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Machine Learning Basics for a Newbie
6 Steps of Machine learning Lifecycle Introduction to Predictive Modeling
Introduction to Exploratory Data Analysis & Data Insights Descriptive Statistics Inferential Statistics How to Understand Population Distributions?
Reading Data Files into Python Different Variable Datatypes
Probability for Data Science Basic Concepts of Probability Axioms of Probability Conditional Probability
Central Tendencies for Continuous Variables Spread of Data KDE plots for Continuous Variable Overview of Distribution for Continuous variables Normal Distribution Skewed Distribution Skeweness and Kurtosis Distribution for Continuous Variable
Central Tendencies for Categorical Variables Understanding Discrete Distributions Performing EDA on Categorical Variables
Dealing with Missing Values Understanding Outliers Identifying Outliers in Data Outlier Detection in Python Outliers Detection Using IQR, Z-score, LOF and DBSCAN
Sample and Population Central Limit Theorem Confidence Interval and Margin of Error
Bivariate Analysis Introduction
Covariance Pearson Correlation Spearman's Correlation & Kendall's Tau Correlation versus Causation Tabular and Graphical methods for Bivariate Analysis Performing Bivariate Analysis on Continuous-Continuous Variables
Tabular and Graphical methods for Continuous-Categorical Variables Introduction to Hypothesis Testing P-value Two sample Z-test T-test T-test vs Z-test Performing Bivariate Analysis on Continuous-Catagorical variables
Chi-Squares Test Bivariate Analysis on Categorical Categorical Variables
Multivariate Analysis A Comprehensive Guide to Data Exploration The Data Science behind IPL
Supervised Learning vs Unsupervised Learning Reinforcement Learning Generative and Descriminative Models Parametric and Non Parametric model
Machine Learning Pipeline Preparing Dataset Build a Benchmark Model: Regression Build a Benchmark Model: Classification
Evaluation Metrics for Machine Learning Everyone should know Confusion Matrix Accuracy Precision and Recall AUC-ROC Log Loss R2 and Adjusted R2
Dealing with Missing Values Replacing Missing Values Imputing Missing Values in Data Working with Categorical Variables Working with Outliers Preprocessing Data for Model Building
Understanding Cost Function Understanding Gradient Descent Math Behind Gradient Descent Assumptions of Linear Regression Implement Linear Regression from Scratch Train Linear Regression in Python Implementing Linear Regression in R Diagnosing Residual Plots in Linear Regression Models Generalized Linear Models Introduction to Logistic Regression Odds Ratio Implementing Logistic Regression from Scratch Introduction to Scikit-learn in Python Train Logistic Regression in python Multiclass using Logistic Regression How to use Multinomial and Ordinal Logistic Regression in R ? Challenges with Linear Regression Introduction to Regularisation Implementing Regularisation Ridge Regression Lasso Regression
Introduction to K Nearest Neighbours Determining the Right Value of K in KNN Implement KNN from Scratch Implement KNN in Python
Bias Variance Tradeoff Introduction to Overfitting and Underfitting Visualizing Overfitting and Underfitting Selecting the Right Model What is Validation? Hold-Out Validation Understanding K Fold Cross Validation
Introduction to Feature Selection Feature Selection Algorithms Missing Value Ratio Low Variance Filter High Correlation Filter Backward Feature Elimination Forward Feature Selection Implement Feature Selection in Python Implement Feature Selection in R
Introduction to Decision Tree Purity in Decision Tree Terminologies Related to Decision Tree How to Select Best Split Point in Decision Tree? Chi-Squares Information Gain Reduction in Variance Optimizing Performance of Decision Tree Train Decision Tree using Scikit Learn Pruning of Decision Trees
