Replication pack, FSE2018 submission #164:
------------------------------------------

**Working title:** Ecosystem-Level Factors Affecting the Survival of Open-Source Projects: 
A Case Study of the PyPI Ecosystem

**Note:** link to data artifacts is already included in the paper. 
Link to the code will be included in the Camera Ready version as well.


Content description
===================

- **ghd-0.1.0.zip** - the code archive. This code produces the dataset files 
 described below
- **settings.py** - settings template for the code archive.
- **dataset_minimal_Jan_2018.zip** - the minimally sufficient version of the dataset.
 This dataset only includes stats aggregated by the ecosystem (PyPI)
- **dataset_full_Jan_2018.tgz** - full version of the dataset, including project-level
 statistics. It is ~34Gb unpacked. This dataset still doesn't include PyPI packages
 themselves, which take around 2TB.
- **build_model.r, helpers.r** - R files to process the survival data 
  (`survival_data.csv` in **dataset_minimal_Jan_2018.zip**, 
  `common.cache/survival_data.pypi_2008_2017-12_6.csv` in 
  **dataset_full_Jan_2018.tgz**)
- **Interview protocol.pdf** - approximate protocol used for semistructured interviews.
- LICENSE - text of GPL v3, under which this dataset is published
- INSTALL.md - replication guide (~2 pages)

Replication guide
=================

Step 0 - prerequisites
----------------------

- Unix-compatible OS (Linux or OS X)
- Python interpreter (2.7 was used; Python 3 compatibility is highly likely)
- R 3.4 or higher (3.4.4 was used, 3.2 is known to be incompatible)

Depending on detalization level (see Step 2 for more details):
- up to 2Tb of disk space (see Step 2 detalization levels)
- at least 16Gb of RAM (64 preferable)
- few hours to few month of processing time

Step 1 - software
----------------

- unpack **ghd-0.1.0.zip**, or clone from gitlab:

   git clone https://gitlab.com/user2589/ghd.git
   git checkout 0.1.0
 
 `cd` into the extracted folder. 
 All commands below assume it as a current directory.
  
- copy `settings.py` into the extracted folder. Edit the file:
  * set `DATASET_PATH` to some newly created folder path
  * add at least one GitHub API token to `SCRAPER_GITHUB_API_TOKENS` 
- install docker. For Ubuntu Linux, the command is 
  `sudo apt-get install docker-compose`
- install libarchive and headers: `sudo apt-get install libarchive-dev`
- (optional) to replicate on NPM, install yajl: `sudo apt-get install yajl-tools`
 Without this dependency, you might get an error on the next step, 
 but it's safe to ignore.
- install Python libraries: `pip install --user -r requirements.txt` . 
- disable all APIs except GitHub (Bitbucket and Gitlab support were
 not yet implemented when this study was in progress): edit
 `scraper/init.py`, comment out everything except GitHub support
 in `PROVIDERS`.

Step 2 - obtaining the dataset
-----------------------------

The ultimate goal of this step is to get output of the Python function 
`common.utils.survival_data()` and save it into a CSV file:

  # copy and paste into a Python console
  from common import utils
  survival_data = utils.survival_data('pypi', '2008', smoothing=6)
  survival_data.to_csv('survival_data.csv')

Since full replication will take several months, here are some ways to speedup
the process:

####Option 2.a, difficulty level: easiest

Just use the precomputed data. Step 1 is not necessary under this scenario.

- extract **dataset_minimal_Jan_2018.zip**
- get `survival_data.csv`, go to the next step

####Option 2.b, difficulty level: easy

Use precomputed longitudinal feature values to build the final table.
The whole process will take 15..30 minutes.

- create a folder `

Writing process data of 116 participants (50 - 90 years) were obtained. Each of them completed a typed sentence production task that consisted of 40 trials. Pause times between and within all words, target nouns and target verbs were logged with a keystroke logging tool (ScriptLog). The data were used to perform a Generalizability and a Decision study to determine the minimum number of trials and of items per trial that are necessary to generalize over tasks.

This data set contains the data that remained after eliminating the trials during which participants made deletions and corrections. The R script that was used for the analyses is also available.

Writing process data of 15 cognitively impaired patients and 15 age- and gender-matched healthy controls were obtained. Each of them completed two typed picture description tasks that were logged with Inputlog, a keystroke logging tool. Variables included time on task; number of characters, pauses and Pause-bursts per minute; proportion of pause time; duration of Pause-bursts; and pause time between words. For pause time between words, also the effect of pauses preceeding specific word categories was analyzed.

The data were used to explore if the observation of writing behavior can assist in the screening and follow-up of mild cognitive impairment (MCI) and mild dementia due to Alzheimer’s disease (AD). This data set contains the CSV files that were used for the analyses and the corresponding R script.

Context

To make this a seamless process, I cleaned the data and delete many variables that I thought were not important to our dataset. I then uploaded all of those files to Kaggle for each of you to download. The rideshare_data has both lyft and uber but it is still a cleaned version from the dataset we downloaded from Kaggle.

Use of Data Files

You can easily subset the data into the car types that you will be modeling by first loading the csv into R, here is the code for how you do this:

This loads the file into R

df<-read.csv('uber.csv')

The next codes is to subset the data into specific car types. The example below only has Uber 'Black' car types.

df_black<-subset(uber_df, uber_df$name == 'Black')

This next portion of code will be to load it into R. First, we must write this dataframe into a csv file on our computer in order to load it into R.

write.csv(df_black, "nameofthefileyouwanttosaveas.csv")

The file will appear in you working directory. If you are not familiar with your working directory. Run this code:

getwd()

The output will be the file path to your working directory. You will find the file you just created in that folder.

