Exploratory Data Analysis for the Physical Properties of Lakes

This lesson was adapted from educational material written by Dr. Kateri Salk for her Fall 2019 Hydrologic Data Analysis course at Duke University. This is the first part of a two-part exercise focusing on the physical properties of lakes.

Introduction

Lakes are dynamic, nonuniform bodies of water in which the physical, biological, and chemical properties interact. Lakes also contain the majority of Earth's fresh water supply. This lesson introduces exploratory data analysis using R statistical software in the context of the physical properties of lakes.

Learning Objectives

After successfully completing this exercise, you will be able to:

1. Apply exploratory data analytics skills to applied questions about physical properties of lakes
2. Communicate findings with peers through oral, visual, and written modes

The zipped file contains the following: - data (as csv, in the 'data' folder), - R scripts (as Rmd, in the rro folder), - figures (as pdf, in the 'figs' folder), and - presentation (as html, in the root folder).

The Exploratory Data Analysis (EDA) tools market is experiencing robust growth, driven by the increasing volume and complexity of data across industries. The rising need for data-driven decision-making, coupled with the expanding adoption of cloud-based analytics solutions, is fueling market expansion. While precise figures for market size and CAGR are not provided, a reasonable estimation, based on the prevalent growth in the broader analytics market and the crucial role of EDA in the data science workflow, would place the 2025 market size at approximately $3 billion, with a projected Compound Annual Growth Rate (CAGR) of 15% through 2033. This growth is segmented across various applications, with large enterprises leading the adoption due to their higher investment capacity and complex data needs. However, SMEs are witnessing rapid growth in EDA tool adoption, driven by the increasing availability of user-friendly and cost-effective solutions. Further segmentation by tool type reveals a strong preference for graphical EDA tools, which offer intuitive visualizations facilitating better data understanding and communication of findings. Geographic regions, such as North America and Europe, currently hold a significant market share, but the Asia-Pacific region shows promising potential for future growth owing to increasing digitalization and data generation. Key restraints to market growth include the need for specialized skills to effectively utilize these tools and the potential for data bias if not handled appropriately. The competitive landscape is dynamic, with both established players like IBM and emerging companies specializing in niche areas vying for market share. Established players benefit from brand recognition and comprehensive enterprise solutions, while specialized vendors provide innovative features and agile development cycles. Open-source options like KNIME and R packages (Rattle, Pandas Profiling) offer cost-effective alternatives, particularly attracting academic institutions and smaller businesses. The ongoing development of advanced analytics functionalities, such as automated machine learning integration within EDA platforms, will be a significant driver of future market growth. Further, the integration of EDA tools within broader data science platforms is streamlining the overall analytical workflow, contributing to increased adoption and reduced complexity. The market's evolution hinges on enhanced user experience, more robust automation features, and seamless integration with other data management and analytics tools.

The high-resolution and mass accuracy of Fourier transform mass spectrometry (FT-MS) has made it an increasingly popular technique for discerning the composition of soil, plant and aquatic samples containing complex mixtures of proteins, carbohydrates, lipids, lignins, hydrocarbons, phytochemicals and other compounds. Thus, there is a growing demand for informatics tools to analyze FT-MS data that will aid investigators seeking to understand the availability of carbon compounds to biotic and abiotic oxidation and to compare fundamental chemical properties of complex samples across groups. We present ftmsRanalysis, an R package which provides an extensive collection of data formatting and processing, filtering, visualization, and sample and group comparison functionalities. The package provides a suite of plotting methods and enables expedient, flexible and interactive visualization of complex datasets through functions which link to a powerful and interactive visualization user interface, Trelliscope. Example analysis using FT-MS data from a soil microbiology study demonstrates the core functionality of the package and highlights the capabilities for producing interactive visualizations.

Parallel Coordinate Plots (PCP) are a valuable tool for exploratory data analysis of high-dimensional numerical data. The use of PCPs is limited when working with categorical variables or a mix of categorical and continuous variables. In this article, we propose Generalized Parallel Coordinate Plots (GPCP) to extend the ability of PCPs from just numeric variables to dealing seamlessly with a mix of categorical and numeric variables in a single plot. In this process we find that existing solutions for categorical values only, such as hammock plots or parsets become edge cases in the new framework. By focusing on individual observations rather than a marginal frequency we gain additional flexibility. The resulting approach is implemented in the R package ggpcp. Supplementary materials for this article are available online.

