library(knitr)
opts_chunk$set(cache = FALSE,
tidy = FALSE,
fig.width = 8,
fig.height = 8,
fig.align = "center",
eval.after= "fig.cap",
message = FALSE,
error = FALSE,
warning = FALSE,
dpi = 96,
dev = "png",
warning = FALSE,
dev.args = list(family = "Palatino"))
options(width = 68)
#-----------------------------------------------------------------------
# Fazer análise exploratória.
setwd("~/Dropbox/Consultorias/Milson Serafim/faixa-otima")
rm(list = ls())
load(file = "high_soybean.RData")
str(high_soybean)
## List of 3
## $ atrib:'data.frame': 390 obs. of 38 variables:
## ..$ faz : chr [1:390] "FAZ. ARGEMIRA" "FAZ. ARGEMIRA" "FAZ. ARGEMIRA" "FAZ. ARGEMIRA" ...
## ..$ tal : chr [1:390] "AG2" "AG2" "AG2" "AG2" ...
## ..$ cam : chr [1:390] "0-0.1" "0-0.1" "0.1-0.2" "0.1-0.2" ...
## ..$ rpt : int [1:390] 1 2 1 2 1 2 1 2 1 2 ...
## ..$ prod : num [1:390] 3.89 NA NA NA NA ...
## ..$ glic : num [1:390] 65 NA NA NA NA NA 76.2 NA NA NA ...
## ..$ phos : num [1:390] 192 NA NA NA NA ...
## ..$ sulf : num [1:390] 74.4 NA NA NA NA NA 74 NA NA NA ...
## ..$ LFF : num [1:390] 14.4 NA NA NA NA ...
## ..$ LFO : num [1:390] 6.21 NA NA NA NA NA 3.1 NA NA NA ...
## ..$ HF : num [1:390] 22.6 NA NA NA NA ...
## ..$ rp : num [1:390] 2.09 1.75 2.39 2.9 2.35 1.14 0.54 1.26 0.94 2.65 ...
## ..$ dens : num [1:390] 1.23 1.19 1.28 1.3 1.23 1.2 1.01 1.08 1.15 1.24 ...
## ..$ poro : num [1:390] 0.53 0.54 0.53 0.52 0.5 0.51 0.61 0.59 0.57 0.53 ...
## ..$ clay : int [1:390] 653 NA 725 NA 775 NA 644 NA 724 NA ...
## ..$ sand : int [1:390] 162 NA 139 NA 120 NA 175 NA 138 NA ...
## ..$ pH : num [1:390] 6.2 NA 5.3 NA 5.1 NA 6.1 NA 5.2 NA ...
## ..$ pH_Ca: num [1:390] 5.4 NA 4.5 NA 4.4 NA 5.2 NA 4.5 NA ...
## ..$ P : num [1:390] 16.4 NA 2.1 NA 0.9 NA 14.4 NA 1.7 NA ...
## ..$ K : num [1:390] 97.3 NA 76.9 NA 67.7 NA 78.6 NA 25.6 NA ...
## ..$ Ca_Mg: num [1:390] 5.5 NA 2.1 NA 1.1 NA 5.1 NA 1.8 NA ...
## ..$ Ca : num [1:390] 4 NA 1.5 NA 0.8 NA 3.7 NA 1.3 NA ...
## ..$ Mg : num [1:390] 1.5 NA 0.6 NA 0.3 NA 1.4 NA 0.5 NA ...
## ..$ Al : num [1:390] 0 NA 0.4 NA 0.5 NA 0 NA 0.4 NA ...
## ..$ MO : num [1:390] 43.3 NA 31.2 NA 21.3 NA 44.5 NA 29.5 NA ...
## ..$ base : num [1:390] 5.75 NA 2.3 NA 1.27 NA 5.3 NA 1.87 NA ...
## ..$ CTC : num [1:390] 10.15 NA 7.6 NA 5.77 ...
## ..$ V : num [1:390] 56.6 NA 30.2 NA 22.1 ...
## ..$ CaMg : num [1:390] 2.67 NA 2.5 NA 2.67 NA 2.64 NA 2.6 NA ...
## ..$ CaK : num [1:390] 16.03 NA 7.61 NA 4.61 ...
## ..$ MgK : num [1:390] 6.01 NA 3.04 NA 1.73 NA 6.95 NA 7.62 NA ...
## ..$ Ca_ : num [1:390] 39.4 NA 19.7 NA 13.9 NA 36.6 NA 17.9 NA ...
## ..$ Mg_ : num [1:390] 14.8 NA 7.9 NA 5.2 NA 13.9 NA 6.9 NA ...
## ..$ K_ : num [1:390] 2.5 NA 2.6 NA 3 NA 2 NA 0.9 NA ...
## ..$ H_ : num [1:390] 43.4 NA 64.5 NA 69.3 NA 47.5 NA 68.8 NA ...
## ..$ m_ : num [1:390] 0 NA 14.8 NA 28.2 NA 0 NA 17.7 NA ...
## ..$ S : num [1:390] 21.1 NA 33.9 NA 56 NA 10.8 NA 32.7 NA ...
## ..$ dp : num [1:390] 2.59 2.59 2.73 2.73 2.45 2.45 2.63 2.63 2.65 2.65 ...
## $ swrc :'data.frame': 390 obs. of 15 variables:
## ..$ faz : chr [1:390] "FAZ. ARGEMIRA" "FAZ. ARGEMIRA" "FAZ. ARGEMIRA" "FAZ. ARGEMIRA" ...
## ..$ tal : chr [1:390] "AG2" "AG2" "AG2" "AG2" ...
## ..$ cam : chr [1:390] "0-0.1" "0-0.1" "0.1-0.2" "0.1-0.2" ...
## ..$ rpt : int [1:390] 1 2 1 2 1 2 1 2 1 2 ...
## ..$ S0 : num [1:390] 0.54 0.53 0.49 0.5 0.52 0.53 0.56 0.56 0.55 0.5 ...
## ..$ S1 : num [1:390] 0.52 0.5 0.45 0.48 0.49 0.49 0.53 0.54 0.5 0.49 ...
## ..$ S2 : num [1:390] 0.49 0.48 0.44 0.47 0.48 0.49 0.46 0.5 0.49 0.48 ...
## ..$ S4 : num [1:390] 0.46 0.46 0.44 0.45 0.47 0.49 0.41 0.46 0.45 0.47 ...
## ..$ S6 : num [1:390] 0.45 0.44 0.43 0.44 0.45 0.47 0.39 0.44 0.44 0.45 ...
## ..$ S8 : num [1:390] 0.44 0.43 0.42 0.43 0.44 0.46 0.38 0.43 0.43 0.45 ...
## ..$ S10 : num [1:390] 0.44 0.42 0.41 0.42 0.43 0.45 0.36 0.43 0.43 0.44 ...
## ..$ S33 : num [1:390] 0.39 0.38 0.37 0.37 0.36 0.35 0.32 0.39 0.38 0.38 ...
## ..$ S66 : num [1:390] 0.36 0.37 0.36 0.36 0.35 0.34 0.29 0.33 0.37 0.35 ...
## ..$ S300 : num [1:390] 0.37 0.34 0.32 0.33 0.32 0.31 0.28 0.32 0.33 0.33 ...
## ..$ S1500: num [1:390] 0.273 0.273 0.288 0.288 0.291 0.291 0.265 0.265 0.327 0.327 ...
## $ fract:'data.frame': 390 obs. of 10 variables:
## ..$ faz : chr [1:390] "FAZ. ARGEMIRA" "FAZ. ARGEMIRA" "FAZ. ARGEMIRA" "FAZ. ARGEMIRA" ...
## ..$ tal : chr [1:390] "AG2" "AG2" "AG2" "AG2" ...
## ..$ cam : chr [1:390] "0-0.1" "0-0.1" "0.1-0.2" "0.1-0.2" ...
## ..$ rpt : int [1:390] 1 2 1 2 1 2 1 2 1 2 ...
## ..$ lightfree : num [1:390] 14.4 NA NA NA NA ...
## ..$ filter1 : num [1:390] 0.13 NA NA NA NA ...
## ..$ filterC1 : num [1:390] 0.274 NA NA NA NA ...
## ..$ lightocluded: num [1:390] 6.21 NA NA NA NA NA 3.1 NA NA NA ...
## ..$ filter2 : num [1:390] 0.128 NA NA NA NA ...
## ..$ filterC2 : num [1:390] 0.19 NA NA NA NA ...
library(reshape2)
library(data.table)
#-----------------------------------------------------------------------
# Curvas de retenção.
swrc <- high_soybean$swrc
swrc <- as.data.table(swrc)
str(swrc)
## Classes 'data.table' and 'data.frame': 390 obs. of 15 variables:
## $ faz : chr "FAZ. ARGEMIRA" "FAZ. ARGEMIRA" "FAZ. ARGEMIRA" "FAZ. ARGEMIRA" ...
## $ tal : chr "AG2" "AG2" "AG2" "AG2" ...
## $ cam : chr "0-0.1" "0-0.1" "0.1-0.2" "0.1-0.2" ...
## $ rpt : int 1 2 1 2 1 2 1 2 1 2 ...
## $ S0 : num 0.54 0.53 0.49 0.5 0.52 0.53 0.56 0.56 0.55 0.5 ...
## $ S1 : num 0.52 0.5 0.45 0.48 0.49 0.49 0.53 0.54 0.5 0.49 ...
## $ S2 : num 0.49 0.48 0.44 0.47 0.48 0.49 0.46 0.5 0.49 0.48 ...
## $ S4 : num 0.46 0.46 0.44 0.45 0.47 0.49 0.41 0.46 0.45 0.47 ...
## $ S6 : num 0.45 0.44 0.43 0.44 0.45 0.47 0.39 0.44 0.44 0.45 ...
## $ S8 : num 0.44 0.43 0.42 0.43 0.44 0.46 0.38 0.43 0.43 0.45 ...
## $ S10 : num 0.44 0.42 0.41 0.42 0.43 0.45 0.36 0.43 0.43 0.44 ...
## $ S33 : num 0.39 0.38 0.37 0.37 0.36 0.35 0.32 0.39 0.38 0.38 ...
## $ S66 : num 0.36 0.37 0.36 0.36 0.35 0.34 0.29 0.33 0.37 0.35 ...
## $ S300 : num 0.37 0.34 0.32 0.33 0.32 0.31 0.28 0.32 0.33 0.33 ...
## $ S1500: num 0.273 0.273 0.288 0.288 0.291 0.291 0.265 0.265 0.327 0.327 ...
## - attr(*, ".internal.selfref")=<externalptr>
class(swrc)
## [1] "data.table" "data.frame"
methods(class = "data.table")
## [1] all.equal anyDuplicated as.data.frame as.data.table
## [5] as.list as.matrix coerce coerce<-
## [9] [<- [[<- $<- [
## [13] dcast dim dimnames<- dimnames
## [17] duplicated format head initialize
## [21] is.na melt merge names<-
## [25] na.omit Ops print show
## [29] slotsFromS3 split subset tail
## [33] transform unique within
## see '?methods' for accessing help and source code
swrc
## faz tal cam rpt S0 S1 S2 S4 S6 S8
## 1: FAZ. ARGEMIRA AG2 0-0.1 1 0.54 0.52 0.49 0.46 0.45 0.44
## 2: FAZ. ARGEMIRA AG2 0-0.1 2 0.53 0.50 0.48 0.46 0.44 0.43
## 3: FAZ. ARGEMIRA AG2 0.1-0.2 1 0.49 0.45 0.44 0.44 0.43 0.42
## 4: FAZ. ARGEMIRA AG2 0.1-0.2 2 0.50 0.48 0.47 0.45 0.44 0.43
## 5: FAZ. ARGEMIRA AG2 0.2-0.4 1 0.52 0.49 0.48 0.47 0.45 0.44
## ---
## 386: FAZ. SUCURI SU20 0-0.1 2 0.50 0.45 0.42 0.34 0.30 0.28
## 387: FAZ. SUCURI SU20 0.1-0.2 1 0.34 0.32 0.30 0.28 0.26 0.26
## 388: FAZ. SUCURI SU20 0.1-0.2 2 0.34 0.31 0.30 0.28 0.25 0.24
## 389: FAZ. SUCURI SU20 0.2-0.4 1 0.38 0.34 0.33 0.31 0.27 0.25
## 390: FAZ. SUCURI SU20 0.2-0.4 2 0.27 0.26 0.26 0.26 0.26 0.25
## S10 S33 S66 S300 S1500
## 1: 0.44 0.39 0.36 0.37 0.273
## 2: 0.42 0.38 0.37 0.34 0.273
## 3: 0.41 0.37 0.36 0.32 0.288
## 4: 0.42 0.37 0.36 0.33 0.288
## 5: 0.43 0.36 0.35 0.32 0.291
## ---
## 386: 0.27 0.22 0.21 0.21 0.124
## 387: 0.25 0.20 0.19 0.17 0.138
## 388: 0.23 0.19 0.19 0.16 0.138
## 389: 0.25 0.20 0.19 0.17 0.151
## 390: 0.25 0.21 0.19 0.17 0.151
swrc <- melt(data = swrc, id.vars = 1:4)
names(swrc)[ncol(swrc) - 1:0] <- c("tens", "umid")
swrc$tens <- as.numeric(sub("S", "", as.character(swrc$tens)))
swrc <- subset(swrc, umid > 0 & umid < 0.95)
unique(swrc$tens) # R-ônico.
## [1] 0 1 2 4 6 8 10 33 66 300 1500
swrc[, unique(tens)] # DT-ônico.
## [1] 0 1 2 4 6 8 10 33 66 300 1500
# swrc$tens[swrc$tens == 0] <- 0.1 # R-ônico
swrc[tens == 0, tens := 0.1] # DT-ônico.
swrc[, unique(tens)]
## [1] 0.1 1.0 2.0 4.0 6.0 8.0 10.0 33.0 66.0
## [10] 300.0 1500.0
#-----------------------------------------------------------------------
# Pacotes.
library(ggplot2)
library(lattice)
library(latticeExtra)
#-----------------------------------------------------------------------
xyplot(umid ~ tens | tal,
data = swrc,
groups = cam,
xlab = "Tensão",
ylab = "Umidade",
type = c("p", "a"),
scales = list(x = list(log = 10)),
ylim = c(0, 1),
auto.key = list(space = "top", columns = 3),
as.table = TRUE)
ggplot(data = swrc,
mapping = aes(x = tens, y = umid, color = cam)) +
xlab(label = "Tensão") +
ylab(label = "Umidade") +
geom_point() +
stat_summary(fun.y = mean, geom = "line") +
scale_x_log10() +
scale_y_continuous(limits = c(0, 1)) +
facet_wrap(facets = ~tal) +
theme(legend.position = "top")
#-----------------------------------------------------------------------
# Exploratória dos dados de química e física.
str(high_soybean)
