The whole data and source can be found at https://emilhvitfeldt.github.io/friends/

"The goal of friends to provide the complete script transcription of the Friends sitcom. The data originates from the Character Mining repository which includes references to scientific explorations using this data. This package simply provides the data in tibble format instead of json files."

Content

• friends.csv - Contains the scenes and lines for each character, including season and episodes.
• friends_emotions.csv - Contains sentiments for each scene - for the first four seasons only.
• friends_info.csv - Contains information regarding each episode, such as imdb_rating, views, episode title and directors.

Uses

• Text mining, sentiment analysis and word statistics.
• Data visualizations.

This repository was created for my Master's thesis in Computational Intelligence and Internet of Things at the University of Córdoba, Spain. The purpose of this repository is to store the datasets found that were used in some of the studies that served as research material for this Master's thesis. Also, the datasets used in the experimental part of this work are included.

Below are the datasets specified, along with the details of their references, authors, and download sources.

----------- STS-Gold Dataset ----------------

The dataset consists of 2026 tweets. The file consists of 3 columns: id, polarity, and tweet. The three columns denote the unique id, polarity index of the text and the tweet text respectively.

Reference: Saif, H., Fernandez, M., He, Y., & Alani, H. (2013). Evaluation datasets for Twitter sentiment analysis: a survey and a new dataset, the STS-Gold.

File name: sts_gold_tweet.csv

----------- Amazon Sales Dataset ----------------

This dataset is having the data of 1K+ Amazon Product's Ratings and Reviews as per their details listed on the official website of Amazon. The data was scraped in the month of January 2023 from the Official Website of Amazon.

Owner: Karkavelraja J., Postgraduate student at Puducherry Technological University (Puducherry, Puducherry, India)

Features:

• product_id - Product ID
• product_name - Name of the Product
• category - Category of the Product
• discounted_price - Discounted Price of the Product
• actual_price - Actual Price of the Product
• discount_percentage - Percentage of Discount for the Product
• rating - Rating of the Product
• rating_count - Number of people who voted for the Amazon rating
• about_product - Description about the Product
• user_id - ID of the user who wrote review for the Product
• user_name - Name of the user who wrote review for the Product
• review_id - ID of the user review
• review_title - Short review
• review_content - Long review
• img_link - Image Link of the Product
• product_link - Official Website Link of the Product

License: CC BY-NC-SA 4.0

File name: amazon.csv

----------- Rotten Tomatoes Reviews Dataset ----------------

This rating inference dataset is a sentiment classification dataset, containing 5,331 positive and 5,331 negative processed sentences from Rotten Tomatoes movie reviews. On average, these reviews consist of 21 words. The first 5331 rows contains only negative samples and the last 5331 rows contain only positive samples, thus the data should be shuffled before usage.

This data is collected from https://www.cs.cornell.edu/people/pabo/movie-review-data/ as a txt file and converted into a csv file. The file consists of 2 columns: reviews and labels (1 for fresh (good) and 0 for rotten (bad)).

Reference: Bo Pang and Lillian Lee. Seeing stars: Exploiting class relationships for sentiment categorization with respect to rating scales. In Proceedings of the 43rd Annual Meeting of the Association for Computational Linguistics (ACL'05), pages 115–124, Ann Arbor, Michigan, June 2005. Association for Computational Linguistics

File name: data_rt.csv

----------- Preprocessed Dataset Sentiment Analysis ----------------

Preprocessed amazon product review data of Gen3EcoDot (Alexa) scrapped entirely from amazon.in
Stemmed and lemmatized using nltk.
Sentiment labels are generated using TextBlob polarity scores.

The file consists of 4 columns: index, review (stemmed and lemmatized review using nltk), polarity (score) and division (categorical label generated using polarity score).

DOI: 10.34740/kaggle/dsv/3877817

Citation: @misc{pradeesh arumadi_2022, title={Preprocessed Dataset Sentiment Analysis}, url={https://www.kaggle.com/dsv/3877817}, DOI={10.34740/KAGGLE/DSV/3877817}, publisher={Kaggle}, author={Pradeesh Arumadi}, year={2022} }

This dataset was used in the experimental phase of my research.

File name: EcoPreprocessed.csv

----------- Amazon Earphones Reviews ----------------

This dataset consists of a 9930 Amazon reviews, star ratings, for 10 latest (as of mid-2019) bluetooth earphone devices for learning how to train Machine for sentiment analysis.

This dataset was employed in the experimental phase of my research. To align it with the objectives of my study, certain reviews were excluded from the original dataset, and an additional column was incorporated into this dataset.

The file consists of 5 columns: ReviewTitle, ReviewBody, ReviewStar, Product and division (manually added - categorical label generated using ReviewStar score)

License: U.S. Government Works

Source: www.amazon.in

File name (original): AllProductReviews.csv (contains 14337 reviews)

File name (edited - used for my research) : AllProductReviews2.csv (contains 9930 reviews)

----------- Amazon Musical Instruments Reviews ----------------

This dataset contains 7137 comments/reviews of different musical instruments coming from Amazon.

This dataset was employed in the experimental phase of my research. To align it with the objectives of my study, certain reviews were excluded from the original dataset, and an additional column was incorporated into this dataset.

The file consists of 10 columns: reviewerID, asin (ID of the product), reviewerName, helpful (helpfulness rating of the review), reviewText, overall (rating of the product), summary (summary of the review), unixReviewTime (time of the review - unix time), reviewTime (time of the review (raw) and division (manually added - categorical label generated using overall score).

Source: http://jmcauley.ucsd.edu/data/amazon/

File name (original): Musical_instruments_reviews.csv (contains 10261 reviews)

File name (edited - used for my research) : Musical_instruments_reviews2.csv (contains 7137 reviews)

Cyclistic ride share service 12-month data. Used to Categorize and analyze how the two user types; annual members and casual riders use the service differently. The data set involves 12 separate csv files merged together using R-studio resulting in 5.8million+ rows of data. (https://public.tableau.com/app/profile/richgg/viz/CyclisticCapstoneDashboard/Dashboard1 )-DashBoard (Check the **PowerPoint **presentation for more analysis information from the data set.) https://www.kaggle.com/code/therichgg/cyclistic-data-analysis-on-user-type-differences/notebook <-notebook reference for analysis

The Canada Trademarks Dataset

18 Journal of Empirical Legal Studies 908 (2021), prepublication draft available at https://papers.ssrn.com/abstract=3782655, published version available at https://onlinelibrary.wiley.com/share/author/CHG3HC6GTFMMRU8UJFRR?target=10.1111/jels.12303

Dataset Selection and Arrangement (c) 2021 Jeremy Sheff

Python and Stata Scripts (c) 2021 Jeremy Sheff

Contains data licensed by Her Majesty the Queen in right of Canada, as represented by the Minister of Industry, the minister responsible for the administration of the Canadian Intellectual Property Office.

This individual-application-level dataset includes records of all applications for registered trademarks in Canada since approximately 1980, and of many preserved applications and registrations dating back to the beginning of Canada’s trademark registry in 1865, totaling over 1.6 million application records. It includes comprehensive bibliographic and lifecycle data; trademark characteristics; goods and services claims; identification of applicants, attorneys, and other interested parties (including address data); detailed prosecution history event data; and data on application, registration, and use claims in countries other than Canada. The dataset has been constructed from public records made available by the Canadian Intellectual Property Office. Both the dataset and the code used to build and analyze it are presented for public use on open-access terms.