Unsupervised exploratory data analysis (EDA) is often the first step in understanding complex data sets. While summary statistics are among the most efficient and convenient tools for exploring and describing sets of data, they are often overlooked in EDA. In this paper, we show multiple case studies that compare the performance, including clustering, of a series of summary statistics in EDA. The summary statistics considered here are pattern recognition entropy (PRE), the mean, standard deviation (STD), 1-norm, range, sum of squares (SSQ), and X4, which are compared with principal component analysis (PCA), multivariate curve resolution (MCR), and/or cluster analysis. PRE and the other summary statistics are direct methods for analyzing datathey are not factor-based approaches. To quantify the performance of summary statistics, we use the concept of the “critical pair,” which is employed in chromatography. The data analyzed here come from different analytical methods. Hyperspectral images, including one of a biological material, are also analyzed. In general, PRE outperforms the other summary statistics, especially in image analysis, although a suite of summary statistics is useful in exploring complex data sets. While PRE results were generally comparable to those from PCA and MCR, PRE is easier to apply. For example, there is no need to determine the number of factors that describe a data set. Finally, we introduce the concept of divided spectrum-PRE (DS-PRE) as a new EDA method. DS-PRE increases the discrimination power of PRE. We also show that DS-PRE can be used to provide the inputs for the k-nearest neighbor (kNN) algorithm. We recommend PRE and DS-PRE as rapid new tools for unsupervised EDA.

Context

Reddit is a massive platform for news, content, and discussions, hosting millions of active users daily. Among its vast number of subreddits, we focus on the r/AskScience community, where users engage in science-related discussions and questions.

Content

This dataset is derived from the r/AskScience subreddit, collected between January 1, 2016, and May 20, 2022. It includes 612,668 datapoints across 22 columns, featuring diverse information such as the content of the questions, submission descriptions, associated flairs, NSFW/SFW status, year of submission, and more. The data was extracted using Python and Pushshift's API, followed by some cleaning with NumPy and pandas. Detailed column descriptions are available for clarity.

Mendeley Data

Ideas for Usage

• Flair Prediction:Train models to predict post flairs (e.g., 'Science', 'Ask', 'Discussion') to automate content categorization for platforms like Reddit.
• NSFW Classification: Classify posts as SFW or NSFW based on textual content, enabling content moderation tools for online forums.
• Text Mining / NLP Tasks: Apply NLP techniques like Sentiment Analysis, Topic Modeling, and Text Classification to explore the content and themes of science-related discussions.
• Community Engagement Analysis: Investigate which post types or flairs generate more engagement (e.g., upvotes or comments), offering insights into user interaction.
• Trend Detection in Science Topics: Identify emerging science topics and analyze shifts in interest areas, which can help predict future trends in scientific discussions.

Reddit is a social news, content rating and discussion website. It's one of the most popular sites on the internet. Reddit has 52 million daily active users and approximately 430 million users who use it once a month. Reddit has different subreddits and here We'll use the r/AskScience Subreddit.

The dataset is extracted from the subreddit /r/AskScience from Reddit. The data was collected between 01-01-2016 and 20-05-2022. It contains 612,668 Datapoints and 25 Columns. The database contains a number of information about the questions asked on the subreddit, the description of the submission, the flair of the question, NSFW or SFW status, the year of the submission, and more. The data is extracted using python and Pushshift's API. A little bit of cleaning is done using NumPy and pandas as well. (see the descriptions of individual columns below).