## List of 3
## $ atrib:'data.frame': 390 obs. of 38 variables:
## ..$ faz : chr [1:390] "FAZ. ARGEMIRA" "FAZ. ARGEMIRA" "FAZ. ARGEMIRA" "FAZ. ARGEMIRA" ...
## ..$ tal : chr [1:390] "AG2" "AG2" "AG2" "AG2" ...
## ..$ cam : chr [1:390] "0-0.1" "0-0.1" "0.1-0.2" "0.1-0.2" ...
## ..$ rpt : int [1:390] 1 2 1 2 1 2 1 2 1 2 ...
## ..$ prod : num [1:390] 3.89 NA NA NA NA ...
## ..$ glic : num [1:390] 65 NA NA NA NA NA 76.2 NA NA NA ...
## ..$ phos : num [1:390] 192 NA NA NA NA ...
## ..$ sulf : num [1:390] 74.4 NA NA NA NA NA 74 NA NA NA ...
## ..$ LFF : num [1:390] 14.4 NA NA NA NA ...
## ..$ LFO : num [1:390] 6.21 NA NA NA NA NA 3.1 NA NA NA ...
## ..$ HF : num [1:390] 22.6 NA NA NA NA ...
## ..$ rp : num [1:390] 2.09 1.75 2.39 2.9 2.35 1.14 0.54 1.26 0.94 2.65 ...
## ..$ dens : num [1:390] 1.23 1.19 1.28 1.3 1.23 1.2 1.01 1.08 1.15 1.24 ...
## ..$ poro : num [1:390] 0.53 0.54 0.53 0.52 0.5 0.51 0.61 0.59 0.57 0.53 ...
## ..$ clay : int [1:390] 653 NA 725 NA 775 NA 644 NA 724 NA ...
## ..$ sand : int [1:390] 162 NA 139 NA 120 NA 175 NA 138 NA ...
## ..$ pH : num [1:390] 6.2 NA 5.3 NA 5.1 NA 6.1 NA 5.2 NA ...
## ..$ pH_Ca: num [1:390] 5.4 NA 4.5 NA 4.4 NA 5.2 NA 4.5 NA ...
## ..$ P : num [1:390] 16.4 NA 2.1 NA 0.9 NA 14.4 NA 1.7 NA ...
## ..$ K : num [1:390] 97.3 NA 76.9 NA 67.7 NA 78.6 NA 25.6 NA ...
## ..$ Ca_Mg: num [1:390] 5.5 NA 2.1 NA 1.1 NA 5.1 NA 1.8 NA ...
## ..$ Ca : num [1:390] 4 NA 1.5 NA 0.8 NA 3.7 NA 1.3 NA ...
## ..$ Mg : num [1:390] 1.5 NA 0.6 NA 0.3 NA 1.4 NA 0.5 NA ...
## ..$ Al : num [1:390] 0 NA 0.4 NA 0.5 NA 0 NA 0.4 NA ...
## ..$ MO : num [1:390] 43.3 NA 31.2 NA 21.3 NA 44.5 NA 29.5 NA ...
## ..$ base : num [1:390] 5.75 NA 2.3 NA 1.27 NA 5.3 NA 1.87 NA ...
## ..$ CTC : num [1:390] 10.15 NA 7.6 NA 5.77 ...
## ..$ V : num [1:390] 56.6 NA 30.2 NA 22.1 ...
## ..$ CaMg : num [1:390] 2.67 NA 2.5 NA 2.67 NA 2.64 NA 2.6 NA ...
## ..$ CaK : num [1:390] 16.03 NA 7.61 NA 4.61 ...
## ..$ MgK : num [1:390] 6.01 NA 3.04 NA 1.73 NA 6.95 NA 7.62 NA ...
## ..$ Ca_ : num [1:390] 39.4 NA 19.7 NA 13.9 NA 36.6 NA 17.9 NA ...
## ..$ Mg_ : num [1:390] 14.8 NA 7.9 NA 5.2 NA 13.9 NA 6.9 NA ...
## ..$ K_ : num [1:390] 2.5 NA 2.6 NA 3 NA 2 NA 0.9 NA ...
## ..$ H_ : num [1:390] 43.4 NA 64.5 NA 69.3 NA 47.5 NA 68.8 NA ...
## ..$ m_ : num [1:390] 0 NA 14.8 NA 28.2 NA 0 NA 17.7 NA ...
## ..$ S : num [1:390] 21.1 NA 33.9 NA 56 NA 10.8 NA 32.7 NA ...
## ..$ dp : num [1:390] 2.59 2.59 2.73 2.73 2.45 2.45 2.63 2.63 2.65 2.65 ...
## $ swrc :'data.frame': 390 obs. of 15 variables:
## ..$ faz : chr [1:390] "FAZ. ARGEMIRA" "FAZ. ARGEMIRA" "FAZ. ARGEMIRA" "FAZ. ARGEMIRA" ...
## ..$ tal : chr [1:390] "AG2" "AG2" "AG2" "AG2" ...
## ..$ cam : chr [1:390] "0-0.1" "0-0.1" "0.1-0.2" "0.1-0.2" ...
## ..$ rpt : int [1:390] 1 2 1 2 1 2 1 2 1 2 ...
## ..$ S0 : num [1:390] 0.54 0.53 0.49 0.5 0.52 0.53 0.56 0.56 0.55 0.5 ...
## ..$ S1 : num [1:390] 0.52 0.5 0.45 0.48 0.49 0.49 0.53 0.54 0.5 0.49 ...
## ..$ S2 : num [1:390] 0.49 0.48 0.44 0.47 0.48 0.49 0.46 0.5 0.49 0.48 ...
## ..$ S4 : num [1:390] 0.46 0.46 0.44 0.45 0.47 0.49 0.41 0.46 0.45 0.47 ...
## ..$ S6 : num [1:390] 0.45 0.44 0.43 0.44 0.45 0.47 0.39 0.44 0.44 0.45 ...
## ..$ S8 : num [1:390] 0.44 0.43 0.42 0.43 0.44 0.46 0.38 0.43 0.43 0.45 ...
## ..$ S10 : num [1:390] 0.44 0.42 0.41 0.42 0.43 0.45 0.36 0.43 0.43 0.44 ...
## ..$ S33 : num [1:390] 0.39 0.38 0.37 0.37 0.36 0.35 0.32 0.39 0.38 0.38 ...
## ..$ S66 : num [1:390] 0.36 0.37 0.36 0.36 0.35 0.34 0.29 0.33 0.37 0.35 ...
## ..$ S300 : num [1:390] 0.37 0.34 0.32 0.33 0.32 0.31 0.28 0.32 0.33 0.33 ...
## ..$ S1500: num [1:390] 0.273 0.273 0.288 0.288 0.291 0.291 0.265 0.265 0.327 0.327 ...
## $ fract:'data.frame': 390 obs. of 10 variables:
## ..$ faz : chr [1:390] "FAZ. ARGEMIRA" "FAZ. ARGEMIRA" "FAZ. ARGEMIRA" "FAZ. ARGEMIRA" ...
## ..$ tal : chr [1:390] "AG2" "AG2" "AG2" "AG2" ...
## ..$ cam : chr [1:390] "0-0.1" "0-0.1" "0.1-0.2" "0.1-0.2" ...
## ..$ rpt : int [1:390] 1 2 1 2 1 2 1 2 1 2 ...
## ..$ lightfree : num [1:390] 14.4 NA NA NA NA ...
## ..$ filter1 : num [1:390] 0.13 NA NA NA NA ...
## ..$ filterC1 : num [1:390] 0.274 NA NA NA NA ...
## ..$ lightocluded: num [1:390] 6.21 NA NA NA NA NA 3.1 NA NA NA ...
## ..$ filter2 : num [1:390] 0.128 NA NA NA NA ...
## ..$ filterC2 : num [1:390] 0.19 NA NA NA NA ...
atrib <- as.data.table(high_soybean$atrib)
atrib <- transform(atrib,
cam = factor(cam),
tal = factor(tal),
faz = factor(faz))
fivenum(atrib$prod)
## [1] 3.226 3.930 4.128 4.343 4.974
bk <- seq(from = 3.2, to = 5, by = 0.1)
histogram(~prod,
data = atrib,
breaks = bk,
type = "density",
xlab = "Produção",
ylab = "Densidade")
ggplot(data = atrib,
mapping = aes(x = prod,
y = ..density..,
color = I("black"))) +
xlab(label = "Produção") +
ylab(label = "Densidade") +
geom_histogram(breaks = bk)
densityplot(~prod,
data = atrib,
plot.points = "rug",
xlab = "Produção",
ylab = "Densidade")
ggplot(data = atrib,
mapping = aes(x = prod,
color = I("black"))) +
xlab(label = "Produção") +
ylab(label = "Densidade") +
geom_density() +
geom_rug()
#-----------------------------------------------------------------------
# A variável resposta e todas as variáveis preditoras.
m <- tail(names(atrib), n = -4)
m
## [1] "prod" "glic" "phos" "sulf" "LFF" "LFO" "HF" "rp"
## [9] "dens" "poro" "clay" "sand" "pH" "pH_Ca" "P" "K"
## [17] "Ca_Mg" "Ca" "Mg" "Al" "MO" "base" "CTC" "V"
## [25] "CaMg" "CaK" "MgK" "Ca_" "Mg_" "K_" "H_" "m_"
## [33] "S" "dp"
atrib2 <- melt(data = atrib, measure.vars = m)
str(atrib2)
## Classes 'data.table' and 'data.frame': 13260 obs. of 6 variables:
## $ faz : Factor w/ 14 levels "FAZ. ARGEMIRA",..: 1 1 1 1 1 1 1 1 1 1 ...
## $ tal : Factor w/ 65 levels "AG10","AG2","AG3",..: 2 2 2 2 2 2 3 3 3 3 ...
## $ cam : Factor w/ 3 levels "0-0.1","0.1-0.2",..: 1 1 2 2 3 3 1 1 2 2 ...
## $ rpt : int 1 2 1 2 1 2 1 2 1 2 ...
## $ variable: Factor w/ 34 levels "prod","glic",..: 1 1 1 1 1 1 1 1 1 1 ...
## $ value : num 3.89 NA NA NA NA ...
## - attr(*, ".internal.selfref")=<externalptr>
atrib2 <- atrib2[!is.na(value)]
# densityplot(~value | variable,
# groups = cam,
# data = atrib2,
# scales = "free",
# auto.key = list(columns = 3),
# as.table = TRUE) +
# glayer({
# mx <- mean(x)
# dens <- density(x)
# fx <- approxfun(x = dens$x, y = dens$y)
# hy <- fx(mx)
# panel.segments(x0 = mx,
# x1 = mx,
# y0 = 0,
# y1 = hy,
# col = col.line)
# })
# Todas as variáveis juntas.
bwplot(value ~ cam | variable,
data = atrib2,
scales = "free",
as.table = TRUE,
# panel = panel.violin,
par.settings = list(
plot.symbol = list(col = 1),
box.dot = list(col = 1, pch = "|"),
box.umbrella = list(col = 1, lty = 1),
box.rectangle = list(col = 1, fill = c("gray70")))) +
layer({
panel.xyplot(x = x, y = y, type = "a", col = 1)
})
#-----------------------------------------------------------------------
# Desempilhar para combinar variável com camada.
str(atrib2)
## Classes 'data.table' and 'data.frame': 6466 obs. of 6 variables:
## $ faz : Factor w/ 14 levels "FAZ. ARGEMIRA",..: 1 1 1 1 1 1 1 1 5 5 ...
## $ tal : Factor w/ 65 levels "AG10","AG2","AG3",..: 2 3 4 5 6 1 38 39 52 58 ...
## $ cam : Factor w/ 3 levels "0-0.1","0.1-0.2",..: 1 1 1 1 1 1 1 1 1 1 ...
## $ rpt : int 1 1 1 1 1 1 1 1 1 1 ...
## $ variable: Factor w/ 34 levels "prod","glic",..: 1 1 1 1 1 1 1 1 1 1 ...
## $ value : num 3.89 4.12 4.25 4.12 4.38 ...
## - attr(*, ".internal.selfref")=<externalptr>
# Desempilhar.
atrib2[, camvar := interaction(variable,
as.integer(cam),
sep = ":",
drop = TRUE)]
atrib2[, levels(camvar)]
## [1] "prod:1" "glic:1" "phos:1" "sulf:1" "LFF:1" "LFO:1"
## [7] "HF:1" "rp:1" "dens:1" "poro:1" "clay:1" "sand:1"
## [13] "pH:1" "pH_Ca:1" "P:1" "K:1" "Ca_Mg:1" "Ca:1"
## [19] "Mg:1" "Al:1" "MO:1" "base:1" "CTC:1" "V:1"
## [25] "CaMg:1" "CaK:1" "MgK:1" "Ca_:1" "Mg_:1" "K_:1"
## [31] "H_:1" "m_:1" "S:1" "dp:1" "rp:2" "dens:2"
## [37] "poro:2" "clay:2" "sand:2" "pH:2" "pH_Ca:2" "P:2"
## [43] "K:2" "Ca_Mg:2" "Ca:2" "Mg:2" "Al:2" "MO:2"
## [49] "base:2" "CTC:2" "V:2" "CaMg:2" "CaK:2" "MgK:2"
## [55] "Ca_:2" "Mg_:2" "K_:2" "H_:2" "m_:2" "S:2"
## [61] "dp:2" "rp:3" "dens:3" "poro:3" "clay:3" "sand:3"
## [67] "pH:3" "pH_Ca:3" "P:3" "K:3" "Ca_Mg:3" "Ca:3"
## [73] "Mg:3" "Al:3" "MO:3" "base:3" "CTC:3" "V:3"
## [79] "CaMg:3" "CaK:3" "MgK:3" "Ca_:3" "Mg_:3" "K_:3"
## [85] "H_:3" "m_:3" "S:3" "dp:3"
names(atrib2)
## [1] "faz" "tal" "cam" "rpt" "variable"
## [6] "value" "camvar"
# Tira a médias das repetições.
atrib3 <- dcast(data = atrib2,
formula = faz + tal ~ camvar,
value.var = "value",
# fun.aggregate = identity, fill = NA,
fun.aggregate = mean,
sep = ":")
nrow(atrib3)
## [1] 65
names(atrib3)
## [1] "faz" "tal" "prod:1" "glic:1" "phos:1" "sulf:1"
## [7] "LFF:1" "LFO:1" "HF:1" "rp:1" "dens:1" "poro:1"
## [13] "clay:1" "sand:1" "pH:1" "pH_Ca:1" "P:1" "K:1"
## [19] "Ca_Mg:1" "Ca:1" "Mg:1" "Al:1" "MO:1" "base:1"
## [25] "CTC:1" "V:1" "CaMg:1" "CaK:1" "MgK:1" "Ca_:1"
## [31] "Mg_:1" "K_:1" "H_:1" "m_:1" "S:1" "dp:1"
## [37] "rp:2" "dens:2" "poro:2" "clay:2" "sand:2" "pH:2"
## [43] "pH_Ca:2" "P:2" "K:2" "Ca_Mg:2" "Ca:2" "Mg:2"
## [49] "Al:2" "MO:2" "base:2" "CTC:2" "V:2" "CaMg:2"
## [55] "CaK:2" "MgK:2" "Ca_:2" "Mg_:2" "K_:2" "H_:2"
## [61] "m_:2" "S:2" "dp:2" "rp:3" "dens:3" "poro:3"
## [67] "clay:3" "sand:3" "pH:3" "pH_Ca:3" "P:3" "K:3"
## [73] "Ca_Mg:3" "Ca:3" "Mg:3" "Al:3" "MO:3" "base:3"
## [79] "CTC:3" "V:3" "CaMg:3" "CaK:3" "MgK:3" "Ca_:3"
## [85] "Mg_:3" "K_:3" "H_:3" "m_:3" "S:3" "dp:3"
# Variâncias.
atrib3[,
lapply(.SD, FUN = var, na.rm = TRUE),
.SDcols = 3:ncol(atrib3)]
## prod:1 glic:1 phos:1 sulf:1 LFF:1 LFO:1 HF:1
## 1: 0.1250321 578.1434 12663.52 488.7893 14.5678 9.2511 35.9463
## rp:1 dens:1 poro:1 clay:1 sand:1 pH:1
## 1: 0.5881918 0.02088047 0.00735369 14703 21784.57 0.0436875
## pH_Ca:1 P:1 K:1 Ca_Mg:1 Ca:1 Mg:1 Al:1
## 1: 0.0421875 174.8634 986.0294 0.4862596 0.2614279 0.03559135 0
## MO:1 base:1 CTC:1 V:1 CaMg:1 CaK:1
## 1: 20.74578 0.5354701 0.813834 35.60101 0.006489087 22.88028
## MgK:1 Ca_:1 Mg_:1 K_:1 H_:1 m_:1 S:1
## 1: 3.233015 16.80674 2.305351 0.773101 35.59554 0 37.75078
## dp:1 rp:2 dens:2 poro:2 clay:2 sand:2
## 1: 0.005371004 0.293748 0.01540459 0.008098534 15431.62 20716.28
## pH:2 pH_Ca:2 P:2 K:2 Ca_Mg:2 Ca:2
## 1: 0.07859135 0.08034615 52.71091 532.8338 0.619149 0.3377788
## Mg:2 Al:2 MO:2 base:2 CTC:2 V:2
## 1: 0.04290865 0.0406875 26.62002 0.6604085 1.024687 94.37282
## CaMg:2 CaK:2 MgK:2 Ca_:2 Mg_:2 K_:2 H_:2
## 1: 0.02664529 35.25331 5.215659 49.02754 6.152322 0.6768029 49.8511
## m_:2 S:2 dp:2 rp:3 dens:3 poro:3
## 1: 112.9342 119.6136 0.004443654 0.1582381 0.01444369 0.005287837
## clay:3 sand:3 pH:3 pH_Ca:3 P:3 K:3
## 1: 14972.4 18987.86 0.03571154 0.03453365 2.588885 259.6855
## Ca_Mg:3 Ca:3 Mg:3 Al:3 MO:3 base:3
## 1: 0.2128029 0.1087163 0.01802885 0.01967788 23.31874 0.2252013
## CTC:3 V:3 CaMg:3 CaK:3 MgK:3 Ca_:3 Mg_:3
## 1: 0.7687975 51.04202 0.0694249 33.6436 6.217125 24.43953 4.308212
## K_:3 H_:3 m_:3 S:3 dp:3
## 1: 0.6090529 26.46215 105.053 347.3378 0.00998375
# Mantém só as variáveis numéricas com variância não nula.
atrib3 <- atrib3[,
Filter(function(x) {
if (is.numeric(x)) {
var(x, na.rm = TRUE) > 0
} else {
TRUE
}
}, .SD)]
