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added mushroom and census income datasets;
removed config variables from utils functions
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README.md
122
README.md
@ -3,7 +3,7 @@ Andrzej Wójtowicz
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Document generation date: 2016-07-17 02:59:19.
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Document generation date: 2016-08-11 18:12:19.
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This project preprocesses a few datasets from [UC Irvine Machine Learning
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Repository](https://archive.ics.uci.edu/ml/) into tidy R object files.
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@ -27,9 +27,11 @@ within a dataset.
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1. [Breast Cancer Wisconsin (Diagnostic)](#breast-cancer-wisconsin-diagnostic)
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1. [Breast Cancer Wisconsin (Original)](#breast-cancer-wisconsin-original)
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1. [Cardiotocography](#cardiotocography)
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1. [Census income](#census-income)
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1. [Default of credit card clients](#default-of-credit-card-clients)
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1. [ILPD (Indian Liver Patient Dataset)](#ilpd-indian-liver-patient-dataset)
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1. [MAGIC Gamma Telescope](#magic-gamma-telescope)
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1. [Mushroom](#mushroom)
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1. [Seismic bumps](#seismic-bumps)
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1. [Spambase](#spambase)
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1. [Wine Quality](#wine-quality)
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@ -279,6 +281,62 @@ Ayres de Campos et al. (2000) SisPorto 2.0 A Program for Automated Analysis of C
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---
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# Census income
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**Local directory**: census-income
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**Details**: [link](https://archive.ics.uci.edu/ml/datasets/Census+Income)
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**Source data files**:
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* [adult.data](https://archive.ics.uci.edu/ml/machine-learning-databases/adult/adult.data)
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* [adult.test](https://archive.ics.uci.edu/ml/machine-learning-databases/adult/adult.test)
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* [adult.names](https://archive.ics.uci.edu/ml/machine-learning-databases/adult/adult.names)
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**Cite**:
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```nohighlight
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https://archive.ics.uci.edu/ml/citation_policy.html
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@misc{Lichman:2013 , author = "M. Lichman", year = "2013", title = "{UCI} Machine Learning Repository", url = "http://archive.ics.uci.edu/ml", institution = "University of California, Irvine, School of Information and Computer Sciences" }
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```
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**Dataset**:
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```nohighlight
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'data.frame': 45222 obs. of 14 variables:
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$ age : int 39 50 38 53 28 37 49 52 31 42 ...
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$ workclass : Factor w/ 8 levels "federal.gov",..: 7 6 4 4 4 4 4 6 4 4 ...
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$ fnlwgt : int 77516 83311 215646 234721 338409 284582 160187 209642 45781 159449 ...
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$ education : Ord.factor w/ 16 levels "preschool"<"x1st.4th"<..: 13 13 9 7 13 14 5 9 14 13 ...
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$ marital.status: Factor w/ 7 levels "divorced","married.af.spouse",..: 5 3 1 3 3 3 4 3 5 3 ...
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$ occupation : Factor w/ 14 levels "adm.clerical",..: 1 4 6 6 10 4 8 4 10 4 ...
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$ relationship : Factor w/ 6 levels "husband","not.in.family",..: 2 1 2 1 6 6 2 1 2 1 ...
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$ race : Factor w/ 5 levels "amer.indian.eskimo",..: 5 5 5 3 3 5 3 5 5 5 ...
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$ sex : Factor w/ 2 levels "female","male": 2 2 2 2 1 1 1 2 1 2 ...
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$ capital.gain : int 2174 0 0 0 0 0 0 0 14084 5178 ...
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$ capital.loss : int 0 0 0 0 0 0 0 0 0 0 ...
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$ hours.per.week: int 40 13 40 40 40 40 16 45 50 40 ...
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$ native.country: Factor w/ 41 levels "cambodia","canada",..: 39 39 39 39 5 39 23 39 39 39 ...
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$ class : Factor w/ 2 levels "x..50k","x.50k": 1 1 1 1 1 1 1 2 2 2 ...