Scripts are licensed for reuse subject to the Creative Commons Attribution License 4.0 (CC-BY-4.0), https://creativecommons.org/licenses/by/4.0/. Data files are licensed for reuse subject to the Creative Commons Attribution License 4.0 (CC-BY-4.0), https://creativecommons.org/licenses/by/4.0/, and also subject to additional conditions imposed by the Canadian Intellectual Property Office (CIPO) as described below.

Terms of Use:

As per the terms of use of CIPO's government data, all users are required to include the above-quoted attribution to CIPO in any reproductions of this dataset. They are further required to cease using any record within the datasets that has been modified by CIPO and for which CIPO has issued a notice on its website in accordance with its Terms and Conditions, and to use the datasets in compliance with applicable laws. These requirements are in addition to the terms of the CC-BY-4.0 license, which require attribution to the author (among other terms). For further information on CIPO’s terms and conditions, see https://www.ic.gc.ca/eic/site/cipointernet-internetopic.nsf/eng/wr01935.html. For further information on the CC-BY-4.0 license, see https://creativecommons.org/licenses/by/4.0/.

The following attribution statement, if included by users of this dataset, is satisfactory to the author, but the author makes no representations as to whether it may be satisfactory to CIPO:

The Canada Trademarks Dataset is (c) 2021 by Jeremy Sheff and licensed under a CC-BY-4.0 license, subject to additional terms imposed by the Canadian Intellectual Property Office. It contains data licensed by Her Majesty the Queen in right of Canada, as represented by the Minister of Industry, the minister responsible for the administration of the Canadian Intellectual Property Office. For further information, see https://creativecommons.org/licenses/by/4.0/ and https://www.ic.gc.ca/eic/site/cipointernet-internetopic.nsf/eng/wr01935.html.

Details of Repository Contents:

This repository includes a number of .zip archives which expand into folders containing either scripts for construction and analysis of the dataset or data files comprising the dataset itself. These folders are as follows:

• /csv: contains the .csv versions of the data files
• /do: contains Stata do-files used to convert the .csv files to .dta format and perform the statistical analyses set forth in the paper reporting this dataset
• /dta: contains the .dta versions of the data files
• /py: contains the python scripts used to download CIPO’s historical trademarks data via SFTP and generate the .csv data files

If users wish to construct rather than download the datafiles, the first script that they should run is /py/sftp_secure.py. This script will prompt the user to enter their IP Horizons SFTP credentials; these can be obtained by registering with CIPO at https://ised-isde.survey-sondage.ca/f/s.aspx?s=59f3b3a4-2fb5-49a4-b064-645a5e3a752d&lang=EN&ds=SFTP. The script will also prompt the user to identify a target directory for the data downloads. Because the data archives are quite large, users are advised to create a target directory in advance and ensure they have at least 70GB of available storage on the media in which the directory is located.

The sftp_secure.py script will generate a new subfolder in the user’s target directory called /XML_raw. Users should note the full path of this directory, which they will be prompted to provide when running the remaining python scripts. Each of the remaining scripts, the filenames of which begin with “iterparse”, corresponds to one of the data files in the dataset, as indicated in the script’s filename. After running one of these scripts, the user’s target directory should include a /csv subdirectory containing the data file corresponding to the script; after running all the iterparse scripts the user’s /csv directory should be identical to the /csv directory in this repository. Users are invited to modify these scripts as they see fit, subject to the terms of the licenses set forth above.

With respect to the Stata do-files, only one of them is relevant to construction of the dataset itself. This is /do/CA_TM_csv_cleanup.do, which converts the .csv versions of the data files to .dta format, and uses Stata’s labeling functionality to reduce the size of the resulting files while preserving information. The other do-files generate the analyses and graphics presented in the paper describing the dataset (Jeremy N. Sheff, The Canada Trademarks Dataset, 18 J. Empirical Leg. Studies (forthcoming 2021)), available at https://papers.ssrn.com/abstract=3782655). These do-files are also licensed for reuse subject to the terms of the CC-BY-4.0 license, and users are invited to adapt the scripts to their needs.

The python and Stata scripts included in this repository are separately maintained and updated on Github at https://github.com/jnsheff/CanadaTM.

This repository also includes a copy of the current version of CIPO's data dictionary for its historical XML trademarks archive as of the date of construction of this dataset.

We present a tool for multi-omics data analysis that enables simultaneous visualization of up to four types of omics data on organism-scale metabolic network diagrams. The tool’s interactive web-based metabolic charts depict the metabolic reactions, pathways, and metabolites of a single organism as described in a metabolic pathway database for that organism; the charts are constructed using automated graphical layout algorithms. The multi-omics visualization facility paints each individual omics dataset onto a different “visual channel” of the metabolic-network diagram. For example, a transcriptomics dataset might be displayed by coloring the reaction arrows within the metabolic chart, while a companion proteomics dataset is displayed as reaction arrow thicknesses, and a complementary metabolomics dataset is displayed as metabolite node colors. Once the network diagrams are painted with omics data, semantic zooming provides more details within the diagram as the user zooms in. Datasets containing multiple time points can be displayed in an animated fashion. The tool will also graph data values for individual reactions or metabolites designated by the user. The user can interactively adjust the mapping from data value ranges to the displayed colors and thicknesses to provide more informative diagrams.

Researchers engaged in the scholarship of teaching and learning seek tools for rigorous, quantitative analysis. Here we present a brief introduction to computational techniques for the researcher with interest in analyzing data pertaining to pedagogical study. Sample dataset and fully executable code in the open-source R programming language are provided, along with illustrative vignettes relevant to common forms of inquiry in the educational setting.

Explanation/Overview: Corresponding dataset for the analyses and results achieved in the CS Track project in the research line on participation analyses, which is also reported in the publication "Does Volunteer Engagement Pay Off? An Analysis of User Participation in Online Citizen Science Projects", a conference paper for the conference CollabTech 2022: Collaboration Technologies and Social Computing and published as part of the Lecture Notes in Computer Science book series (LNCS,volume 13632) here. The usernames have been anonymised. Purpose: The purpose of this dataset is to provide the basis to reproduce the results reported in the associated deliverable, and in the above-mentioned publication. As such, it does not represent raw data, but rather files that already include certain analysis steps (like calculated degrees or other SNA-related measures), ready for analysis, visualisation and interpretation with R. Relatedness: The data of the different projects was derived from the forums of 7 Zooniverse projects based on similar discussion board features. The projects are: 'Galaxy Zoo', 'Gravity Spy', 'Seabirdwatch', 'Snapshot Wisconsin', 'Wildwatch Kenya', 'Galaxy Nurseries', 'Penguin Watch'. Content: In this Zenodo entry, several files can be found. The structure is as follows (files and folders and descriptions). corresponding_calculations.html Quarto-notebook to view in browser corresponding_calculations.qmd Quarto-notebook to view in RStudio assets data annotations annotations.csv List of annotations made per day for each of the analysed projects comments comments.csv Total list of comments with several data fields (i.e., comment id, text, reply_user_id) rolechanges 478_rolechanges.csv List of roles per user to determine number of role changes 1104_rolechanges.csv ... ... totalnetworkdata Edges 478_edges.csv Network data (edge set) for the given projects (without time slices) 1104_edges.csv ... ... Nodes 478_nodes.csv Network data (node set) for the given projects (without time slices) 1104_nodes.csv ... ... trajectories Network data (edge and node sets) for the given projects and all time slices (Q1 2016 - Q4 2021) 478 Edges edges_4782016_q1.csv edges_4782016_q2.csv edges_4782016_q3.csv edges_4782016_q4.csv ... Nodes nodes_4782016_q1.csv nodes_4782016_q4.csv nodes_4782016_q3.csv nodes_4782016_q2.csv ... 1104 Edges ... Nodes ... ... scripts datavizfuncs.R script for the data visualisation functions, automatically executed from within corresponding_calculations.qmd import.R script for the import of data, automatically executed from within corresponding_calculations.qmd corresponding_calculations_files files for the html/qmd view in the browser/RStudio Grouping: The data is grouped according to given criteria (e.g., project_title or time). Accordingly, the respective files can be found in the data structure

hello everyone. I wanted to share here my data set, which is completely my own product of imagination and has no connection with the real data that I wrote for my own data analysis training, for analysts working on data analysis. have fun:))))))