The dataset contains the following columns and descriptions: author - Redditor Name author_fullname - Redditor Full name contest_mode - Contest mode [implement obscured scores and randomized sorting]. created_utc - Time the submission was created, represented in Unix Time. domain - Domain of submission. edited - If the post is edited or not. full_link - Link of the post on the subreddit. id - ID of the submission. is_self - Whether or not the submission is a self post (text-only). link_flair_css_class - CSS Class used to identify the flair. link_flair_text - Flair on the post or The link flair’s text content. locked - Whether or not the submission has been locked. num_comments - The number of comments on the submission. over_18 - Whether or not the submission has been marked as NSFW. permalink - A permalink for the submission. retrieved_on - time ingested. score - The number of upvotes for the submission. description - Description of the Submission. spoiler - Whether or not the submission has been marked as a spoiler. stickied - Whether or not the submission is stickied. thumbnail - Thumbnail of Submission. question - Question Asked in the Submission. url - The URL the submission links to, or the permalink if a self post. year - Year of the Submission. banned - Banned by the moderator or not.

This dataset can be used for Flair Prediction, NSFW Classification, and different Text Mining/NLP tasks. Exploratory Data Analysis can also be done to get the insights and see the trend and patterns over the years.

Why this Dataset

This dataset brings to you Iris Dataset in several data formats (see more details in the next sections).

You can use it to test the ingestion of data in all these formats using Python or R libraries. We also prepared Python Jupyter Notebook and R Markdown report that input all these formats:

• Test Data Formats in Python
• Test Data Formats in R

Iris Dataset

Iris Dataset was created by R. A. Fisher and donated by Michael Marshall.

Repository on UCI site: https://archive.ics.uci.edu/ml/datasets/iris

Data Source: https://archive.ics.uci.edu/ml/machine-learning-databases/iris/

The file downloaded is iris.data and is formatted as a comma delimited file.

This small data collection was created to help you test your skills with ingesting various data formats.

Content

This file was processed to convert the data in the following formats: * csv - comma separated values format * tsv - tab separated values format * parquet - parquet format
* feather - feather format * parquet.gzip - compressed parquet format * h5 - hdf5 format * pickle - Python binary object file - pickle format * xslx - Excel format
* npy - Numpy (Python library) binary format * npz - Numpy (Python library) binary compressed format * rds - Rds (R specific data format) binary format

Acknowledgements

I would like to acknowledge the work of the creator of the dataset - R. A. Fisher and of the donor - Michael Marshall.

Inspiration

Use these data formats to test your skills in ingesting data in various formats.

This is version 3.1.0.2019f of Met Office Hadley Centre's Integrated Surface Database, HadISD. These data are global sub-daily surface meteorological data that extends HadISD v3.0.0.2018f to include 2019 and so spans 1931-2019. The quality controlled variables in this dataset are: temperature, dewpoint temperature, sea-level pressure, wind speed and direction, cloud data (total, low, mid and high level). Past significant weather and precipitation data are also included, but have not been quality controlled, so their quality and completeness cannot be guaranteed. Quality control flags and data values which have been removed during the quality control process are provided in the qc_flags and flagged_values fields, and ancillary data files show the station listing with a station listing with IDs, names and location information. The data are provided as one NetCDF file per station. Files in the station_data folder station data files have the format "station_code"_HadISD_HadOBS_19310101-20200101_v3-1-0-2019f.nc. The station codes can be found under the docs tab or on the archive beside the station_data folder. The station codes file has five columns as follows: 1) station code, 2) station name 3) station latitude 4) station longitude 5) station height. To keep informed about updates, news and announcements follow the HadOBS team on twitter @metofficeHadOBS. For more detailed information e.g bug fixes, routine updates and other exploratory analysis, see the HadISD blog: http://hadisd.blogspot.co.uk/ References: When using the dataset in a paper you must cite the following papers (see Docs for link to the publications) and this dataset (using the "citable as" reference) : Dunn, R. J. H., (2019), HadISD version 3: monthly updates, Hadley Centre Technical Note. Dunn, R. J. H., Willett, K. M., Parker, D. E., and Mitchell, L.: Expanding HadISD: quality-controlled, sub-daily station data from 1931, Geosci. Instrum. Method. Data Syst., 5, 473-491, doi:10.5194/gi-5-473-2016, 2016. Dunn, R. J. H., et al. (2012), HadISD: A Quality Controlled global synoptic report database for selected variables at long-term stations from 1973-2011, Clim. Past, 8, 1649-1679, 2012, doi:10.5194/cp-8-1649-2012 Smith, A., N. Lott, and R. Vose, 2011: The Integrated Surface Database: Recent Developments and Partnerships. Bulletin of the American Meteorological Society, 92, 704–708, doi:10.1175/2011BAMS3015.1 For a homogeneity assessment of HadISD please see this following reference Dunn, R. J. H., K. M. Willett, C. P. Morice, and D. E. Parker. "Pairwise homogeneity assessment of HadISD." Climate of the Past 10, no. 4 (2014): 1501-1522. doi:10.5194/cp-10-1501-2014, 2014.