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```
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**Predictors**:
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|Type | Frequency|
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|:--------------|---------:|
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|factor | 7|
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|integer | 5|
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|ordered factor | 1|
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**Class imbalance**:
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| class A | class B |
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|:-------:|:-------:|
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| 25 % | 75 % |
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| 11208 | 34014 |
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---
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# Default of credit card clients
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**Local directory**: credit-card
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@ -442,6 +500,68 @@ https://archive.ics.uci.edu/ml/citation_policy.html
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---
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# Mushroom
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**Local directory**: mushroom
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**Details**: [link](https://archive.ics.uci.edu/ml/datasets/Mushroom)
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**Source data files**:
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* [agaricus-lepiota.data](https://archive.ics.uci.edu/ml/machine-learning-databases/mushroom/agaricus-lepiota.data)
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* [agaricus-lepiota.names](https://archive.ics.uci.edu/ml/machine-learning-databases/mushroom/agaricus-lepiota.names)
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**Cite**:
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```nohighlight
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https://archive.ics.uci.edu/ml/citation_policy.html
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@misc{Lichman:2013 , author = "M. Lichman", year = "2013", title = "{UCI} Machine Learning Repository", url = "http://archive.ics.uci.edu/ml", institution = "University of California, Irvine, School of Information and Computer Sciences" }
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```
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**Dataset**:
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```nohighlight
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'data.frame': 5644 obs. of 22 variables:
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$ cap.shape : Factor w/ 6 levels "b","c","f","k",..: 6 6 1 6 6 6 1 1 6 1 ...
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$ cap.surface : Factor w/ 4 levels "f","g","s","y": 3 3 3 4 3 4 3 4 4 3 ...
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$ cap.color : Factor w/ 10 levels "b","c","e","g",..: 5 10 9 9 4 10 9 9 9 10 ...
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$ bruises : Factor w/ 2 levels "f","t": 2 2 2 2 1 2 2 2 2 2 ...
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$ odor : Factor w/ 9 levels "a","c","f","l",..: 7 1 4 7 6 1 1 4 7 1 ...
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$ gill.attachment : Factor w/ 2 levels "a","f": 2 2 2 2 2 2 2 2 2 2 ...
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$ gill.spacing : Factor w/ 2 levels "c","w": 1 1 1 1 2 1 1 1 1 1 ...
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$ gill.size : Factor w/ 2 levels "b","n": 2 1 1 2 1 1 1 1 2 1 ...
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$ gill.color : Factor w/ 12 levels "b","e","g","h",..: 5 5 6 6 5 6 3 6 8 3 ...
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$ stalk.shape : Factor w/ 2 levels "e","t": 1 1 1 1 2 1 1 1 1 1 ...
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$ stalk.root : Factor w/ 4 levels "b","c","e","r": 3 2 2 3 3 2 2 2 3 2 ...
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$ stalk.surface.above.ring: Factor w/ 4 levels "f","k","s","y": 3 3 3 3 3 3 3 3 3 3 ...
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$ stalk.surface.below.ring: Factor w/ 4 levels "f","k","s","y": 3 3 3 3 3 3 3 3 3 3 ...
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$ stalk.color.above.ring : Factor w/ 9 levels "b","c","e","g",..: 8 8 8 8 8 8 8 8 8 8 ...
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$ stalk.color.below.ring : Factor w/ 9 levels "b","c","e","g",..: 8 8 8 8 8 8 8 8 8 8 ...
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$ veil.color : Factor w/ 4 levels "n","o","w","y": 3 3 3 3 3 3 3 3 3 3 ...
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$ ring.number : int 1 1 1 1 1 1 1 1 1 1 ...
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$ ring.type : Factor w/ 5 levels "e","f","l","n",..: 5 5 5 5 1 5 5 5 5 5 ...
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$ spore.print.color : Factor w/ 9 levels "b","h","k","n",..: 3 4 4 3 4 3 3 4 3 3 ...
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$ population : Factor w/ 6 levels "a","c","n","s",..: 4 3 3 4 1 3 3 4 5 4 ...
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$ habitat : Factor w/ 7 levels "d","g","l","m",..: 6 2 4 6 2 2 4 4 2 4 ...
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$ class : Factor w/ 2 levels "e","p": 2 1 1 2 1 1 1 1 2 1 ...
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```
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**Predictors**:
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|Type | Frequency|
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|:-------|---------:|
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|factor | 20|
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|integer | 1|
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**Class imbalance**:
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| class A | class B |
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|:-------:|:-------:|
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| 38 % | 62 % |
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| 2156 | 3488 |
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---
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# Seismic bumps
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**Local directory**: seismic-bumps
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19
data-collection/census-income/config.yaml
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19
data-collection/census-income/config.yaml
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---
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name: Census income
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info: https://archive.ics.uci.edu/ml/datasets/Census+Income
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urls:
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- https://archive.ics.uci.edu/ml/machine-learning-databases/adult/adult.data
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- https://archive.ics.uci.edu/ml/machine-learning-databases/adult/adult.test
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- https://archive.ics.uci.edu/ml/machine-learning-databases/adult/adult.names
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cite: >
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https://archive.ics.uci.edu/ml/citation_policy.html
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@misc{Lichman:2013 ,
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author = "M. Lichman",
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year = "2013",
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title = "{UCI} Machine Learning Repository",
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url = "http://archive.ics.uci.edu/ml",
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institution = "University of California, Irvine, School of Information and Computer Sciences" }
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49
data-collection/census-income/preprocess.R
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49
data-collection/census-income/preprocess.R
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@ -0,0 +1,49 @@
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preprocess.dataset = function()
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{
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csv.file.1 = "adult.data"
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csv.file.2 = "adult.test"
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dataset.1 = read.csv(file.path(orig.dir, csv.file.1), header = FALSE,
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na.strings = " ?")