Inspiration

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

Writing process data of 90 healthy elderly (50 - 90 years) were obtained. Each of them completed a typed sentence production task that consisted of 40 trials. Time on task, production time, and pause times before sentences, between words and within words were logged with a keystroke logging tool (ScriptLog). The data were used to examine the influences of normal ageing and verb transitivity on sentence production. The underlying aim was to provide a foundation for further research on sentence production in Alzheimer's disease (AD).

This data set contains the CSV files that were used for the analyses and the corresponding R script. Note that the files contain the data before data reduction (still containing, e.g., participants that were eventually not included in the analyses, or sentences with errors); the R script includes the necessary code for data reduction. This data set also contains the stimuli that were used in the experiment (a subset of images from the Open Linguistic Picture Database; Paesen & Meulemans, 2020).

The paper is currently under review. The data will be available as soon as it is accepted for publication.

Categorical scatterplots with R for biologists: a step-by-step guide

Benjamin Petre1, Aurore Coince2, Sophien Kamoun1

1 The Sainsbury Laboratory, Norwich, UK; 2 Earlham Institute, Norwich, UK

Weissgerber and colleagues (2015) recently stated that ‘as scientists, we urgently need to change our practices for presenting continuous data in small sample size studies’. They called for more scatterplot and boxplot representations in scientific papers, which ‘allow readers to critically evaluate continuous data’ (Weissgerber et al., 2015). In the Kamoun Lab at The Sainsbury Laboratory, we recently implemented a protocol to generate categorical scatterplots (Petre et al., 2016; Dagdas et al., 2016). Here we describe the three steps of this protocol: 1) formatting of the data set in a .csv file, 2) execution of the R script to generate the graph, and 3) export of the graph as a .pdf file.

Protocol

• Step 1: format the data set as a .csv file. Store the data in a three-column excel file as shown in Powerpoint slide. The first column ‘Replicate’ indicates the biological replicates. In the example, the month and year during which the replicate was performed is indicated. The second column ‘Condition’ indicates the conditions of the experiment (in the example, a wild type and two mutants called A and B). The third column ‘Value’ contains continuous values. Save the Excel file as a .csv file (File -> Save as -> in ‘File Format’, select .csv). This .csv file is the input file to import in R.

• Step 2: execute the R script (see Notes 1 and 2). Copy the script shown in Powerpoint slide and paste it in the R console. Execute the script. In the dialog box, select the input .csv file from step 1. The categorical scatterplot will appear in a separate window. Dots represent the values for each sample; colors indicate replicates. Boxplots are superimposed; black dots indicate outliers.

• Step 3: save the graph as a .pdf file. Shape the window at your convenience and save the graph as a .pdf file (File -> Save as). See Powerpoint slide for an example.

Notes

• Note 1: install the ggplot2 package. The R script requires the package ‘ggplot2’ to be installed. To install it, Packages & Data -> Package Installer -> enter ‘ggplot2’ in the Package Search space and click on ‘Get List’. Select ‘ggplot2’ in the Package column and click on ‘Install Selected’. Install all dependencies as well.

• Note 2: use a log scale for the y-axis. To use a log scale for the y-axis of the graph, use the command line below in place of command line #7 in the script.

7 Display the graph in a separate window. Dot colors indicate

replicates

graph + geom_boxplot(outlier.colour='black', colour='black') + geom_jitter(aes(col=Replicate)) + scale_y_log10() + theme_bw()

References

Dagdas YF, Belhaj K, Maqbool A, Chaparro-Garcia A, Pandey P, Petre B, et al. (2016) An effector of the Irish potato famine pathogen antagonizes a host autophagy cargo receptor. eLife 5:e10856.

Petre B, Saunders DGO, Sklenar J, Lorrain C, Krasileva KV, Win J, et al. (2016) Heterologous Expression Screens in Nicotiana benthamiana Identify a Candidate Effector of the Wheat Yellow Rust Pathogen that Associates with Processing Bodies. PLoS ONE 11(2):e0149035

Weissgerber TL, Milic NM, Winham SJ, Garovic VD (2015) Beyond Bar and Line Graphs: Time for a New Data Presentation Paradigm. PLoS Biol 13(4):e1002128

https://cran.r-project.org/

http://ggplot2.org/

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

Online Retail Transaction Records

Online Retail Sales: Product Transactions and Customer Details

By Ali Prasla [source]

About this dataset

The Online Retail Sales Dataset, often referred to as the Online Retail.csv file, is an extensive and comprehensive collection of data points relating to e-commerce transactions. This dataset provides a detailed view of sales activities within the online retail sector, covering numerous essential attributes necessary for a quantitative understanding of consumer behavior and the overall business performance.

One of the key elements covered in this dataset is 'InvoiceNo', which is a unique identifier for each transaction taking place in this retail environment. Given its uniqueness, it serves as a primary key for distinguishing individual transactions. It's worthwhile to note that these Invoice Numbers are numerical values.

Another important attribute included here is 'StockCode'. Each product listed or sold on this online retail platform has been assigned with its unique identification code or StockCode. These codes are also numerical values that offer another layer to clearly classify items and distinguish one from another.

For further understanding, every product comes with a basic description noted under the 'Description' column. In textual form, these descriptions provide insights into what exactly each product item entails. Aside from aiding identification efforts, they can potentially open avenues for text-based analysis such as sentiment analysis or keyword flagging based on product trends.

