Data 624 Hw4
Scott Reed
9/29/2021
library(mlbench)
library(mice)##
## Attaching package: 'mice'## The following object is masked from 'package:stats':
##
## filter## The following objects are masked from 'package:base':
##
## cbind, rbindlibrary(corrplot)## corrplot 0.90 loadedlibrary(tidyverse)## -- Attaching packages --------------------------------------- tidyverse 1.3.1 --## v ggplot2 3.3.5 v purrr 0.3.4
## v tibble 3.1.4 v dplyr 1.0.7
## v tidyr 1.1.3 v stringr 1.4.0
## v readr 2.0.1 v forcats 0.5.1## -- Conflicts ------------------------------------------ tidyverse_conflicts() --
## x dplyr::filter() masks mice::filter(), stats::filter()
## x dplyr::lag() masks stats::lag()library(caret)## Loading required package: lattice##
## Attaching package: 'caret'## The following object is masked from 'package:purrr':
##
## lift3.1
- The UC Irvine Machine Learning Repository6 contains a data set related to glass identification. The data consist of 214 glass samples labeled as one of seven class categories. There are nine predictors, including the refractive index and percentages of eight elements: Na, Mg, Al, Si, K, Ca, Ba, and Fe
library(mlbench)
data(Glass)
str(Glass)## 'data.frame': 214 obs. of 10 variables:
## $ RI : num 1.52 1.52 1.52 1.52 1.52 ...
## $ Na : num 13.6 13.9 13.5 13.2 13.3 ...
## $ Mg : num 4.49 3.6 3.55 3.69 3.62 3.61 3.6 3.61 3.58 3.6 ...
## $ Al : num 1.1 1.36 1.54 1.29 1.24 1.62 1.14 1.05 1.37 1.36 ...
## $ Si : num 71.8 72.7 73 72.6 73.1 ...
## $ K : num 0.06 0.48 0.39 0.57 0.55 0.64 0.58 0.57 0.56 0.57 ...
## $ Ca : num 8.75 7.83 7.78 8.22 8.07 8.07 8.17 8.24 8.3 8.4 ...
## $ Ba : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Fe : num 0 0 0 0 0 0.26 0 0 0 0.11 ...
## $ Type: Factor w/ 6 levels "1","2","3","5",..: 1 1 1 1 1 1 1 1 1 1 ...- Using visualizations, explore the predictor variables to understand their distributions as well as the relationships between predictors.
mice::md.pattern(Glass)## /\ /\
## { `---' }
## { O O }
## ==> V <== No need for mice. This data set is completely observed.
## \ \|/ /
## `-----'
## RI Na Mg Al Si K Ca Ba Fe Type
## 214 1 1 1 1 1 1 1 1 1 1 0
## 0 0 0 0 0 0 0 0 0 0 0Shockingly it is completely observed
glassCor<-cor(Glass%>% select(-Type))
corrplot(glassCor)
There are some strong correlations observed, between CA and RI.
- Do there appear to be any outliers in the data? Are any predictors skewed?
Glass%>% mutate(Type=as.numeric(Type)) %>%
gather %>%
ggplot2::ggplot(aes(value)) +
ggplot2::facet_wrap(~ key, scales = "free") +
ggplot2::geom_histogram()## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Glass%>% mutate(Type=as.numeric(Type)) %>%
gather %>%
ggplot2::ggplot(aes(value)) +
ggplot2::facet_wrap(~ key, scales = "free") +
ggplot2::geom_boxplot()
Ba, Fe are strongly skewed.K has some truly extreme outliers.
- Are there any relevant transformations of one or more predictors that might improve the classification model?
A fairly standard response would be Box-Cox, we could further use PCA (principal component analysis).
GlassPCA<-caret::preProcess(Glass%>% mutate(Type=as.numeric(Type)), method=c("BoxCox","scale","center","pca"))
glassTransformed<-predict(GlassPCA,Glass%>% mutate(Type=as.numeric(Type)))
glassTransformed %>% gather %>%
ggplot2::ggplot(aes(value)) +
ggplot2::facet_wrap(~ key, scales = "free") +
ggplot2::geom_histogram()## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
GlassPCA$rotation ## PC1 PC2 PC3 PC4 PC5 PC6
## RI -0.3274656 0.50414413 0.1891739054 -0.13708941 0.100281367 -0.11947306
## Na 0.2893926 0.10685812 -0.3392707880 -0.55481687 -0.187749770 0.46040369
## Mg -0.3449803 -0.44354901 -0.0141699787 -0.29389494 -0.148890503 -0.10998763
## Al 0.4561552 -0.02332162 0.3028533907 0.15932041 -0.005249685 -0.07394593
## Si 0.1388741 -0.18465205 -0.5399643923 0.58555246 -0.030349971 -0.14948586
## K 0.1270115 -0.31145790 0.5920656883 0.08671292 0.341738683 0.24467309
## Ca -0.2759822 0.52597006 -0.0410126561 0.27180692 0.183761688 0.13441080
## Ba 0.3809849 0.23847928 0.1425561724 -0.19938707 -0.254691258 -0.68824318
## Fe -0.1593390 0.04593504 0.3050899613 0.29409863 -0.845834619 0.25497189
## Type 0.4469975 0.26535092 -0.0003041303 0.10539681 0.026815742 0.34237816
## PC7
## RI 0.08145839
## Na 0.13205052
## Mg -0.30780979
## Al -0.69218465
## Si 0.23341903
## K 0.47623559
## Ca -0.14024636
## Ba 0.29398454
## Fe 0.10178615
## Type -0.06572347Looking at the contributions we see 7 required to have a 95% CI. This suggests a certain no overriding variables. PCA in this instance will not be terribly easy to interpret.
3.2
The soybean data can also be found at the UC Irvine Machine Learning Repository. Data were collected to predict disease in 683 soybeans. The 35 predictors are mostly categorical and include information on the environmental conditions (e.g., temperature, precipitation) and plant conditions (e.g., left spots, mold growth). The outcome labels consist of 19 distinct classes. 6 http://archive.ics.uci.edu/ml/index.html. 3.8 Computing 59 The data can be loaded via:
library(mlbench)
data(Soybean)
## See ?Soybean for details- Investigate the frequency distributions for the categorical predictors. Are any of the distributions degenerate in the ways discussed earlier in this chapter?