This is version v3.3.0.2022f of Met Office Hadley Centre's Integrated Surface Database, HadISD. These data are global sub-daily surface meteorological data. The quality controlled variables in this dataset are: temperature, dewpoint temperature, sea-level pressure, wind speed and direction, cloud data (total, low, mid and high level). Past significant weather and precipitation data are also included, but have not been quality controlled, so their quality and completeness cannot be guaranteed. Quality control flags and data values which have been removed during the quality control process are provided in the qc_flags and flagged_values fields, and ancillary data files show the station listing with a station listing with IDs, names and location information. The data are provided as one NetCDF file per station. Files in the station_data folder station data files have the format "station_code"_HadISD_HadOBS_19310101-20230101_v3.3.1.2022f.nc. The station codes can be found under the docs tab. The station codes file has five columns as follows: 1) station code, 2) station name 3) station latitude 4) station longitude 5) station height. To keep informed about updates, news and announcements follow the HadOBS team on twitter @metofficeHadOBS. For more detailed information e.g bug fixes, routine updates and other exploratory analysis, see the HadISD blog: http://hadisd.blogspot.co.uk/ References: When using the dataset in a paper you must cite the following papers (see Docs for link to the publications) and this dataset (using the "citable as" reference) : Dunn, R. J. H., (2019), HadISD version 3: monthly updates, Hadley Centre Technical Note. Dunn, R. J. H., Willett, K. M., Parker, D. E., and Mitchell, L.: Expanding HadISD: quality-controlled, sub-daily station data from 1931, Geosci. Instrum. Method. Data Syst., 5, 473-491, doi:10.5194/gi-5-473-2016, 2016. Dunn, R. J. H., et al. (2012), HadISD: A Quality Controlled global synoptic report database for selected variables at long-term stations from 1973-2011, Clim. Past, 8, 1649-1679, 2012, doi:10.5194/cp-8-1649-2012 Smith, A., N. Lott, and R. Vose, 2011: The Integrated Surface Database: Recent Developments and Partnerships. Bulletin of the American Meteorological Society, 92, 704–708, doi:10.1175/2011BAMS3015.1 For a homogeneity assessment of HadISD please see this following reference Dunn, R. J. H., K. M. Willett, C. P. Morice, and D. E. Parker. "Pairwise homogeneity assessment of HadISD." Climate of the Past 10, no. 4 (2014): 1501-1522. doi:10.5194/cp-10-1501-2014, 2014.

Location codes that start with a “1” indicate the front of the body and codes that begin with a “2” indicate the back of the body.

Context

Data Visualization

Content

a. Scatter plot

  i. The webapp should allow the user to select genes from datasets and plot 2D scatter plots between 2 variables(expression/copy_number/chronos) for 
    any pair of genes.

  ii. The user should be able to filter and color data points using metadata information available in the file “metadata.csv”.

  iii. The visualization could be interactive - It would be great if the user can hover over the data-points on the plot and get the relevant information (hint - 
    visit https://plotly.com/r/, https://plotly.com/python)

  iv. Here is a quick reference for you. The scatter plot is between chronos score for TTBK2 gene and expression for MORC2 gene with coloring defined by
    Gender/Sex column from the metadata file.

b. Boxplot/violin plot

  i. User should be able to select a gene and a variable (expression / chronos / copy_number) and generate a boxplot to display its distribution across 
   multiple categories as defined by user selected variable (a column from the metadata file)

 ii. Here is an example for your reference where violin plot for CHRONOS score for gene CCL22 is plotted and grouped by ‘Lineage’

Acknowledgements

We wouldn't be here without the help of others. If you owe any attributions or thanks, include them here along with any citations of past research.

Inspiration

Your data will be in front of the world's largest data science community. What questions do you want to see answered?