'Moving onto details about transactions themselves', we have two crucial columns: 'Quantity' and 'UnitPrice'. As their names suggest, these show respectively how many particular units of an item were sold per transaction and at what price per unit was sold at.

Further adding detail to our transactions information comes 'InvoiceDate', which records when each separate purchase occurred down to accurate date & time records. This data can be pivotal in recognizing sales patterns throughout different periods or predicting future trends based on historical timing behavior.

Finally yet importantly comes our global indicator - The ‘Country’ column specifies various countries where customers reside who interacts with this particular online platform regularly by making purchases. This application allows us insights into the geographical dispersion of user base across various countries, potentially providing us insights into regional preferences or global market segmentation.

Ith such a wealth of detailed transaction records and customer information, the Online Retail.csv dataset stands as an invaluable tool for those looking to delve deep into online retail sales data analysis. The possibilities with this dataset are vast, ranging from shaping efficient marketing strategies based on geographical data to predicting sales & growth metrics using historical behavior and much more

How to use the dataset

Here's how to make best use of this dataset:

Getting Started Before you start analyzing your data – you'll have to load it into statistical software such as Python (using pandas library) or R. The dataset is saved in .csv file format which supports easy reading into most data manipulation software.

Understand The Fields

• InvoiceNo: Each transaction made has an associated unique numerical identifier called InvoiceNo. Consider it like a receipt code - these allow for tracking individual transactions.

• StockCode: To identify each product uniquely during analysis, refer to each StockCode value which is essentially a product identification code.

• Description: A brief textual description about each product that can be invaluable when dealing with categories for market-basket type analysis.

• Quantity: Each row lists out how many units of a particular item were involved in a single transaction - watch out for very large values as they might represent bulk orders.

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This data and code archive provides all the data and code for replicating the empirical analysis that is presented in the journal article "A Ray-Based Input Distance Function to Model Zero-Valued Output Quantities: Derivation and an Empirical Application" authored by Juan José Price and Arne Henningsen and published in the Journal of Productivity Analysis (DOI: 10.1007/s11123-023-00684-1).

We conducted the empirical analysis with the "R" statistical software (version 4.3.0) using the add-on packages "combinat" (version 0.0.8), "miscTools" (version 0.6.28), "quadprog" (version 1.5.8), sfaR (version 1.0.0), stargazer (version 5.2.3), and "xtable" (version 1.8.4) that are available at CRAN. We created the R package "micEconDistRay" that provides the functions for empirical analyses with ray-based input distance functions that we developed for the above-mentioned paper. Also this R package is available at CRAN (https://cran.r-project.org/package=micEconDistRay).

This replication package contains the following files and folders:

README This file

MuseumsDk.csv The original data obtained from the Danish Ministry of Culture and from Statistics Denmark. It includes the following variables:

museum: Name of the museum.

type: Type of museum (Kulturhistorisk museum = cultural history museum; Kunstmuseer = arts museum; Naturhistorisk museum = natural history museum; Blandet museum = mixed museum).

munic: Municipality, in which the museum is located.

yr: Year of the observation.

units: Number of visit sites.

resp: Whether or not the museum has special responsibilities (0 = no special responsibilities; 1 = at least one special responsibility).

vis: Number of (physical) visitors.

aarc: Number of articles published (archeology).

ach: Number of articles published (cultural history).

aah: Number of articles published (art history).

anh: Number of articles published (natural history).

exh: Number of temporary exhibitions.

edu: Number of primary school classes on educational visits to the museum.

ev: Number of events other than exhibitions.

ftesc: Scientific labor (full-time equivalents).

ftensc: Non-scientific labor (full-time equivalents).

expProperty: Running and maintenance costs [1,000 DKK].

expCons: Conservation expenditure [1,000 DKK].

ipc: Consumer Price Index in Denmark (the value for year 2014 is set to 1).

prepare_data.R This R script imports the data set MuseumsDk.csv, prepares it for the empirical analysis (e.g., removing unsuitable observations, preparing variables), and saves the resulting data set as DataPrepared.csv.

DataPrepared.csv This data set is prepared and saved by the R script prepare_data.R. It is used for the empirical analysis.

make_table_descriptive.R This R script imports the data set DataPrepared.csv and creates the LaTeX table /tables/table_descriptive.tex, which provides summary statistics of the variables that are used in the empirical analysis.

IO_Ray.R This R script imports the data set DataPrepared.csv, estimates a ray-based Translog input distance functions with the 'optimal' ordering of outputs, imposes monotonicity on this distance function, creates the LaTeX table /tables/idfRes.tex that presents the estimated parameters of this function, and creates several figures in the folder /figures/ that illustrate the results.

IO_Ray_ordering_outputs.R This R script imports the data set DataPrepared.csv, estimates a ray-based Translog input distance functions, imposes monotonicity for each of the 720 possible orderings of the outputs, and saves all the estimation results as (a huge) R object allOrderings.rds.

allOrderings.rds (not included in the ZIP file, uploaded separately) This is a saved R object created by the R script IO_Ray_ordering_outputs.R that contains the estimated ray-based Translog input distance functions (with and without monotonicity imposed) for each of the 720 possible orderings.

IO_Ray_model_averaging.R This R script loads the R object allOrderings.rds that contains the estimated ray-based Translog input distance functions for each of the 720 possible orderings, does model averaging, and creates several figures in the folder /figures/ that illustrate the results.

/tables/ This folder contains the two LaTeX tables table_descriptive.tex and idfRes.tex (created by R scripts make_table_descriptive.R and IO_Ray.R, respectively) that provide summary statistics of the data set and the estimated parameters (without and with monotonicity imposed) for the 'optimal' ordering of outputs.

