_12_28 0.3123232 18.898289 0.4980297 42.00390
## 3 274329 2015_2_2_8_28 3.2772275 3.761705 -0.3312209 40.99989
## 4 279185 2015_2_2_13_28 1.3103609 8.440208 -1.6763318 40.58780
## 5 265363 2015_2_2_8_27 5.9211512 4.149025 1.2514863 42.88398
## 6 280375 2014_2_2_12_28 3.7105109 6.820598 0.2213109 40.86701
## wetnes_ind Gradient surface_ar terrain_ru Converge_1 Diurnal.An
## 1 6.563148 0.2829149 233.3569 2.4195110 0.3101727 -0.23499100
## 2 6.632017 0.3690671 237.8749 -0.2186071 0.1139183 -0.31500167
## 3 7.861132 0.4918054 225.5698 -0.7272798 4.1136608 0.03749138
## 4 9.269210 0.3255108 227.6864 -3.7561426 -33.5199394 -0.04094237
## 5 6.241852 0.1312212 225.6591 2.5306769 17.5198746 -0.08574492
## 6 7.004273 0.1528517 226.6132 0.6137341 -1.7239873 0.11350797
## Gradient.D Mass.Balan Melton.Rug MRRTF MRVBF Negative.O
## 1 -0.03976338 0.23262992 1.6009030 0.0003552800 0.0005643136 1.427715
## 2 -0.01695556 0.18331428 4.2749519 0.0000018064 0.0000055822 1.408556
## 3 -0.04021820 -0.03022123 0.7437500 0.1611664891 1.4445400238 1.508586
## 4 0.04925732 -0.36373237 0.3612482 0.0055610202 0.9109805822 1.511821
## 5 -0.03851040 0.03049402 0.3359920 0.7745479941 0.1156171635 1.462601
## 6 -0.02882987 0.07301509 0.7019782 0.1395121664 0.4252680242 1.497216
## Positive.O Protection Terrain.Ru Texture Valley.Dep Vector.Ter
## 1 1.497043 0.00000000 3.2192051 3.9732645 68.85468 0.0009425436
## 2 1.393731 0.15862396 4.2942548 5.6545472 79.65411 0.0007203591
## 3 1.542816 0.00000000 0.5153882 0.4501843 19.11548 0.0002357820
## 4 1.450135 0.11122490 1.4585416 4.5214396 48.59698 0.0034538379
## 5 1.532068 0.03266432 1.2279302 3.3236787 22.89575 0.0008372103
## 6 1.522332 0.04395977 1.4644219 0.6872351 14.27087 0.0000661986
## WI.values Zabaged10m Downslope PC1 PC2
## 1 0.3385665 569.6250 -0.02241760 1.2088343 -1.77500080
## 2 0.3677483 579.9375 -0.65973765 4.2114942 0.74560581
## 3 1.0000000 698.7500 -0.02724636 -1.8869956 -0.05171784
## 4 1.0000000 648.8750 -0.33420649 0.2263589 3.70443186
## 5 0.1576759 553.3750 -0.01631729 -0.6387082 -2.29420431
## 6 0.6152093 644.3750 -0.05017763 -0.9282104 -0.72378779cor(data_morfo_only, PCA2_morfo[,26:27])## Zabaged10m Downslope
## aspect 0.072650386 -0.0430313057
## slope 0.130950056 -0.3700637326
## TPI 0.062324580 0.6674699299
## Convexity 0.294709583 -0.0515845690
## wetnes_ind -0.130979713 -0.0967342424
## Gradient -0.017450113 -0.1965435836
## surface_ar 0.062172185 -0.3684125222
## terrain_ru 0.074982418 0.7180766950
## Converge_1 0.041002516 0.4641239049
## Diurnal.An -0.009989047 -0.0065337196
## Gradient.D 0.105597886 -0.2385098871
## Mass.Balan 0.041005038 0.4885290099
## Melton.Rug 0.239537671 -0.2716824742
## MRRTF -0.175871137 0.2195950680
## MRVBF -0.259865516 0.1010677138
## Negative.O -0.234104813 0.0251858042
## Positive.O -0.042770264 0.6488235154
## Protection 0.002839166 -0.5982908189
## Terrain.Ru 0.121774359 -0.3794599829
## Texture -0.154678804 -0.5087144886
## Valley.Dep 0.016876401 -0.3408142212
## Vector.Ter -0.119733860 -0.4589264977
## WI.values -0.025975812 -0.0002991106
## Zabaged10m 1.000000000 0.1750684280
## Downslope 0.175068428 1.0000000000RDA Použito z videa https://www.youtube.com/watch?v=paO9-PLXwD0&ab_channel=KeithMcGuinness
RDA_morfo <- rda(data_morfo_only, scale = TRUE)
RDA_morfo## Call: rda(X = data_morfo_only, scale = TRUE)
##
## Inertia Rank
## Total 25
## Unconstrained 25 25
## Inertia is correlations
##
## Eigenvalues for unconstrained axes:
## PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8
## 8.279 4.934 1.946 1.398 1.192 0.942 0.851 0.794
## (Showing 8 of 25 unconstrained eigenvalues)# species score # site score
# summary(RDA_morfo)
# Výpočet Eigenvalues
(ev <- RDA_morfo$CA$eig)## PC1 PC2 PC3 PC4 PC5 PC6
## 8.27939940 4.93370599 1.94560016 1.39841045 1.19179174 0.94202888
## PC7 PC8 PC9 PC10 PC11 PC12
## 0.85111963 0.79364819 0.74563760 0.60633993 0.57709859 0.47237704
## PC13 PC14 PC15 PC16 PC17 PC18
## 0.40753996 0.36412235 0.32506106 0.28624737 0.21522919 0.18458947
## PC19 PC20 PC21 PC22 PC23 PC24
## 0.14515116 0.12649788 0.08781621 0.04740103 0.03203845 0.03093534
## PC25
## 0.01021293ev [ev > mean(ev)]## PC1 PC2 PC3 PC4 PC5
## 8.279399 4.933706 1.945600 1.398410 1.191792# Graph eigenvalues
barplot(ev, main = "Eigenvalues for PCA on ENV", col = "gold", las=2)
abline(h=mean(ev), col="red")
legend("topright", "Averige eigenvalue", lwd = 1, col = 2, bty = "n")
# Graph biplots
# Two biplots - scaling 1 and scaling 2, using cleanplot.pca
par(mfrow=c(1,2))
cleanplot.pca(RDA_morfo, point = TRUE)
# One biplot - nefunkčí, stejné jako biplot
# Get site scores, scaling 1, display = "wa" gives weighted average
# par(mfrow=c(1,1))
# cleanplot.pca(morpho_RDA, point = TRUE)Závoslost mezi vegetačními a morfometrickými daty ve vícerozměnrné analýze
NMDS
# pouze druhy (odstranění 1 sloupce)
# data_vege_100_only <- data_vege_100[,-1]
# NMDS aplikovaná na druzích
# nmds_vege <- metaMDS(data_vege_100)
# nmds_vege
# Grah NMDS
# plot(nmds_vege, type = "t")
# Výpočet NMDS (vege + morpho)
# nmds_vege_morfo <- envfit(nmds_vege, data_morfo)
# Graph NMDS (vege + morpho)
# plot(nmds_vege_morfo, p.max = 0.05)RDA
# rda_vege_morfo_1 <- rda(data_vege_100 ~ 1, data_morfo)