Introduction to Feature Engineering Feature Transformation Feature Scaling Feature Engineering Frequency Encoding Automated Feature Engineering: Feature Tools
Introduction to Naive Bayes Conditional Probability and Bayes Theorem Introduction to Bayesian Adjustment Rating: The Incredible Concept Behind Online Ratings! Working of Naive Bayes Math behind Naive Bayes Types of Naive Bayes Implementation of Naive Bayes
Understanding how to solve Multiclass and Multilabled Classification Problem Evaluation Metrics: Multi Class Classification
Introduction to Ensemble Techniques Basic Ensemble Techniques Implementing Basic Ensemble Techniques Finding Optimal Weights of Ensemble Learner using Neural Network Why Ensemble Models Work well?
Introduction to Stacking Implementing Stacking Variants of Stacking Implementing Variants of Stacking Introduction to Blending Bootstrap Sampling Introduction to Random Sampling Hyper-parameters of Random Forest Implementing Random Forest Out-of-Bag (OOB) Score in the Random Forest IPL Team Win Prediction Project Using Machine Learning Introduction to Boosting Gradient Boosting Algorithm Math behind GBM Implementing GBM in python Regularized Greedy Forests Extreme Gradient Boosting Implementing XGBM in python Tuning Hyperparameters of XGBoost in Python Implement XGBM in R/H2O Adaptive Boosting Implementing Adaptive Boosing LightGBM Implementing LightGBM in Python Catboost Implementing Catboost in Python
Different Hyperparameter Tuning methods Implementing Different Hyperparameter Tuning methods GridsearchCV RandomizedsearchCV Bayesian Optimization for Hyperparameter Tuning Hyperopt
Understanding SVM Algorithm SVM Kernels In-depth Intuition and Practical Implementation SVM Kernel Tricks Kernels and Hyperparameters in SVM Implementing SVM from Scratch in Python and R
Introduction to Principal Component Analysis Steps to Perform Principal Compound Analysis Computation of Covariance Matrix Finding Eigenvectors and Eigenvalues Implementing PCA in python Visualizing PCA A Brief Introduction to Linear Discriminant Analysis Introduction to Factor Analysis
Introduction to Clustering Applications of Clustering Evaluation Metrics for Clustering Understanding K-Means Implementation of K-Means in Python Implementation of K-Means in R Choosing Right Value for K Profiling Market Segments using K-Means Clustering Hierarchical Clustering Implementation of Hierarchial Clustering DBSCAN Defining Similarity between clusters Build Better and Accurate Clusters with Gaussian Mixture Models
Understand Basics of Recommendation Engine with Case Study
8 Ways to Improve Accuracy of Machine Learning Models
Introduction to Dask Working with CuML
Introduction to Machine Learning Interpretability Framework and Interpretable Models model Agnostic Methods for Interpretability Implementing Interpretable Model Understanding SHAP Out-of-Core ML Introduction to Interpretable Machine Learning Models Model Agnostic Methods for Interpretability Game Theory & Shapley Values
Introduction to Machine Learning Interpretability Framework and Interpretable Models model Agnostic Methods for Interpretability Implementing Interpretable Model Understanding SHAP Out-of-Core ML Introduction to Interpretable Machine Learning Models Model Agnostic Methods for Interpretability Game Theory & Shapley Values
Introduction to AutoML Implementation of MLBox Introduction to PyCaret TPOT Auto-Sklearn EvalML
Pickle and Joblib Introduction to Model Deployment
Deploying Machine Learning Model using Streamlit Deploying ML Models in Docker Deploy Using Streamlit Deploy on Heroku Deploy Using Netlify Introduction to Amazon Sagemaker Setting up Amazon SageMaker Using SageMaker Endpoint to Generate Inference Deploy on Microsoft Azure Cloud Introduction to Flask for Model Deploying ML model using Flask
Model Deployment in Android Model Deployment in Iphone