/figures/ This folder contains 48 figures (created by the R scripts IO_Ray.R and IO_Ray_model_averaging.R) that illustrate the results obtained with the 'optimal' ordering of outputs and the model-averaged results and that compare these two sets of results.

This reference contains the R-code for the analysis and summary of detections of Bachman's sparrow, bobwhite quail and brown-headed nuthatch through 2020. Specifically generates probability of detection and occupancy of the species based on call counts and elicited calls with playback. The code loads raw point count (CSV files) and fire history data (CSV) and cleans/transforms into a tidy format for occupancy analysis. It then creates the necessary data structure for occupancy analysis, performs the analysis for the three focal species, and provides functionality for generating tables and figures summarizing the key findings of the occupancy analysis. The raw data, point count locations and other spatial data (ShapeFiles) are contained in the dataset.

Corresponding peer-reviewed publication

This dataset corresponds to all the RAPID input and output files that were used in the study reported in:

David, Cédric H., Florence Habets, David R. Maidment and Zong-Liang Yang (2011), RAPID applied to the SIM-France model, Hydrological Processes, 25(22), 3412-3425. DOI: 10.1002/hyp.8070.

When making use of any of the files in this dataset, please cite both the aforementioned article and the dataset herein.

Time format

The times reported in this description all follow the ISO 8601 format. For example 2000-01-01T16:00-06:00 represents 4:00 PM (16:00) on Jan 1st 2000 (2000-01-01), Central Standard Time (-06:00). Additionally, when time ranges with inner time steps are reported, the first time corresponds to the beginning of the first time step, and the second time corresponds to the end of the last time step. For example, the 3-hourly time range from 2000-01-01T03:00+00:00 to 2000-01-01T09:00+00:00 contains two 3-hourly time steps. The first one starts at 3:00 AM and finishes at 6:00AM on Jan 1st 2000, Universal Time; the second one starts at 6:00 AM and finishes at 9:00AM on Jan 1st 2000, Universal Time.

Data sources

The following sources were used to produce files in this dataset:

The hydrographic network of SIM-France, as published in Habets, F., A. Boone, J. L. Champeaux, P. Etchevers, L. Franchistéguy, E. Leblois, E. Ledoux, P. Le Moigne, E. Martin, S. Morel, J. Noilhan, P. Quintana Seguí, F. Rousset-Regimbeau, and P. Viennot (2008), The SAFRAN-ISBA-MODCOU hydrometeorological model applied over France, Journal of Geophysical Research: Atmospheres, 113(D6), DOI: 10.1029/2007JD008548.

The observed flows are from Banque HYDRO, Service Central d'Hydrométéorologie et d'Appui à la Prévision des Inondations. Available at http://www.hydro.eaufrance.fr/index.php.

Outputs from a simulation using SIM-France (Habets et al. 2008). The simulation was run by Florence Habets, and produced 3-hourly time steps from 1995-08-01T00:00+02:00 to 2005-07-31T21:02+00:00. Further details on the inputs and options used for this simulation are provided in David et al. (2011).

Software

The following software were used to produce files in this dataset:

The Routing Application for Parallel computation of Discharge (RAPID, David et al. 2011, http://rapid-hub.org), Version 1.1.0. Further details on the inputs and options used for this series of simulations are provided below and in David et al. (2011).

ESRI ArcGIS (http://www.arcgis.com).

Microsoft Excel (https://products.office.com/en-us/excel).

The GNU Compiler Collection (https://gcc.gnu.org) and the Intel compilers (https://software.intel.com/en-us/intel-compilers).

Study domain

The files in this dataset correspond to one study domain:

The river network of SIM-France is made of 24264 river reaches. The temporal range corresponding to this domain is from 1995-08-01T00:00+02:00 to 2005-07-31 T21:00+02:00.

Description of files

All files below were prepared by Cédric H. David, using the data sources and software mentioned above.

rapid_connect_France.csv. This CSV file contains the river network connectivity information and is based on the unique IDs of the SIM-France river reaches (the IDs). For each river reach, this file specifies: the ID of the reach, the ID of the unique downstream reach, the number of upstream reaches with a maximum of four reaches, and the IDs of all upstream reaches. A value of zero is used in place of NoData. The river reaches are sorted in increasing value of ID. The values were computed based on the SIM-France FICVID file. This file was prepared using a Fortran program.

m3_riv_France_1995_2005_ksat_201101_c_zvol_ext.nc. This netCDF file contains the 3-hourly accumulated inflows of water (in cubic meters) from surface and subsurface runoff into the upstream point of each river reach. The river reaches have the same IDs and are sorted similarly to rapid_connect_France.csv. The time range for this file is from 1995-08-01T00:00+02:00 to 2005/07/31T21:00+02:00. The values were computed using the outputs of SIM-France. This file was prepared using a Fortran program.

kfac_modcou_1km_hour.csv. This CSV file contains a first guess of Muskingum k values (in seconds) for all river reaches. The river reaches have the same IDs and are sorted similarly to rapid_connect_France.csv. The values were computed based on the following information: ID, size of the side of the grid cell, Equation (5) in David et al. (2011), and using a wave celerity of 1 km/h. This file was prepared using a Fortran program.

kfac_modcou_ttra_length.csv. This CSV file contains a second guess of Muskingum k values (in seconds) for all river reaches. The river reaches have the same IDs and are sorted similarly to rapid_connect_France.csv. The values were computed based on the following information: ID, size of the side of the grid cell, travel time, and Equation (9) in David et al. (2011).