UserId: Unique identifier for each user in the data set

UsageDuration: Total time spent by the user on social media in hours

Age: Age of the user in years

Country: Country of residence of the user

TotalLikes: Total number of likes giving by the user in a day

Our dataset comprises 1000 tweets, which were taken from Twitter using the Python programming language. The dataset was stored in a CSV file and generated using various modules. The random module was used to generate random IDs and text, while the faker module was used to generate random user names and dates. Additionally, the textblob module was used to assign a random sentiment to each tweet.

This systematic approach ensures that the dataset is well-balanced and represents different types of tweets, user behavior, and sentiment. It is essential to have a balanced dataset to ensure that the analysis and visualization of the dataset are accurate and reliable. By generating tweets with a range of sentiments, we have created a diverse dataset that can be used to analyze and visualize sentiment trends and patterns.

In addition to generating the tweets, we have also prepared a visual representation of the data sets. This visualization provides an overview of the key features of the dataset, such as the frequency distribution of the different sentiment categories, the distribution of tweets over time, and the user names associated with the tweets. This visualization will aid in the initial exploration of the dataset and enable us to identify any patterns or trends that may be present.

This data release supports an analysis of changes in dissolved organic carbon (DOC) and nitrate concentrations in Buck Creek watershed near Inlet, New York 2001 to 2021. The Buck Creek watershed is a 310-hectare forested watershed that is recovering from acidic deposition within the Adirondack region. The data release includes pre-processed model inputs and model outputs for the Weighted Regressions on Time, Discharge and Season (WRTDS) model (Hirsch and others, 2010) to estimate daily flow normalized concentrations of DOC and nitrate during a 20-year period of analysis. WRTDS uses daily discharge and concentration observations implemented through the Exploration and Graphics for River Trends R package (EGRET) to predict solute concentration using decimal time and discharge as explanatory variables (Hirsch and De Cicco, 2015; Hirsch and others, 2010). Discharge and concentration data are available from the U.S. Geological Survey National Water Information System (NWIS) database (U.S. Geological Survey, 2016). The time series data were analyzed for the entire period, water years 2001 (WY2001) to WY2021 where WY2001 is the period from October 1, 2000 to September 30, 2001. This data release contains 5 comma-separated values (CSV) files, one R script, and one XML metadata file. There are four input files (“Daily.csv”, “INFO.csv”, “Sample_doc.csv”, and “Sample_nitrate.csv”) that contain site information, daily mean discharge, and mean daily DOC or nitrate concentrations. The R script (“Buck Creek WRTDS R script.R”) uses the four input datasets and functions from the EGRET R package to generate estimations of flow normalized concentrations. The output file (“WRTDS_results.csv”) contains model output at daily time steps for each sub-watershed and for each solute. Files are automatically associated with the R script when opened in RStudio using the provided R project file ("Files.Rproj"). All input, output, and R files are in the "Files.zip" folder.

This replication package contains datasets and scripts related to the paper: "*How do Hugging Face Models Document Datasets, Bias, and Licenses? An Empirical Study*"

## Root directory

- `statistics.r`: R script used to compute the correlation between usage and downloads, and the RQ1/RQ2 inter-rater agreements

- `modelsInfo.zip`: zip file containing all the downloaded model cards (in JSON format)

- `script`: directory containing all the scripts used to collect and process data. For further details, see README file inside the script directory.

## Dataset

- `Dataset/Dataset_HF-models-list.csv`: list of HF models analyzed

- `Dataset/Dataset_github-prj-list.txt`: list of GitHub projects using the *transformers* library

- `Dataset/Dataset_github-Prj_model-Used.csv`: contains usage pairs: project, model

- `Dataset/Dataset_prj-num-models-reused.csv`: number of models used by each GitHub project

- `Dataset/Dataset_model-download_num-prj_correlation.csv` contains, for each model used by GitHub projects: the name, the task, the number of reusing projects, and the number of downloads

## RQ1

- `RQ1/RQ1_dataset-list.txt`: list of HF datasets

- `RQ1/RQ1_datasetSample.csv`: sample set of models used for the manual analysis of datasets

- `RQ1/RQ1_analyzeDatasetTags.py`: Python script to analyze model tags for the presence of datasets. it requires to unzip the `modelsInfo.zip` in a directory with the same name (`modelsInfo`) at the root of the replication package folder. Produces the output to stdout. To redirect in a file fo be analyzed by the `RQ2/countDataset.py` script

- `RQ1/RQ1_countDataset.py`: given the output of `RQ2/analyzeDatasetTags.py` (passed as argument) produces, for each model, a list of Booleans indicating whether (i) the model only declares HF datasets, (ii) the model only declares external datasets, (iii) the model declares both, and (iv) the model is part of the sample for the manual analysis

- `RQ1/RQ1_datasetTags.csv`: output of `RQ2/analyzeDatasetTags.py`

- `RQ1/RQ1_dataset_usage_count.csv`: output of `RQ2/countDataset.py`

## RQ2

- `RQ2/tableBias.pdf`: table detailing the number of occurrences of different types of bias by model Task

- `RQ2/RQ2_bias_classification_sheet.csv`: results of the manual labeling

- `RQ2/RQ2_isBiased.csv`: file to compute the inter-rater agreement of whether or not a model documents Bias

- `RQ2/RQ2_biasAgrLabels.csv`: file to compute the inter-rater agreement related to bias categories

- `RQ2/RQ2_final_bias_categories_with_levels.csv`: for each model in the sample, this file lists (i) the bias leaf category, (ii) the first-level category, and (iii) the intermediate category

## RQ3

- `RQ3/RQ3_LicenseValidation.csv`: manual validation of a sample of licenses

- `RQ3/RQ3_{NETWORK-RESTRICTIVE|RESTRICTIVE|WEAK-RESTRICTIVE|PERMISSIVE}-license-list.txt`: lists of licenses with different permissiveness

- `RQ3/RQ3_prjs_license.csv`: for each project linked to models, among other fields it indicates the license tag and name

- `RQ3/RQ3_models_license.csv`: for each model, indicates among other pieces of info, whether the model has a license, and if yes what kind of license

- `RQ3/RQ3_model-prj-license_contingency_table.csv`: usage contingency table between projects' licenses (columns) and models' licenses (rows)