# Dimensões.
# c(linhas = nrow(atrib3), colunas = ncol(atrib3) - 2)
structure(dim(atrib3) - c(0, 2),
.Names = c("linhas", "colunas"))
## linhas colunas
## 65 86
#-----------------------------------------------------------------------
# Explorando as correlações.
library(corrplot)
k <- cor(atrib3[, 3:ncol(atrib3)], use = "pairwise.complete.obs")
# Diagrama de correlações.
corrplot::corrplot(k,
type = "upper",
order = c("original", "AOE", "FPC", "hclust", "alphabet")[1],
# tl.pos = c("lt", "d", "td")[3],
# outline = TRUE,
method = "ellipse")
# Separando as variáveis por camada.
par(mfrow = c(2, 2))
sapply(1:3,
FUN = function(cam) {
i <- grep(pattern = sprintf(":%d$", cam),
x = colnames(k))
corrplot::corrplot(k[i, i],
type = "upper",
tl.pos = c("lt", "d", "td")[3],
outline = TRUE,
method = "ellipse")
})
## [[1]]
## prod:1 glic:1 phos:1 sulf:1
## prod:1 1.00000000 0.26180390 -0.12604529 0.063195246
## glic:1 0.26180390 1.00000000 -0.18222094 0.430285359
## phos:1 -0.12604529 -0.18222094 1.00000000 0.152037262
## sulf:1 0.06319525 0.43028536 0.15203726 1.000000000
## LFF:1 -0.07601192 0.01105054 0.14278886 0.018263157
## LFO:1 0.06709591 -0.16713474 0.13731589 -0.085106030
## HF:1 0.03049029 0.30258729 0.02039905 0.315142956
## rp:1 -0.39207874 -0.11284608 0.22372772 0.143759729
## dens:1 -0.22955518 -0.16022396 -0.08132025 -0.107142336
## poro:1 0.23172295 0.18164550 -0.04854562 -0.050500519
## clay:1 -0.12648334 0.24175216 0.15086226 0.191000124
## sand:1 0.12369779 -0.20837318 -0.16393789 -0.166815904
## pH:1 0.10891971 0.03839387 -0.12947074 0.073017103
## pH_Ca:1 0.10718180 -0.02044939 -0.10975644 -0.001429465
## P:1 -0.12344554 -0.09407243 -0.25932817 -0.078468845
## K:1 0.25437028 0.10749443 -0.22926722 -0.072917137
## Ca_Mg:1 0.05162701 0.17747163 0.05774925 0.255312536
## Ca:1 0.05729365 0.17519063 0.06147165 0.260850798
## Mg:1 0.03554846 0.18104328 0.04685457 0.237143058
## MO:1 0.02124394 0.29452231 0.23820199 0.354222929
## base:1 0.07728110 0.18102593 0.03072191 0.235609081
## CTC:1 0.00737564 0.22223998 0.21424983 0.303095732
## V:1 0.11091608 0.04011570 -0.16782120 0.040818485
## CaMg:1 0.11427721 -0.02837427 0.04814784 0.111747734
## CaK:1 -0.18287695 0.01030033 0.26734818 0.297643333
## MgK:1 -0.18724185 0.01668743 0.25467888 0.283267214
## Ca_:1 0.08423509 0.03084582 -0.12750184 0.075941882
## Mg_:1 0.05252590 0.04559345 -0.14439617 0.050814618
## K_:1 0.26330897 0.04419680 -0.29784649 -0.162055171
## H_:1 -0.11156581 -0.03967888 0.16710210 -0.040626233
## S:1 -0.23837027 0.02595622 -0.15958335 0.018105201
## dp:1 -0.16668219 -0.04590009 -0.17794589 -0.275791130
## LFF:1 LFO:1 HF:1 rp:1
## prod:1 -0.07601192 0.067095909 0.030490288 -0.392078744
## glic:1 0.01105054 -0.167134741 0.302587287 -0.112846078
## phos:1 0.14278886 0.137315892 0.020399052 0.223727719
## sulf:1 0.01826316 -0.085106030 0.315142956 0.143759729
## LFF:1 1.00000000 0.243192434 -0.597819800 -0.033081843
## LFO:1 0.24319243 1.000000000 -0.474488847 0.142528058
## HF:1 -0.59781980 -0.474488847 1.000000000 -0.006975694
## rp:1 -0.03308184 0.142528058 -0.006975694 1.000000000
## dens:1 -0.30157742 -0.036225890 -0.021719966 0.503274244
## poro:1 0.16823744 0.203465088 0.024401207 -0.524277121
## clay:1 0.21211120 0.229509588 0.084095796 0.242934852
## sand:1 -0.25278261 -0.255574167 -0.073600692 -0.187342339
## pH:1 -0.05374774 0.001214148 0.120430786 -0.015481877
## pH_Ca:1 -0.06326129 0.029387951 0.071168283 0.018664285
## P:1 -0.04194289 -0.273375847 0.051954533 0.058856354
## K:1 0.02608003 0.009053952 0.139667448 0.076462737
## Ca_Mg:1 0.08908162 0.187278606 0.370363906 -0.009483338
## Ca:1 0.09245716 0.190076422 0.368160426 -0.008292563
## Mg:1 0.07868959 0.177081461 0.371165427 -0.012578205
## MO:1 0.21345205 0.246987042 0.498509916 0.058272952
## base:1 0.08818694 0.180040830 0.368000663 -0.001397394
## CTC:1 0.20651960 0.258888440 0.466861216 0.008996976
## V:1 -0.04728956 -0.008036408 0.060041899 -0.040599560
## CaMg:1 0.07931305 0.041117680 -0.040935436 0.027568338
## CaK:1 -0.07971462 0.063386278 0.103767388 -0.129283629
## MgK:1 -0.08531341 0.058342812 0.103861430 -0.133729215
## Ca_:1 -0.03995399 0.008465169 0.061525328 -0.050348943
## Mg_:1 -0.06168956 -0.005059085 0.076954548 -0.054569474
## K_:1 -0.03136438 -0.087664879 -0.010054266 0.049994729
## H_:1 0.04741552 0.008483129 -0.060202367 0.041359775
## S:1 0.06353553 -0.245321752 0.142742865 0.002207732
## dp:1 0.01387195 0.012812504 -0.062955321 -0.013854591
## dens:1 poro:1 clay:1 sand:1
## prod:1 -0.22955518 0.23172295 -0.12648334 0.12369779
## glic:1 -0.16022396 0.18164550 0.24175216 -0.20837318
## phos:1 -0.08132025 -0.04854562 0.15086226 -0.16393789
## sulf:1 -0.10714234 -0.05050052 0.19100012 -0.16681590
## LFF:1 -0.30157742 0.16823744 0.21211120 -0.25278261
## LFO:1 -0.03622589 0.20346509 0.22950959 -0.25557417
## HF:1 -0.02171997 0.02440121 0.08409580 -0.07360069
## rp:1 0.50327424 -0.52427712 0.24293485 -0.18734234
## dens:1 1.00000000 -0.75679504 -0.37780655 0.46422862
## poro:1 -0.75679504 1.00000000 0.30151127 -0.38090619
## clay:1 -0.37780655 0.30151127 1.00000000 -0.97130558
## sand:1 0.46422862 -0.38090619 -0.97130558 1.00000000
## pH:1 0.04643938 -0.05387376 -0.36694534 0.34250572
## pH_Ca:1 0.13538566 -0.12641259 -0.45252344 0.41810140
## P:1 0.49129091 -0.38037633 -0.37540012 0.44374383
## K:1 0.10502915 -0.14861519 -0.16155768 0.18396635
## Ca_Mg:1 -0.11392519 0.18547817 -0.01195604 -0.03278619
## Ca:1 -0.11684720 0.18491351 -0.01207193 -0.03200442
## Mg:1 -0.10441549 0.18441918 -0.01147504 -0.03444726
## MO:1 -0.30549628 0.30896839 0.44170284 -0.47937495
## base:1 -0.09721862 0.16073118 -0.02903470 -0.01119393
## CTC:1 -0.29213204 0.36148519 0.42822218 -0.46978826
## V:1 0.11445180 -0.09652220 -0.45209923 0.43364008
## CaMg:1 -0.07022535 -0.01326176 -0.01049371 0.01936551
## CaK:1 -0.16010712 0.23534163 0.12972758 -0.15350076
## MgK:1 -0.15387770 0.23528934 0.12865982 -0.15285464
## Ca_:1 0.08924175 -0.06440155 -0.43343170 0.40871715
## Mg_:1 0.10685725 -0.06178127 -0.42760342 0.40124100
## K_:1 0.17674007 -0.24751838 -0.31989900 0.35232176
## H_:1 -0.11401961 0.09694559 0.45228752 -0.43375697
## S:1 -0.12889638 0.03555254 0.34495457 -0.33400585
## dp:1 0.18727091 -0.06786170 -0.04381646 0.03779066
## pH:1 pH_Ca:1 P:1 K:1
## prod:1 0.108919711 0.107181801 -0.12344554 0.254370281
## glic:1 0.038393870 -0.020449386 -0.09407243 0.107494428
## phos:1 -0.129470745 -0.109756439 -0.25932817 -0.229267224
## sulf:1 0.073017103 -0.001429465 -0.07846885 -0.072917137
## LFF:1 -0.053747737 -0.063261290 -0.04194289 0.026080026
## LFO:1 0.001214148 0.029387951 -0.27337585 0.009053952
## HF:1 0.120430786 0.071168283 0.05195453 0.139667448
## rp:1 -0.015481877 0.018664285 0.05885635 0.076462737
## dens:1 0.046439376 0.135385657 0.49129091 0.105029153
## poro:1 -0.053873755 -0.126412593 -0.38037633 -0.148615188
## clay:1 -0.366945337 -0.452523445 -0.37540012 -0.161557679
## sand:1 0.342505721 0.418101397 0.44374383 0.183966347
## pH:1 1.000000000 0.953566149 0.19429940 0.507712814
## pH_Ca:1 0.953566149 1.000000000 0.24690981 0.528516228
## P:1 0.194299398 0.246909806 1.00000000 0.204679051
## K:1 0.507712814 0.528516228 0.20467905 1.000000000
## Ca_Mg:1 0.715473464 0.681826768 0.09606006 0.378466663
## Ca:1 0.714362976 0.684400012 0.09562800 0.381952048
## Mg:1 0.708494914 0.665334231 0.09589004 0.363737021
## MO:1 0.114297129 0.060293495 -0.14931253 0.211747854
## base:1 0.737869243 0.707958225 0.11357282 0.470122074
## CTC:1 0.084423323 0.030357270 -0.09106334 0.185054325
## V:1 0.943924054 0.949935380 0.27386672 0.478038965
## CaMg:1 0.051782599 0.115211592 0.01336279 0.078100355
## CaK:1 -0.139941744 -0.199607026 -0.18479921 -0.837218470
## MgK:1 -0.140184293 -0.204010001 -0.18209256 -0.831945192
## Ca_:1 0.926945005 0.933742266 0.25310599 0.365938275
## Mg_:1 0.913208597 0.901344408 0.25039984 0.346356647
## K_:1 0.507571997 0.539876736 0.24491757 0.944779817
## H_:1 -0.944069239 -0.950046606 -0.27415532 -0.478026605
## S:1 -0.230975649 -0.226577230 0.12661279 -0.206143813
## dp:1 -0.029104905 -0.029410205 0.35664898 0.064812287
## Ca_Mg:1 Ca:1 Mg:1 MO:1
## prod:1 0.051627006 0.057293649 0.035548457 0.02124394
## glic:1 0.177471632 0.175190631 0.181043277 0.29452231
## phos:1 0.057749255 0.061471648 0.046854573 0.23820199
## sulf:1 0.255312536 0.260850798 0.237143058 0.35422293
## LFF:1 0.089081622 0.092457156 0.078689594 0.21345205
## LFO:1 0.187278606 0.190076422 0.177081461 0.24698704
## HF:1 0.370363906 0.368160426 0.371165427 0.49850992
## rp:1 -0.009483338 -0.008292563 -0.012578205 0.05827295
## dens:1 -0.113925188 -0.116847197 -0.104415487 -0.30549628
## poro:1 0.185478167 0.184913512 0.184419176 0.30896839
## clay:1 -0.011956036 -0.012071927 -0.011475038 0.44170284
## sand:1 -0.032786192 -0.032004419 -0.034447259 -0.47937495
## pH:1 0.715473464 0.714362976 0.708494914 0.11429713
## pH_Ca:1 0.681826768 0.684400012 0.665334231 0.06029350
## P:1 0.096060065 0.095627995 0.095890041 -0.14931253
## K:1 0.378466663 0.381952048 0.363737021 0.21174785
## Ca_Mg:1 1.000000000 0.998616158 0.989790228 0.68722704
## Ca:1 0.998616158 1.000000000 0.980924687 0.68902349
## Mg:1 0.989790228 0.980924687 1.000000000 0.67276440
## MO:1 0.687227043 0.689023492 0.672764398 1.00000000
## base:1 0.994865863 0.993903347 0.983585881 0.67853331
## CTC:1 0.700392934 0.700481440 0.690375380 0.96047837
## V:1 0.715154484 0.714636533 0.706574488 0.03404039
## CaMg:1 0.023485234 0.075475262 -0.117746781 0.04003576
## CaK:1 0.071784395 0.065139719 0.088790766 0.11212023
## MgK:1 0.068190594 0.057190157 0.097052182 0.10418445
## Ca_:1 0.734418339 0.736994347 0.717184115 0.05315948
## Mg_:1 0.729193974 0.718209176 0.748785388 0.04622420
## K_:1 0.171997485 0.175730136 0.159480064 -0.09805793
## H_:1 -0.714760648 -0.714221933 -0.706242422 -0.03384775
## S:1 -0.127960482 -0.116542618 -0.157118986 0.07731656
## dp:1 -0.023567387 -0.033890937 0.004740659 -0.06268921
## base:1 CTC:1 V:1 CaMg:1
## prod:1 0.077281097 0.0073756401 0.110916082 0.1142772112
## glic:1 0.181025926 0.2222399753 0.040115704 -0.0283742737
## phos:1 0.030721913 0.2142498256 -0.167821200 0.0481478380
## sulf:1 0.235609081 0.3030957318 0.040818485 0.1117477343
## LFF:1 0.088186942 0.2065196030 -0.047289559 0.0793130536
## LFO:1 0.180040830 0.2588884397 -0.008036408 0.0411176796
## HF:1 0.368000663 0.4668612165 0.060041899 -0.0409354362
## rp:1 -0.001397394 0.0089969765 -0.040599560 0.0275683385
## dens:1 -0.097218615 -0.2921320440 0.114451805 -0.0702253482
## poro:1 0.160731185 0.3614851902 -0.096522201 -0.0132617605
## clay:1 -0.029034705 0.4282221836 -0.452099228 -0.0104937111
## sand:1 -0.011193928 -0.4697882585 0.433640076 0.0193655068
## pH:1 0.737869243 0.0844233226 0.943924054 0.0517825992
## pH_Ca:1 0.707958225 0.0303572695 0.949935380 0.1152115922
## P:1 0.113572818 -0.0910633437 0.273866719 0.0133627891
## K:1 0.470122074 0.1850543246 0.478038965 0.0781003545
## Ca_Mg:1 0.994865863 0.7003929336 0.715154484 0.0234852338
## Ca:1 0.993903347 0.7004814401 0.714636533 0.0754752618
## Mg:1 0.983585881 0.6903753800 0.706574488 -0.1177467812
## MO:1 0.678533309 0.9604783720 0.034040385 0.0400357607
## base:1 1.000000000 0.6882408215 0.734007166 0.0304610326
## CTC:1 0.688240821 1.0000000000 0.016374768 -0.0006562792
## V:1 0.734007166 0.0163747682 1.000000000 0.0617526202
## CaMg:1 0.030461033 -0.0006562792 0.061752620 1.0000000000
## CaK:1 -0.022412232 0.1251455301 -0.152683675 -0.1189242676
## MgK:1 -0.025235899 0.1207102906 -0.153935798 -0.2018068997
## Ca_:1 0.740103048 0.0377826219 0.988912071 0.1225591078
## Mg_:1 0.733092752 0.0414736764 0.970948026 -0.1364543142
## K_:1 0.267158816 -0.1343379680 0.500624907 0.0863573357
## H_:1 -0.733631965 -0.0158869115 -0.999988943 -0.0613267683
## S:1 -0.144901845 0.0838342667 -0.260114756 0.2328465930
## dp:1 -0.015538563 -0.0347757331 0.013498422 -0.2032401525
## CaK:1 MgK:1 Ca_:1 Mg_:1
## prod:1 -0.182876949 -0.18724185 0.084235089 0.052525898
## glic:1 0.010300332 0.01668743 0.030845819 0.045593453
## phos:1 0.267348177 0.25467888 -0.127501841 -0.144396165
## sulf:1 0.297643333 0.28326721 0.075941882 0.050814618
## LFF:1 -0.079714616 -0.08531341 -0.039953992 -0.061689561
## LFO:1 