k_modcou_0.csv. This CSV file contains Muskingum k values (in seconds) for all river reaches. The river reaches have the same COMIDs and are sorted similarly to rapid_connect_San_Guad.csv. The values were computed based on the following information: kfac_modcou_1km_hour.csv and using Table (2) in David et al. (2011). This file was prepared using a Fortran program.

k_modcou_1.csv. This CSV file contains Muskingum k values (in seconds) for all river reaches. The river reaches have the same COMIDs and are sorted similarly to rapid_connect_San_Guad.csv. The values were computed based on the following information: kfac_modcou_1km_hour.csv and using Table (2) in David et al. (2011). This file was prepared using a Fortran program.

k_modcou_2.csv. This CSV file contains Muskingum k values (in seconds) for all river reaches. The river reaches have the same COMIDs and are sorted similarly to rapid_connect_San_Guad.csv. The values were computed based on the following information: kfac_modcou_1km_hour.csv and using Table (2) in David et al. (2011). This file was prepared using a Fortran program.

k_modcou_3.csv. This CSV file contains Muskingum k values (in seconds) for all river reaches. The river reaches have the same COMIDs and are sorted similarly to rapid_connect_San_Guad.csv. The values were computed based on the following information: kfac_modcou_1km_hour.csv and using Table (2) in David et al. (2011). This file was prepared using a Fortran program.

k_modcou_4.csv. This CSV file contains Muskingum k values (in seconds) for all river reaches. The river reaches have the same COMIDs and are sorted similarly to rapid_connect_San_Guad.csv. The values were computed based on the following information: kfac_modcou_1km_hour.csv and using Table (2) in David et al. (2011). This file was prepared using a Fortran program.

k_modcou_a.csv. This CSV file contains Muskingum k values (in seconds) for all river reaches. The river reaches have the same COMIDs and are sorted similarly to rapid_connect_San_Guad.csv. The values were computed based on the following information: kfac_modcou_1km_hour.csv and using Table (2) in David et al. (2011). This file was prepared using a Fortran program.

k_modcou_b.csv. This CSV file contains Muskingum k values (in seconds) for all river reaches. The river reaches have the same COMIDs and are sorted similarly to rapid_connect_San_Guad.csv. The values were computed based on the following information: kfac_modcou_1km_hour.csv and using Table (2) in David et al. (2011). This file was prepared using a Fortran program.

k_modcou_c.csv. This CSV file contains Muskingum k values (in seconds) for all river reaches. The river reaches have the same COMIDs and are sorted similarly to rapid_connect_San_Guad.csv. The values were computed based on the following information: kfac_modcou_1km_hour.csv and using Table (2) in David et al. (2011). This file was prepared using a Fortran program.

x_modcou_0.csv. This CSV file contains Muskingum x values (dimensionless) for all river reaches. The river reaches have the same COMIDs and are sorted similarly to rapid_connect_San_Guad.csv. The values were computed based on Table (2) in David et al. (2011). This file was prepared using a Fortran program.

x_modcou_1.csv. This CSV file contains Muskingum x values (dimensionless) for all river reaches. The river reaches have the same COMIDs and are sorted similarly to rapid_connect_San_Guad.csv. The values were computed based on Table (2) in David et al. (2011). This file was prepared using a Fortran program.

x_modcou_2.csv. This CSV file contains Muskingum x values (dimensionless) for all river reaches. The river reaches have the same COMIDs and are sorted similarly to rapid_connect_San_Guad.csv. The values were computed based on Table (2) in David et al. (2011). This file was prepared using a Fortran program.

x_modcou_3.csv. This CSV file contains Muskingum x values (dimensionless) for all river reaches. The river reaches have the same COMIDs and are sorted similarly to rapid_connect_San_Guad.csv. The values were computed based on Table (2) in David et al. (2011). This file was prepared using a Fortran program.

x_modcou_4.csv. This CSV file contains Muskingum x values (dimensionless) for all river reaches. The river reaches have the same COMIDs and are sorted similarly to rapid_connect_San_Guad.csv. The values were computed based on Table (2) in David et al. (2011). This file was prepared using a Fortran program.

x_modcou_a.csv. This CSV file contains Muskingum x values (dimensionless) for all river reaches. The river reaches have the same COMIDs and are sorted similarly to rapid_connect_San_Guad.csv. The values were computed based on Table (2) in David et al. (2011). This file was prepared using a Fortran program.