- `RQ3/RQ3_models_prjs_licenses_with_type.csv`: pairs project-model, with their respective licenses and permissiveness level

## scripts

Contains the scripts used to mine Hugging Face and GitHub. Details are in the enclosed README

Overview

Data points present in this dataset were obtained following the subsequent steps: To assess the secretion efficiency of the constructs, 96 colonies from the selection plates were evaluated using the workflow presented in Figure Workflow. We picked transformed colonies and cultured in 400 μL TAP medium for 7 days in Deep-well plates (Corning Axygen®, No.: PDW500CS, Thermo Fisher Scientific Inc., Waltham, MA), covered with Breathe-Easy® (Sigma-Aldrich®). Cultivation was performed on a rotary shaker, set to 150 rpm, under constant illumination (50 μmol photons/m²s). Then 100 μL sample were transferred clear bottom 96-well plate (Corning Costar, Tewksbury, MA, USA) and fluorescence was measured using an Infinite® M200 PRO plate reader (Tecan, Männedorf, Switzerland). Fluorescence was measured at excitation 575/9 nm and emission 608/20 nm. Supernatant samples were obtained by spinning Deep-well plates at 3000 × g for 10 min and transferring 100 μL from each well to the clear bottom 96-well plate (Corning Costar, Tewksbury, MA, USA), followed by fluorescence measurement. To compare the constructs, R Statistic version 3.3.3 was used to perform one-way ANOVA (with Tukey's test), and to test statistical hypotheses, the significance level was set at 0.05. Graphs were generated in RStudio v1.0.136. The codes are deposit herein.

Info

ANOVA_Turkey_Sub.R -> code for ANOVA analysis in R statistic 3.3.3

barplot_R.R -> code to generate bar plot in R statistic 3.3.3

boxplotv2.R -> code to generate boxplot in R statistic 3.3.3

pRFU_+_bk.csv -> relative supernatant mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of Chlamydomonas reinhardtii

sup_+_bl.csv -> supernatant mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of Chlamydomonas reinhardtii

sup_raw.csv -> supernatant mCherry fluorescence dataset of 96 colonies for each construct.

who_+_bl2.csv -> whole culture mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of Chlamydomonas reinhardtii

who_raw.csv -> whole culture mCherry fluorescence dataset of 96 colonies for each construct.

who_+_Chlo.csv -> whole culture chlorophyll fluorescence dataset of 96 colonies for each construct.

Anova_Output_Summary_Guide.pdf -> Explain the ANOVA files content

ANOVA_pRFU_+_bk.doc -> ANOVA of relative supernatant mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of Chlamydomonas reinhardtii

ANOVA_sup_+_bk.doc -> ANOVA of supernatant mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of Chlamydomonas reinhardtii

ANOVA_who_+_bk.doc -> ANOVA of whole culture mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of Chlamydomonas reinhardtii

ANOVA_Chlo.doc -> ANOVA of whole culture chlorophyll fluorescence of all constructs, plus average and standard deviation values.

Consider citing our work.

Molino JVD, de Carvalho JCM, Mayfield SP (2018) Comparison of secretory signal peptides for heterologous protein expression in microalgae: Expanding the secretion portfolio for Chlamydomonas reinhardtii. PLoS ONE 13(2): e0192433. https://doi.org/10.1371/journal. pone.0192433

This data description contains code (written in the R programming language), as well as processed data and results presented in a research article (see references). No raw data are provided and the data that are made available cannot be linked to study participants. The sample consists of 180 of 308 eligible participants (adult primary care patients in Sweden, living with chronic illness) who responded to a Swedish web-based questionnaire at two time points. Using a confirmatory factor analysis, we calculated latent factor scores for 9 constructs, based on 34 questionnaire items. In this dataset, we share the latent factor scores and the latent profile analysis results. Although raw data are not shared, we provide the questionnaire item, including response scales. The code that was used to produce the latent factor scores and latent profile analysis results is also provided.

The study was performed as part of a research project exploring how the use of eHealth services in chronic care influence interaction and collaboration between patients and healthcare. The purpose of the study was to identify subgroups of primary care patients who are similar with respect to their experiences of co-care, as measured by the DoCCA scale (von Thiele Schwarz, 2021). Baseline data were collected after patients had been introduced to an eHealth service that aimed to support them in their self-care and digital communication with healthcare; follow-up data were collected 7 months later. All patients were treated at the same primary care center, located in the Stockholm Region in Sweden.

Cited reference: von Thiele Schwarz U, Roczniewska M, Pukk Härenstam K, Karlgren K, Hasson H, Menczel S, Wannheden C. The work of having a chronic condition: Development and psychometric evaluation of the Distribution of Co-Care Activities (DoCCA) Scale. BMC Health Services Research (2021) 21:480. doi: 10.1186/s12913-021-06455-8

The DATASET consists of two files: factorscores_docca.csv and latent-profile-analysis-results_docca.csv.

• factorscores_docca.csv: This file contains 18 variables (columns) and 180 cases (rows). The variables represent latent factors (measured at two time points, T1 and T2) and the values are latent factor scores. The questionnaire data that were used to produce the latent factor scores consist of 20 items that measure experiences of collaboration with healthcare, based on the DoCCA scale. These items were included in the latent profile analysis. Additionally, latent factor scores reflecting perceived self-efficacy in self-care (6 items), satisfaction with healthcare (2 items), self-rated health (2 items), and perceived impact of e-health (4 items) were calculated. These items were used to make comparisons between profiles resulting from the latent profile analysis. Variable definitions are provided in a separate file (see below).

• latent-profile-analysis-results_docca.csv: This file contains 14 variables (columns) and 180 cases (rows). The variables represent profile classifications (numbers and labels) and posterior classification probabilities for each of the identified profiles, 4 profiles at T1 and 5 profiles at T2. Transition probabilities (from T1 to T2 profiles) were not calculated due to lacking configural similarity of profiles at T1 and T2; hence no transition probabilities are provided.

The ASSOCIATED DOCUMENTATION consists of one file with variable definitions in English and Swedish, and four script files (written in the R programming language):

• variable-definitions_swe-eng.xlsx: This file consists of four sheets. Sheet 1 (scale-items_original_swedish) specifies the questionnaire items (in Swedish) that were used to calculate the latent factor scores; response scales are included. Sheet 2 (scale-items_translated_english) provides an English translation of the questionnaire items and response scales provided in Sheet 1. Sheet 3 (factorscores_docca) defines the variables in the factorscores_docca.csv dataset. Sheet 4 (latent-profile-analysis-results) defines the variables in the latent-profile-analysis-results_docca.csv dataset.

• R-script_Step-0_Factor-scores.R: R script file with the code that was used to calculate the latent factor scores. This script can only be run with access to the raw data file which is not publicly shared due to ethical constraints. Hence, the purpose of the script file is code transparency. Also, the script shows the model specification that was used in the confirmatory factor analysis (CFA). Missingness in data was accounted for by using Full Information Maximum Likelihood (FIML).

• R-script_Step-1_Latent-profile-analysis.R: R script file with the code that was used to run the latent profile analyses at T1 and T2 and produce profile plots. This code can be run with the provided dataset factorscores_docca.csv. Note that the script generates the results that are provided in the latent-profile-analysis-results_docca.csv dataset.

• R-script_Step-2_Non-parametric-tests.R: R script file with the code that was used to run non-parametric tests for comparing exogenous variables between profiles at T1 and T2. This script uses the following datasets: factorscores_docca.csv and latent-profile-analysis-results_docca.csv.

