Misclassification of Cores
Kristen Noelle Finch
2/15/2017
Details
This is an R Markdown document. These data pretain to Finch et al. 2017 Applications in Plant Sciences.
Structure
two or three annuals rings per increment core random forest classification
Question
How many annual rings/core were misclassified?
Purpose
I investigated this because we were interested in understanding why Cascades samples are easier to classify than Coast samples.
Sample totals for this analysis
Cascades: 103
Coast: 84
Total: 187 (one sample deleted for this analysis because it was a single ring from the core)
library(randomForest)
library(ggplot2)Data
quest2<-read.csv("quest_test_2.csv")
quest2## Sample.ID Region Mis.class.score
## 1 PSME1024.1 Cascades 0
## 2 PSME1026.1 Cascades 0
## 3 PSME1026.2 Cascades 0
## 4 PSME1191.2 Coast 0
## 5 PSME1191.3 Coast 0
## 6 PSME1195.2 Coast 0
## 7 PSME1195.4 Coast 0
## 8 PSME1202.1 Cascades 0
## 9 PSME1202.2 Cascades 0
## 10 PSME1202.3 Cascades 0
## 11 PSME1202.5 Cascades 0
## 12 PSME1223.1 Cascades 0
## 13 PSME1223.2 Cascades 0
## 14 PSME1223.3 Cascades 0
## 15 PSME1223.4 Cascades 0
## 16 PSME2034.1 Cascades 0
## 17 PSME2034.2 Cascades 0
## 18 PSME2034.3 Cascades 0
## 19 PSME2034.4 Cascades 0
## 20 PSME2092.2 Cascades 0
## 21 PSME2092.3 Cascades 0
## 22 PSME2092.4 Cascades 0
## 23 PSME3054.3 Cascades 0
## 24 PSME3061.1 Cascades 0
## 25 PSME3061.3 Cascades 0
## 26 PSME3061.4 Cascades 0
## 27 PSME3061.5 Cascades 0
## 28 PSME3061.6 Cascades 0
## 29 PSME3175.1 Coast 0
## 30 PSME3175.2 Coast 0
## 31 PSME3198.1 Coast 0
## 32 PSME3198.2 Coast 0
## 33 PSME3198.3 Coast 0
## 34 PSME3198.4 Coast 0
## 35 PSME3202.1 Coast 0
## 36 PSME3202.2 Coast 0
## 37 PSME3202.4 Coast 0
## 38 PSME3205.1 Coast 0
## 39 PSME3205.2 Coast 0
## 40 PSME3205.3 Coast 0
## 41 PSME3218.1 Coast 0
## 42 PSME3218.2 Coast 0
## 43 PSME3218.3 Coast 0
## 44 PSME3238.1 Coast 0
## 45 PSME3238.4 Coast 0
## 46 PSME3240.1 Coast 0
## 47 PSME3240.2 Coast 0
## 48 PSME3313.2 Coast 0
## 49 PSME3353.1 Coast 0
## 50 PSME3358.1 Coast 0
## 51 PSME3358.3 Coast 0
## 52 PSME3358.4 Coast 0
## 53 PSME3364.2 Coast 0
## 54 PSME4005.2 Cascades 0
## 55 PSME4005.4 Cascades 0
## 56 PSME4069.1 Cascades 0
## 57 PSME4069.2 Cascades 0
## 58 PSME4069.4 Cascades 0
## 59 PSME4085.2 Cascades 0
## 60 PSME4085.3 Cascades 0
## 61 PSME4085.4 Cascades 0
## 62 PSME4146.1 Cascades 0
## 63 PSME4146.2 Cascades 0
## 64 PSME4146.3 Cascades 0
## 65 PSME4153.1 Cascades 0
## 66 PSME4153.2 Cascades 0
## 67 PSME4153.3 Cascades 0
## 68 PSME4153.4 Cascades 0
## 69 PSME4158.1 Cascades 0
## 70 PSME4158.3 Cascades 0
## 71 PSME4158.4 Cascades 0
## 72 PSME4192.1 Cascades 0
## 73 PSME4192.3 Cascades 0
## 74 PSME4193.3 Cascades 0
## 75 PSME4193.4 Cascades 0
## 76 PSME4194.2 Cascades 0
## 77 PSME4194.4 Cascades 0
## 78 PSME4196.1 Cascades 0
## 79 PSME4196.2 Cascades 0
## 80 PSME4199.1 Cascades 0
## 81 PSME4199.3 Cascades 0
## 82 PSME4202.1 Cascades 0
## 83 PSME4202.2 Cascades 0
## 84 PSME4202.3 Cascades 0
## 85 PSME4203.1 Cascades 0
## 86 PSME4203.2 Cascades 0
## 87 PSME4203.3 Cascades 0
## 88 PSME4203.4 Cascades 0
## 89 PSME4203.5 Cascades 0
## 90 PSME4205.3 Cascades 0
## 91 PSME4205.4 Cascades 0
## 92 PSME4209.1 Cascades 0
## 93 PSME4209.2 Cascades 0
## 94 PSME4209.3 Cascades 0
## 95 PSME4209.4 Cascades 0
## 96 PSME6015.1 Coast 0
## 97 PSME6015.3 Coast 0
## 98 PSME6024.2 Coast 0
## 99 PSME6024.4 Coast 0
## 100 PSME6090.2 Coast 0
## 101 PSME6090.3 Coast 0
## 102 PSME6090.4 Coast 0
## 103 PSME6095.1 Coast 0
## 104 PSME6095.2 Coast 0
## 105 PSME6095.4 Coast 0
## 106 PSME6105.1 Coast 0
## 107 PSME6105.2 Coast 0
## 108 PSME6105.3 Coast 0
## 109 PSME6105.4 Coast 0
## 110 PSME6107.1 Coast 0
## 111 PSME6107.2 Coast 0
## 112 PSME6107.3 Coast 0
## 113 PSME6107.4 Coast 0
## 114 PSME6118.2 Coast 0
## 115 PSME6118.3 Coast 0
## 