x_modcou_b.csv. This CSV file contains Muskingum x values

LScD (Leicester Scientific Dictionary)April 2020 by Neslihan Suzen, PhD student at the University of Leicester (ns433@leicester.ac.uk/suzenneslihan@hotmail.com)Supervised by Prof Alexander Gorban and Dr Evgeny Mirkes[Version 3] The third version of LScD (Leicester Scientific Dictionary) is created from the updated LSC (Leicester Scientific Corpus) - Version 2*. All pre-processing steps applied to build the new version of the dictionary are the same as in Version 2** and can be found in description of Version 2 below. We did not repeat the explanation. After pre-processing steps, the total number of unique words in the new version of the dictionary is 972,060. The files provided with this description are also same as described as for LScD Version 2 below.* Suzen, Neslihan (2019): LSC (Leicester Scientific Corpus). figshare. Dataset. https://doi.org/10.25392/leicester.data.9449639.v2** Suzen, Neslihan (2019): LScD (Leicester Scientific Dictionary). figshare. Dataset. https://doi.org/10.25392/leicester.data.9746900.v2[Version 2] Getting StartedThis document provides the pre-processing steps for creating an ordered list of words from the LSC (Leicester Scientific Corpus) [1] and the description of LScD (Leicester Scientific Dictionary). This dictionary is created to be used in future work on the quantification of the meaning of research texts. R code for producing the dictionary from LSC and instructions for usage of the code are available in [2]. The code can be also used for list of texts from other sources, amendments to the code may be required.LSC is a collection of abstracts of articles and proceeding papers published in 2014 and indexed by the Web of Science (WoS) database [3]. Each document contains title, list of authors, list of categories, list of research areas, and times cited. The corpus contains only documents in English. The corpus was collected in July 2018 and contains the number of citations from publication date to July 2018. The total number of documents in LSC is 1,673,824.LScD is an ordered list of words from texts of abstracts in LSC.The dictionary stores 974,238 unique words, is sorted by the number of documents containing the word in descending order. All words in the LScD are in stemmed form of words. The LScD contains the following information:1.Unique words in abstracts2.Number of documents containing each word3.Number of appearance of a word in the entire corpusProcessing the LSCStep 1.Downloading the LSC Online: Use of the LSC is subject to acceptance of request of the link by email. To access the LSC for research purposes, please email to ns433@le.ac.uk. The data are extracted from Web of Science [3]. You may not copy or distribute these data in whole or in part without the written consent of Clarivate Analytics.Step 2.Importing the Corpus to R: The full R code for processing the corpus can be found in the GitHub [2].All following steps can be applied for arbitrary list of texts from any source with changes of parameter. The structure of the corpus such as file format and names (also the position) of fields should be taken into account to apply our code. The organisation of CSV files of LSC is described in README file for LSC [1].Step 3.Extracting Abstracts and Saving Metadata: Metadata that include all fields in a document excluding abstracts and the field of abstracts are separated. Metadata are then saved as MetaData.R. Fields of metadata are: List_of_Authors, Title, Categories, Research_Areas, Total_Times_Cited and Times_cited_in_Core_Collection.Step 4.Text Pre-processing Steps on the Collection of Abstracts: In this section, we presented our approaches to pre-process abstracts of the LSC.1.Removing punctuations and special characters: This is the process of substitution of all non-alphanumeric characters by space. We did not substitute the character “-” in this step, because we need to keep words like “z-score”, “non-payment” and “pre-processing” in order not to lose the actual meaning of such words. A processing of uniting prefixes with words are performed in later steps of pre-processing.2.Lowercasing the text data: Lowercasing is performed to avoid considering same words like “Corpus”, “corpus” and “CORPUS” differently. Entire collection of texts are converted to lowercase.3.Uniting prefixes of words: Words containing prefixes joined with character “-” are united as a word. The list of prefixes united for this research are listed in the file “list_of_prefixes.csv”. The most of prefixes are extracted from [4]. We also added commonly used prefixes: ‘e’, ‘extra’, ‘per’, ‘self’ and ‘ultra’.4.Substitution of words: Some of words joined with “-” in the abstracts of the LSC require an additional process of substitution to avoid losing the meaning of the word before removing the character “-”. Some examples of such words are “z-test”, “well-known” and “chi-square”. These words have been substituted to “ztest”, “wellknown” and “chisquare”. Identification of such words is done by sampling of abstracts form LSC. The full list of such words and decision taken for substitution are presented in the file “list_of_substitution.csv”.5.Removing the character “-”: All remaining character “-” are replaced by space.6.Removing numbers: All digits which are not included in a word are replaced by space. All words that contain digits and letters are kept because alphanumeric characters such as chemical formula might be important for our analysis. Some examples are “co2”, “h2o” and “21st”.7.Stemming: Stemming is the process of converting inflected words into their word stem. This step results in uniting several forms of words with similar meaning into one form and also saving memory space and time [5]. All words in the LScD are stemmed to their word stem.8.Stop words removal: Stop words are words that are extreme common but provide little value in a language. Some common stop words in English are ‘I’, ‘the’, ‘a’ etc. We used ‘tm’ package in R to remove stop words [6]. There are 174 English stop words listed in the package.Step 5.Writing the LScD into CSV Format: There are 1,673,824 plain processed texts for further analysis. All unique words in the corpus are extracted and written in the file “LScD.csv”.The Organisation of the LScDThe total number of words in the file “LScD.csv” is 974,238. Each field is described below:Word: It contains unique words from the corpus. All words are in lowercase and their stem forms. The field is sorted by the number of documents that contain words in descending order.Number of Documents Containing the Word: In this content, binary calculation is used: if a word exists in an abstract then there is a count of 1. If the word exits more than once in a document, the count is still 1. Total number of document containing the word is counted as the sum of 1s in the entire corpus.Number of Appearance in Corpus: It contains how many times a word occurs in the corpus when the corpus is considered as one large document.Instructions for R CodeLScD_Creation.R is an R script for processing the LSC to create an ordered list of words from the corpus [2]. Outputs of the code are saved as RData file and in CSV format. Outputs of the code are:Metadata File: It includes all fields in a document excluding abstracts. Fields are List_of_Authors, Title, Categories, Research_Areas, Total_Times_Cited and Times_cited_in_Core_Collection.File of Abstracts: It contains all abstracts after pre-processing steps defined in the step 4.DTM: It is the Document Term Matrix constructed from the LSC[6]. Each entry of the matrix is the number of times the word occurs in the corresponding document.LScD: An ordered list of words from LSC as defined in the previous section.The code can be used by:1.Download the folder ‘LSC’, ‘list_of_prefixes.csv’ and ‘list_of_substitution.csv’2.Open LScD_Creation.R script3.Change parameters in the script: replace with the full path of the directory with source files and the full path of the directory to write output files4.Run the full code.References[1]N. Suzen. (2019). LSC (Leicester Scientific Corpus) [Dataset]. Available: https://doi.org/10.25392/leicester.data.9449639.v1[2]N. Suzen. (2019). LScD-LEICESTER SCIENTIFIC DICTIONARY CREATION. Available: https://github.com/neslihansuzen/LScD-LEICESTER-SCIENTIFIC-DICTIONARY-CREATION[3]Web of Science. (15 July). Available: https://apps.webofknowledge.com/[4]A. Thomas, "Common Prefixes, Suffixes and Roots," Center for Development and Learning, 2013.[5]C. Ramasubramanian and R. Ramya, "Effective pre-processing activities in text mining using improved porter’s stemming algorithm," International Journal of Advanced Research in Computer and Communication Engineering, vol. 2, no. 12, pp. 4536-4538, 2013.[6]I. Feinerer, "Introduction to the tm Package Text Mining in R," Accessible en ligne: https://cran.r-project.org/web/packages/tm/vignettes/tm.pdf, 2013.