• R-script_Step-3_Class-transitions.R: R script file with the code that was used to create a sankey diagram for illustrating class transitions. This script uses the following dataset: latent-profile-analysis-results_docca.csv.

Software requirements: To run the code, the R software environment and R packages specified in the script files need to be installed (open source). The scripts were produced in R version 4.2.1.

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Pathogen diversity resulting in quasispecies can enable persistence and adaptation to host defenses and therapies. However, accurate quasispecies characterization can be impeded by errors introduced during sample handling and sequencing which can require extensive optimizations to overcome. We present complete laboratory and bioinformatics workflows to overcome many of these hurdles. The Pacific Biosciences single molecule real-time platform was used to sequence PCR amplicons derived from cDNA templates tagged with universal molecular identifiers (SMRT-UMI). Optimized laboratory protocols were developed through extensive testing of different sample preparation conditions to minimize between-template recombination during PCR and the use of UMI allowed accurate template quantitation as well as removal of point mutations introduced during PCR and sequencing to produce a highly accurate consensus sequence from each template. Handling of the large datasets produced from SMRT-UMI sequencing was facilitated by a novel bioinformatic pipeline, Probabilistic Offspring Resolver for Primer IDs (PORPIDpipeline), that automatically filters and parses reads by sample, identifies and discards reads with UMIs likely created from PCR and sequencing errors, generates consensus sequences, checks for contamination within the dataset, and removes any sequence with evidence of PCR recombination or early cycle PCR errors, resulting in highly accurate sequence datasets. The optimized SMRT-UMI sequencing method presented here represents a highly adaptable and established starting point for accurate sequencing of diverse pathogens. These methods are illustrated through characterization of human immunodeficiency virus (HIV) quasispecies. Methods This serves as an overview of the analysis performed on PacBio sequence data that is summarized in Analysis Flowchart.pdf and was used as primary data for the paper by Westfall et al. "Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations – application to HIV-1 quasispecies" Five different PacBio sequencing datasets were used for this analysis: M027, M2199, M1567, M004, and M005 For the datasets which were indexed (M027, M2199), CCS reads from PacBio sequencing files and the chunked_demux_config files were used as input for the chunked_demux pipeline. Each config file lists the different Index primers added during PCR to each sample. The pipeline produces one fastq file for each Index primer combination in the config. For example, in dataset M027 there were 3–4 samples using each Index combination. The fastq files from each demultiplexed read set were moved to the sUMI_dUMI_comparison pipeline fastq folder for further demultiplexing by sample and consensus generation with that pipeline. More information about the chunked_demux pipeline can be found in the README.md file on GitHub. The demultiplexed read collections from the chunked_demux pipeline or CCS read files from datasets which were not indexed (M1567, M004, M005) were each used as input for the sUMI_dUMI_comparison pipeline along with each dataset's config file. Each config file contains the primer sequences for each sample (including the sample ID block in the cDNA primer) and further demultiplexes the reads to prepare data tables summarizing all of the UMI sequences and counts for each family (tagged.tar.gz) as well as consensus sequences from each sUMI and rank 1 dUMI family (consensus.tar.gz). More information about the sUMI_dUMI_comparison pipeline can be found in the paper and the README.md file on GitHub. The consensus.tar.gz and tagged.tar.gz files were moved from sUMI_dUMI_comparison pipeline directory on the server to the Pipeline_Outputs folder in this analysis directory for each dataset and appended with the dataset name (e.g. consensus_M027.tar.gz). Also in this analysis directory is a Sample_Info_Table.csv containing information about how each of the samples was prepared, such as purification methods and number of PCRs. There are also three other folders: Sequence_Analysis, Indentifying_Recombinant_Reads, and Figures. Each has an .Rmd file with the same name inside which is used to collect, summarize, and analyze the data. All of these collections of code were written and executed in RStudio to track notes and summarize results. Sequence_Analysis.Rmd has instructions to decompress all of the consensus.tar.gz files, combine them, and create two fasta files, one with all sUMI and one with all dUMI sequences. Using these as input, two data tables were created, that summarize all sequences and read counts for each sample that pass various criteria. These are used to help create Table 2 and as input for Indentifying_Recombinant_Reads.Rmd and Figures.Rmd. Next, 2 fasta files containing all of the rank 1 dUMI sequences and the matching sUMI sequences were created. These were used as input for the python script compare_seqs.py which identifies any matched sequences that are different between sUMI and dUMI read collections. This information was also used to help create Table 2. Finally, to populate the table with the number of sequences and bases in each sequence subset of interest, different sequence collections were saved and viewed in the Geneious program. To investigate the cause of sequences where the sUMI and dUMI sequences do not match, tagged.tar.gz was decompressed and for each family with discordant sUMI and dUMI sequences the reads from the UMI1_keeping directory were aligned using geneious. Reads from dUMI families failing the 0.7 filter were also aligned in Genious. The uncompressed tagged folder was then removed to save space. These read collections contain all of the reads in a UMI1 family and still include the UMI2 sequence. By examining the alignment and specifically the UMI2 sequences, the site of the discordance and its case were identified for each family as described in the paper. These alignments were saved as "Sequence Alignments.geneious". The counts of how many families were the result of PCR recombination were used in the body of the paper. Using Identifying_Recombinant_Reads.Rmd, the dUMI_ranked.csv file from each sample was extracted from all of the tagged.tar.gz files, combined and used as input to create a single dataset containing all UMI information from all samples. This file dUMI_df.csv was used as input for Figures.Rmd. Figures.Rmd used dUMI_df.csv, sequence_counts.csv, and read_counts.csv as input to create draft figures and then individual datasets for eachFigure. These were copied into Prism software to create the final figures for the paper.