```r
md.pattern(Soybean, rotate.names = T)
## Class leaves date area.dam crop.hist plant.growth stem temp roots
## 562 1 1 1 1 1 1 1 1 1
## 13 1 1 1 1 1 1 1 1 1
## 55 1 1 1 1 1 1 1 1 1
## 8 1 1 1 1 1 1 1 1 1
## 9 1 1 1 1 1 1 1 1 0
## 6 1 1 1 1 1 1 1 1 0
## 14 1 1 1 1 1 1 1 0 1
## 15 1 1 1 1 0 0 0 0 0
## 1 1 1 0 0 0 0 0 0 0
## 0 0 1 1 16 16 16 30 31
## plant.stand precip stem.cankers canker.lesion ext.decay mycelium
## 562 1 1 1 1 1 1
## 13 1 1 1 1 1 1
## 55 1 1 1 1 1 1
## 8 1 0 0 0 0 0
## 9 1 1 1 1 1 1
## 6 0 1 1 1 1 1
## 14 0 0 0 0 0 0
## 15 0 0 0 0 0 0
## 1 0 0 0 0 0 0
## 36 38 38 38 38 38
## int.discolor sclerotia leaf.halo leaf.marg leaf.size leaf.malf fruit.pods
## 562 1 1 1 1 1 1 1
## 13 1 1 1 1 1 1 0
## 55 1 1 0 0 0 0 0
## 8 0 0 1 1 1 1 1
## 9 1 1 0 0 0 0 1
## 6 1 1 0 0 0 0 1
## 14 0 0 0 0 0 0 1
## 15 0 0 1 1 1 1 0
## 1 0 0 1 1 1 1 0
## 38 38 84 84 84 84 84
## seed mold.growth seed.size leaf.shread fruiting.bodies fruit.spots
## 562 1 1 1 1 1 1
## 13 0 0 0 1 0 0
## 55 0 0 0 0 0 0
## 8 0 0 0 1 0 0
## 9 1 1 1 0 1 1
## 6 1 1 1 0 1 1
## 14 1 1 1 0 0 0
## 15 0 0 0 0 0 0
## 1 0 0 0 0 0 0
## 92 92 92 100 106 106
## seed.discolor shriveling leaf.mild germ hail sever seed.tmt lodging
## 562 1 1 1 1 1 1 1 1 0
## 13 0 0 1 0 0 0 0 0 13
## 55 0 0 0 0 0 0 0 0 19
## 8 0 0 0 0 0 0 0 0 20
## 9 1 1 0 1 0 0 0 0 11
## 6 1 1 0 0 0 0 0 0 13
## 14 0 0 0 0 0 0 0 0 24
## 15 0 0 0 0 0 0 0 0 28
## 1 0 0 0 0 0 0 0 0 30
## 106 106 108 112 121 121 121 121 2337We see a significant amount of missing data. Class and Leaves are the only complete data runs.
summary(Soybean)## Class date plant.stand precip temp
## brown-spot : 92 5 :149 0 :354 0 : 74 0 : 80
## alternarialeaf-spot: 91 4 :131 1 :293 1 :112 1 :374
## frog-eye-leaf-spot : 91 3 :118 NA's: 36 2 :459 2 :199
## phytophthora-rot : 88 2 : 93 NA's: 38 NA's: 30
## anthracnose : 44 6 : 90
## brown-stem-rot : 44 (Other):101
## (Other) :233 NA's : 1
## hail crop.hist area.dam sever seed.tmt germ plant.growth
## 0 :435 0 : 65 0 :123 0 :195 0 :305 0 :165 0 :441
## 1 :127 1 :165 1 :227 1 :322 1 :222 1 :213 1 :226
## NA's:121 2 :219 2 :145 2 : 45 2 : 35 2 :193 NA's: 16
## 3 :218 3 :187 NA's:121 NA's:121 NA's:112
## NA's: 16 NA's: 1
##
##
## leaves leaf.halo leaf.marg leaf.size leaf.shread leaf.malf leaf.mild
## 0: 77 0 :221 0 :357 0 : 51 0 :487 0 :554 0 :535
## 1:606 1 : 36 1 : 21 1 :327 1 : 96 1 : 45 1 : 20
## 2 :342 2 :221 2 :221 NA's:100 NA's: 84 2 : 20
## NA's: 84 NA's: 84 NA's: 84 NA's:108
##
##
##
## stem lodging stem.cankers canker.lesion fruiting.bodies ext.decay
## 0 :296 0 :520 0 :379 0 :320 0 :473 0 :497
## 1 :371 1 : 42 1 : 39 1 : 83 1 :104 1 :135
## NA's: 16 NA's:121 2 : 36 2 :177 NA's:106 2 : 13
## 3 :191 3 : 65 NA's: 38
## NA's: 38 NA's: 38
##
##
## mycelium int.discolor sclerotia fruit.pods fruit.spots seed
## 0 :639 0 :581 0 :625 0 :407 0 :345 0 :476
## 1 : 6 1 : 44 1 : 20 1 :130 1 : 75 1 :115
## NA's: 38 2 : 20 NA's: 38 2 : 14 2 : 57 NA's: 92
## NA's: 38 3 : 48 4 :100
## NA's: 84 NA's:106
##
##
## mold.growth seed.discolor seed.size shriveling roots
## 0 :524 0 :513 0 :532 0 :539 0 :551
## 1 : 67 1 : 64 1 : 59 1 : 38 1 : 86
## NA's: 92 NA's:106 NA's: 92 NA's:106 2 : 15
## NA's: 31
##
##
## Most of the data consists of factors and most of the order of the factors are relatively low order, and unbalanced in distribution. In particular some of them are clearly degenerate:
- leaf.malf
- lodging
- sclerotia
- seed.discolor
- seed.size
- shriveling
- roots
- Roughly 18 % of the data are missing. Are there particular predictors that are more likely to be missing? Is the pattern of missing data related to the classes?