0.063386278 0.05834281 0.008465169 -0.005059085
## HF:1 0.103767388 0.10386143 0.061525328 0.076954548
## rp:1 -0.129283629 -0.13372922 -0.050348943 -0.054569474
## dens:1 -0.160107116 -0.15387770 0.089241746 0.106857250
## poro:1 0.235341626 0.23528934 -0.064401549 -0.061781273
## clay:1 0.129727577 0.12865982 -0.433431700 -0.427603415
## sand:1 -0.153500757 -0.15285464 0.408717148 0.401241003
## pH:1 -0.139941744 -0.14018429 0.926945005 0.913208597
## pH_Ca:1 -0.199607026 -0.20401000 0.933742266 0.901344408
## P:1 -0.184799214 -0.18209256 0.253105991 0.250399841
## K:1 -0.837218470 -0.83194519 0.365938275 0.346356647
## Ca_Mg:1 0.071784395 0.06819059 0.734418339 0.729193974
## Ca:1 0.065139719 0.05719016 0.736994347 0.718209176
## Mg:1 0.088790766 0.09705218 0.717184115 0.748785388
## MO:1 0.112120231 0.10418445 0.053159476 0.046224199
## base:1 -0.022412232 -0.02523590 0.740103048 0.733092752
## CTC:1 0.125145530 0.12071029 0.037782622 0.041473676
## V:1 -0.152683675 -0.15393580 0.988912071 0.970948026
## CaMg:1 -0.118924268 -0.20180690 0.122559108 -0.136454314
## CaK:1 1.000000000 0.99620169 -0.034336480 -0.003362239
## MgK:1 0.996201687 1.00000000 -0.042458504 0.010055336
## Ca_:1 -0.034336480 -0.04245850 1.000000000 0.966049016
## Mg_:1 -0.003362239 0.01005534 0.966049016 1.000000000
## K_:1 -0.874939617 -0.86921543 0.382174819 0.359176994
## H_:1 0.152565575 0.15378022 -0.988845415 -0.970974345
## S:1 0.071473728 0.05215062 -0.224948693 -0.280336297
## dp:1 -0.134202235 -0.11288144 -0.011296161 0.043413022
## K_:1 H_:1 S:1 dp:1
## prod:1 0.26330897 -0.111565810 -0.238370273 -0.166682194
## glic:1 0.04419680 -0.039678883 0.025956221 -0.045900092
## phos:1 -0.29784649 0.167102103 -0.159583349 -0.177945893
## sulf:1 -0.16205517 -0.040626233 0.018105201 -0.275791130
## LFF:1 -0.03136438 0.047415517 0.063535526 0.013871948
## LFO:1 -0.08766488 0.008483129 -0.245321752 0.012812504
## HF:1 -0.01005427 -0.060202367 0.142742865 -0.062955321
## rp:1 0.04999473 0.041359775 0.002207732 -0.013854591
## dens:1 0.17674007 -0.114019614 -0.128896382 0.187270911
## poro:1 -0.24751838 0.096945595 0.035552542 -0.067861704
## clay:1 -0.31989900 0.452287523 0.344954572 -0.043816465
## sand:1 0.35232176 -0.433756970 -0.334005848 0.037790663
## pH:1 0.50757200 -0.944069239 -0.230975649 -0.029104905
## pH_Ca:1 0.53987674 -0.950046606 -0.226577230 -0.029410205
## P:1 0.24491757 -0.274155322 0.126612795 0.356648977
## K:1 0.94477982 -0.478026605 -0.206143813 0.064812287
## Ca_Mg:1 0.17199748 -0.714760648 -0.127960482 -0.023567387
## Ca:1 0.17573014 -0.714221933 -0.116542618 -0.033890937
## Mg:1 0.15948006 -0.706242422 -0.157118986 0.004740659
## MO:1 -0.09805793 -0.033847753 0.077316555 -0.062689211
## base:1 0.26715882 -0.733631965 -0.144901845 -0.015538563
## CTC:1 -0.13433797 -0.015886912 0.083834267 -0.034775733
## V:1 0.50062491 -0.999988943 -0.260114756 0.013498422
## CaMg:1 0.08635734 -0.061326768 0.232846593 -0.203240153
## CaK:1 -0.87493962 0.152565575 0.071473728 -0.134202235
## MgK:1 -0.86921543 0.153780215 0.052150621 -0.112881439
## Ca_:1 0.38217482 -0.988845415 -0.224948693 -0.011296161
## Mg_:1 0.35917699 -0.970974345 -0.280336297 0.043413022
## K_:1 1.00000000 -0.500817104 -0.236133892 0.069050564
## H_:1 -0.50081710 1.000000000 0.260461655 -0.013639980
## S:1 -0.23613389 0.260461655 1.000000000 -0.009010252
## dp:1 0.06905056 -0.013639980 -0.009010252 1.000000000
##
## [[2]]
## rp:2 dens:2 poro:2 clay:2
## rp:2 1.00000000 0.221496602 0.08015625 0.071044699
## dens:2 0.22149660 1.000000000 -0.42406158 -0.703310767
## poro:2 0.08015625 -0.424061577 1.00000000 0.227036070
## clay:2 0.07104470 -0.703310767 0.22703607 1.000000000
## sand:2 -0.10607784 0.694519032 -0.27739830 -0.975317405
## pH:2 0.26176668 0.245893250 0.05434475 -0.278955354
## pH_Ca:2 0.19787216 0.250248070 0.09075955 -0.314750519
## P:2 -0.10000742 0.383676266 -0.14704192 -0.575099343
## K:2 0.06055575 -0.095044892 0.25616853 -0.017157499
## Ca_Mg:2 0.21080224 -0.009651189 0.31271280 -0.114414329
## Ca:2 0.20911656 -0.010758857 0.31844835 -0.115322084
## Mg:2 0.21403455 -0.006474838 0.29439941 -0.111054798
## Al:2 -0.18634298 -0.207268502 -0.06094240 0.217313452
## MO:2 0.21845821 -0.466701630 0.53239747 0.325071449
## base:2 0.20806498 -0.016365276 0.32100456 -0.111628197
## CTC:2 0.19515814 -0.475384010 0.52046119 0.308287568
## V:2 0.14639576 0.217560633 0.08038362 -0.285964127
## CaMg:2 -0.01079947 -0.096139337 0.26897578 0.009265045
## CaK:2 0.07978376 0.008189011 -0.06354027 0.036610664
## MgK:2 0.07779068 0.014773855 -0.09572377 0.044036127
## Ca_:2 0.15199112 0.209105393 0.08829229 -0.277949016
## Mg_:2 0.15469527 0.234424952 0.04478323 -0.287723476
## K_:2 -0.03299839 0.078725739 0.06190264 -0.144623561
## H_:2 -0.10439054 -0.262237530 -0.05443335 0.342160249
## m_:2 -0.17091516 -0.106482799 -0.08603267 0.141660619
## S:2 -0.13601990 -0.338368045 0.11257758 0.274991043
## dp:2 -0.07754103 0.093928421 -0.20784780 -0.093555852
## sand:2 pH:2 pH_Ca:2 P:2
## rp:2 -0.10607784 0.26176668 0.19787216 -0.100007418
## dens:2 0.69451903 0.24589325 0.25024807 0.383676266
## poro:2 -0.27739830 0.05434475 0.09075955 -0.147041922
## clay:2 -0.97531741 -0.27895535 -0.31475052 -0.575099343
## sand:2 1.00000000 0.28221827 0.32009873 0.555216287
## pH:2 0.28221827 1.00000000 0.89796453 0.259990891
## pH_Ca:2 0.32009873 0.89796453 1.00000000 0.289696364
## P:2 0.55521629 0.25999089 0.28969636 1.000000000
## K:2 0.04705137 0.39730285 0.39623940 0.148982330
## Ca_Mg:2 0.09930666 0.81226818 0.89005568 0.236004893
## Ca:2 0.09955776 0.81305089 0.89262219 0.237225475
## Mg:2 0.09789681 0.80430295 0.87653315 0.230904057
## Al:2 -0.22501620 -0.83501950 -0.92423110 -0.212427389
## MO:2 -0.38033145 0.12860084 0.11802516 -0.136165107
## base:2 0.09902525 0.81533953 0.89062286 0.238950987
## CTC:2 -0.36589239 0.10485647 0.10795262 -0.061921305
## V:2 0.29812249 0.89396799 0.98124634 0.263985541
## CaMg:2 -0.01562866 0.34076869 0.43202363 -0.001446225
## CaK:2 -0.06561692 0.27867103 0.35006130 -0.050040480
## MgK:2 -0.06927070 0.22053071 0.28171380 -0.062969990
## Ca_:2 0.28463350 0.88861307 0.98047856 0.253056539
## Mg_:2 0.29930788 0.88130418 0.96606092 0.259855212
## K_:2 0.19548137 0.33890031 0.33090098 0.176858071
## H_:2 -0.36081326 -0.88666009 -0.96978871 -0.313333146
## m_:2 -0.15093319 -0.81743516 -0.89114563 -0.127570378
## S:2 -0.32362796 -0.53513827 -0.49476784 -0.337676485
## dp:2 0.09611545 -0.26000397 -0.21694758 0.008123381
## K:2 Ca_Mg:2 Ca:2 Mg:2
## rp:2 0.06055575 0.210802238 0.20911656 0.214034548
## dens:2 -0.09504489 -0.009651189 -0.01075886 -0.006474838
## poro:2 0.25616853 0.312712800 0.31844835 0.294399413
## clay:2 -0.01715750 -0.114414329 -0.11532208 -0.111054798
## sand:2 0.04705137 0.099306658 0.09955776 0.097896813
## pH:2 0.39730285 0.812268179 0.81305089 0.804302949
## pH_Ca:2 0.39623940 0.890055683 0.89262219 0.876533150
## P:2 0.14898233 0.236004893 0.23722547 0.230904057
## K:2 1.00000000 0.407911920 0.41037731 0.398097540
## Ca_Mg:2 0.40791192 1.000000000 0.99933595 0.994760603
## Ca:2 0.41037731 0.999335953 1.00000000 0.990375018
## Mg:2 0.39809754 0.994760603 0.99037502 1.000000000
## Al:2 -0.37770660 -0.836188477 -0.84021321 -0.818957177
## MO:2 0.19866556 0.503023968 0.49895662 0.510863064
## base:2 0.46775683 0.997776882 0.99730666 0.992009464
## CTC:2 0.20490830 0.503185077 0.49882180 0.511853304
## V:2 0.40828896 0.895160925 0.89620975 0.885860315
## CaMg:2 0.21960870 0.401963507 0.43269730 0.312878254
## CaK:2 -0.57503247 0.416728472 0.41375756 0.422104187
## MgK:2 -0.61735753 0.357025953 0.34949444 0.375621459
## Ca_:2 0.34222519 0.903466990 0.90567666 0.890850377
## Mg_:2 0.32311570 0.888622782 0.88505430 0.892323468
## K_:2 0.93052972 0.204908353 0.20939888 0.190853848
## H_:2 -0.40883563 -0.860106567 -0.86056573 -0.852709343
## m_:2 -0.36389623 -0.865619712 -0.86523791 -0.860542865
## S:2 -0.29072706 -0.409195258 -0.41410407 -0.392516211
## dp:2 -0.05070105 -0.250665477 -0.24909363 -0.253295286
## Al:2 MO:2 base:2 CTC:2 V:2
## rp:2 -0.18634298 0.21845821 0.20806498 0.19515814 0.14639576
## dens:2 -0.20726850 -0.46670163 -0.01636528 -0.47538401 0.21756063
## poro:2 -0.06094240 0.53239747 0.32100456 0.52046119 0.08038362
## clay:2 0.21731345 0.32507145 -0.11162820 0.30828757 -0.28596413
## sand:2 -0.22501620 -0.38033145 0.09902525 -0.36589239 0.29812249
## pH:2 -0.83501950 0.12860084 0.81533953 0.10485647 0.89396799
## pH_Ca:2 -0.92423110 0.11802516 0.89062286 0.10795262 0.98124634
## P:2 -0.21242739 -0.13616511 0.23895099 -0.06192131 0.26398554
## K:2 -0.37770660 0.19866556 0.46775683 0.20490830 0.40828896
## Ca_Mg:2 -0.83618848 0.50302397 0.99777688 0.50318508 0.89516093
## Ca:2 -0.84021321 0.49895662 0.99730666 0.49882180 0.89620975
## Mg:2 -0.81895718 0.51086306 0.99200946 0.51185330 0.88586032
## Al:2 1.00000000 -0.05795256 -0.83698424 -0.04505694 -0.94735757
## MO:2 -0.05795256 1.00000000 0.50163839 0.98589574 0.09859526
## base:2 -0.83698424 0.50163839 1.00000000 0.50215315 0.89639018
## CTC:2 -0.04505694 0.98589574 0.50215315 1.00000000 0.08850901
## V:2 -0.94735757 0.09859526 0.89639018 0.08850901 1.00000000
## CaMg:2 -0.44692844 0.13314370 0.40513301 0.11213667 0.40985706
## CaK:2 -0.37183971 0.17945461 0.36164764 0.18225062 0.36577535
## MgK:2 -0.29980444 0.16780917 0.30074183 0.17165537 0.30154870
## Ca_:2 -0.94683043 0.12020407 0.89961941 0.10904240 0.99597725
## Mg_:2 -0.92702706 0.09905061 0.88388751 0.08984126 0.98846545
## K_:2 -0.33237866 -0.15184502 0.26611984 -0.14668611 0.35225353
## H_:2 0.89583831 -0.02714351 -0.86246448 -0.02051036 -0.98666525
## m_:2 0.96330469 -0.17005563 -0.86454088 -0.15687014 -0.94086527
## S:2 0.56528493 0.08503904 -0.41706525 0.09606284 -0.52374370
## dp:2 0.20963121 -0.10266900 -0.24621096 -0.10440356 -0.21155565
## CaMg:2 CaK:2 MgK:2 Ca_:2
## rp:2 -0.010799470 0.079783758 0.077790683 0.15199112
## dens:2 -0.096139337 0.008189011 0.014773855 0.20910539
## poro:2 0.268975779 -0.063540275 -0.095723771 0.08829229
## clay:2 0.009265045 0.036610664 0.044036127 -0.27794902
## sand:2 -0.015628661 -0.065616922 -0.069270696 0.28463350
## pH:2 0.340768690 0.278671031 0.220530708 0.88861307
## pH_Ca:2 0.432023629 0.350061296 0.281713801 0.98047856
## P:2 -0.001446225 -0.050040480 -0.062969990 0.25305654
## K:2 0.219608703 -0.575032469 -0.617357528 0.34222519
## Ca_Mg:2 0.401963507 0.416728472 0.357025953 0.90346699
## Ca:2 0.432697296 0.413757559 0.349494440 0.90567666
## Mg:2 0.312878254 0.422104187 0.375621459 0.89085038
## Al:2 -0.446928445 -0.371839710 -0.299804437 -0.94683043
## MO:2 0.133143696 0.179454607 0.167809173 0.12020407
## base:2 0.405133010 0.361647639 0.300741826 0.89961941
## CTC:2 0.112136668 0.182250624 0.171655368 0.10904240
## V:2 0.409857056 0.365775352 0.301548696 0.99597725
## CaMg:2 1.000000000 0.137057508 0.002165645 0.44249915
## CaK:2 0.137057508 1.000000000 0.988958729 0.43072990
## MgK:2 0.002165645 0.988958729 1.000000000 0.36276557
## Ca_:2 0.442499155 0.430729901 0.362765570 1.00000000
## Mg_:2 0.297807879 0.436876731 0.389774012 0.98643254
## K_:2 0.179040881 -0.656229047 -0.695246169 0.27758626
## H_:2 -0.376999079 -0.320138148 -0.260901505 -0.97839260
## m_:2 -0.369454925 -0.432678194 -0.372780940 -0.94062659
## S:2 -0.267951485 -0.044604632 0.003632438 -0.51294666
## dp:2 -0.089033397 -0.148344773 -0.123281166 -0.21795987
## Mg_:2 K_:2 H_:2 m_:2
## rp:2 0.15469527 -0.03299839 -0.10439054 -0.17091516
## dens:2 0.23442495 0.07872574 -0.26223753 -0.10648280
## poro:2 0.04478323 0.06190264 -0.05443335 -0.08603267
## clay:2 -0.28772348 -0.14462356 0.34216025 0.14166062
## sand:2 0.29930788 0.19548137 -0.36081326 -0.15093319
## pH:2 0.88130418 0.33890031 -0.88666009 -0.81743516
## pH_Ca:2 0.96606092 0.33090098 -0.96978871 -0.89114563
## P:2 0.25985521 0.17685807 -0.31333315 -0.12757038
## K:2 0.32311570 0.93052972 -0.40883563 -0.36389623
## Ca_Mg:2 0.88862278 0.20490835 -0.86010657 -0.86561971
## Ca:2 0.88505430 0.20939888 -0.86056573 -0.86523791
## Mg:2 0.89232347 0.19085385 -0.85270934 -0.86054286
## Al:2 -0.92702706 -0.33237866 0.89583831 0.96330469
## MO:2 0.09905061 -0.15184502 -0.02714351 -0.17005563
## base:2 0.88388751 0.26611984 -0.86246448 -0.86454088
## CTC:2 0.08984126 -0.14668611 -0.02051036 -0.15687014
## V:2 0.98846545 0.35225353 -0.98666525 -0.94086527
## CaMg:2 0.29780788 0.17904088 -0.37699908 -0.36945492
## CaK:2 0.43687673 -0.65622905 -0.32013815 -0.43267819
## MgK:2 0.38977401 -0.69524617 -0.26090151 -0.37278094
## Ca_:2 0.98643254 0.27758626 -0.97839260 -0.94062659
## Mg_:2 1.00000000 0.26289487 -0.97692208 -0.93489728
## K_:2 0.26289487 1.00000000 -0.37918592 -0.28553744
## H_:2 -0.97692208 -0.37918592 1.00000000 0.88477849
## m_:2 -0.93489728 -0.28553744 0.88477849 1.00000000
## S:2 -0.49381678 -0.32093216 0.50678577 0.52818259
## dp:2 -0.22028750 0.02693564 0.20049119 0.20269747
## S:2 dp:2
## rp:2 -0.136019901 -0.077541031
## dens:2 -0.338368045 0.093928421
## poro:2 0.112577580 -0.207847797
## clay:2 0.274991043 -0.093555852
## sand:2 -0.323627959 0.096115454
## pH:2 -0.535138273 -0.260003965
## pH_Ca:2 -0.494767837 -0.216947578
## P:2 -0.337676485 0.008123381
## K:2 -0.290727056 -0.050701049
## Ca_Mg:2 -0.409195258 -0.250665477
## Ca:2 -0.414104068 -0.249093626
## Mg:2 -0.392516211 -0.253295286
## Al:2 0.565284931 0.209631212
## MO:2 0.085039043 -0.102669004
## base:2 -0.417065252 -0.246210962
## CTC:2 0.096062841 -0.104403558
## V:2 -0.523743702 -0.211555647
## CaMg:2 -0.267951485 -0.089033397
## CaK:2 -0.044604632 -0.148344773
## MgK:2 0.003632438 -0.123281166
## Ca_:2 -0.512946663 -0.217959870
## Mg_:2 -0.493816780 -0.220287500
## K_:2 -0.320932159 0.026935643
## H_:2 0.506785774 0.200491189
## m_:2 0.528182589 0.202697471
## S:2 1.000000000 0.175412417
## dp:2 0.175412417 1.000000000
##
## [[3]]
## rp:3 dens:3 poro:3 clay:3
## rp:3 1.00000000 0.2162312397 0.034096182 0.11486770
## dens:3 0.21623124 1.0000000000 -0.415190409 -0.78388466
## poro:3 0.03409618 -0.4151904088 1.000000000 0.37667407
## clay:3 0.11486770 -0.7838846634 0.376674075 1.00000000
## sand:3 -0.11718744 0.7773112268 -0.408156424 -0.97901615
## pH:3 0.16108435 0.3002244786 -0.136891182 -0.30028704
## pH_Ca:3 0.15236198 0.2639166510 -0.137382820 -0.27143577
## P:3 -0.08214880 0.4777072709 -0.245596824 -0.62142559
## K:3 0.15992305 0.1220570677 0.006229290 -0.16133110
## Ca_Mg:3 0.13137591 0.0155875454 -0.004822741 -0.01997308
## Ca:3 0.13053595 0.0221418055 -0.021034186 -0.03310364
## Mg:3 0.13080898 -0.0008193063 0.035083148 0.01267053
## Al:3 -0.06493674 -0.2857433314 0.171333676 0.29571485
## MO:3 0.17051280 -0.3766384266 0.258831199 0.38830826
## base:3 0.14062706 0.0249160845 -0.002808683 -0.03327852
## CTC:3 0.15281223 -0.3726062825 0.245237914 0.37847121
## V:3 0.12307037 0.2672157578 -0.144994838 -0.27639097
## CaMg:3 0.02929475 0.1370589627 -0.229901055 -0.21269493
## CaK:3 -0.05199719 -0.1777057027 0.071118394 0.20890384
## MgK:3 -0.07155763 -0.1941025267 0.090563132 0.23350322
## Ca_:3 0.11678346 0.2521722872 -0.158218757 -0.26481088
## Mg_:3 0.11099413 0.2089649759 -0.089029686 -0.19496777
## K_:3 0.09680156 0.3013131859 -0.099269168 -0.34690665
## H_:3 -0.07691454 -0.3246490715 0.188389552 0.34625262
## m_:3 -0.13950125 -0.1748923382 0.069665578 0.16778760
## S:3 -0.01848788 -0.4855034443 0.337354670 0.51263250
## dp:3 0.12254127 0.2418224767 0.237863913 -0.19550692
## sand:3 pH:3 pH_Ca:3 P:3
## rp:3 -0.117187445 0.16108435 0.15236198 -0.08214880
## dens:3 0.777311227 0.30022448 0.26391665 0.47770727
## poro:3 -0.408156424 -0.13689118 -0.13738282 -0.24559682
## clay:3 -0.979016150 -0.30028704 -0.27143577 -0.62142559
## sand:3 1.000000000 0.30170394 0.26378344 0.59555278
## pH:3 0.301703940 1.00000000 0.96591501 0.45746144
## pH_Ca:3 0.263783445 0.96591501 1.00000000 0.43653683
## P:3 0.595552778 0.45746144 0.43653683 1.00000000
## K:3 0.190855678 0.26974777 0.30386148 0.28798576
## Ca_Mg:3 -0.012620837 0.78742828 0.82121468 0.34235252
## Ca:3 -0.001943839 0.78705743 0.82233728 0.35267303
## Mg:3 -0.038587012 0.77257809 0.80202089 0.31015675
## Al:3 -0.280780440 -0.91550881 -0.91439263 -0.41140975
## MO:3 -0.435049046 -0.12179518 -0.04658621 -0.06486049
## base:3 0.004032974 0.78892405 0.82491738 0.35776069
## CTC:3 -0.432238340 -0.08933942 -0.01279230 -0.04351064
## V:3 0.275183786 0.96910243 0.96490641 0.42668442
## CaMg:3 0.170494688 -0.04999618 -0.04580954 0.09743601
## CaK:3 -0.261440830 0.25780599 0.23845260 -0.15084274
## MgK:3 -0.278187379 0.23696640 0.21559722 -0.17040208
## Ca_:3 0.254437196 0.96552584 0.96230793 0.41323149
## Mg_:3 0.195809753 0.93025048 0.92145864 0.36226265
## K_:3 0.398914534 0.28762138 0.29115938 0.33073189
## H_:3 -0.362715007 -0.93336256 -0.91341402 -0.44409529
## m_:3 -0.149994727 -0.89033022 -0.89759981 -0.28539139
## S:3 -0.520144301 -0.39706604 -0.34098056 -0.43263603
## dp:3 0.178326708 0.13140727 0.12184858 0.18040210
## K:3 Ca_Mg:3 Ca:3 Mg:3
## rp:3 0.15992305 0.131375909 0.130535947 0.1308089768
## dens:3 0.12205707 0.015587545 0.022141806 -0.0008193063
## poro:3 0.00622929 -0.004822741 -0.021034186 0.0350831481
## clay:3 -0.16133110 -0.019973081 -0.033103643 0.0126705334
## sand:3 0.19085568 -0.012620837 -0.001943839 -0.0385870117
## pH:3 0.26974777 0.787428278 0.787057427 0.7725780913
## pH_Ca:3 0.30386148 0.821214684 0.822337277 0.8020208883
## P:3 0.28798576 0.342352522 0.352673029 0.3101567460
## K:3 1.00000000 0.269629522 0.281671202 0.2346627736
## Ca_Mg:3 0.26962952 1.000000000 0.997651273 0.9857519941
## Ca:3 0.28167120 0.997651273 1.000000000 0.9719150565
## Mg:3 0.23466277 0.985751994 0.971915056 1.0000000000
## Al:3 -0.29853365 -0.813565745 -0.811336033 -0.8027570782
## MO:3 0.15387591 0.417700486 0.416562757 0.4121337983
## base:3 0.34941168 0.996459003 0.995269839 0.9794344092
## CTC:3 0.13975340 0.452690124 0.450238784 0.4496488428
## V:3 0.28222258 0.829440301 0.825961680 0.8213807584
## CaMg:3 0.15267247 -0.130985006 -0.065856221 -0.2882956512
## CaK:3 -0.70918105 0.379247185 0.367409599 0.4007250844
## MgK:3 -0.71219417 0.359239930 0.337056420 0.4065240805
## Ca_:3 0.20485710 0.844065204 0.844746521 0.8254976518
## Mg_:3 0.14808482 0.825309170 0.807060236 0.8536027827
## K_:3 0.90513545 0.050719547 0.064140973 0.0167462689
## H_:3 -0.24512140 -0.703193607 -0.701873520 -0.6923604023
## m_:3 -0.28193685 -0.876702026 -0.867378685 -0.8820489983
## S:3 -0.19475817 -0.288115550 -0.279697932 -0.3030193195
## dp:3 0.10887464 0.023322380 0.030732703 0.0046585333
## Al:3 MO:3 base:3 CTC:3
## rp:3 -0.06493674 0.17051280 0.140627059 0.15281223
## dens:3 -0.28574333 -0.37663843 0.024916084 -0.37260628
## poro:3 0.17133368 0.25883120 -0.002808683 0.24523791
## clay:3 0.29571485 0.38830826 -0.033278520 0.37847121
## sand:3 -0.28078044 -0.43504905 0.004032974 -0.43223834
## pH:3 -0.91550881 -0.12179518 0.788924053 -0.08933942
## pH_Ca:3 -0.91439263 -0.04658621 0.824917383 -0.01279230
## P:3 -0.41140975 -0.06486049 0.357760688 -0.04351064
## K:3 -0.29853365 0.15387591 0.349411678 0.13975340
## Ca_Mg:3 -0.81356574 0.41770049 0.996459003 0.45269012
## Ca:3 -0.81133603 0.41656276 0.995269839 0.45023878
## Mg:3 -0.80275708 0.41213380 0.979434409 0.44964884
## Al:3 1.00000000 0.10701352 -0.816794969 0.07779649
## MO:3 0.10701352 1.00000000 0.420354521 0.98756965
## base:3 -0.81679497 0.42035452 1.000000000 0.45328698
## CTC:3 0.07779649 0.98756965 0.453286978 1.00000000
## V:3 -0.95211987 -0.11600955 0.830993894 -0.08040113
## CaMg:3 0.06845784 -0.07206170 -0.113713985 -0.09710425
## CaK:3 -0.27650094 0.10569528 0.307445517 0.14044262
## MgK:3 -0.26366690 0.10359984 0.287507300 0.13983732
## Ca_:3 -0.94415789 -0.09383450 0.838555166 -0.05672192
## Mg_:3 -0.91737216 -0.08492086 0.815220165 -0.04321425
## K_:3 -0.29952713 -0.24656294 0.127805109 -0.26643903
## H_:3 0.88726030 0.31263889 -0.705088585 0.27971378
## m_:3 0.95081776 -0.07061948 -0.877122817 -0.09974861
## S:3 0.41125041 0.13655473 -0.296341553 0.11554531
## dp:3 -0.06777781 -0.03969541 0.032135227 -0.05573005
## V:3 CaMg:3 CaK:3 MgK:3 Ca_:3
## rp:3 0.12307037 0.02929475 -0.05199719 -0.07155763 0.11678346
## dens:3 0.26721576 0.13705896 -0.17770570 -0.19410253 0.25217229
## poro:3 -0.14499484 -0.22990105 0.07111839 0.09056313 -0.15821876
## clay:3 -0.27639097 -0.21269493 0.20890384 0.23350322 -0.26481088
## sand:3 0.27518379 0.17049469 -0.26144083 -0.27818738 0.25443720
## pH:3 0.96910243 -0.04999618 0.25780599 0.23696640 0.96552584
## pH_Ca:3 0.96490641 -0.04580954 0.23845260 0.21559722 0.96230793
## P:3 0.42668442 0.09743601 -0.15084274 -0.17040208 0.41323149
## K:3 0.28222258 0.15267247 -0.70918105 -0.71219417 0.20485710
## Ca_Mg:3 0.82944030 -0.13098501 0.37924718 0.35923993 0.84406520
## Ca:3 0.82596168 -0.06585622 0.36740960 0.33705642 0.84474652
## Mg:3 0.82138076 -0.28829565 0.40072508 0.40652408 0.82549765
## Al:3 -0.95211987 0.06845784 -0.27650094 -0.26366690 -0.94415789
## MO:3 -0.11600955 -0.07206170 0.10569528 0.10359984 -0.09383450
## base:3 0.83099389 -0.11371398 0.30744552 0.28750730 0.83855517
## CTC:3 -0.08040113 -0.09710425 0.14044262 0.13983732 -0.05672192
## V:3 1.00000000 -0.10917298 0.27946552 0.26327680 0.99282241
## CaMg:3 -0.10917298 1.00000000 -0.20808391 -0.34700491 -0.05380487
## CaK:3 0.27946552 -0.20808391 1.00000000 0.98565927 0.35684072
## MgK:3 0.26327680 -0.34700491 0.98565927 1.00000000 0.32787037
## Ca_:3 0.99282241 -0.05380487 0.35684072 0.32787037 1.00000000
## Mg_:3 0.97022669 -0.31671472 0.39061555 0.40423973 0.96033412
## K_:3 0.28846471 0.20190593 -0.75398259 -0.75682760 0.20349833
## H_:3 -0.96564666 0.08141722 -0.21826540 -0.19898496 -0.95495683
## m_:3 -0.93894467 0.17405935 -0.35282146 -0.34779561 -0.93278631
## S:3 -0.42323988 0.10283260 0.02782960 0.01266145 -0.40001453
## dp:3 0.10251494 0.14702006 -0.11970405 -0.16267654 0.10065937
## Mg_:3 K_:3 H_:3 m_:3 S:3
## rp:3 0.11099413 0.09680156 -0.07691454 -0.13950125 -0.01848788
## dens:3 0.20896498 0.30131319 -0.32464907 -0.17489234 -0.48550344
## poro:3 -0.08902969 -0.09926917 0.18838955 0.06966558 0.33735467
## clay:3 -0.19496777 -0.34690665 0.34625262 0.16778760 0.51263250
## sand:3 0.19580975 0.39891453 -0.36271501 -0.14999473 -0.52014430
## pH:3 0.93025048 0.28762138 -0.93336256 -0.89033022 -0.39706604
## pH_Ca:3 0.92145864 0.29115938 -0.91341402 -0.89759981 -0.34098056
## P:3 0.36226265 0.33073189 -0.44409529 -0.28539139 -0.43263603
## K:3 0.14808482 0.90513545 -0.24512140 -0.28193685 -0.19475817
## Ca_Mg:3 0.82530917 0.05071955 -0.70319361 -0.87670203 -0.28811555
## Ca:3 0.80706024 0.06414097 -0.70187352 -0.86737868 -0.27969793
## Mg:3 0.85360278 0.01674627 -0.69236040 -0.88204900 -0.30301932
## Al:3 -0.91737216 -0.29952713 0.88726030 0.95081776 0.41125041
## MO:3 -0.08492086 -0.24656294 0.31263889 -0.07061948 0.13655473
## base:3 0.81522017 0.12780511 -0.70508858 -0.87712282 -0.29634155
## CTC:3 -0.04321425 -0.26643903 0.27971378 -0.09974861 0.11554531
## V:3 0.97022669 0.28846471 -0.96564666 -0.93894467 -0.42323988
## CaMg:3 -0.31671472 0.20190593 0.08141722 0.17405935 0.10283260
## CaK:3 0.39061555 -0.75398259 -0.21826540 -0.35282146 0.02782960
## MgK:3 0.40423973 -0.75682760 -0.19898496 -0.34779561 0.01266145
## Ca_:3 0.96033412 0.20349833 -0.95495683 -0.93278631 -0.40001453
## Mg_:3 1.00000000 0.13825731 -0.92607259 -0.93310835 -0.41272962
## K_:3 0.13825731 1.00000000 -0.33223314 -0.20716754 -0.24140090
## H_:3 -0.92607259 -0.33223314 1.00000000 0.83942734 0.42695095
## m_:3 -0.93310835 -0.20716754 0.83942734 1.00000000 0.40632807
## S:3 -0.41272962 -0.24140090 0.42695095 0.40632807 1.00000000
## dp:3 0.06040748 0.14262763 -0.10997783 -0.05702760 -0.05690559
## dp:3
## rp:3 0.122541266
## dens:3 0.241822477
## poro:3 0.237863913
## clay:3 -0.195506921
## sand:3 0.178326708
## pH:3 0.131407271
## pH_Ca:3 0.121848580
## P:3 0.180402104
## K:3 0.108874639
## Ca_Mg:3 0.023322380
## Ca:3 0.030732703
## Mg:3 0.004658533
## Al:3 -0.067777813
## MO:3 -0.039695406
## base:3 0.032135227
## CTC:3 -0.055730049
## V:3 0.102514944
## CaMg:3 0.147020063
## CaK:3 -0.119704046
## MgK:3 -0.162676539
## Ca_:3 0.100659366
## Mg_:3 0.060407480
## K_:3 0.142627628
## H_:3 -0.109977828
## m_:3 -0.057027596
## S:3 -0.056905590
## dp:3 1.000000000
layout(1)
#-----------------------------------------------------------------------
# Conjunto de variáveis criadas como função de outras.
# DANGER: VERIFICAR COM O MILSON PORQUE ESSAS VARIÁVEIS NÃO ESTÃO
# BATENDO COM O PREVISTO.
atrib[, list(Ca_Mg, Ca + Mg)] # OK.