This archive contains code and data for reproducing the analysis for “Replication Data for Revisiting ‘The Rise and Decline’ in a Population of Peer Production Projects”. Depending on what you hope to do with the data you probabbly do not want to download all of the files. Depending on your computation resources you may not be able to run all stages of the analysis. The code for all stages of the analysis, including typesetting the manuscript and running the analysis, is in code.tar. If you only want to run the final analysis or to play with datasets used in the analysis of the paper, you want intermediate_data.7z or the uncompressed tab and csv files. The data files are created in a four-stage process. The first stage uses the program “wikiq” to parse mediawiki xml dumps and create tsv files that have edit data for each wiki. The second stage generates all.edits.RDS file which combines these tsvs into a dataset of edits from all the wikis. This file is expensive to generate and at 1.5GB is pretty big. The third stage builds smaller intermediate files that contain the analytical variables from these tsv files. The fourth stage uses the intermediate files to generate smaller RDS files that contain the results. Finally, knitr and latex typeset the manuscript. A stage will only run if the outputs from the previous stages do not exist. So if the intermediate files exist they will not be regenerated. Only the final analysis will run. The exception is that stage 4, fitting models and generating plots, always runs. If you only want to replicate from the second stage onward, you want wikiq_tsvs.7z. If you want to replicate everything, you want wikia_mediawiki_xml_dumps.7z.001 wikia_mediawiki_xml_dumps.7z.002, and wikia_mediawiki_xml_dumps.7z.003. These instructions work backwards from building the manuscript using knitr, loading the datasets, running the analysis, to building the intermediate datasets. Building the manuscript using knitr This requires working latex, latexmk, and knitr installations. Depending on your operating system you might install these packages in different ways. On Debian Linux you can run apt install r-cran-knitr latexmk texlive-latex-extra. Alternatively, you can upload the necessary files to a project on Overleaf.com. Download code.tar. This has everything you need to typeset the manuscript. Unpack the tar archive. On a unix system this can be done by running tar xf code.tar. Navigate to code/paper_source. Install R dependencies. In R. run install.packages(c("data.table","scales","ggplot2","lubridate","texreg")) On a unix system you should be able to run make to build the manuscript generalizable_wiki.pdf. Otherwise you should try uploading all of the files (including the tables, figure, and knitr folders) to a new project on Overleaf.com. Loading intermediate datasets The intermediate datasets are found in the intermediate_data.7z archive. They can be extracted on a unix system using the command 7z x intermediate_data.7z. The files are 95MB uncompressed. These are RDS (R data set) files and can be loaded in R using the readRDS. For example newcomer.ds <- readRDS("newcomers.RDS"). If you wish to work with these datasets using a tool other than R, you might prefer to work with the .tab files. Running the analysis Fitting the models may not work on machines with less than 32GB of RAM. If you have trouble, you may find the functions in lib-01-sample-datasets.R useful to create stratified samples of data for fitting models. See line 89 of 02_model_newcomer_survival.R for an example. Download code.tar and intermediate_data.7z to your working folder and extract both archives. On a unix system this can be done with the command tar xf code.tar && 7z x intermediate_data.7z. Install R dependencies. install.packages(c("data.table","ggplot2","urltools","texreg","optimx","lme4","bootstrap","scales","effects","lubridate","devtools","roxygen2")). On a unix system you can simply run regen.all.sh to fit the models, build the plots and create the RDS files. Generating datasets Building the intermediate files The intermediate files are generated from all.edits.RDS. This process requires about 20GB of memory. Download all.edits.RDS, userroles_data.7z,selected.wikis.csv, and code.tar. Unpack code.tar and userroles_data.7z. On a unix system this can be done using tar xf code.tar && 7z x userroles_data.7z. Install R dependencies. In R run install.packages(c("data.table","ggplot2","urltools","texreg","optimx","lme4","bootstrap","scales","effects","lubridate","devtools","roxygen2")). Run 01_build_datasets.R. Building all.edits.RDS The intermediate RDS files used in the analysis are created from all.edits.RDS. To replicate building all.edits.RDS, you only need to run 01_build_datasets.R when the int... Visit https://dataone.org/datasets/sha256%3Acfa4980c107154267d8eb6dc0753ed0fde655a73a062c0c2f5af33f237da3437 for complete metadata about this dataset.

Abstract \r

\r The dataset was derived by the Bioregional Assessment Programme from multiple source datasets. The source datasets are identified in the Lineage field in this metadata statement. The processes undertaken to produce this derived dataset are described in the History field in this metadata statement.\r \r \r \r This dataset contains all the scripts used to carry out the uncertainty analysis for the maximum drawdown and time to maximum drawdown at the groundwater receptors in the Hunter bioregion and all the resulting posterior predictions. This is described in product 2.6.2 Groundwater numerical modelling (Herron et al. 2016). See History for a detailed explanation of the dataset contents.\r \r \r \r References:\r \r Herron N, Crosbie R, Peeters L, Marvanek S, Ramage A and Wilkins A (2016) Groundwater numerical modelling for the Hunter subregion. Product 2.6.2 for the Hunter subregion from the Northern Sydney Basin Bioregional Assessment. Department of the Environment, Bureau of Meteorology, CSIRO and Geoscience Australia, Australia.\r \r

Dataset History \r

\r This dataset uses the results of the design of experiment runs of the groundwater model of the Hunter subregion to train emulators to (a) constrain the prior parameter ensembles into the posterior parameter ensembles and to (b) generate the predictive posterior ensembles of maximum drawdown and time to maximum drawdown. This is described in product 2.6.2 Groundwater numerical modelling (Herron et al. 2016).\r \r \r \r A flow chart of the way the various files and scripts interact is provided in HUN_GW_UA_Flowchart.png (editable version in HUN_GW_UA_Flowchart.gliffy).\r \r \r \r R-script HUN_DoE_Parameters.R creates the set of parameters for the design of experiment in HUN_DoE_Parameters.csv. Each of these parameter combinations is evaluated with the groundwater model (dataset HUN GW Model v01). Associated with this spreadsheet is file HUN_GW_Parameters.csv. This file contains, for each parameter, if it is included in the sensitivity analysis, tied to another parameters, the initial value and range, the transformation, the type of prior distribution with its mean and covariance structure.\r \r \r \r The results of the design of experiment model runs are summarised in files HUN_GW_dmax_DoE_Predictions.csv, HUN_GW_tmax_DoE_Predictions.csv, HUN_GW_DoE_Observations.csv, HUN_GW_DoE_mean_BL_BF_hist.csv which have the maximum additional drawdown, the time to maximum additional drawdown for each receptor and the simulated equivalents to observed groundwater levels and SW-GW fluxes respectively. These are generated with post-processing scripts in dataset HUN GW Model v01 from the output (as exemplified in dataset HUN GW Model simulate ua999 pawsey v01).\r \r \r \r Spreadsheets HUN_GW_dmax_Predictions.csv and HUN_GW_tmax_Predictions.csv capture additional information on each prediction; the name of the prediction, transformation, min, max and median of design of experiment, a boolean to indicate the prediction is to be included in the uncertainty analysis, the layer it is assigned to and which objective function to use to constrain the prediction.\r \r Spreadsheet HUN_GW_Observations.csv has additional information on each observation; the name of the observation, a boolean to indicate to use the observation, the min and max of the design of experiment, a metadata statement describing the observation, the spatial coordinates, the observed value and the number of observations at this location (from dataset HUN bores v01). Further it has the distance of each bore to the nearest blue line network and the distance to each prediction (both in km). Spreadsheet HUN_GW_mean_BL_BF_hist.csv has similar information, but on the SW-GW flux. The observed values are from dataset HUN Groundwater Flowrate Time Series v01\r \r \r \r These files are used in script HUN_GW_SI.py to generate sensitivity indices (based on the Plischke et al. (2013) method) for each group of observations and predictions. These indices are saved in spreadsheets HUN_GW_dmax_SI.csv, HUN_GW_tmax_SI.csv, HUN_GW_hobs_SI.py, HUN_GW_mean_BF_hist_SI.csv\r \r \r \r Script HUN_GW_dmax_ObjFun.py calculates the objective function values for the design of experiment runs. Each prediction has a tailored objective function which is a weighted sum of the residuals between observations and predictions with weights based on the distance between observation and prediction. In addition to that there is an objective function for the baseflow rates. The results are stored in HUN_GW_DoE_ObjFun.csv and HUN_GW_ObjFun.csv. \r \r \r \r The latter files are used in scripts HUN_GW_dmax_CreatePosteriorParameters.R to carry out the Monte Carlo sampling of the prior parameter distributions with the Approximate Bayesian Computation methodology as described in Herron et al (2016) by generating and applying emulators for each objective function. The scripts use the scripts in dataset R-scripts for uncertainty analysis v01. These files are run on the high performance computation cluster machines with batch file HUN_GW_dmax_CreatePosterior.slurm. These scripts result in posterior parameter combinations for each objective function, stored in directory PosteriorParameters, with filename convention HUN_GW_dmax_Posterior_Parameters_OO_$OFName$.csv where $OFName$ is the name of the objective function. Python script HUN_GW_PosteriorParameters_Percentiles.py summarizes these posterior parameter combinations and stores the results in HUN_GW_PosteriorParameters_Percentiles.csv.\r \r \r \r The same set of spreadsheets is used to test convergence of the emulator performance with script HUN_GW_emulator_convergence.R and batch file HUN_GW_emulator_convergence.slurm to produce spreadsheet HUN_GW_convergence_objfun_BF.csv.\r \r \r \r The posterior parameter distributions are sampled with scripts HUN_GW_dmax_tmax_MCsampler.R and associated .slurm batch file. The script create and apply an emulator for each prediction. The emulator and results are stored in directory Emulators. This directory is not part of the this dataset but can be regenerated by running the scripts on the high performance computation clusters. A single emulator and associated output is included for illustrative purposes.\r \r \r \r Script HUN_GW_collate_predictions.csv collates all posterior predictive distributions in spreadsheets HUN_GW_dmax_PosteriorPredictions.csv and HUN_GW_tmax_PosteriorPredictions.csv. These files are further summarised in spreadsheet HUN_GW_dmax_tmax_excprob.csv with script HUN_GW_exc_prob. This spreadsheet contains for all predictions the coordinates, layer, number of samples in the posterior parameter distribution and the 5th, 50th and 95th percentile of dmax and tmax, the probability of exceeding 1 cm and 20 cm drawdown, the maximum dmax value from the design of experiment and the threshold of the objective function and the acceptance rate.\r \r \r \r The script HUN_GW_dmax_tmax_MCsampler.R is also used to evaluate parameter distributions HUN_GW_dmax_Posterior_Parameters_HUN_OF_probe439.csv and HUN_GW_dmax_Posterior_Parameters_Mackie_OF_probe439.csv. These are, for one predictions, different parameter distributions, in which the latter represents local information. The corresponding dmax values are stored in HUN_GW_dmax_probe439_HUN.csv and HUN_GW_dmax_probe439_Mackie.csv\r \r