soybeanSplit<-split(Soybean,Soybean$Class)
for(n in soybeanSplit){
print(summary(n))
}## Class date plant.stand precip temp hail
## 2-4-d-injury :16 0 :3 0 : 0 0 : 0 0 : 0 0 : 0
## alternarialeaf-spot: 0 1 :2 1 : 0 1 : 0 1 : 0 1 : 0
## anthracnose : 0 2 :2 NA's:16 2 : 0 2 : 0 NA's:16
## bacterial-blight : 0 3 :2 NA's:16 NA's:16
## bacterial-pustule : 0 4 :2
## brown-spot : 0 (Other):4
## (Other) : 0 NA's :1
## crop.hist area.dam sever seed.tmt germ plant.growth leaves leaf.halo
## 0 : 0 0 :4 0 : 0 0 : 0 0 : 0 0 : 0 0: 0 0:16
## 1 : 0 1 :4 1 : 0 1 : 0 1 : 0 1 : 0 1:16 1: 0
## 2 : 0 2 :4 2 : 0 2 : 0 2 : 0 NA's:16 2: 0
## 3 : 0 3 :3 NA's:16 NA's:16 NA's:16
## NA's:16 NA's:1
##
##
## leaf.marg leaf.size leaf.shread leaf.malf leaf.mild stem lodging
## 0: 0 0: 0 0 : 0 0: 0 0 : 0 0 : 0 0 : 0
## 1: 0 1: 0 1 : 0 1:16 1 : 0 1 : 0 1 : 0
## 2:16 2:16 NA's:16 2 : 0 NA's:16 NA's:16
## NA's:16
##
##
##
## stem.cankers canker.lesion fruiting.bodies ext.decay mycelium int.discolor
## 0 : 0 0 : 0 0 : 0 0 : 0 0 : 0 0 : 0
## 1 : 0 1 : 0 1 : 0 1 : 0 1 : 0 1 : 0
## 2 : 0 2 : 0 NA's:16 2 : 0 NA's:16 2 : 0
## 3 : 0 3 : 0 NA's:16 NA's:16
## NA's:16 NA's:16
##
##
## sclerotia fruit.pods fruit.spots seed mold.growth seed.discolor seed.size
## 0 : 0 0 : 0 0 : 0 0 : 0 0 : 0 0 : 0 0 : 0
## 1 : 0 1 : 0 1 : 0 1 : 0 1 : 0 1 : 0 1 : 0
## NA's:16 2 : 0 2 : 0 NA's:16 NA's:16 NA's:16 NA's:16
## 3 : 0 4 : 0
## NA's:16 NA's:16
##
##
## shriveling roots
## 0 : 0 0 : 0
## 1 : 0 1 : 0
## NA's:16 2 : 0
## NA's:16
##
##
##
## Class date plant.stand precip temp hail crop.hist
## alternarialeaf-spot:91 0: 0 0:58 0: 0 0: 0 0:81 0:11
## 2-4-d-injury : 0 1: 0 1:33 1: 9 1:40 1:10 1:20
## anthracnose : 0 2: 0 2:82 2:51 2:30
## bacterial-blight : 0 3: 3 3:30
## bacterial-pustule : 0 4:18
## brown-spot : 0 5:40
## (Other) : 0 6:30
## area.dam sever seed.tmt germ plant.growth leaves leaf.halo leaf.marg
## 0:18 0:53 0:42 0:30 0:91 0: 0 0: 0 0:91
## 1:25 1:38 1:43 1:31 1: 0 1:91 1: 0 1: 0
## 2:24 2: 0 2: 6 2:30 2:91 2: 0
## 3:24
##
##
##
## leaf.size leaf.shread leaf.malf leaf.mild stem lodging stem.cankers
## 0: 0 0:80 0:91 0:91 0:91 0:91 0:91
## 1:91 1:11 1: 0 1: 0 1: 0 1: 0 1: 0
## 2: 0 2: 0 2: 0
## 3: 0
##
##
##
## canker.lesion fruiting.bodies ext.decay mycelium int.discolor sclerotia
## 0:91 0:91 0:91 0:91 0:91 0:91
## 1: 0 1: 0 1: 0 1: 0 1: 0 1: 0
## 2: 0 2: 0 2: 0
## 3: 0
##
##
##
## fruit.pods fruit.spots seed mold.growth seed.discolor seed.size shriveling
## 0:91 0:91 0:81 0:91 0:81 0:91 0:91
## 1: 0 1: 0 1:10 1: 0 1:10 1: 0 1: 0
## 2: 0 2: 0
## 3: 0 4: 0
##
##
##
## roots
## 0:91
## 1: 0
## 2: 0
##
##
##
##
## Class date plant.stand precip temp hail crop.hist
## anthracnose :44 0: 2 0:21 0: 0 0: 0 0:33 0: 5
## 2-4-d-injury : 0 1: 2 1:23 1: 0 1:33 1:11 1:13
## alternarialeaf-spot: 0 2: 2 2:44 2:11 2:13
## bacterial-blight : 0 3: 2 3:13
## bacterial-pustule : 0 4: 7
## brown-spot : 0 5:17
## (Other) : 0 6:12
## area.dam sever seed.tmt germ plant.growth leaves leaf.halo leaf.marg
## 0: 5 0:11 0:21 0:15 0:32 0:24 0:44 0: 0
## 1:13 1:31 1:19 1:19 1:12 1:20 1: 0 1: 0
## 2:13 2: 2 2: 4 2:10 2: 0 2:44
## 3:13
##
##
##
## leaf.size leaf.shread leaf.malf leaf.mild stem lodging stem.cankers
## 0: 0 0:44 0:44 0:44 0: 0 0:39 0: 0
## 1: 0 1: 0 1: 0 1: 0 1:44 1: 5 1: 0
## 2:44 2: 0 2: 5
## 3:39
##
##
##
## canker.lesion fruiting.bodies ext.decay mycelium int.discolor sclerotia
## 0: 0 0:14 0:24 0:44 0:44 0:44
## 1:10 1:30 1:20 1: 0 1: 0 1: 0
## 2:34 2: 0 2: 0
## 3: 0
##
##
##
## fruit.pods fruit.spots seed mold.growth seed.discolor seed.size shriveling
## 0: 6 0: 6 0:17 0:22 0:36 0:22 0:22
## 1:38 1: 0 1:27 1:22 1: 8 1:22 1:22
## 2: 0 2:38
## 3: 0 4: 0
##
##
##
## roots
## 0:44
## 1: 0
## 2: 0
##
##
##
##
## Class date plant.stand precip temp hail crop.hist
## bacterial-blight :20 0:0 0:15 0: 0 0: 0 0:10 0:2
## 2-4-d-injury : 0 1:0 1: 5 1:10 1:17 1:10 1:6
## alternarialeaf-spot: 0 2:3 2:10 2: 3 2:6
## anthracnose : 0 3:7 3:6