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dataset.2 = read.csv(file.path(orig.dir, csv.file.2), header = FALSE,
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na.strings = " ?", skip = 1)
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column.names = c("age", "workclass", "fnlwgt", "education",
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"education.num", "marital.status", "occupation",
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"relationship", "race", "sex", "capital.gain",
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"capital.loss", "hours.per.week", "native.country",
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"class")
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colnames(dataset.1) = column.names
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colnames(dataset.2) = column.names
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levels(dataset.2$class) = gsub("\\.", "", levels(dataset.2$class))
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dataset = rbind(dataset.1, dataset.2)
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for (column.name in column.names)
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{
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if (is.factor(dataset[[column.name]]))
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{
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levels(dataset[[column.name]]) = trimws(levels(dataset[[column.name]]))
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}
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}
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education.ordered.levels = dataset %>%
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select(education.num, education) %>%
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unique %>%
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arrange(education.num) %>%
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select(education) %>%
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c %>%
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unlist %>%
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unname %>%
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as.character
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dataset = dataset %>%
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mutate(education = factor(education, levels = education.ordered.levels,
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ordered = TRUE)) %>%
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select(-education.num) %>%
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filter(complete.cases(.))
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return(dataset)
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}
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18
data-collection/mushroom/config.yaml
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data-collection/mushroom/config.yaml
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---
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name: Mushroom
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info: https://archive.ics.uci.edu/ml/datasets/Mushroom
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urls:
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- https://archive.ics.uci.edu/ml/machine-learning-databases/mushroom/agaricus-lepiota.data
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- https://archive.ics.uci.edu/ml/machine-learning-databases/mushroom/agaricus-lepiota.names
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cite: >
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https://archive.ics.uci.edu/ml/citation_policy.html
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@misc{Lichman:2013 ,
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author = "M. Lichman",
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year = "2013",
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title = "{UCI} Machine Learning Repository",
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url = "http://archive.ics.uci.edu/ml",
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institution = "University of California, Irvine, School of Information and Computer Sciences" }
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22
data-collection/mushroom/preprocess.R
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22
data-collection/mushroom/preprocess.R
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preprocess.dataset = function()
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{
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csv.file = "agaricus-lepiota.data"
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dataset = read.csv(file.path(orig.dir, csv.file), header = FALSE,
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na.strings = "?")
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colnames(dataset) = c("class", "cap.shape", "cap.surface", "cap.color",
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"bruises", "odor", "gill.attachment", "gill.spacing",
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"gill.size", "gill.color", "stalk.shape", "stalk.root",
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"stalk.surface.above.ring", "stalk.surface.below.ring",
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"stalk.color.above.ring", "stalk.color.below.ring",
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"veil.type", "veil.color", "ring.number", "ring.type",
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"spore.print.color", "population", "habitat")
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dataset = dataset %>%
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select(cap.shape:habitat, class, -veil.type) %>%
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filter(complete.cases(.)) %>%
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mutate(ring.number = as.integer(as.integer(ring.number) - 1))
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return(dataset)
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}
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@ -3,7 +3,7 @@
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source("init.R")
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source("utils.R")
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setup.logger(LOGGER.OUTPUT.S1.FILE)
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setup.logger(LOGGER.OUTPUT.S1.FILE, LOGGER.OVERWRITE.EXISTING.FILES)
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flog.info("Step 1: download dataset collection")
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@ -3,7 +3,7 @@
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source("init.R")
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source("utils.R")
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setup.logger(LOGGER.OUTPUT.S2.FILE)
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setup.logger(LOGGER.OUTPUT.S2.FILE, LOGGER.OVERWRITE.EXISTING.FILES)
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flog.info("Step 2: preprocess dataset collection")
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4
utils.R
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utils.R
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", classes: ", perc.classes[1], "%/", perc.classes[2], "%"))
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}
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setup.logger = function(output.file)
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setup.logger = function(output.file, overwrite.existing.files)
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{
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if (LOGGER.OVERWRITE.EXISTING.FILES & file.exists(output.file))
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if (overwrite.existing.files & file.exists(output.file))
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{
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file.remove(output.file)
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}
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