Dataset Citation \r

\r Bioregional Assessment Programme (XXXX) HUN GW Uncertainty Analysis v01. Bioregional Assessment Derived Dataset. Viewed 13 March 2019, http://data.bioregionalassessments.gov.au/dataset/c25db039-5082-4dd6-bb9d-de7c37f6949a.\r \r

Dataset Ancestors \r

\r * Derived From HUN GW Model code v01\r \r * Derived From Hydstra Groundwater Measurement Update - NSW Office of Water, Nov2013\r \r * Derived From Groundwater Economic Elements Hunter NSW 20150520 PersRem v02\r \r * Derived From NSW Office of Water - National Groundwater Information System 20140701\r \r * Derived From Travelling Stock Route Conservation Values\r \r * Derived From HUN GW Model v01\r \r * Derived From NSW Wetlands\r \r * Derived From Climate Change Corridors Coastal North East NSW\r \r * Derived From Communities of National Environmental Significance Database - RESTRICTED - Metadata only\r \r * Derived From Climate Change Corridors for Nandewar and New England Tablelands\r \r * Derived From National Groundwater Dependent Ecosystems (GDE) Atlas\r \r * Derived From Fauna Corridors for North East NSW\r \r * Derived From R-scripts for uncertainty analysis v01\r \r * Derived From Asset database for the Hunter subregion on 27 August 2015\r \r * Derived From Hunter CMA GDEs (DRAFT DPI pre-release)\r \r * Derived From [Estuarine Macrophytes of Hunter Subregion NSW DPI Hunter

We hereby publish the dataset (with metadata) and the R script (R Core team, 2018) used for implementing the analysis presented in the paper "Food waste between environmental education, peers, and family influence. Insights from primary school students in Northern Italy", Journal of Cleaner Production (Piras et al., 2023). The dataset is provided in csv format with semicolons as separators and "NA" for missing data. The dataset includes all the variables used in at least one of the models presented in the paper, either in the main text or in the Supplementary Material. Other variables gathered by means of the questionnaires included as Supplementary Material of the paper have been removed. The dataset includes inputted values for missing data on independent variables. These were inputted using two approaches: last observation carried forward (LOCF) - preferred when possible - and last observation carried backward (LOCB). The metadata are presented as a PDF file.

Ransomware is considered as a significant threat for most enterprises since past few years. In scenarios wherein users can access all files on a shared server, one infected host is capable of locking the access to all shared files. In the article related to this repository, we detect ransomware infection based on file-sharing traffic analysis, even in the case of encrypted traffic. We compare three machine learning models and choose the best for validation. We train and test the detection model using more than 70 ransomware binaries from 26 different families and more than 2500 h of ‘not infected’ traffic from real users. The results reveal that the proposed tool can detect all ransomware binaries, including those not used in the training phase (zero-days). This paper provides a validation of the algorithm by studying the false positive rate and the amount of information from user files that the ransomware could encrypt before being detected.

This dataset directory contains the 'infected' and 'not infected' samples and the models used for each T configuration, each one in a separated folder.

The folders are named NxSy where x is the number of 1-second interval per sample and y the sliding step in seconds.

Each folder (for example N10S10/) contains: - tree.py -> Python script with the Tree model. - ensemble.json -> JSON file with the information about the Ensemble model. - NN_XhiddenLayer.json -> JSON file with the information about the NN model with X hidden layers (1, 2 or 3). - N10S10.csv -> All samples used for training each model in this folder. It is in csv format for using in bigML application. - zeroDays.csv -> All zero-day samples used for testing each model in this folder. It is in csv format for using in bigML application. - userSamples_test -> All samples used for validating each model in this folder. It is in csv format for using in bigML application. - userSamples_train -> User samples used for training the models. - ransomware_train -> Ransomware samples used for training the models - scaler.scaler -> Standard Scaler from python library used for scale the samples. - zeroDays_notFiltered -> Folder with the zeroDay samples.

In the case of N30S30 folder, there is an additional folder (SMBv2SMBv3NFS) with the samples extracted from the SMBv2, SMBv3 and NFS traffic traces. There are more binaries than the ones presented in the article, but it is because some of them are not "unseen" binaries (the families are present in the training set).

The files containing samples (NxSy.csv, zeroDays.csv and userSamples_test.csv) are structured as follows: - Each line is one sample. - Each sample has 3*T features and the label (1 if it is 'infected' sample and 0 if it is not). - The features are separated by ',' because it is a csv file. - The last column is the label of the sample.

Additionally we have placed two pcap files in root directory. There are the traces used for compare both versions of SMB.

This artifact accompanies the SEET@ICSE article "Assessing the impact of hints in learning formal specification", which reports on a user study to investigate the impact of different types of automated hints while learning a formal specification language, both in terms of immediate performance and learning retention, but also in the emotional response of the students. This research artifact provides all the material required to replicate this study (except for the proprietary questionnaires passed to assess the emotional response and user experience), as well as the collected data and data analysis scripts used for the discussion in the paper.

Dataset

The artifact contains the resources described below.