{# General information# The script runs with R (Version 3.1.1; 2014-07-10) and packages plyr (Version 1.8.1), XLConnect (Version 0.2-9), utilsMPIO (Version 0.0.25), sp (Version 1.0-15), rgdal (Version 0.8-16), tools (Version 3.1.1) and lattice (Version 0.20-29)# --------------------------------------------------------------------------------------------------------# Questions can be directed to: Martin Bulla (bulla.mar@gmail.com)# -------------------------------------------------------------------------------------------------------- # Data collection and how the individual variables were derived is described in: #Steiger, S.S., et al., When the sun never sets: diverse activity rhythms under continuous daylight in free-living arctic-breeding birds. Proceedings of the Royal Society B: Biological Sciences, 2013. 280(1764): p. 20131016-20131016. # Dale, J., et al., The effects of life history and sexual selection on male and female plumage colouration. Nature, 2015. # Data are available as Rdata file # Missing values are NA. # --------------------------------------------------------------------------------------------------------# For better readability the subsections of the script can be collapsed # --------------------------------------------------------------------------------------------------------}{# Description of the method # 1 - data are visualized in an interactive actogram with time of day on x-axis and one panel for each day of data # 2 - red rectangle indicates the active field, clicking with the mouse in that field on the depicted light signal generates a data point that is automatically (via custom made function) saved in the csv file. For this data extraction I recommend, to click always on the bottom line of the red rectangle, as there is always data available due to a dummy variable ("lin") that creates continuous data at the bottom of the active panel. The data are captured only if greenish vertical bar appears and if new line of data appears in R console). # 3 - to extract incubation bouts, first click in the new plot has to be start of incubation, then next click depict end of incubation and the click on the same stop start of the incubation for the other sex. If the end and start of incubation are at different times, the data will be still extracted, but the sex, logger and bird_ID will be wrong. These need to be changed manually in the csv file. Similarly, the first bout for a given plot will be always assigned to male (if no data are present in the csv file) or based on previous data. Hence, whenever a data from a new plot are extracted, at a first mouse click it is worth checking whether the sex, logger and bird_ID information is correct and if not adjust it manually. # 4 - if all information from one day (panel) is extracted, right-click on the plot and choose "stop". This will activate the following day (panel) for extraction. # 5 - If you wish to end extraction before going through all the rectangles, just press "escape". }{# Annotations of data-files from turnstone_2009_Barrow_nest-t401_transmitter.RData dfr-- contains raw data on signal strength from radio tag attached to the rump of female and male, and information about when the birds where captured and incubation stage of the nest1. who: identifies whether the recording refers to female, male, capture or start of hatching2. datetime_: date and time of each recording3. logger: unique identity of the radio tag 4. signal_: signal strength of the radio tag5. sex: sex of the bird (f = female, m = male)6. nest: unique identity of the nest7. day: datetime_ variable truncated to year-month-day format8. time: time of day in hours9. datetime_utc: date and time of each recording, but in UTC time10. cols: colors assigned to "who"--------------------------------------------------------------------------------------------------------m-- contains metadata for a given nest1. sp: identifies species (RUTU = Ruddy turnstone)2. nest: unique identity of the nest3. year_: year of observation4. IDfemale: unique identity of the female5. IDmale: unique identity of the male6. lat: latitude coordinate of the nest7. lon: longitude coordinate of the nest8. hatch_start: date and time when the hatching of the eggs started 9. scinam: scientific name of the species10. breeding_site: unique identity of the breeding site (barr = Barrow, Alaska)11. logger: type of device used to record incubation (IT - radio tag)12. sampling: mean incubation sampling interval in seconds--------------------------------------------------------------------------------------------------------s-- contains metadata for the incubating parents1. year_: year of capture2. species: identifies species (RUTU = Ruddy turnstone)3. author: identifies the author who measured the bird4. nest: unique identity of the nest5. caught_date_time: date and time when the bird was captured6. recapture: was the bird capture before? (0 - no, 1 - yes)7. sex: sex of the bird (f = female, m = male)8. bird_ID: unique identity of the bird9. logger: unique identity of the radio tag --------------------------------------------------------------------------------------------------------}

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 repository contains the raw data for the study:

Characterizing Intraspecific Resource Utilization in an Aquatic Consumer Using High-Throughput Phenotyping

Data are provided separately for the first experiment (numerical response experiment with 16 rotifer clones across six food concentrations) and the second experiment (growth rate measurements with 98 rotifer clones across two food concentrations).