## bacterial-pustule : 0 4:7
## brown-spot : 0 5:3
## (Other) : 0 6:0
## area.dam sever seed.tmt germ plant.growth leaves leaf.halo leaf.marg
## 0:5 0:10 0:10 0:7 0:16 0: 0 0: 0 0:20
## 1:5 1:10 1:10 1:8 1: 4 1:20 1:10 1: 0
## 2:5 2: 0 2: 0 2:5 2:10 2: 0
## 3:5
##
##
##
## leaf.size leaf.shread leaf.malf leaf.mild stem lodging stem.cankers
## 0:20 0: 3 0:18 0:20 0:20 0:20 0:20
## 1: 0 1:17 1: 2 1: 0 1: 0 1: 0 1: 0
## 2: 0 2: 0 2: 0
## 3: 0
##
##
##
## canker.lesion fruiting.bodies ext.decay mycelium int.discolor sclerotia
## 0:20 0:20 0:20 0:20 0:20 0:20
## 1: 0 1: 0 1: 0 1: 0 1: 0 1: 0
## 2: 0 2: 0 2: 0
## 3: 0
##
##
##
## fruit.pods fruit.spots seed mold.growth seed.discolor seed.size shriveling
## 0:20 0:20 0:20 0:20 0:20 0:20 0:20
## 1: 0 1: 0 1: 0 1: 0 1: 0 1: 0 1: 0
## 2: 0 2: 0
## 3: 0 4: 0
##
##
##
## roots
## 0:20
## 1: 0
## 2: 0
##
##
##
##
## Class date plant.stand precip temp hail crop.hist
## bacterial-pustule :20 0:0 0:11 0: 0 0: 5 0:10 0:3
## 2-4-d-injury : 0 1:2 1: 9 1:12 1:11 1:10 1:6
## alternarialeaf-spot: 0 2:7 2: 8 2: 4 2:6
## anthracnose : 0 3:7 3:5
## bacterial-blight : 0 4:2
## brown-spot : 0 5:2
## (Other) : 0 6:0
## area.dam sever seed.tmt germ plant.growth leaves leaf.halo leaf.marg
## 0:5 0:12 0:14 0: 1 0:17 0: 0 0: 0 0: 3
## 1:5 1: 8 1: 6 1:10 1: 3 1:20 1:16 1:17
## 2:5 2: 0 2: 0 2: 9 2: 4 2: 0
## 3:5
##
##
##
## leaf.size leaf.shread leaf.malf leaf.mild stem lodging stem.cankers
## 0:20 0: 6 0:17 0:20 0:20 0:20 0:20
## 1: 0 1:14 1: 3 1: 0 1: 0 1: 0 1: 0
## 2: 0 2: 0 2: 0
## 3: 0
##
##
##
## canker.lesion fruiting.bodies ext.decay mycelium int.discolor sclerotia
## 0:20 0:20 0:20 0:20 0:20 0:20
## 1: 0 1: 0 1: 0 1: 0 1: 0 1: 0
## 2: 0 2: 0 2: 0
## 3: 0
##
##
##
## fruit.pods fruit.spots seed mold.growth seed.discolor seed.size shriveling
## 0:20 0:20 0:10 0:10 0:10 0:13 0:20
## 1: 0 1: 0 1:10 1:10 1:10 1: 7 1: 0
## 2: 0 2: 0
## 3: 0 4: 0
##
##
##
## roots
## 0:10
## 1: 9
## 2: 1
##
##
##
##
## Class date plant.stand precip temp hail crop.hist
## brown-spot :92 0: 5 0:57 0: 0 0: 0 0:81 0: 2
## 2-4-d-injury : 0 1:27 1:35 1:10 1:82 1:11 1:17
## alternarialeaf-spot: 0 2:28 2:82 2:10 2:37
## anthracnose : 0 3:17 3:36
## bacterial-blight : 0 4: 8
## bacterial-pustule : 0 5: 7
## (Other) : 0 6: 0
## area.dam sever seed.tmt germ plant.growth leaves leaf.halo leaf.marg
## 0: 7 0:11 0:63 0:27 0:83 0: 0 0: 0 0:92
## 1:17 1:75 1:15 1:33 1: 9 1:92 1: 0 1: 0
## 2:17 2: 6 2:14 2:32 2:92 2: 0
## 3:51
##
##
##
## leaf.size leaf.shread leaf.malf leaf.mild stem lodging stem.cankers
## 0: 0 0:48 0:92 0:92 0:54 0:92 0:59
## 1:92 1:44 1: 0 1: 0 1:38 1: 0 1: 0
## 2: 0 2: 0 2: 0
## 3:33
##
##
##
## canker.lesion fruiting.bodies ext.decay mycelium int.discolor sclerotia
## 0:54 0:56 0:87 0:92 0:92 0:92
## 1:33 1:36 1: 5 1: 0 1: 0 1: 0
## 2: 0 2: 0 2: 0
## 3: 5
##
##
##
## fruit.pods fruit.spots seed mold.growth seed.discolor seed.size shriveling
## 0:90 0:88 0:92 0:92 0:92 0:92 0:92
## 1: 2 1: 2 1: 0 1: 0 1: 0 1: 0 1: 0
## 2: 0 2: 2
## 3: 0 4: 0
##
##
##
## roots
## 0:92
## 1: 0
## 2: 0
##
##
##
##
## Class date plant.stand precip temp hail crop.hist
## brown-stem-rot :44 0: 0 0:33 0:35 0:13 0:35 0: 0
## 2-4-d-injury : 0 1: 0 1:11 1: 9 1:25 1: 9 1:10
## alternarialeaf-spot: 0 2: 0 2: 0 2: 6 2:16
## anthracnose : 0 3: 8 3:18
## bacterial-blight : 0 4:17
## bacterial-pustule : 0 5:16
## (Other) : 0 6: 3
## area.dam sever seed.tmt germ plant.growth leaves leaf.halo leaf.marg
## 0:11 0: 0 0:22 0:15 0:24 0:10 0:35 0: 9
## 1: 2 1:37 1:22 1:15 1:20 1:34 1: 0 1: 0
## 2:17 2: 7 2: 0 2:14 2: 9 2:35
## 3:14
##
##
##
## leaf.size leaf.shread leaf.malf leaf.mild stem lodging stem.cankers
## 0: 0 0:44 0:44 0:44 0: 0 0:28 0:44
## 1: 9 1: 0 1: 0 1: 0 1:44 1:16 1: 0
## 2:35 2: 0 2: 0
## 3: 0
##
##
##
## canker.lesion fruiting.bodies ext.decay mycelium int.discolor sclerotia
## 0:24 0:44 0:44 0:44 0: 0 0:44
## 1: 0 1: 0 1: 0 1: 0 1:44 1: 0
## 2: 0 2: 0 2: 0
## 3:20
##
##
##
## fruit.pods fruit.spots