Experiment resources

The resources needed for replicating the experiment, namely in directory experiment:

alloy_sheet_pt.pdf: the 1-page Alloy sheet that participants had access to during the 2 sessions of the experiment. The sheet was passed in Portuguese due to the population of the experiment.

alloy_sheet_en.pdf: a version the 1-page Alloy sheet that participants had access to during the 2 sessions of the experiment translated into English.

docker-compose.yml: a Docker Compose configuration file to launch Alloy4Fun populated with the tasks in directory data/experiment for the 2 sessions of the experiment.

api and meteor: directories with source files for building and launching the Alloy4Fun platform for the study.

Experiment data

The task database used in our application of the experiment, namely in directory data/experiment:

Model.json, Instance.json, and Link.json: JSON files with to populate Alloy4Fun with the tasks for the 2 sessions of the experiment.

identifiers.txt: the list of all (104) available participant identifiers that can participate in the experiment.

Collected data

Data collected in the application of the experiment as a simple one-factor randomised experiment in 2 sessions involving 85 undergraduate students majoring in CSE. The experiment was validated by the Ethics Committee for Research in Social and Human Sciences of the Ethics Council of the University of Minho, where the experiment took place. Data is shared the shape of JSON and CSV files with a header row, namely in directory data/results:

data_sessions.json: data collected from task-solving in the 2 sessions of the experiment, used to calculate variables productivity (PROD1 and PROD2, between 0 and 12 solved tasks) and efficiency (EFF1 and EFF2, between 0 and 1).

data_socio.csv: data collected from socio-demographic questionnaire in the 1st session of the experiment, namely:

participant identification: participant's unique identifier (ID);

socio-demographic information: participant's age (AGE), sex (SEX, 1 through 4 for female, male, prefer not to disclosure, and other, respectively), and average academic grade (GRADE, from 0 to 20, NA denotes preference to not disclosure).

data_emo.csv: detailed data collected from the emotional questionnaire in the 2 sessions of the experiment, namely:

participant identification: participant's unique identifier (ID) and the assigned treatment (column HINT, either N, L, E or D);

detailed emotional response data: the differential in the 5-point Likert scale for each of the 14 measured emotions in the 2 sessions, ranging from -5 to -1 if decreased, 0 if maintained, from 1 to 5 if increased, or NA denoting failure to submit the questionnaire. Half of the emotions are positive (Admiration1 and Admiration2, Desire1 and Desire2, Hope1 and Hope2, Fascination1 and Fascination2, Joy1 and Joy2, Satisfaction1 and Satisfaction2, and Pride1 and Pride2), and half are negative (Anger1 and Anger2, Boredom1 and Boredom2, Contempt1 and Contempt2, Disgust1 and Disgust2, Fear1 and Fear2, Sadness1 and Sadness2, and Shame1 and Shame2). This detailed data was used to compute the aggregate data in data_emo_aggregate.csv and in the detailed discussion in Section 6 of the paper.

data_umux.csv: data collected from the user experience questionnaires in the 2 sessions of the experiment, namely:

participant identification: participant's unique identifier (ID);

user experience data: summarised user experience data from the UMUX surveys (UMUX1 and UMUX2, as a usability metric ranging from 0 to 100).

participants.txt: the list of participant identifiers that have registered for the experiment.

Analysis scripts

The analysis scripts required to replicate the analysis of the results of the experiment as reported in the paper, namely in directory analysis:

analysis.r: An R script to analyse the data in the provided CSV files; each performed analysis is documented within the file itself.

requirements.r: An R script to install the required libraries for the analysis script.

normalize_task.r: A Python script to normalize the task JSON data from file data_sessions.json into the CSV format required by the analysis script.

normalize_emo.r: A Python script to compute the aggregate emotional response in the CSV format required by the analysis script from the detailed emotional response data in the CSV format of data_emo.csv.

Dockerfile: Docker script to automate the analysis script from the collected data.

Setup

To replicate the experiment and the analysis of the results, only Docker is required.

If you wish to manually replicate the experiment and collect your own data, you'll need to install:

A modified version of the Alloy4Fun platform, which is built in the Meteor web framework. This version of Alloy4Fun is publicly available in branch study of its repository at https://github.com/haslab/Alloy4Fun/tree/study.

If you wish to manually replicate the analysis of the data collected in our experiment, you'll need to install:

Python to manipulate the JSON data collected in the experiment. Python is freely available for download at https://www.python.org/downloads/, with distributions for most platforms.

R software for the analysis scripts. R is freely available for download at https://cran.r-project.org/mirrors.html, with binary distributions available for Windows, Linux and Mac.

Usage

Experiment replication

This section describes how to replicate our user study experiment, and collect data about how different hints impact the performance of participants.

To launch the Alloy4Fun platform populated with tasks for each session, just run the following commands from the root directory of the artifact. The Meteor server may take a few minutes to launch, wait for the "Started your app" message to show.

cd experimentdocker-compose up

This will launch Alloy4Fun at http://localhost:3000. The tasks are accessed through permalinks assigned to each participant. The experiment allows for up to 104 participants, and the list of available identifiers is given in file identifiers.txt. The group of each participant is determined by the last character of the identifier, either N, L, E or D. The task database can be consulted in directory data/experiment, in Alloy4Fun JSON files.

In the 1st session, each participant was given one permalink that gives access to 12 sequential tasks. The permalink is simply the participant's identifier, so participant 0CAN would just access http://localhost:3000/0CAN. The next task is available after a correct submission to the current task or when a time-out occurs (5mins). Each participant was assigned to a different treatment group, so depending on the permalink different kinds of hints are provided. Below are 4 permalinks, each for each hint group:

Group N (no hints): http://localhost:3000/0CAN

Group L (error locations): http://localhost:3000/CA0L

Group E (counter-example): http://localhost:3000/350E

Group D (error description): http://localhost:3000/27AD

In the 2nd session, likewise the 1st session, each permalink gave access to 12 sequential tasks, and the next task is available after a correct submission or a time-out (5mins). The permalink is constructed by prepending the participant's identifier with P-. So participant 0CAN would just access http://localhost:3000/P-0CAN. In the 2nd sessions all participants were expected to solve the tasks without any hints provided, so the permalinks from different groups are undifferentiated.

Before the 1st session the participants should answer the socio-demographic questionnaire, that should ask the following information: unique identifier, age, sex, familiarity with the Alloy language, and average academic grade.

Before and after both sessions the participants should answer the standard PrEmo 2 questionnaire. PrEmo 2 is published under an Attribution-NonCommercial-NoDerivatives 4.0 International Creative Commons licence (CC BY-NC-ND 4.0). This means that you are free to use the tool for non-commercial purposes as long as you give appropriate credit, provide a link to the license, and do not modify the original material. The original material, namely the depictions of the diferent emotions, can be downloaded from https://diopd.org/premo/. The questionnaire should ask for the unique user identifier, and for the attachment with each of the depicted 14 emotions, expressed in a 5-point Likert scale.

After both sessions the participants should also answer the standard UMUX questionnaire. This questionnaire can be used freely, and should ask for the user unique identifier and answers for the standard 4 questions in a 7-point Likert scale. For information about the questions, how to implement the questionnaire, and how to compute the usability metric ranging from 0 to 100 score from the answers, please see the original paper:

Kraig Finstad. 2010. The usability metric for user experience. Interacting with computers 22, 5 (2010), 323–327.

Analysis of other applications of the experiment

This section describes how to replicate the analysis of the data collected in an application of the experiment described in Experiment replication.

The analysis script expects data in 4 CSV files,