library(aqp)
## Warning: package 'aqp' was built under R version 4.1.3
## This is aqp 1.42
library(soilDB)
## Warning: package 'soilDB' was built under R version 4.1.3
library(ggplot2)
## Warning: package 'ggplot2' was built under R version 4.1.3
data("loafercreek")
# Construct generalized horizon designations
n <- c("A","BAt", "Bt1","Bt2","Cr", "R")
p <- c("A", "BA|AB", "bt|Bw", "Bt3|Bt4|2B|C" ,"Cr","R")
loafercreek$genhz <- generalize.hz(
loafercreek$hzname,
n,p)
h <- horizons(loafercreek)
table(h$genhz, h$hzname)
##
## 2BC 2BCt 2Bt1 2Bt2 2Bt3 2Bt4 2Bt5 2CB 2CBt 2Cr 2Crt 2R A A1 A2 AB
## A 0 0 0 0 0 0 0 0 0 0 0 0 97 7 7 0
## BAt 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
## Bt1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## Bt2 1 1 3 8 8 6 1 1 1 0 0 0 0 0 0 0
## Cr 0 0 0 0 0 0 0 0 0 4 2 0 0 0 0 0
## R 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0
## not-used 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
##
## ABt Ad Ap B BA BAt BC BCt Bt Bt1 Bt2 Bt3 Bt4 Bw Bw1 Bw2 Bw3 C CBt
## A 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## BAt 2 0 0 0 31 8 0 0 0 0 0 0 0 0 0 0 0 0 0
## Bt1 0 0 0 0 0 0 0 0 0 0 0 0 0 10 2 2 1 0 0
## Bt2 0 0 0 0 0 0 4 16 0 0 0 47 8 0 0 0 0 6 6
## Cr 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## R 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## not-used 0 0 0 1 0 0 0 0 8 93 88 0 0 0 0 0 0 0 0
##
## Cd Cr Cr/R Crt H1 Oi R Rt
## A 0 0 0 0 0 0 0 0
## BAt 0 0 0 0 0 0 0 0
## Bt1 0 0 0 0 0 0 0 0
## Bt2 1 0 0 0 0 0 0 0
## Cr 0 49 0 20 0 0 0 0
## R 0 0 1 0 0 0 40 1
## not-used 0 0 0 0 1 24 0 0
vars <- c("genhz", "clay","total_frags_pct",
"phfield", "effclass")
summary(h[, vars])
## genhz clay total_frags_pct phfield
## A :113 Min. :10.00 Min. : 0.00 Min. :4.90
## BAt : 42 1st Qu.:18.00 1st Qu.: 0.00 1st Qu.:6.00
## Bt1 : 15 Median :22.00 Median : 5.00 Median :6.30
## Bt2 :118 Mean :23.63 Mean :13.88 Mean :6.18
## Cr : 75 3rd Qu.:28.00 3rd Qu.:20.00 3rd Qu.:6.50
## R : 48 Max. :60.00 Max. :95.00 Max. :7.00
## not-used:215 NA's :167 NA's :381
## effclass
## Length:626
## Class :character
## Mode :character
##
##
##
##
sort(unique(h$hzname))
## [1] "2BC" "2BCt" "2Bt1" "2Bt2" "2Bt3" "2Bt4" "2Bt5" "2CB" "2CBt" "2Cr"
## [11] "2Crt" "2R" "A" "A1" "A2" "AB" "ABt" "Ad" "Ap" "B"
## [21] "BA" "BAt" "BC" "BCt" "Bt" "Bt1" "Bt2" "Bt3" "Bt4" "Bw"
## [31] "Bw1" "Bw2" "Bw3" "C" "CBt" "Cd" "Cr" "Cr/R" "Crt" "H1"
## [41] "Oi" "R" "Rt"
h$hzname <- ifelse(h$hzname == "BT",
"Bt", h$hzname)
clay <- na.exclude(h$clay)
mean(clay)
## [1] 23.62767
median(clay)
## [1] 22
sort(table(round(h$clay)),
decreasing = TRUE)[1]
## 25
## 42
table(h$genhz, h$hzname)