Context

Every story has a question that triggered it. Mine was - What are the vaccinations being administered in USA? What are people's reported incidents post the vaccine doses ?

I look at awe at which folks do EDA in kaggle and I have a long way to go.But I want to start small and I have already started my journey.The folks who do wonderful EDA are my source of inspiration and I learn by doing their notebooks in R. Iam a R fan for now.

Content

The data here was downloaded on 29th March from CDC Wonder site which helps take reports on VAERS.

Acknowledgements

My google search on VAERS and Kaggle search for VAERS got me a wonderful notebook and dataset. Thanks to folks like Ayush Garg and jmreuter for helping folks like me learn more.

Inspiration

What are the vaccinations being administered in USA? What are people's reported incidents post the vaccine doses ? Which vaccine has most side effects in all age groups ? Which vaccine has most side effects in each state?

Wetlands Ecological Integrity Depth to Water Logger data from 2009-2019 at Great Sand Dunes National Park. This includes Raw dataset (primarily hourly), daily summaries, weekly summaries, and monthly summaries. Included in the data package are exploratory data analysis figures at the daily, weekly and monthly time steps. Lastly included is the R code used to extract the depth to water logger data from the National Park Service Aquarius data system, and to create the exploratory data analysis figures.

Wetlands Ecological Integrity Depth to Water Logger data from 2009-2019 at Florissant Fossil Beds National Monument. This includes Raw dataset (primarily hourly), daily summaries, weekly summaries, and monthly summaries. Included in the data package are exploratory data analysis figures at the daily, weekly and monthly time steps. Lastly included is the R code used to extract the depth to water logger data from the National Park Service Aquarius data system, and to create the exploratory data analysis figures.

Wetlands Ecological Integrity Depth to Water Logger data from 2007-2019 at Rocky Mountain National Park. This includes Raw dataset (primarily hourly), daily summaries, weekly summaries, and monthly summaries. Included in the data package are exploratory data analysis figures at the daily, weekly and monthly time steps. Lastly included is the R code used to extract the depth to water logger data from the National Park Service Aquarius data system, and to create the exploratory data analysis figures.

This package contains data and code to replicate the findings presented in our paper titled "GUI Testing of Android Applications: Investigating the Impact of the Number of Testers on Different Exploratory Testing Strategies".

Abstract

Graphical User Interface (GUI) testing plays a pivotal role in ensuring the quality and functionality of mobile apps. In this context, Exploratory Testing (ET), a distinctive methodology in which individual testers pursue a creative, and experience-based approach to test design, is often used as an alternative or in addition to traditional scripted testing. Managing the exploratory testing process is a challenging task, that can easily result either in wasteful spending or in inadequate software quality, due to the relative unpredictability of exploratory testing activities, which depend on the skills and abilities of individual testers. A number of works have investigated the diversity of testers’ performance when using ET strategies, often in a crowdtesting setting. These works, however, investigated ET effectiveness in detecting bugs, and not in scenarios in which the goal is to generate a re-executable test suite, as well. Moreover, less work has been conducted on evaluating the impact of adopting different exploratory testing strategies. As a first step towards filling this gap in the literature, in this work we conduct an empirical evaluation involving four open-source Android apps and twenty masters students, that we believe can be representative of practitioners partaking in exploratory testing activities. The students were asked to generate test suites for the apps using a Capture and Replay tool and different exploratory testing strategies. We then compare the effectiveness, in terms of aggregate code coverage, that different-sized groups of students using different exploratory testing strategies may achieve. Results provide deeper insights into code coverage dynamics to project managers interested in using exploratory approaches to test simple Android apps, on which they can make more informed decisions.