seed mold.growth seed.discolor seed.size shriveling
## 0:44 0:24 0:44 0:44 0:44 0:44 0:44
## 1: 0 1: 0 1: 0 1: 0 1: 0 1: 0 1: 0
## 2: 0 2: 0
## 3: 0 4:20
##
##
##
## roots
## 0:44
## 1: 0
## 2: 0
##
##
##
##
## Class date plant.stand precip temp hail crop.hist
## charcoal-rot :20 0:0 0:20 0:20 0: 0 0: 9 0:3
## 2-4-d-injury : 0 1:0 1: 0 1: 0 1: 5 1:11 1:5
## alternarialeaf-spot: 0 2:0 2: 0 2:15 2:6
## anthracnose : 0 3:3 3:6
## bacterial-blight : 0 4:5
## bacterial-pustule : 0 5:6
## (Other) : 0 6:6
## area.dam sever seed.tmt germ plant.growth leaves leaf.halo leaf.marg
## 0: 0 0: 0 0:10 0:6 0: 0 0: 0 0:20 0: 0
## 1: 0 1:20 1:10 1:7 1:20 1:20 1: 0 1: 0
## 2:10 2: 0 2: 0 2:7 2: 0 2:20
## 3:10
##
##
##
## leaf.size leaf.shread leaf.malf leaf.mild stem lodging stem.cankers
## 0: 0 0:20 0:20 0:20 0: 0 0:17 0:20
## 1: 0 1: 0 1: 0 1: 0 1:20 1: 3 1: 0
## 2:20 2: 0 2: 0
## 3: 0
##
##
##
## canker.lesion fruiting.bodies ext.decay mycelium int.discolor sclerotia
## 0: 0 0:20 0:20 0:20 0: 0 0: 0
## 1: 0 1: 0 1: 0 1: 0 1: 0 1:20
## 2: 0 2: 0 2:20
## 3:20
##
##
##
## fruit.pods fruit.spots seed mold.growth seed.discolor seed.size shriveling
## 0:20 0: 0 0:20 0:20 0:20 0:20 0:20
## 1: 0 1: 0 1: 0 1: 0 1: 0 1: 0 1: 0
## 2: 0 2: 0
## 3: 0 4:20
##
##
##
## roots
## 0:20
## 1: 0
## 2: 0
##
##
##
##
## Class date plant.stand precip temp hail
## cyst-nematode :14 0:0 0 : 0 0 : 0 0 : 0 0 : 0
## 2-4-d-injury : 0 1:0 1 : 0 1 : 0 1 : 0 1 : 0
## alternarialeaf-spot: 0 2:3 NA's:14 2 : 0 2 : 0 NA's:14
## anthracnose : 0 3:6 NA's:14 NA's:14
## bacterial-blight : 0 4:5
## bacterial-pustule : 0 5:0
## (Other) : 0 6:0
## crop.hist area.dam sever seed.tmt germ plant.growth leaves leaf.halo
## 0:0 0:0 0 : 0 0 : 0 0 : 0 0: 0 0: 0 0 : 0
## 1:2 1:8 1 : 0 1 : 0 1 : 0 1:14 1:14 1 : 0
## 2:7 2:6 2 : 0 2 : 0 2 : 0 2 : 0
## 3:5 3:0 NA's:14 NA's:14 NA's:14 NA's:14
##
##
##
## leaf.marg leaf.size leaf.shread leaf.malf leaf.mild stem lodging
## 0 : 0 0 : 0 0 : 0 0 : 0 0 : 0 0:14 0 : 0
## 1 : 0 1 : 0 1 : 0 1 : 0 1 : 0 1: 0 1 : 0
## 2 : 0 2 : 0 NA's:14 NA's:14 2 : 0 NA's:14
## NA's:14 NA's:14 NA's:14
##
##
##
## stem.cankers canker.lesion fruiting.bodies ext.decay mycelium int.discolor
## 0 : 0 0 : 0 0 : 0 0 : 0 0 : 0 0 : 0
## 1 : 0 1 : 0 1 : 0 1 : 0 1 : 0 1 : 0
## 2 : 0 2 : 0 NA's:14 2 : 0 NA's:14 2 : 0
## 3 : 0 3 : 0 NA's:14 NA's:14
## NA's:14 NA's:14
##
##
## sclerotia fruit.pods fruit.spots seed mold.growth seed.discolor seed.size
## 0 : 0 0: 0 0 : 0 0: 0 0:14 0 : 0 0: 0
## 1 : 0 1: 0 1 : 0 1:14 1: 0 1 : 0 1:14
## NA's:14 2:14 2 : 0 NA's:14
## 3: 0 4 : 0
## NA's:14
##
##
## shriveling roots
## 0 : 0 0: 0
## 1 : 0 1: 0
## NA's:14 2:14
##
##
##
##
## Class date plant.stand precip temp hail
## diaporthe-pod-&-stem-blight:15 0:0 0 :7 0: 0 0: 0 0 : 0
## 2-4-d-injury : 0 1:2 1 :2 1: 2 1: 0 1 : 0
## alternarialeaf-spot : 0 2:0 NA's:6 2:13 2:15 NA's:15
## anthracnose : 0 3:0
## bacterial-blight : 0 4:0
## bacterial-pustule : 0 5:7
## (Other) : 0 6:6
## crop.hist area.dam sever seed.tmt germ plant.growth leaves leaf.halo
## 0:2 0: 2 0 : 0 0 : 0 0 :5 0:15 0:15 0 : 0
## 1:3 1: 0 1 : 0 1 : 0 1 :2 1: 0 1: 0 1 : 0
## 2:4 2: 0 2 : 0 2 : 0 2 :2 2 : 0
## 3:6 3:13 NA's:15 NA's:15 NA's:6 NA's:15
##
##
##
## leaf.marg leaf.size leaf.shread leaf.malf leaf.mild stem lodging
## 0 : 0 0 : 0 0 : 0 0 : 0 0 : 0 0: 0 0 : 0
## 1 : 0 1 : 0 1 : 0 1 : 0 1 : 0 1:15 1 : 0
## 2 : 0 2 : 0 NA's:15 NA's:15 2 : 0 NA's:15
## NA's:15 NA's:15 NA's:15
##
##
##
## stem.cankers canker.lesion fruiting.bodies ext.decay mycelium int.discolor
## 0:15 0:15 0: 0 0:15 0:15 0:15
## 1: 0 1: 0 1:15 1: 0 1: 0 1: 0
## 2: 0 2: 0 2: 0 2: 0
## 3: 0 3: 0
##
##
##
## sclerotia fruit.pods fruit.spots seed mold.growth seed.discolor seed.size
## 0:15 0: 0 0: 0 0: 3 0: 0 0: 0 0: 0
## 1: 0 1:15 1: 0 1:12 1:15 1:15 1:15
## 2: 0 2:15
## 3: 0 4: 0
##
##
##
## shriveling roots
## 0: 0 0 : 0
## 1:15 1 : 0
## 2 : 0
## NA's:15
##
##
##
## Class date plant.stand precip temp hail crop.hist