## Ca_Mg V2
## 1: 5.5 5.5
## 2: NA NA
## 3: 2.1 2.1
## 4: NA NA
## 5: 1.1 1.1
## ---
## 386: NA NA
## 387: 3.7 3.7
## 388: NA NA
## 389: 2.1 2.1
## 390: NA NA
atrib[, list(CaMg, Ca/Mg)] # OK.
## CaMg V2
## 1: 2.67 2.666667
## 2: NA NA
## 3: 2.50 2.500000
## 4: NA NA
## 5: 2.67 2.666667
## ---
## 386: NA NA
## 387: 2.70 2.700000
## 388: NA NA
## 389: 2.50 2.500000
## 390: NA NA
atrib[, list(MgK, Mg/K)] # FAIL.
## MgK V2
## 1: 6.01 0.015416238
## 2: NA NA
## 3: 3.04 0.007802341
## 4: NA NA
## 5: 1.73 0.004431315
## ---
## 386: NA NA
## 387: 6.89 0.017667845
## 388: NA NA
## 389: 4.45 0.011406844
## 390: NA NA
atrib[, list(CaK, Ca/K)] # FAIL.
## CaK V2
## 1: 16.03 0.04110997
## 2: NA NA
## 3: 7.61 0.01950585
## 4: NA NA
## 5: 4.61 0.01181684
## ---
## 386: NA NA
## 387: 18.60 0.04770318
## 388: NA NA
## 389: 11.12 0.02851711
## 390: NA NA
atrib[, list(V, 100 * base/CTC)] # OK.
## V V2
## 1: 56.65 56.65025
## 2: NA NA
## 3: 30.24 30.26316
## 4: NA NA
## 5: 22.06 22.01040
## ---
## 386: NA NA
## 387: 60.60 60.62992
## 388: NA NA
## 389: 52.77 52.71868
## 390: NA NA
atrib[, list(Ca_, 100 * Ca/CTC)] # OK.
## Ca_ V2
## 1: 39.4 39.40887
## 2: NA NA
## 3: 19.7 19.73684
## 4: NA NA
## 5: 13.9 13.86482
## ---
## 386: NA NA
## 387: 42.6 42.51969
## 388: NA NA
## 389: 35.4 35.46099
## 390: NA NA
atrib[, list(Mg_, 100 * Mg/CTC)] # OK.
## Mg_ V2
## 1: 14.8 14.778325
## 2: NA NA
## 3: 7.9 7.894737
## 4: NA NA
## 5: 5.2 5.199307
## ---
## 386: NA NA
## 387: 15.8 15.748031
## 388: NA NA
## 389: 14.2 14.184397
## 390: NA NA
atrib[, list(K_, 100 * K/CTC)] # FAIL.
## K_ V2
## 1: 2.5 958.6207
## 2: NA NA
## 3: 2.6 1011.8421
## 4: NA NA
## 5: 3.0 1173.3102
## ---
## 386: NA NA
## 387: 2.3 891.3386
## 388: NA NA
## 389: 3.2 1243.4988
## 390: NA NA
atrib[, list(m_, 100 * Al/CTC)] # FAIL. (o denominador é com CTC efetiva e não essa CTC é que é pH 7).
## m_ V2
## 1: 0.0 0.000000
## 2: NA NA
## 3: 14.8 5.263158
## 4: NA NA
## 5: 28.2 8.665511
## ---
## 386: NA NA
## 387: 0.0 0.000000
## 388: NA NA
## 389: 0.0 0.000000
## 390: NA NA
# ATTENTION: a suspeita é que o problema está no K.
#-----------------------------------------------------------------------
# Remover as variáveis sintetizadas a partir das outras.
keep <- c("prod", "glic", "phos", "sulf", "LFF", "LFO", "HF", "pH",
"pH_Ca", "P", "K", "Ca", "Mg", "Al", "MO", "CTC", "V", "S",
"dp", "rp", "dens", "poro", "clay", "sand")
i <- sapply(sprintf("^%s:", keep),
FUN = grep,
x = names(atrib3))
i <- unlist(i, use.names = FALSE)
i
## [1] 3 4 5 6 7 8 9 15 40 67 16 41 68 17 42 69 18 43 70 20 45
## [22] 72 21 46 73 47 74 22 48 75 24 50 77 25 51 78 33 60 87 34 61 88
## [43] 10 35 62 11 36 63 12 37 64 13 38 65 14 39 66
# Seleciona as variáveis "orgânicas" ou genuínas (sintaxe estranha).
atrib4 <- atrib3[, .SD, .SDcols = c(1:2, i)]
dim(atrib4)
## [1] 65 59
names(atrib4) <- sub(":", "", names(atrib4))
names(atrib4)
## [1] "faz" "tal" "prod1" "glic1" "phos1" "sulf1" "LFF1"
## [8] "LFO1" "HF1" "pH1" "pH2" "pH3" "pH_Ca1" "pH_Ca2"
## [15] "pH_Ca3" "P1" "P2" "P3" "K1" "K2" "K3"
## [22] "Ca1" "Ca2" "Ca3" "Mg1" "Mg2" "Mg3" "Al2"
## [29] "Al3" "MO1" "MO2" "MO3" "CTC1" "CTC2" "CTC3"
## [36] "V1" "V2" "V3" "S1" "S2" "S3" "dp1"
## [43] "dp2" "dp3" "rp1" "rp2" "rp3" "dens1" "dens2"
## [50] "dens3" "poro1" "poro2" "poro3" "clay1" "clay2" "clay3"
## [57] "sand1" "sand2" "sand3"
#-----------------------------------------------------------------------
# Regressão múltipla.
m0 <- lm(prod1 ~ .,
data = subset(atrib4, select = -c(faz, tal)))
par(mfrow = c(2, 2))
plot(m0)
layout(1)
# Nada é significativo.
summary(m0)$coefficients
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -7.4884472574 51.844416972 -0.14444077 0.8943101
## glic1 0.0058897319 0.010164954 0.57941548 0.6029525
## phos1 0.0021400819 0.001816190 1.17833602 0.3236182
## sulf1 0.0046234169 0.009640972 0.47955919 0.6643312
## LFF1 0.1150339231 0.192080456 0.59888406 0.5914554
## LFO1 0.0488475102 0.172933896 0.28246348 0.7959552
## HF1 0.0405048404 0.161108576 0.25141331 0.8177325
## pH1 1.3822175207 3.773529100 0.36629306 0.7384544
## pH2 1.0310966276 1.609885194 0.64047836 0.5674255
## pH3 2.5179549277 3.284400152 0.76664073 0.4991007
## pH_Ca1 3.3195870650 3.637733371 0.91254271 0.4287683
## pH_Ca2 8.2017755672 5.043584937 1.62617973 0.2023855
## pH_Ca3 2.5835290024 3.517480073 0.73448291 0.5158564
## P1 0.0201393204 0.032279613 0.62390216 0.5769141
## P2 -0.0231520974 0.052807795 -0.43842197 0.6907317
## P3 -0.3570041174 0.327436666 -1.09029976 0.3553224
## K1 0.0317585141 0.017352278 1.83022163 0.1646334
## K2 -0.0420614071 0.021968019 -1.91466543 0.1514295
## K3 0.0842388671 0.046202628 1.82324841 0.1657823
## Ca1 2.9034322271 6.014395493 0.48274714 0.6623115
## Ca2 -4.9679922270 3.655887447 -1.35890185 0.2673194
## Ca3 -0.5569436594 3.968856871 -0.14032848 0.8972926
## Mg1 16.3392847467 8.200917929 1.99237267 0.1403603
## Mg2 5.5012644829 7.048301369 0.78050926 0.4920147
## Mg3 26.7728023921 15.568839774 1.71964018 0.1839873
## Al2 4.8738497998 5.635084316 0.86491160 0.4507091
## Al3 0.3571095741 4.760095554 0.07502151 0.9449202
## MO2 -0.3826211262 0.326478119 -1.17196560 0.3258142
## MO3 0.2972693334 0.193150961 1.53905179 0.2214164
## CTC1 -4.2477673060 3.722639610 -1.14106326 0.3366812
## CTC2 2.7028444550 1.737232826 1.55583317 0.2176013
## CTC3 -3.7524911391 1.792184740 -2.09380822 0.1273139
## V1 -0.7790318012 0.461230488 -1.68902929 0.1897961
## V2 0.0091100794 0.158528249 0.05746660 0.9577870
## V3 -0.5430038584 0.302699096 -1.79387341 0.1707246
## S1 0.0455134665 0.048331688 0.94168998 0.4158227
## S2 -0.0554279620 0.027242781 -2.03459263 0.1347463
## S3 0.0053522061 0.014162779 0.37790649 0.7306540
## dp1 -4.4525190830 2.820555250 -1.57859665 0.2125423
## dp2 2.4473919671 1.914589851 1.27828525 0.2910780
## dp3 0.3442945271 1.943944351 0.17711131 0.8707037
## rp1 -0.3665261428 0.315924720 -1.16016924 0.3299202
## rp2 -1.0720389477 0.675509615 -1.58700768 0.2107062
## rp3 -0.7830094166 0.618159588 -1.26667843 0.2946769
## dens1 -2.3641113884 1.799072960 -1.31407199 0.2802678
## dens2 -0.9016881629 2.181397667 -0.41335341 0.7071180
## dens3 4.2165829270 4.319731978 0.97612142 0.4009943
## poro1 3.0339641142 4.189274752 0.72422180 0.5212983
## poro2 -1.5533824213 1.564947840 -0.99260971 0.3940694
## poro3 -6.8664205227 4.448964183 -1.54337510 0.2204265
## clay1 0.0006833161 0.007210263 0.09476993 0.9304728
## clay2 -0.0112805832 0.009598776 -1.17521063 0.3246937
## clay3 -0.0076787936 0.008064316 -0.95219410 0.4112459
## sand1 -0.0035562612 0.011220941 -0.31693075 0.7720710
## sand2 -0.0184661724 0.021182716 -0.87175659 0.4474957
## sand3 0.0047512564 0.014656888 0.32416543 0.7670992
drop1(m0, test = "F")
## Single term deletions
##
## Model:
## prod1 ~ glic1 + phos1 + sulf1 + LFF1 + LFO1 + HF1 + pH1 + pH2 +
## pH3 + pH_Ca1 + pH_Ca2 + pH_Ca3 + P1 + P2 + P3 + K1 + K2 +
## K3 + Ca1 + Ca2 + Ca3 + Mg1 + Mg2 + Mg3 + Al2 + Al3 + MO1 +
## MO2 + MO3 + CTC1 + CTC2 + CTC3 + V1 + V2 + V3 + S1 + S2 +
## S3 + dp1 + dp2 + dp3 + rp1 + rp2 + rp3 + dens1 + dens2 +
## dens3 + poro1 + poro2 + poro3 + clay1 + clay2 + clay3 + sand1 +
## sand2 + sand3
## Df Sum of Sq RSS AIC F value Pr(>F)
## <none> 0.35539 -189.61
## glic1 1 0.03977 0.39516 -185.35 0.3357 0.6030
## phos1 1 0.16448 0.51988 -169.17 1.3885 0.3236
## sulf1 1 0.02724 0.38264 -187.25 0.2300 0.6643
## LFF1 0 0.00000 0.35539 -189.61
## LFO1 0 0.00000 0.35539 -189.61
## HF1 0 0.00000 0.35539 -189.61
## pH1 1 0.01589 0.37129 -189.03 0.1342 0.7385
## pH2 1 0.04860 0.40399 -184.05 0.4102 0.5674
## pH3 1 0.06963 0.42502 -181.06 0.5877 0.4991
## pH_Ca1 1 0.09865 0.45404 -177.16 0.8327 0.4288
## pH_Ca2 1 0.31327 0.66867 -154.32 2.6445 0.2024
## pH_Ca3 1 0.06391 0.41930 -181.86 0.5395 0.5159
## P1 1 0.04611 0.40151 -184.41 0.3893 0.5769
## P2 1 0.02277 0.37816 -187.95 0.1922 0.6907
## P3 1 0.14082 0.49622 -171.92 1.1888 0.3553
## K1 1 0.39682 0.75221 -147.37 3.3497 0.1646
## K2 1 0.43428 0.78968 -144.51 3.6659 0.1514
## K3 1 0.39380 0.74920 -147.61 3.3242 0.1658
## Ca1 1 0.02761 0.38300 -187.20 0.2330 0.6623
## Ca2 1 0.21876 0.57415 -163.31 1.8466 0.2673
## Ca3 1 0.00233 0.35773 -191.23 0.0197 0.8973
## Mg1 1 0.47025 0.82564 -141.88 3.9695 0.1404
## Mg2 1 0.07217 0.42756 -180.71 0.6092 0.4920
## Mg3 1 0.35032 0.70571 -151.14 2.9572 0.1840
## Al2 1 0.08862 0.44401 -178.48 0.7481 0.4507
## Al3 1 0.00067 0.35606 -191.50 0.0056 0.9449
## MO1 0 0.00000 0.35539 -189.61
## MO2 1 0.16271 0.51810 -169.37 1.3735 0.3258
## MO3 1 0.28060 0.63600 -157.28 2.3687 0.2214
## CTC1 1 0.15424 0.50964 -170.34 1.3020 0.3367
## CTC2 1 0.28676 0.64215 -156.71 2.4206 0.2176
## CTC3 1 0.51935 0.87474 -138.47 4.3840 0.1273
## V1 1 0.33796 0.69335 -152.18 2.8528 0.1898
## V2 1 0.00039 0.35578 -191.55 0.0033 0.9578
## V3 1 0.38122 0.73661 -148.61 3.2180 0.1707
## S1 1 0.10505 0.46044 -176.33 0.8868 0.4158
## S2 1 0.49039 0.84578 -140.46 4.1396 0.1347
## S3 1 0.01692 0.37231 -188.87 0.1428 0.7307
## dp1 1 0.29521 0.65060 -155.94 2.4920 0.2125
## dp2 1 0.19357 0.54896 -165.96 1.6340 0.2911
## dp3 1 0.00372 0.35911 -191.00 0.0314 0.8707
## rp1 1 0.15945 0.51484 -169.74 1.3460 0.3299
## rp2 1 0.29836 0.65376 -155.65 2.5186 0.2107
## rp3 1 0.19007 0.54547 -166.34 1.6045 0.2947
## dens1 1 0.20456 0.55995 -164.79 1.7268 0.2803
## dens2 1 0.02024 0.37563 -188.34 0.1709 0.7071
## dens3 1 0.11287 0.46827 -175.34 0.9528 0.4010
## poro1 1 0.06213 0.41753 -182.11 0.5245 0.5213
## poro2 1 0.11672 0.47211 -174.86 0.9853 0.3941
## poro3 1 0.28218 0.63758 -157.13 2.3820 0.2204
## clay1 1 0.00106 0.35646 -191.44 0.0090 0.9305
## clay2 1 0.16361 0.51901 -169.27 1.3811 0.3247
## clay3 1 0.10741 0.46280 -176.03 0.9067 0.4112
## sand1 1 0.01190 0.36729 -189.67 0.1004 0.7721
## sand2 1 0.09003 0.44542 -178.29 0.7600 0.4475
## sand3 1 0.01245 0.36784 -189.58 0.1051 0.7671
# Modelo nulo.
m00 <- update(m0, formula = . ~ 1, data = model.frame(m0))
# Razão entre modelos encaixados.
anova(m00, m0)