Contents and Instructions

This package contains:

apps-under-test.zip A zip archive containing the source code of the four Android applications we considered in our study, namely MunchLife, TippyTipper, Trolly, and SimplyDo.

apps-under-test-instrumented.zip A zip archive containing the instrumented source code of the four Android applications we used to compute branch coverage.

students-test-suites.zip A zip archive containing the test suites developed by the students using Uninformed Exploratory Testing (referred to as "Black Box" in the subdirectories) and Informed Exploratory Testing (referred to as "White Box" in the subdirectories). This also includes coverage reports.

compute-coverage-unions.zip A zip archive containing Python scripts we developed to compute the aggregate LOC coverage of all possible subsets of students. The scripts have been tested on MS Windows. To compute the LOC coverage achieved by any possible subsets of testers using IET and UET strategies, run the analysisAndReport.py script. To compute the LOC coverage achieved by mixed crowds in which some testers use a U+IET approach and others use a UET approach, run the analysisAndReport_UET_IET_combinations_emma.py script.

branch-coverage-computation.zip A zip archive containing Python scripts we developed to compute the aggregate branch coverage of all considered subsets of students. The scripts have been tested on MS Windows. To compute the branch coverage achieved by any possible subsets of testers using UET and I+UET strategies, run the branch_coverage_analysis.py script. To compute the code coverage achieved by mixed crowds in which some testers use a U+IET approach and others use a UET approach, run the mixed_branch_coverage_analysis.py script.

data-analysis-scripts.zip A zip archive containing R scripts to merge and manipulate coverage data, to carry out statistical analysis and draw plots. All data concerning RQ1 and RQ2 is available as a ready-to-use R data frame in the ./data/all_coverage_data.rds file. All data concerning RQ3 is available in the ./data/all_mixed_coverage_data.rds file.

This is version v3.2.0.2021f of Met Office Hadley Centre's Integrated Surface Database, HadISD. These data are global sub-daily surface meteorological data. The quality controlled variables in this dataset are: temperature, dewpoint temperature, sea-level pressure, wind speed and direction, cloud data (total, low, mid and high level). Past significant weather and precipitation data are also included, but have not been quality controlled, so their quality and completeness cannot be guaranteed. Quality control flags and data values which have been removed during the quality control process are provided in the qc_flags and flagged_values fields, and ancillary data files show the station listing with a station listing with IDs, names and location information. The data are provided as one NetCDF file per station. Files in the station_data folder station data files have the format "station_code"_HadISD_HadOBS_19310101-20220101_v3.2.1.2021f.nc. The station codes can be found under the docs tab. The station codes file has five columns as follows: 1) station code, 2) station name 3) station latitude 4) station longitude 5) station height. To keep informed about updates, news and announcements follow the HadOBS team on twitter @metofficeHadOBS. For more detailed information e.g bug fixes, routine updates and other exploratory analysis, see the HadISD blog: http://hadisd.blogspot.co.uk/ References: When using the dataset in a paper you must cite the following papers (see Docs for link to the publications) and this dataset (using the "citable as" reference) : Dunn, R. J. H., (2019), HadISD version 3: monthly updates, Hadley Centre Technical Note. Dunn, R. J. H., Willett, K. M., Parker, D. E., and Mitchell, L.: Expanding HadISD: quality-controlled, sub-daily station data from 1931, Geosci. Instrum. Method. Data Syst., 5, 473-491, doi:10.5194/gi-5-473-2016, 2016. Dunn, R. J. H., et al. (2012), HadISD: A Quality Controlled global synoptic report database for selected variables at long-term stations from 1973-2011, Clim. Past, 8, 1649-1679, 2012, doi:10.5194/cp-8-1649-2012 Smith, A., N. Lott, and R. Vose, 2011: The Integrated Surface Database: Recent Developments and Partnerships. Bulletin of the American Meteorological Society, 92, 704–708, doi:10.1175/2011BAMS3015.1 For a homogeneity assessment of HadISD please see this following reference Dunn, R. J. H., K. M. Willett, C. P. Morice, and D. E. Parker. "Pairwise homogeneity assessment of HadISD." Climate of the Past 10, no. 4 (2014): 1501-1522. doi:10.5194/cp-10-1501-2014, 2014.

Wetlands Ecological Integrity Depth to Water Logger data from 2007-2019 at Rocky Mountain National Park. This includes Raw dataset (primarily hourly), daily summaries, weekly summaries, and monthly summaries. Included in the data package are exploratory data analysis figures at the daily, weekly and monthly time steps. Lastly included is the R code used to extract the depth to water logger data from the National Park Service Aquarius data system, and to create the exploratory data analysis figures.