## diaporthe-stem-canker:20 0:0 0:20 0: 0 0: 0 0:19 0:0
## 2-4-d-injury : 0 1:0 1: 0 1: 0 1:20 1: 1 1:6
## alternarialeaf-spot : 0 2:0 2:20 2: 0 2:7
## anthracnose : 0 3:5 3:7
## bacterial-blight : 0 4:5
## bacterial-pustule : 0 5:5
## (Other) : 0 6:5
## area.dam sever seed.tmt germ plant.growth leaves leaf.halo leaf.marg
## 0:17 0: 0 0:11 0:3 0: 0 0: 0 0:20 0: 0
## 1: 3 1:14 1: 9 1:9 1:20 1:20 1: 0 1: 0
## 2: 0 2: 6 2: 0 2:8 2: 0 2:20
## 3: 0
##
##
##
## leaf.size leaf.shread leaf.malf leaf.mild stem lodging stem.cankers
## 0: 0 0:20 0:20 0:20 0: 0 0:14 0: 0
## 1: 0 1: 0 1: 0 1: 0 1:20 1: 6 1: 0
## 2:20 2: 0 2: 0
## 3:20
##
##
##
## canker.lesion fruiting.bodies ext.decay mycelium int.discolor sclerotia
## 0:10 0: 0 0: 0 0:20 0:20 0:20
## 1:10 1:20 1:20 1: 0 1: 0 1: 0
## 2: 0 2: 0 2: 0
## 3: 0
##
##
##
## fruit.pods fruit.spots seed mold.growth seed.discolor seed.size shriveling
## 0:20 0: 0 0:20 0:20 0:20 0:20 0:20
## 1: 0 1: 0 1: 0 1: 0 1: 0 1: 0 1: 0
## 2: 0 2: 0
## 3: 0 4:20
##
##
##
## roots
## 0:20
## 1: 0
## 2: 0
##
##
##
##
## Class date plant.stand precip temp hail crop.hist
## downy-mildew :20 0:0 0: 9 0: 0 0:8 0:11 0:2
## 2-4-d-injury : 0 1:2 1:11 1: 0 1:9 1: 9 1:6
## alternarialeaf-spot: 0 2:4 2:20 2:3 2:6
## anthracnose : 0 3:4 3:6
## bacterial-blight : 0 4:4
## bacterial-pustule : 0 5:4
## (Other) : 0 6:2
## area.dam sever seed.tmt germ plant.growth leaves leaf.halo leaf.marg
## 0:5 0: 6 0:10 0: 0 0:20 0: 0 0: 0 0:20
## 1:5 1:14 1:10 1:10 1: 0 1:20 1:10 1: 0
## 2:5 2: 0 2: 0 2:10 2:10 2: 0
## 3:5
##
##
##
## leaf.size leaf.shread leaf.malf leaf.mild stem lodging stem.cankers
## 0: 0 0:20 0:14 0: 0 0:20 0:20 0:20
## 1:20 1: 0 1: 6 1: 0 1: 0 1: 0 1: 0
## 2: 0 2:20 2: 0
## 3: 0
##
##
##
## canker.lesion fruiting.bodies ext.decay mycelium int.discolor sclerotia
## 0:20 0:20 0:20 0:20 0:20 0:20
## 1: 0 1: 0 1: 0 1: 0 1: 0 1: 0
## 2: 0 2: 0 2: 0
## 3: 0
##
##
##
## fruit.pods fruit.spots seed mold.growth seed.discolor seed.size shriveling
## 0:20 0:20 0: 0 0: 0 0:20 0:20 0:20
## 1: 0 1: 0 1:20 1:20 1: 0 1: 0 1: 0
## 2: 0 2: 0
## 3: 0 4: 0
##
##
##
## roots
## 0:20
## 1: 0
## 2: 0
##
##
##
##
## Class date plant.stand precip temp hail crop.hist
## frog-eye-leaf-spot :91 0: 0 0:63 0: 0 0: 0 0:81 0: 5
## 2-4-d-injury : 0 1: 0 1:28 1:10 1:54 1:10 1:27
## alternarialeaf-spot: 0 2: 0 2:81 2:37 2:29
## anthracnose : 0 3:13 3:30
## bacterial-blight : 0 4:33
## bacterial-pustule : 0 5:31
## (Other) : 0 6:14
## area.dam sever seed.tmt germ plant.growth leaves leaf.halo leaf.marg
## 0:23 0:48 0:44 0:35 0:87 0: 0 0: 0 0:91
## 1:23 1:43 1:42 1:28 1: 4 1:91 1: 0 1: 0
## 2:22 2: 0 2: 5 2:28 2:91 2: 0
## 3:23
##
##
##
## leaf.size leaf.shread leaf.malf leaf.mild stem lodging stem.cankers
## 0: 0 0:91 0:91 0:91 0:26 0:88 0:24
## 1:91 1: 0 1: 0 1: 0 1:65 1: 3 1: 0
## 2: 0 2: 0 2: 1
## 3:66
##
##
##
## canker.lesion fruiting.bodies ext.decay mycelium int.discolor sclerotia
## 0:26 0:88 0:27 0:91 0:91 0:91
## 1:10 1: 3 1:64 1: 0 1: 0 1: 0
## 2:55 2: 0 2: 0
## 3: 0
##
##
##
## fruit.pods fruit.spots seed mold.growth seed.discolor seed.size shriveling
## 0:27 0:27 0:89 0:91 0:90 0:90 0:90
## 1:64 1:62 1: 2 1: 0 1: 1 1: 1 1: 1
## 2: 0 2: 2
## 3: 0 4: 0
##
##
##
## roots
## 0:91
## 1: 0
## 2: 0
##
##
##
##
## Class date plant.stand precip temp hail crop.hist
## herbicide-injury :8 0:3 0:0 0 :0 0:8 0 :0 0:4
## 2-4-d-injury :0 1:3 1:8 1 :0 1:0 1 :0 1:4
## alternarialeaf-spot:0 2:2 2 :0 2:0 NA's:8 2:0
## anthracnose :0 3:0 NA's:8 3:0
## bacterial-blight :0 4:0
## bacterial-pustule :0 5:0
## (Other) :0 6:0
## area.dam sever seed.tmt germ plant.growth leaves leaf.halo leaf.marg
## 0:4 0 :0 0 :0 0 :0 0:0 0:0 0:4 0:0
## 1:0 1 :0 1 :0 1 :0 1:8 1:8 1:0 1:4
## 2:0 2 :0 2 :0 2 :0 2:4 2:4
## 3:4 NA's:8 NA's:8 NA's:8
##
##
##
## leaf.size leaf.shread leaf.malf leaf.mild stem lodging stem.cankers
## 0:0 0:8 0:0 0 :0 0:0 0 :0 0 :0
## 1:4 1:0 1:8 1 :0 1:8 1 :0 1 :0
## 2:4 2 :0 NA's:8 2 :0
## NA's:8 3 :0
## NA's:8