Unleash the Power of Data using R with Covid Trial Dataset

A
Anu Last Updated : 31 Mar, 2021
3 min read
This article was published as a part of the Data Science Blogathon.

Introduction

Data is the universal truth guiding today’s world of Data Science. At the same time, it is not as simple as it looks to extract actionable insights. Turning data into meaningful insights require deep insights into the domain and the environment from where the data originates.

The year 2020 turned into a painful year. Covid has changed our lives forever. These difficult times have taught us how to be resilient and empathetic. Hope is setting its foot with the arrival of Covid Vaccines. Let’s learn the power of data using Covid Trial Datasets which has led to the emergence of vaccines in record time.

We will be using R as the programming language to explore and visualize Covid Trial Datasets.

Below is a visualization of Covid Vaccine Trial Datasets in R that we will be analyzing:

Step 1: Load the Covid Trial Dataset

CovidDF = data.frame(read.csv(“CovidTrials.csv”))

Step 2: Analyze Datasets and their variables

> str(COVID)
‘data.frame’: 5061 obs. of 27 variables:

There are 5061 observations(rows) with 27 variables(columns)

Analyze Gender Variable:

> unique(CovidDF$Gender)
[1] “All” “Female” “Male” “”

> length(which(CovidDF$Gender == “All”))
[1] 4881

> length(which(CovidDF$Gender == “Male”))
[1] 40

> length(which(CovidDF$Gender == “Female”))
[1] 131

> length(which(CovidDF$Gender == “”))
[1] 9

> nrow(CovidDF);
[1] 5061

There is a total of 5061 observations (rows) with 40 males, 131females,4881 all, and 9 unspecified genders.

The value “All” for the gender variable indicates that it can be of any gender. It is hard to achieve precise results when modeling data with gender. Here comes the nightmare of every data engineer trying to deal with incomplete data.

Analyze Study Results Variable:

> unique(CovidDF$Study.Results)
[1] “No Results Available” “Has Results”

> length(which(CovidDF$Study.Results == “No Results Available”))
[1] 5033

> length(which(CovidDF$Study.Results == “Has Results”))
[1] 28

The above result indicates that the Covid Trial datasets were captured when the study was still happening with 5033 results under “No Results Available”.

Step 3: Analyze Age Variable

Age variable consists of free-form values with different formats used to capture the age of volunteers in different locations.

Below is sample age values captured in trial datasets

18 Years and older (Adult, Older Adult)
18 Years and older (Adult, Older Adult)
Child, Adult, Older Adult
18 Years to 48 Years (Adult)

It would have been much better if age was captured as an integer or in a range format. Since it is having different values and formats, we will use convertAge function to approximate age to a certain numeric value.

convertAge <- function(age) {
newage = str_replace_all(age, “Child”, “”)
newage = str_replace_all(newage, “Adult”, “”)
newage = str_replace_all(newage, “Older”, “”)
newage = str_replace_all(newage, “older”, “”)
newage = str_replace_all(newage, “and”, “”)
newage = str_replace_all(newage, “Years”, “”)
newage = str_replace_all(newage, “to”, “”)
newage = str_replace_all(newage, “up”, “”)
newage = str_replace_all(newage, “\(“, “”)
newage = str_replace_all(newage, “\)”, “”)
newage = str_replace_all(newage, “,”, “”)
newage = str_trim(newage, side = c(“both”, “left”, “right”))
newage = ifelse(grepl(“Months”, newage, fixed = TRUE) == TRUE,str_replace_all(newage, newage, “2”), ageStrip)
newage = ifelse(grepl(“Month”, newage, fixed = TRUE) == TRUE,str_replace_all(newage, newage, “2”), ageStrip)
newage = ifelse(grepl(“Days”, newage, fixed = TRUE) == TRUE,str_replace_all(newage, newage, “1”), ageStrip)
newage = substr(newage, nchar(newage)-2+1, nchar(newage))
newage = as.numeric(newage)
}
ageVector <- sapply(CovidDF$Age, convertAge)
CovidDF$NewAge =ageVector
CovidDF$NewAge[is.na(CovidDF$NewAge)] <- 0
CovidDF$NewAge = as.numeric(CovidDF$NewAge)

Step 4: Visualize using plots in R

hist(CovidDF$NewAge, xlab=”Age group”, main=”Age of Volunteers in Covid Vaccine Trails”)

The above histogram provides information about the number of volunteers grouped by age.

Box plot of the same information gives the median, 1’st, and 3’rd quartile information

Convert Variable Conditions to a factor, a vector of integer values with a corresponding set of character values. The integer value of the conditions factor can then be used to plot a scatter plot against the new age variable which is also numeric.

ConditionFactor = as.factor(CovidDF$Conditions)
CovidDF$NewConditions = as.numeric(ConditionFactor)
plot(x=CovidDF$NewAge, y=CovidDF$NewConditions, xlab = “Age”)

The above scatter plot shows more conditions to be registered for age groups 18 and 0. The age group 0 indicates that the trial data did not have any age value.

Data is the oil for all new-age technologies but it is also important to understand the need to properly engineer data without which highly accurate machine learning models would be near to impossible.

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A
Anu

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