## Analysis of Variance Table
##
## Model 1: prod1 ~ 1
## Model 2: prod1 ~ glic1 + phos1 + sulf1 + LFF1 + LFO1 + HF1 + pH1 + pH2 +
## pH3 + pH_Ca1 + pH_Ca2 + pH_Ca3 + P1 + P2 + P3 + K1 + K2 +
## K3 + Ca1 + Ca2 + Ca3 + Mg1 + Mg2 + Mg3 + Al2 + Al3 + MO1 +
## MO2 + MO3 + CTC1 + CTC2 + CTC3 + V1 + V2 + V3 + S1 + S2 +
## S3 + dp1 + dp2 + dp3 + rp1 + rp2 + rp3 + dens1 + dens2 +
## dens3 + poro1 + poro2 + poro3 + clay1 + clay2 + clay3 + sand1 +
## sand2 + sand3
## Res.Df RSS Df Sum of Sq F Pr(>F)
## 1 58 7.4221
## 2 3 0.3554 55 7.0667 1.0846 0.5637
# ATTENTION: Isso não é um bom sinal.
#-----------------------------------------------------------------------
# Stepwise.
m1 <- step(m0,
direction = "both",
trace = FALSE,
k = log(nrow(atrib4)))
c(antes = length(coef(m0)), depois = length(coef(m1)))
## antes depois
## 57 50
# Razão entre modelos encaixados.
anova(m00, m1)
## Analysis of Variance Table
##
## Model 1: prod1 ~ 1
## Model 2: prod1 ~ glic1 + phos1 + sulf1 + LFF1 + LFO1 + HF1 + pH1 + pH2 +
## pH3 + pH_Ca1 + pH_Ca2 + pH_Ca3 + P1 + P2 + P3 + K1 + K2 +
## K3 + Ca1 + Ca2 + Ca3 + Mg1 + Mg2 + Mg3 + Al2 + MO2 + MO3 +
## CTC1 + CTC2 + CTC3 + V1 + V3 + S1 + S2 + S3 + dp1 + dp2 +
## rp1 + rp2 + rp3 + dens1 + dens3 + poro1 + poro2 + poro3 +
## clay2 + clay3 + sand1 + sand2
## Res.Df RSS Df Sum of Sq F Pr(>F)
## 1 58 7.4221
## 2 9 0.3844 49 7.0378 3.3632 0.02787 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
# ATTENTION: Um pouco melhor.
#-----------------------------------------------------------------------
# Least Absolute Shrinkage and Selection Operator (LASSO). Usa norma
# L1 que a penalização pela soma do valor absoluto dos coeficientes.
X <- model.matrix(m0)
y <- model.response(model.frame(m0))
str(X)
## num [1:59, 1:57] 1 1 1 1 1 1 1 1 1 1 ...
## - attr(*, "dimnames")=List of 2
## ..$ : chr [1:59] "1" "2" "3" "4" ...
## ..$ : chr [1:57] "(Intercept)" "glic1" "phos1" "sulf1" ...
## - attr(*, "assign")= int [1:57] 0 1 2 3 4 5 6 7 8 9 ...
# library(lars)
# l0 <- lars(x = X, y = y, type = "lasso")
#
# methods(class = class(l0))
#
# coef(l0)
# summary(l0)
# plot(l0)
library(glmnet)
lambda <- exp(seq(10, -12, length = 100))
#--------------------------------------------
# Regressão Ridge.
l2 <- glmnet(x = X[, -1],
y = y,
alpha = 0,
lambda = lambda)
cv_l2 <- cv.glmnet(x = X[, -1],
y = y,
alpha = 0)
plot(cv_l2)
abline(v = log(cv_l2$lambda.min), col = "green")
round(cbind(OLS = coef(m0),
L2 = predict(l2,
s = cv_l2$lambda.min,
type = "coefficients")),
digits = 4)
## 57 x 2 sparse Matrix of class "dgCMatrix"
## OLS 1
## (Intercept) -7.4884 3.6691
## glic1 0.0059 0.0006
## phos1 0.0021 0.0000
## sulf1 0.0046 0.0000
## LFF1 0.1150 -0.0013
## LFO1 0.0488 -0.0003
## HF1 0.0405 0.0005
## pH1 1.3822 0.0098
## pH2 1.0311 0.0168
## pH3 2.5180 0.0334
## pH_Ca1 3.3196 0.0091
## pH_Ca2 8.2018 0.0223
## pH_Ca3 2.5835 0.0370
## P1 0.0201 -0.0006
## P2 -0.0232 0.0001
## P3 -0.3570 -0.0034
## K1 0.0318 0.0004
## K2 -0.0421 0.0000
## K3 0.0842 0.0001
## Ca1 2.9034 -0.0040
## Ca2 -4.9680 0.0094
## Ca3 -0.5569 0.0140
## Mg1 16.3393 -0.0226
## Mg2 5.5013 0.0198
## Mg3 26.7728 0.0374
## Al2 4.8738 -0.0376
## Al3 0.3571 -0.0649
## MO1 NA -0.0001
## MO2 -0.3826 0.0005
## MO3 0.2973 -0.0009
## CTC1 -4.2478 -0.0021
## CTC2 2.7028 -0.0002
## CTC3 -3.7525 -0.0075
## V1 -0.7790 0.0002
## V2 0.0091 0.0008
## V3 -0.5430 0.0013
## S1 0.0455 -0.0015
## S2 -0.0554 -0.0007
## S3 0.0054 0.0002
## dp1 -4.4525 -0.1372
## dp2 2.4474 0.1408
## dp3 0.3443 -0.0036
## rp1 -0.3665 -0.0281
## rp2 -1.0720 0.0044
## rp3 -0.7830 -0.0056
## dens1 -2.3641 -0.0936
## dens2 -0.9017 0.0040
## dens3 4.2166 0.0124
## poro1 3.0340 0.1406
## poro2 -1.5534 -0.0207
## poro3 -6.8664 -0.1837
## clay1 0.0007 0.0000
## clay2 -0.0113 0.0000
## clay3 -0.0077 0.0000
## sand1 -0.0036 0.0000
## sand2 -0.0185 0.0000
## sand3 0.0048 0.0000
#--------------------------------------------
# Regressão LASSO.
l1 <- glmnet(x = X[, -1],
y = y,
alpha = 1,
lambda = lambda)
cv_l1 <- cv.glmnet(x = X[, -1],
y = y,
alpha = 1)
plot(cv_l1)
abline(v = log(cv_l1$lambda.min), col = "green")
round(cbind(OLS = coef(m0),
L1 = predict(l1,
s = cv_l1$lambda.min,
type = "coefficients")),
digits = 4)
## 57 x 2 sparse Matrix of class "dgCMatrix"
## OLS 1
## (Intercept) -7.4884 5.1688
## glic1 0.0059 0.0013
## phos1 0.0021 .
## sulf1 0.0046 .
## LFF1 0.1150 .
## LFO1 0.0488 .
## HF1 0.0405 .
## pH1 1.3822 .
## pH2 1.0311 .
## pH3 2.5180 .
## pH_Ca1 3.3196 .
## pH_Ca2 8.2018 .
## pH_Ca3 2.5835 .
## P1 0.0201 -0.0010
## P2 -0.0232 .
## P3 -0.3570 .
## K1 0.0318 0.0018
## K2 -0.0421 .
## K3 0.0842 .
## Ca1 2.9034 .
## Ca2 -4.9680 .
## Ca3 -0.5569 .
## Mg1 16.3393 .
## Mg2 5.5013 .
## Mg3 26.7728 .
## Al2 4.8738 -0.1212
## Al3 0.3571 -0.0776
## MO1 NA .
## MO2 -0.3826 .
## MO3 0.2973 .
## CTC1 -4.2478 .
## CTC2 2.7028 .
## CTC3 -3.7525 -0.0002
## V1 -0.7790 .
## V2 0.0091 .
## V3 -0.5430 0.0029
## S1 0.0455 -0.0008
## S2 -0.0554 .
## S3 0.0054 .
## dp1 -4.4525 -0.2900
## dp2 2.4474 .
## dp3 0.3443 .
## rp1 -0.3665 -0.1217
## rp2 -1.0720 .
## rp3 -0.7830 .
## dens1 -2.3641 .
## dens2 -0.9017 .
## dens3 4.2166 .
## poro1 3.0340 .
## poro2 -1.5534 .
## poro3 -6.8664 -0.5643
## clay1 0.0007 .
## clay2 -0.0113 .
## clay3 -0.0077 .
## sand1 -0.0036 .
## sand2 -0.0185 .
## sand3 0.0048 .
# Correlação entre valores observados e preditos.
cor(cbind(obs = y,
ols = fitted(m0),
l1 = predict(l1,
s = cv_l1$lambda.min,
newx = X[, -1],
type = "response"),
l2 = predict(l2,
s = cv_l2$lambda.min,
newx = X[, -1],
type = "response")))
## obs ols 1 1
## obs 1.0000000 0.9757648 0.6639294 0.6165197
## ols 0.9757648 1.0000000 0.6804194 0.6318322
## 1 0.6639294 0.6804194 1.0000000 0.8711226
## 1 0.6165197 0.6318322 0.8711226 1.0000000
#-----------------------------------------------------------------------
# Árvore de regressão.
library(rpart)
library(rpart.plot)
t0 <- rpart(prod1 ~ ., data = model.frame(m0))
# summary(t1)
t0
## n= 59
##
## node), split, n, deviance, yval
## * denotes terminal node
##
## 1) root 59 7.4221060 4.128220
## 2) pH_Ca3< 4.55 52 5.6315720 4.075365
## 4) rp1>=1.31 28 2.7845230 3.963214
## 8) P1>=30.9 11 1.4038800 3.774818 *
## 9) P1< 30.9 17 0.7375918 4.085118 *
## 5) rp1< 1.31 24 2.0839920 4.206208
## 10) glic1< 48.1 15 0.8447153 4.076667 *
## 11) glic1>=48.1 9 0.5680349 4.422111 *
## 3) pH_Ca3>=4.55 7 0.5661189 4.520857 *
# Usa `minsplit` como tamanho mínimo para permitir a partição.
t1 <- rpart(prod1 ~ ., data = model.frame(m0),
control = rpart.control(minsplit = 7, cp = 0.001))
# summary(t1)
t1
## n= 59
##
## node), split, n, deviance, yval
## * denotes terminal node
##
## 1) root 59 7.4221060000 4.128220
## 2) V3< 31.75 53 5.6331920000 4.076132
## 4) rp1>=3.2325 2 0.0808020000 3.471000 *
## 5) rp1< 3.2325 51 4.7913000000 4.099863
## 10) V1< 48.17 11 1.3189950000 3.851545
## 20) LFO1< 4.315 6 0.2344413000 3.597667 *
## 21) LFO1>=4.315 5 0.2337548000 4.156200 *
## 11) V1>=48.17 40 2.6075030000 4.168150
## 22) rp2>=2.745 4 0.0503760000 3.782000 *
## 23) rp2< 2.745 36 1.8944080000 4.211056
## 46) rp1>=1.585 14 0.3251877000 4.071143
## 92) phos1< 192.9 3 0.0367280000 3.860000 *
## 93) phos1>=192.9 11 0.1182402000 4.128727
## 186) clay3< 749.5 8 0.0637615000 4.085750
## 372) LFF1>=13.8 6 0.0147035000 4.047500 *
## 373) LFF1< 13.8 2 0.0139445000 4.200500 *
## 187) clay3>=749.5 3 0.0002986667 4.243333 *
## 47) rp1< 1.585 22 1.1207620000 4.300091
## 94) dp2< 2.685 11 0.1947309000 4.166909
## 188) LFF1>=11.48 9 0.0495288900 4.114889
## 376) P1>=27.55 2 0.0087120000 3.996000 *
## 377) P1< 27.55 7 0.0044708570 4.148857 *
## 189) LFF1< 11.48 2 0.0112500000 4.401000 *
## 95) dp2>=2.685 11 0.5358082000 4.433273
## 190) poro1< 0.5825 9 0.1728816000 4.357778
## 380) HF1< 14.055 2 0.0006480000 4.170000 *
## 381) HF1>=14.055 7 0.0815637100 4.411429
## 762) HF1>=20.425 5 0.0256828000 4.357200 *
## 763) HF1< 20.425 2 0.0044180000 4.547000 *
## 191) poro1>=0.5825 2 0.0808020000 4.773000 *
## 3) V3>=31.75 6 0.3748913000 4.588333 *
# Visualização da árvore de regressão.
rpart.plot(t0)
rpart.plot(t1)
# Variáveis preditoras.
spl <- t0$splits[t0$splits[, "count"] > 0, ]
prd <- unique(rownames(spl)[seq(1, nrow(spl), by = 5)])
prd
## [1] "pH_Ca3" "rp1" "P1" "glic1"
# # Apenas teste.
# t2 <- rpart(prod1 ~ ., data = model.frame(m0)[, c("prod1", prd)])
# rpart.plot(t2)
# sum(residuals(t0)^2)
# sum(residuals(t2)^2)
# str(t0)
# t1$frame
# str(summary(t1))
plot(CP ~ nsplit, data = t1$cptable, type = "o")
abline(h = 0.025)
t2 <- prune(t1, cp = 0.025)
rpart.plot(t2)
# Variáveis preditoras.
spl <- t2$splits[t2$splits[, "count"] > 0, ]
prd <- unique(rownames(spl)[seq(1, nrow(spl), by = 5)])
prd
## [1] "V3" "rp1" "V1" "LFO1" "rp2" "dp2" "poro1"
cor(cbind(obs = y,
m00 = fitted(m00),
m0 = fitted(m0),
t0 = predict(t0),
t1 = predict(t1),
t2 = predict(t2)))[1, ]
## obs m00 m0 t0 t1
## 1.00000000 -0.01088224 0.97576484 0.66697498 0.91736834
## t2
## 0.87435986
#-----------------------------------------------------------------------
# Partial Leasts Squares.
# QUESTION: é necessário padronizar as covariáveis para normal padrão?
library(pls)
ncol(atrib4)
## [1] 59
p0 <- plsr(prod1 ~ .,
ncomp = 40,
# data = scale(model.frame(m0)),
data = model.frame(m0),
validation = c("LOO", "CV", "none")[2])
summary(p0)
## Data: X dimension: 59 56
## Y dimension: 59 1
## Fit method: kernelpls
## Number of components considered: 40
##
## VALIDATION: RMSEP
## Cross-validated using 10 random segments.
## (Intercept) 1 comps 2 comps 3 comps 4 comps 5 comps
## CV 0.3608 0.3577 0.3674 0.3500 0.3649 0.3780
## adjCV 0.3608 0.3575 0.3654 0.3489 0.3621 0.3738
## 6 comps 7 comps 8 comps 9 comps 10 comps 11 comps
## CV 0.3915 0.4123 0.4233 0.4366 0.4609 0.4767
## adjCV 0.3864 0.4058 0.4163 0.4285 0.4510 0.4660
## 12 comps 13 comps 14 comps 15 comps 16 comps 17 comps
## CV 0.4877 0.5113 0.5211 0.5356 0.5362 0.5632
## adjCV 0.4762 0.4982 0.5074 0.5205 0.5201 0.5441
## 18 comps 19 comps 20 comps 21 comps 22 comps 23 comps
## CV 0.5691 0.5495 0.5343 0.5158 0.5143 0.5154
## adjCV 0.5490 0.5314 0.5177 0.5011 0.4998 0.5000
## 24 comps 25 comps 26 comps 27 comps 28 comps 29 comps
## CV 0.5334 0.5384 0.5327 0.5347 0.5419 0.5547
## adjCV 0.5165 0.5206 0.5168 0.5190 0.5250 0.5362
## 30 comps 31 comps 32 comps 33 comps 34 comps 35 comps
## CV 0.5847 0.6583 0.7081 0.7419 0.7943 0.8397
## adjCV 0.5639 0.6333 0.6785 0.7098 0.7582 0.8010
## 36 comps 37 comps 38 comps 39 comps 40 comps
## CV 0.8873 0.9417 1.0133 1.078 1.128
## adjCV 0.8464 0.8978 0.9655 1.026 1.073
##
## TRAINING: % variance explained
## 1 comps 2 comps 3 comps 4 comps 5 comps 6 comps
## X 86.955 92.70 96.65 97.28 97.8 98.30
## prod1 1.767 11.23 19.75 26.96 30.3 31.77
## 7 comps 8 comps 9 comps 10 comps 11 comps 12 comps
## X 98.59 99.02 99.13 99.27 99.46 99.59
## prod1 33.68 34.39 35.56 36.14 36.51 37.22
## 13 comps 14 comps 15 comps 16 comps 17 comps 18 comps
## X 99.72 99.78 99.83 99.87 99.89 99.90
## prod1 37.81 38.86 41.03 43.44 47.33 50.95
## 19 comps 20 comps 21 comps 22 comps 23 comps 24 comps
## X 99.92 99.93 99.95 99.97 99.97 99.99
## prod1 51.81 52.72 53.00 53.14 54.32 55.06
## 25 comps 26 comps 27 comps 28 comps 29 comps 30 comps
## X 99.99 99.99 100.00 100.00 100.00 100.00
## prod1 56.60 56.98 57.28 61.41 66.08 69.29
## 31 comps 32 comps 33 comps 34 comps 35 comps 36 comps
## X 100.00 100.00 100.00 100.00 100.00 100.00
## prod1 72.19 78.46 81.69 84.77 86.09 86.66
## 37 comps 38 comps 39 comps 40 comps
## X 100.00 100.00 100.0 100.00
## prod1 87.44 88.14 89.5 89.75
# Proporção explicada da variância.
par(mfrow = c(1, 2))
plot(explvar(p0), type = "o")
plot(explvar(p0), log = "y", type = "o")
layout(1)
# Gráfico da Root Mean Square Error of Prediction.
plot(RMSEP(p0))
# Gráficos dos scores.
plot(scores(p0))
plot(p0, plottype = "scores", comps = 1:4)
scoreplot(p0, comps = 1:4)