##
##
## canker.lesion fruiting.bodies ext.decay mycelium int.discolor sclerotia
## 0 :0 0 :0 0 :0 0 :0 0 :0 0 :0
## 1 :0 1 :0 1 :0 1 :0 1 :0 1 :0
## 2 :0 NA's:8 2 :0 NA's:8 2 :0 NA's:8
## 3 :0 NA's:8 NA's:8
## NA's:8
##
##
## fruit.pods fruit.spots seed mold.growth seed.discolor seed.size shriveling
## 0:0 0 :0 0 :0 0 :0 0 :0 0 :0 0 :0
## 1:0 1 :0 1 :0 1 :0 1 :0 1 :0 1 :0
## 2:0 2 :0 NA's:8 NA's:8 NA's:8 NA's:8 NA's:8
## 3:8 4 :0
## NA's:8
##
##
## roots
## 0:0
## 1:8
## 2:0
##
##
##
##
## Class date plant.stand precip temp hail crop.hist
## phyllosticta-leaf-spot:20 0:0 0: 9 0: 9 0: 0 0:11 0:5
## 2-4-d-injury : 0 1:3 1:11 1:11 1:10 1: 9 1:5
## alternarialeaf-spot : 0 2:8 2: 0 2:10 2:5
## anthracnose : 0 3:7 3:5
## bacterial-blight : 0 4:2
## bacterial-pustule : 0 5:0
## (Other) : 0 6:0
## area.dam sever seed.tmt germ plant.growth leaves leaf.halo leaf.marg
## 0:7 0:14 0:10 0:5 0:16 0: 0 0: 0 0:20
## 1:0 1: 6 1: 8 1:8 1: 4 1:20 1: 0 1: 0
## 2:7 2: 0 2: 2 2:7 2:20 2: 0
## 3:6
##
##
##
## leaf.size leaf.shread leaf.malf leaf.mild stem lodging stem.cankers
## 0: 0 0:10 0:10 0:20 0:20 0:20 0:20
## 1:20 1:10 1:10 1: 0 1: 0 1: 0 1: 0
## 2: 0 2: 0 2: 0
## 3: 0
##
##
##
## canker.lesion fruiting.bodies ext.decay mycelium int.discolor sclerotia
## 0:20 0:20 0:20 0:20 0:20 0:20
## 1: 0 1: 0 1: 0 1: 0 1: 0 1: 0
## 2: 0 2: 0 2: 0
## 3: 0
##
##
##
## fruit.pods fruit.spots seed mold.growth seed.discolor seed.size shriveling
## 0:20 0:20 0:20 0:20 0:20 0:20 0:20
## 1: 0 1: 0 1: 0 1: 0 1: 0 1: 0 1: 0
## 2: 0 2: 0
## 3: 0 4: 0
##
##
##
## roots
## 0:20
## 1: 0
## 2: 0
##
##
##
##
## Class date plant.stand precip temp hail crop.hist
## phytophthora-rot :88 0: 7 0: 0 0: 0 0: 9 0 :14 0: 6
## 2-4-d-injury : 0 1:23 1:88 1:30 1:51 1 : 6 1:20
## alternarialeaf-spot: 0 2:25 2:58 2:28 NA's:68 2:32
## anthracnose : 0 3:27 3:30
## bacterial-blight : 0 4: 6
## bacterial-pustule : 0 5: 0
## (Other) : 0 6: 0
## area.dam sever seed.tmt germ plant.growth leaves leaf.halo leaf.marg
## 0: 0 0 : 0 0 :10 0 : 7 0: 0 0: 0 0 :33 0 : 0
## 1:87 1 : 7 1 :10 1 : 7 1:88 1:88 1 : 0 1 : 0
## 2: 0 2 :13 2 : 0 2 : 6 2 : 0 2 :33
## 3: 1 NA's:68 NA's:68 NA's:68 NA's:55 NA's:55
##
##
##
## leaf.size leaf.shread leaf.malf leaf.mild stem lodging stem.cankers
## 0 : 0 0 :33 0 :33 0 :33 0: 0 0 :18 0: 6
## 1 : 0 1 : 0 1 : 0 1 : 0 1:88 1 : 2 1:19
## 2 :33 NA's:55 NA's:55 2 : 0 NA's:68 2:30
## NA's:55 NA's:55 3:33
##
##
##
## canker.lesion fruiting.bodies ext.decay mycelium int.discolor sclerotia
## 0: 0 0 :20 0:69 0:88 0:88 0:88
## 1: 0 1 : 0 1: 6 1: 0 1: 0 1: 0
## 2:88 NA's:68 2:13 2: 0
## 3: 0
##
##
##
## fruit.pods fruit.spots seed mold.growth seed.discolor seed.size
## 0 : 0 0 : 0 0 :20 0 :20 0 :20 0 :20
## 1 : 0 1 : 0 1 : 0 1 : 0 1 : 0 1 : 0
## 2 : 0 2 : 0 NA's:68 NA's:68 NA's:68 NA's:68
## 3 :20 4 :20
## NA's:68 NA's:68
##
##
## shriveling roots
## 0 :20 0:20
## 1 : 0 1:68
## NA's:68 2: 0
##
##
##
##
## Class date plant.stand precip temp hail crop.hist
## powdery-mildew :20 0:0 0: 9 0:10 0:10 0:11 0:5
## 2-4-d-injury : 0 1:3 1:11 1: 9 1:10 1: 9 1:5
## alternarialeaf-spot: 0 2:3 2: 1 2: 0 2:5
## anthracnose : 0 3:2 3:5
## bacterial-blight : 0 4:4
## bacterial-pustule : 0 5:4
## (Other) : 0 6:4
## area.dam sever seed.tmt germ plant.growth leaves leaf.halo leaf.marg
## 0:5 0:10 0:10 0:7 0:20 0: 0 0:20 0: 0
## 1:5 1:10 1: 6 1:7 1: 0 1:20 1: 0 1: 0
## 2:5 2: 0 2: 4 2:6 2: 0 2:20
## 3:5
##
##
##
## leaf.size leaf.shread leaf.malf leaf.mild stem lodging stem.cankers
## 0: 0 0:20 0:20 0: 0 0:20 0:20 0:20
## 1: 0 1: 0 1: 0 1:20 1: 0 1: 0 1: 0
## 2:20 2: 0 2: 0
## 3: 0
##
##
##
## canker.lesion fruiting.bodies ext.decay mycelium int.discolor sclerotia
## 0:20 0:20 0:20 0:20 0:20 0:20
## 1: 0 1: 0 1: 0 1: 0 1: 0 1: 0
## 2: 0 2: 0 2: 0
## 3: 0
##
##
##
## fruit.pods fruit.spots seed mold.growth seed.discolor seed.size shriveling
## 0:20 0:20 0:20 0:20 0:20 0:20 0:20
## 1: 0 1: 0 1: 0 1: 0 1: 0 1: 0 1: 0
## 2: 0 2: 0
## 3: 0 4: 0
##
##