116 PSME6118.4 Coast 0
## 117 PSMEAMY.1 Coast 0
## 118 PSMEAMY.2 Coast 0
## 119 PSMEAMY.4 Coast 0
## 120 PSME1024.2 Cascades 1
## 121 PSME1024.3 Cascades 1
## 122 PSME1195.3 Coast 1
## 123 PSME2092.1 Cascades 1
## 124 PSME3031.3 Cascades 1
## 125 PSME3054.1 Cascades 1
## 126 PSME3054.2 Cascades 1
## 127 PSME3175.4 Coast 1
## 128 PSME3202.3 Coast 1
## 129 PSME3205.4 Coast 1
## 130 PSME3313.3 Coast 1
## 131 PSME3313.4 Coast 1
## 132 PSME3353.2 Coast 1
## 133 PSME3364.1 Coast 1
## 134 PSME4069.3 Cascades 1
## 135 PSME4126.4 Cascades 1
## 136 PSME4158.2 Cascades 1
## 137 PSME4192.2 Cascades 1
## 138 PSME4193.1 Cascades 1
## 139 PSME4194.1 Cascades 1
## 140 PSME4199.2 Cascades 1
## 141 PSME4199.4 Cascades 1
## 142 PSME4202.4 Cascades 1
## 143 PSME4205.2 Cascades 1
## 144 PSME6015.4 Coast 1
## 145 PSME6024.3 Coast 1
## 146 PSME6095.3 Coast 1
## 147 PSME1191.1 Coast 2
## 148 PSME1191.4 Coast 2
## 149 PSME1195.1 Coast 2
## 150 PSME3031.1 Cascades 2
## 151 PSME3061.2 Cascades 2
## 152 PSME3187.3 Coast 2
## 153 PSME3218.4 Coast 2
## 154 PSME3238.3 Coast 2
## 155 PSME3353.3 Coast 2
## 156 PSME3364.3 Coast 2
## 157 PSME4005.1 Cascades 2
## 158 PSME4085.1 Cascades 2
## 159 PSME4126.1 Cascades 2
## 160 PSME4126.2 Cascades 2
## 161 PSME4146.4 Cascades 2
## 162 PSME4173.2 Cascades 2
## 163 PSME4192.4 Cascades 2
## 164 PSME4193.2 Cascades 2
## 165 PSME4194.3 Cascades 2
## 166 PSME4196.3 Cascades 2
## 167 PSME4196.4 Cascades 2
## 168 PSME4205.1 Cascades 2
## 169 PSME6024.1 Coast 2
## 170 PSME6118.1 Coast 2
## 171 PSMEAMY.3 Coast 2
## 172 PSME1024.4 Cascades 3
## 173 PSME3031.2 Cascades 3
## 174 PSME3031.4 Cascades 3
## 175 PSME3054.4 Cascades 3
## 176 PSME3175.3 Coast 3
## 177 PSME3187.1 Coast 3
## 178 PSME3187.2 Coast 3
## 179 PSME3238.2 Coast 3
## 180 PSME3313.1 Coast 3
## 181 PSME3353.4 Coast 3
## 182 PSME3358.2 Coast 3
## 183 PSME4005.3 Cascades 3
## 184 PSME4126.3 Cascades 3
## 185 PSME4173.1 Cascades 3
## 186 PSME6015.2 Coast 3
## 187 PSME6090.1 Coast 3mis.class<-ggplot(data=quest2, aes(x=factor(Mis.class.score), fill=Region))+geom_bar(position="dodge")+
scale_fill_manual(values = c("darkred", "midnightblue"))+
annotate("text", x = .75, y = 70, label = "64.1%", size=2.5)+
annotate("text", x = 1.25, y = 60, label = "63.1%", size=2.5)+
annotate("text", x = 1.75, y = 20, label = "15.5%", size=2.5)+
annotate("text", x = 2.25, y = 15, label = "13.1%", size=2.5)+
annotate("text", x = 2.75, y = 18, label = "13.6%", size=2.5)+
annotate("text", x = 3.25, y = 15, label = "13.1%", size=2.5)+
annotate("text", x = 3.75, y = 10, label = "6.8%", size=2.5)+
annotate("text", x = 4.25, y = 12, label = "10.7%", size=2.5)+
scale_x_discrete(labels=c("0"="0/3 Misclassified", "1"="1/3 Misclassified",
"2"="2/3 Misclassified", "3"="3/3 Misclassified"))+
theme_bw()+
theme(panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
plot.title = element_text(hjust = 0),
axis.title=element_text(size=8),
axis.text=element_text(size=6),
legend.justification=c(1,1),
legend.position=c(1,1),
legend.title=element_blank(),
legend.background = element_blank())+
xlab("Misclassification Score")+ylab("Cores")+ylim(c(0,75))
#ggsave("mis.class.jpg",plot=mis.class, width=3.5, height=3)Results
mis.class
- The majority of annual rings from the same core are all classified accurately.
- There were more Cascades cores where 1/3 rings were misclassified
- There were more Cascades cores where 2/3 rings were misclassified
- There were more Coast cores where 3/3 rings were misclassified
Conclusions
- Cascades samples are easier to classify than Coast samples because they have a more diverse chemical profile.
- Cascades samples are easier to classify than Coast samples because there are more Cascades samples.
Next Steps
- Rerun the asymmetry analysis with equal numbers of Coast and Cascades samples.