##
## 2BC 2BCt 2Bt1 2Bt2 2Bt3 2Bt4 2Bt5 2CB 2CBt 2Cr 2Crt 2R A A1 A2 AB
## A 0 0 0 0 0 0 0 0 0 0 0 0 97 7 7 0
## BAt 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
## Bt1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## Bt2 1 1 3 8 8 6 1 1 1 0 0 0 0 0 0 0
## Cr 0 0 0 0 0 0 0 0 0 4 2 0 0 0 0 0
## R 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0
## not-used 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
##
## ABt Ad Ap B BA BAt BC BCt Bt Bt1 Bt2 Bt3 Bt4 Bw Bw1 Bw2 Bw3 C CBt
## A 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## BAt 2 0 0 0 31 8 0 0 0 0 0 0 0 0 0 0 0 0 0
## Bt1 0 0 0 0 0 0 0 0 0 0 0 0 0 10 2 2 1 0 0
## Bt2 0 0 0 0 0 0 4 16 0 0 0 47 8 0 0 0 0 6 6
## Cr 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## R 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## not-used 0 0 0 1 0 0 0 0 8 93 88 0 0 0 0 0 0 0 0
##
## Cd Cr Cr/R Crt H1 Oi R Rt
## A 0 0 0 0 0 0 0 0
## BAt 0 0 0 0 0 0 0 0
## Bt1 0 0 0 0 0 0 0 0
## Bt2 1 0 0 0 0 0 0 0
## Cr 0 49 0 20 0 0 0 0
## R 0 0 1 0 0 0 40 1
## not-used 0 0 0 0 1 24 0 0
addmargins(table(h$genhz,
h$texcl))
##
## c cl l scl sic sicl sil sl Sum
## A 0 0 78 0 0 0 27 6 111
## BAt 0 2 32 0 0 1 5 1 41
## Bt1 0 0 14 0 0 0 1 0 15
## Bt2 16 54 29 5 1 3 5 0 113
## Cr 1 0 0 0 0 0 0 0 1
## R 0 0 0 0 0 0 0 0 0
## not-used 2 45 112 4 1 5 18 1 188
## Sum 19 101 265 9 2 9 56 8 469
ggplot(h, aes(x = texcl)) +geom_bar()
ggplot(h, aes(x = clay)) +
geom_histogram(bins = nclass.Sturges(h$clay))
## Warning: Removed 167 rows containing non-finite values (stat_bin).
ggplot(h, aes(x = clay)) + geom_density()
## Warning: Removed 167 rows containing non-finite values (stat_density).
ggplot(h, (aes(x = genhz, y = clay))) +
geom_boxplot()
## Warning: Removed 167 rows containing non-finite values (stat_boxplot).
ggplot(h, aes(sample = clay)) +
geom_qq() +
geom_qq_line()
## Warning: Removed 167 rows containing non-finite values (stat_qq).
## Warning: Removed 167 rows containing non-finite values (stat_qq_line).
h$hzdepm <- (h$hzdepb + h$hzdept) / 2
vars <- c("hzdepm", "clay", "sand",
"total_frags_pct", "phfield")
round(cor(h[, vars], use = "complete.obs"), 2)
## hzdepm clay sand total_frags_pct phfield
## hzdepm 1.00 0.59 -0.08 0.50 -0.03
## clay 0.59 1.00 -0.17 0.28 0.13
## sand -0.08 -0.17 1.00 -0.05 0.12
## total_frags_pct 0.50 0.28 -0.05 1.00 -0.16
## phfield -0.03 0.13 0.12 -0.16 1.00
ggplot(h, aes(x = clay, y = hzdepm)) +
geom_point() +
ylim(100, 0)
## Warning: Removed 168 rows containing missing values (geom_point).
ggplot(h, aes(y = clay, x = hzdepm,
group = peiid)) +
geom_line() + coord_flip() + xlim(100, 0)
## Warning: Removed 168 row(s) containing missing values (geom_path).