##
## roots
## 0:20
## 1: 0
## 2: 0
##
##
##
##
## Class date plant.stand precip temp hail crop.hist
## purple-seed-stain :20 0:0 0:20 0: 0 0:7 0:11 0:5
## 2-4-d-injury : 0 1:0 1: 0 1: 0 1:7 1: 9 1:5
## alternarialeaf-spot: 0 2:0 2:20 2:6 2:5
## anthracnose : 0 3:4 3:5
## bacterial-blight : 0 4:5
## bacterial-pustule : 0 5:5
## (Other) : 0 6:6
## area.dam sever seed.tmt germ plant.growth leaves leaf.halo leaf.marg
## 0:5 0:20 0:12 0:2 0:20 0: 9 0: 9 0:11
## 1:5 1: 0 1: 8 1:9 1: 0 1:11 1: 0 1: 0
## 2:5 2: 0 2: 0 2:9 2:11 2: 9
## 3:5
##
##
##
## leaf.size leaf.shread leaf.malf leaf.mild stem lodging stem.cankers
## 0:11 0:20 0:20 0:20 0:11 0:15 0:20
## 1: 0 1: 0 1: 0 1: 0 1: 9 1: 5 1: 0
## 2: 9 2: 0 2: 0
## 3: 0
##
##
##
## canker.lesion fruiting.bodies ext.decay mycelium int.discolor sclerotia
## 0: 0 0:20 0:20 0:20 0:20 0:20
## 1: 0 1: 0 1: 0 1: 0 1: 0 1: 0
## 2: 0 2: 0 2: 0
## 3:20
##
##
##
## fruit.pods fruit.spots seed mold.growth seed.discolor seed.size shriveling
## 0: 9 0: 9 0: 0 0:20 0: 0 0:20 0:20
## 1:11 1:11 1:20 1: 0 1:20 1: 0 1: 0
## 2: 0 2: 0
## 3: 0 4: 0
##
##
##
## roots
## 0:20
## 1: 0
## 2: 0
##
##
##
##
## Class date plant.stand precip temp hail crop.hist
## rhizoctonia-root-rot:20 0:6 0: 2 0: 0 0:20 0:18 0:5
## 2-4-d-injury : 0 1:6 1:18 1: 0 1: 0 1: 2 1:5
## alternarialeaf-spot : 0 2:6 2:20 2: 0 2:5
## anthracnose : 0 3:1 3:5
## bacterial-blight : 0 4:1
## bacterial-pustule : 0 5:0
## (Other) : 0 6:0
## area.dam sever seed.tmt germ plant.growth leaves leaf.halo leaf.marg
## 0: 0 0: 0 0:16 0: 0 0: 0 0:19 0:20 0: 0
## 1:20 1: 9 1: 4 1:10 1:20 1: 1 1: 0 1: 0
## 2: 0 2:11 2: 0 2:10 2: 0 2:20
## 3: 0
##
##
##
## leaf.size leaf.shread leaf.malf leaf.mild stem lodging stem.cankers
## 0: 0 0:20 0:20 0:20 0: 0 0:18 0: 0
## 1: 0 1: 0 1: 0 1: 0 1:20 1: 2 1:20
## 2:20 2: 0 2: 0
## 3: 0
##
##
##
## canker.lesion fruiting.bodies ext.decay mycelium int.discolor sclerotia
## 0: 0 0:20 0: 0 0:14 0:20 0:20
## 1:20 1: 0 1:20 1: 6 1: 0 1: 0
## 2: 0 2: 0 2: 0
## 3: 0
##
##
##
## fruit.pods fruit.spots seed mold.growth seed.discolor seed.size shriveling
## 0: 0 0: 0 0:20 0:20 0:20 0:20 0:20
## 1: 0 1: 0 1: 0 1: 0 1: 0 1: 0 1: 0
## 2: 0 2: 0
## 3:20 4:20
##
##
##
## roots
## 0:19
## 1: 1
## 2: 0
##
##
##
## We see that only some of the classes have any NAs
- 2-4-d-injury
- cyst-nematode
- diaporthe-pod-&-stem-blight
- herbicide-injury
- phytophthora-rot
This suggests that just dropping missing is improper as they are clearly not missing at random.
- Develop a strategy for handling missing data, either by eliminating predictors or imputation.
As the missing values are not exactly numeric nor normally distributed in the untransformed state it is not advisable to use median, mean, or mode.
At this point MICE (Mulivariate Imputation by Chained Equations) is probably the standard response.
set.seed(987655)
SoybeanImputed <- mice(Soybean, method="polyreg")## Warning: Number of logged events: 848md.pattern(complete(SoybeanImputed), rotate.names = T)## /\ /\
## { `---' }
## { O O }
## ==> V <== No need for mice. This data set is completely observed.
## \ \|/ /
## `-----'
## Class date plant.stand precip temp hail crop.hist area.dam sever seed.tmt
## 683 1 1 1 1 1 1 1 1 1 1
## 0 0 0 0 0 0 0 0 0 0
## germ plant.growth leaves leaf.halo leaf.marg leaf.size leaf.shread
## 683 1 1 1 1 1 1 1
## 0 0 0 0 0 0 0
## leaf.malf leaf.mild stem lodging stem.cankers canker.lesion fruiting.bodies
## 683 1 1 1 1 1 1 1
## 0 0 0 0 0 0 0
## ext.decay mycelium int.discolor sclerotia fruit.pods fruit.spots seed
## 683 1 1 1 1 1 1 1
## 0 0 0 0 0 0 0
## mold.growth seed.discolor seed.size shriveling roots
## 683 1 1 1 1 1 0
## 0 0 0 0 0 0We don’t yet have the tools to really determine the appropriateness of this imputation (and arguably without a use case it would be dangerous to make sweeping statements regardless), but the data is no longer missing, and in general imputation will result in better work products.