# Carregamentos.
loadings(p0)
##
## Loadings:
## Comp 1 Comp 2 Comp 3 Comp 4 Comp 5 Comp 6 Comp 7 Comp 8
## glic1 0.215 0.635 -0.201 -0.170 -0.382 0.316
## phos1 -1.284 0.986 -0.167
## sulf1 0.118 0.209 -0.731 -0.206 0.208 0.405
## LFF1
## LFO1
## HF1
## pH1
## pH2
## pH3
## pH_Ca1
## pH_Ca2
## pH_Ca3
## P1 -0.111 -0.342 0.136
## P2
## P3
## K1 0.372 0.167 -0.498 0.557 -0.257 0.392
## K2 0.172 0.163 -0.649 0.172 -0.367
## K3 0.112 -0.412 0.127 -0.248 0.189
## Ca1
## Ca2
## Ca3
## Mg1
## Mg2
## Mg3
## Al2
## Al3
## MO1
## MO2
## MO3
## CTC1
## CTC2
## CTC3
## V1
## V2 0.106 0.125
## V3 0.140
## S1
## S2 -0.166
## S3 0.174 -0.224 -0.177
## dp1
## dp2
## dp3
## rp1
## rp2
## rp3
## dens1
## dens2
## dens3
## poro1
## poro2
## poro3
## clay1 -0.397 0.110 -0.162 -0.191 0.738 -0.818 0.677
## clay2 -0.408 0.426 -0.269 0.556 -0.242 -0.429
## clay3 -0.404 0.351 -0.134 -0.220 0.199 0.375 -0.330
## sand1 0.491 0.113 -0.350 0.377 0.155 -0.272
## sand2 0.483 -0.206 -0.131 -0.110 0.404 -0.243
## sand3 0.461 -0.132 -0.146 0.466 -0.518
## Comp 9 Comp 10 Comp 11 Comp 12 Comp 13 Comp 14 Comp 15
## glic1 -0.140 0.330 -0.253 -0.373 0.507 -0.243
## phos1
## sulf1 -0.161 -0.317 0.191 0.447 -0.376 0.107
## LFF1 -0.278
## LFO1
## HF1 -0.103 -0.131 -0.166 0.284
## pH1
## pH2
## pH3
## pH_Ca1
## pH_Ca2
## pH_Ca3
## P1 -0.285 0.471 0.420 -0.458 -0.239 0.701 -0.168
## P2 0.105 0.423 -0.147 -0.300
## P3
## K1 -0.363 -0.350 0.503 0.167 -0.198 0.101 -0.202
## K2 0.210 0.229 -0.436 0.253 -0.104
## K3 0.192 0.108 -0.409 0.109 -0.221
## Ca1
## Ca2
## Ca3
## Mg1
## Mg2
## Mg3
## Al2
## Al3
## MO1 -0.140
## MO2 0.131 0.297
## MO3 -0.167 0.187
## CTC1
## CTC2
## CTC3
## V1 -0.181 -0.274 -0.121 0.150 0.243
## V2 -0.117 0.254 -0.217 -0.197 0.505 0.341
## V3 0.234 -0.139 -0.122 -0.246 0.155
## S1 -0.106 0.179 0.125 0.204
## S2 0.252 -0.515 0.353 -0.210 0.150 -0.229
## S3 0.815 -0.785 0.588 -0.554 0.118
## dp1
## dp2
## dp3
## rp1
## rp2
## rp3
## dens1
## dens2
## dens3
## poro1
## poro2
## poro3
## clay1 -0.128 -0.143 -0.237 0.276 -0.264
## clay2 0.489 -0.118 -0.191 0.575 -0.444 0.398
## clay3 -0.139 0.545 -0.833 0.470 -0.767 0.485
## sand1 0.243 -0.192 0.146 -0.491 0.271 0.589 -0.868
## sand2 0.133 -0.209 0.263 -0.249 0.642
## sand3 0.126 0.279 -0.257 -0.719 0.545
## Comp 16 Comp 17 Comp 18 Comp 19 Comp 20 Comp 21 Comp 22
## glic1
## phos1
## sulf1 0.114 -0.114
## LFF1 0.393 -0.303 0.216 0.312 -0.378
## LFO1 0.236 -0.130 0.187 -0.173 -0.125
## HF1 -0.239 -0.418 0.681 -0.673 0.236
## pH1
## pH2
## pH3
## pH_Ca1
## pH_Ca2
## pH_Ca3
## P1 -0.328 0.196 -0.351
## P2 0.125 0.618 -0.174 -0.341 0.709
## P3
## K1
## K2 -0.151 0.207 -0.108 0.228 -0.186 0.176
## K3 0.192 -0.501 0.163 0.246 -0.432 0.307 -0.237
## Ca1
## Ca2
## Ca3
## Mg1
## Mg2
## Mg3
## Al2
## Al3
## MO1 -0.195 0.211 0.248 -0.270 0.334 -0.226 -0.267
## MO2 -0.123 0.216 -0.120 -0.304 0.264 -0.305 -0.717
## MO3 -0.172 0.221 -0.105 -0.377 0.806 -0.244
## CTC1
## CTC2 -0.130
## CTC3 0.134
## V1 0.192 0.374 -0.479 -0.117 0.300
## V2 -0.488 0.342 -0.161 -0.249 0.212
## V3 0.361 -0.308 0.214
## S1 -0.195 -0.164 -0.172 -0.112 0.525 -0.328
## S2 -0.340 0.773 -0.157 -0.720 0.527 -0.391
## S3 -0.367 0.248 -0.253 0.315
## dp1
## dp2
## dp3
## rp1
## rp2
## rp3
## dens1
## dens2
## dens3
## poro1
## poro2
## poro3
## clay1 0.195
## clay2 -0.285 0.170
## clay3 -0.141
## sand1 0.425 0.118 -0.103 -0.267
## sand2 -0.684 0.345 -0.179 0.324 0.105 -0.296 0.415
## sand3 0.121 -0.414 0.287 -0.286 -0.152 0.230 -0.160
## Comp 23 Comp 24 Comp 25 Comp 26 Comp 27 Comp 28 Comp 29
## glic1 0.257 -0.106
## phos1
## sulf1
## LFF1 -0.475 0.508 0.115 -0.153
## LFO1 0.297 0.324 -0.582 -1.010 0.526
## HF1 -0.171 0.115 0.388 -0.158
## pH1
## pH2 0.192
## pH3
## pH_Ca1
## pH_Ca2
## pH_Ca3
## P1 0.575 -0.116
## P2 -0.271 0.106 0.123 -0.233 0.102
## P3 0.424 0.135 -0.261 0.186
## K1 0.108
## K2 -0.841 0.439 -0.105 -0.176 0.437 -0.164
## K3 1.233 -0.659 0.140 0.298 -0.498 0.173
## Ca1 -0.172
## Ca2 -0.245
## Ca3 -0.196
## Mg1
## Mg2
## Mg3
## Al2 0.134
## Al3
## MO1 -0.123 -0.162 0.484 -0.507 0.215
## MO2 0.868 -0.144 0.584 -0.227
## MO3 0.928 -0.164 -0.282 -0.150 0.129
## CTC1 -0.104 -0.461
## CTC2 0.152 0.111 -0.232
## CTC3 0.153 -0.243
## V1 0.236 -0.253 0.182 0.311 -0.118
## V2 -0.805 0.476 -0.400 0.438 -0.926 0.307
## V3 -0.269 0.229 -0.460 1.298 -0.448
## S1 -0.531 0.671 -0.320 -0.137
## S2 0.565 -0.278 0.221
## S3 -0.295 -0.191
## dp1
## dp2
## dp3
## rp1 -0.221 0.259 -0.244
## rp2 -0.838
## rp3 -0.265 0.839
## dens1
## dens2
## dens3
## poro1
## poro2
## poro3
## clay1
## clay2 0.339 -0.203
## clay3 -0.224 0.109
## sand1
## sand2 0.422 -0.366 0.166 0.117
## sand3 -0.406 0.292 -0.145 -0.120
## Comp 30 Comp 31 Comp 32 Comp 33 Comp 34 Comp 35 Comp 36
## glic1
## phos1
## sulf1
## LFF1
## LFO1
## HF1
## pH1 0.200 -0.172 0.182
## pH2 -0.138 0.615 -0.626
## pH3 -0.117 -0.235 0.139
## pH_Ca1 -0.108
## pH_Ca2 0.138
## pH_Ca3 -0.132 0.245
## P1
## P2
## P3 -0.395 0.239
## K1
## K2
## K3
## Ca1 0.124 0.126 -0.274 0.215 0.135
## Ca2 -0.196 0.103 -0.153
## Ca3 -0.291 0.133 0.164 -0.271
## Mg1 -0.158
## Mg2 -0.111 -0.129
## Mg3 0.122
## Al2 -0.174
## Al3 -0.174
## MO1
## MO2 -0.133
## MO3 -0.140 0.110
## CTC1 0.227 0.378 -0.401 0.214 -0.192
## CTC2 0.636 -0.391 0.268 -0.372 0.717
## CTC3 -0.167 0.781 -0.268 -0.412 0.521 -0.606
## V1
## V2
## V3
## S1
## S2
## S3
## dp1 -0.203 0.401 -0.167
## dp2 0.243
## dp3 0.567 -0.275 0.264
## rp1 0.413 -0.210 0.108
## rp2 1.440 -0.706
## rp3 0.526 -0.516
## dens1 -0.207 0.451 -0.407 0.325
## dens2 0.178 -0.361 0.123 -0.103
## dens3 0.159 -0.309
## poro1 -0.223 0.426
## poro2 0.100 0.592 -0.423 -0.641
## poro3 -0.383 0.255
## clay1
## clay2
## clay3
## sand1
## sand2
## sand3
## Comp 37 Comp 38 Comp 39 Comp 40
## glic1
## phos1
## sulf1
## LFF1
## LFO1
## HF1
## pH1 0.626 -0.366 -0.124 0.390
## pH2 -0.384 0.573 -0.537 0.592
## pH3 0.160 0.211 -0.329
## pH_Ca1 0.534 -0.520 0.284
## pH_Ca2 0.195 -0.529 -0.241
## pH_Ca3 -0.138 0.204 -0.120 -0.127
## P1
## P2
## P3
## K1
## K2
## K3
## Ca1
## Ca2 0.404 -0.236 0.106
## Ca3 0.493 -0.250 0.108
## Mg1 0.326
## Mg2 0.219
## Mg3 0.192
## Al2 -0.136
## Al3 -0.103 0.129 -0.196
## MO1
## MO2 0.104
## MO3
## CTC1 -0.147 0.139 -0.157
## CTC2 -0.614 0.128
## CTC3 0.321
## V1
## V2
## V3
## S1
## S2
## S3
## dp1 -0.536 0.239 0.163
## dp2 -0.187 -0.222
## dp3 0.156 -0.188 0.299 -0.854
## rp1
## rp2
## rp3 0.184
## dens1 -0.598 0.591
## dens2 0.233 -0.103 0.302 -0.691
## dens3 -0.547
## poro1 -0.280 0.126 -0.114
## poro2 0.120 0.243 0.144
## poro3 0.124 -0.208 -0.125 0.142
## clay1
## clay2
## clay3
## sand1
## sand2
## sand3
##
## Comp 1 Comp 2 Comp 3 Comp 4 Comp 5 Comp 6 Comp 7
## SS loadings 1.185 2.262 1.108 1.406 1.305 1.794 1.714
## Proportion Var 0.021 0.040 0.020 0.025 0.023 0.032 0.031
## Cumulative Var 0.021 0.062 0.081 0.106 0.130 0.162 0.192
## Comp 8 Comp 9 Comp 10 Comp 11 Comp 12 Comp 13
## SS loadings 1.340 1.533 1.931 1.882 2.559 1.450
## Proportion Var 0.024 0.027 0.034 0.034 0.046 0.026
## Cumulative Var 0.216 0.244 0.278 0.312 0.357 0.383
## Comp 14 Comp 15 Comp 16 Comp 17 Comp 18 Comp 19
## SS loadings 2.861 2.342 1.461 2.683 1.230 1.437
## Proportion Var 0.051 0.042 0.026 0.048 0.022 0.026
## Cumulative Var 0.434 0.476 0.502 0.550 0.572 0.598
## Comp 20 Comp 21 Comp 22 Comp 23 Comp 24 Comp 25
## SS loadings 2.024 1.192 2.330 6.850 1.433 1.363
## Proportion Var 0.036 0.021 0.042 0.122 0.026 0.024
## Cumulative Var 0.634 0.655 0.697 0.819 0.845 0.869
## Comp 26 Comp 27 Comp 28 Comp 29 Comp 30 Comp 31
## SS loadings 1.286 5.138 1.070 2.080 2.888 1.099
## Proportion Var 0.023 0.092 0.019 0.037 0.052 0.020
## Cumulative Var 0.892 0.984 1.003 1.040 1.092 1.111
## Comp 32 Comp 33 Comp 34 Comp 35 Comp 36 Comp 37
## SS loadings 1.646 1.453 1.713 1.337 1.760 2.405
## Proportion Var 0.029 0.026 0.031 0.024 0.031 0.043
## Cumulative Var 1.141 1.167 1.197 1.221 1.253 1.296
## Comp 38 Comp 39 Comp 40
## SS loadings 1.599 1.446 2.492
## Proportion Var 0.029 0.026 0.045
## Cumulative Var 1.324 1.350 1.394
# Gráficos dos carregamentos.
v <- rownames(loadings(p0))
loadingplot(p0,
# comps = 1:ncol(scores(p0)),
comps = 1:3,
xaxt = "n")
axis(side = 1,
las = 2,
at = seq_along(v),
labels = v)
abline(v = seq_along(v), lty = 3, col = "gray")
# Só os carregamentos.
plot(p0, plottype = "correlation")
# Biplots.
biplot(p0, var.axes = TRUE)
biplot(p0, comps = c(1, 3), var.axes = TRUE)
par(mfrow = c(2, 2))
cex <- 0.5 + 3 * ((y - min(y))/diff(range(y)))
apply(combn(x = 1:3, m = 2),
MARGIN = 2,
FUN = function(comps) {
plot(p0,
comps = comps,
plottype = "correlation",
col = "red",
# pch = 19,
cex = cex)
})
## NULL
layout(1)
# Correlação observados e preditos.
cor(cbind(obs = y,
m0 = fitted(m0),
p0 = predict(p0, comps = 1:3)))[1, ]
## obs m0 prod1
## 1.0000000 0.9757648 0.4443793
# Coeficientes de regressão.
coef(p0, comps = 1)
## , , Comp 1
##
## prod1
## glic1 2.683943e-05
## phos1 -2.894308e-05
## sulf1 4.665106e-06
## LFF1 -1.529819e-06
## LFO1 -1.842272e-08
## HF1 2.113080e-06
## pH1 8.365887e-08
## pH2 2.255336e-07
## pH3 2.056076e-07
## pH_Ca1 8.333590e-08
## pH_Ca2 2.792477e-07
## pH_Ca3 2.061856e-07
## P1 -5.434301e-06
## P2 2.546518e-06
## P3 8.283338e-08
## K1 3.598813e-05
## K2 8.341255e-06
## K3 8.162407e-06
## Ca1 1.027801e-07
## Ca2 5.235575e-07
## Ca3 2.993916e-07
## Mg1 1.608717e-08
## Mg2 1.633220e-07
## Mg3 1.191647e-07
## Al2 -1.879144e-07
## Al3 -1.681652e-07
## MO1 5.648380e-07
## MO2 1.274867e-06
## MO3 -1.230178e-06
## CTC1 5.501644e-08
## CTC2 8.970678e-08
## CTC3 -3.188845e-07
## V1 2.360920e-06
## V2 9.820746e-06
## V3 8.831054e-06
## S1 -5.518266e-06
## S2 -9.088015e-06
## S3 -3.540160e-06
## dp1 -4.693562e-08
## dp2 2.988199e-08
## dp3 6.860223e-10
## rp1 -1.102630e-06
## rp2 1.611040e-07
## rp3 6.280225e-09
## dens1 -1.165565e-07
## dens2 1.944064e-08
## dens3 4.226264e-08
## poro1 7.471034e-08
## poro2 -3.685479e-09
## poro3 -5.531758e-08
## clay1 -6.527493e-05
## clay2 -3.147436e-05
## clay3 -3.960144e-05
## sand1 7.849613e-05
## sand2 6.038626e-05
## sand3 6.587699e-05
# Gráfico dos coeficientes de regressão.
plot(p0,
plottype = "coef",
# ncomp = 1:ncol(scores(p0)),
ncomp = 1:3,
xaxt = "n",
legend = "topright")
axis(side = 1,
las = 2,
at = seq_len(nrow(loadings(p0))),
labels = rownames(loadings(p0)))
# Predito vs observado.
plot(p0, ncomp = 3, asp = 1, line = TRUE)
# coef(p0)
# predplot(p0)
# residuals(p0)
selectNcomp(p0,
method = c("onesigma", "randomization")[1],
plot = TRUE)
## [1] 0
# TODO: ver https://cran.r-project.org/web/packages/pls/vignettes/pls-manual.pdf.
#-----------------------------------------------------------------------