Contents of first_experiment.zip

input/ This folder contains raw count data (output of the Wellcounter software):
popgrowth_

output/ output files produced by the R-script 'first_experiment_analysis.Rmd'

wellcounter/ contains the Wellcounter software (programs and configuration files) that were used for running the raw analysis of this dataset on a High Performance Computing cluster

first_experiment_analysis.Rmd R-Markdown file with data processing and statistical analysis of the first experiment
numerical_response_2par.R A function required by 'first_experiment_analysis.Rmd'

Contents of second_experiment.zip

input/ This folder contains raw count and behavioral data (output of the Wellcounter software):
popgrowth_

output/ output files produced by the R-script 'second_experiment_analysis.Rmd'

wellcounter/ contains the Wellcounter software (programs and configuration files) that were used for running the raw analysis (image and motion analysis) of this dataset on a High Performance Computing cluster

second_experiment_prep_run1.Rmd R-Markdown file for preprocessing the data from run1
second_experiment_prep_run2.Rmd R-Markdown file for preprocessing the data from run2
second_experiment_analysis.Rmd R-Markdown file with data processing and statistical analysis of the second experiment
extract_fixed_effects_table.R A function required by 'second_experiment_analysis.Rmd'

This data package is associated with the publication "Integrated, Coordinated, Open, and Networked (ICON) Science to Advance the Geosciences: Introduction and Synthesis of a Special Collection of Commentary Articles" in Earth and Space Science (Goldman et al. 2022; https://doi.org/10.1029/2021EA002099). The manuscript is an introductory article for a special collection of commentary articles across 19 geoscience disciplines that explore the challenges and opportunities associated with the use of ICON science principles. These principles focus on research intentionally designed to be Integrated, Coordinated, Open, and Networked (ICON) with the goal of maximizing mutual benefit (among stakeholders) and cross-system transferability of science outcomes. This data package contains data, figures, and R scripts associated with the cost/benefit analysis presented in the manuscript. The writing teams involved in the special collection placed each letter of ICON on a plot with perceived cost on one axis and perceived benefit on the other to summarize their perceptions of pursuing each principle of ICON science. These data were subsequently quantified and analyzed. Files are saved as .csv, .R, and .pdf. This data package also contains (1) the public foundational and instructional documents that enabled the crowdsourced creation of the special collection; (2) file-level metadata (flmd) that lists each file in the data package with a description; (3) data dictionary (dd) that defines column headers that appear in csv files. Files are saved as .pdf and .csv.

The raw data file is available online for public access (https://data.ontario.ca/dataset/lake-simcoe-monitoring). Download the 1980-2019 csv files and open up the file named "Simcoe_Zooplankton&Bythotrephes.csv". Copy and paste the zooplankton sheet into a new excel file called "Simcoe_Zooplankton.csv". The column ZDATE in the excel file needs to be switched from GENERAL to SHORT DATE so that the dates in the ZDATE column read "YYYY/MM/DD". Save as .csv in appropriate R folder. The data file "simcoe_manual_subset_weeks_5" is the raw data that has been subset for the main analysis of the article using the .R file "Simcoe MS - 5 Station Subset Data". The .csv file produced from this must then be manually edited to remove data points that do not have 5 stations per sampling period as well as by combining data points that should fall into a single week. The "simcoe_manual_subset_weeks_5.csv" is then used for the calculation of variability, stabilization, asynchrony, and Shannon Diversity for each year in the .R file "Simcoe MS - 5 Station Calculations". The final .R file "Simcoe MS - 5 Station Analysis contains the final statistical analyses as well as code to reproduce the original figures. Data and code for main and supplementary analyses are also available on GitHub (https://github.com/reillyoc/ZPseasonalPEs).

A routine was developed in R ('bathy_plots.R') to plot bathymetry data over time during individual CEAMARC events. This is so we can analyse benthic data in relation to habitat, ie. did we trawl over a slope or was the sea floor relatively flat. Note that the depth range in the plots is autoscaled to the data, so a small range in depths appears as a scatetring of points. As long as you look at the depth scale though interpretation will be ok. The R files need a file of bathymetry data in '200708V3_one_minute.csv' which is a file containing a data export from the underway PostgreSQL ship database and 'events.csv' which is a stripped down version of the events export from the ship board events database export. If you wish to run the code again you may need to change the pathnames in the R script to relevant locations. If you have opened the csv files in excel at any stage and the R script gets an error you may need to format the date/time columns as yyyy-mm-dd hh;mm:ss, save and close the file as csv without opening it again and then run the R script. However, all output files are here for every CEAMARC event. Filenames contain a reference to CEAMARC event id. Files are in eps format and can be viewed using Ghostview which is available as a free download on the internet.

This data repository provides the Food and Agriculture Biomass Input Output (FABIO) database, a global set of multi-regional physical supply-use and input-output tables covering global agriculture and forestry. The work is based on mostly freely available data from FAOSTAT, IEA, EIA, and UN Comtrade/BACI. FABIO currently covers 191 countries + RoW, 118 processes and 125 commodities (raw and processed agricultural and food products) for 1986-2013. All R codes and auxilliary data are available on GitHub. For more information please refer to https://fabio.fineprint.global. The database consists of the following main components, in compressed .rds format: Z: the inter-commodity input-output matrix, displaying the relationships of intermediate use of each commodity in the production of each commodity, in physical units (tons). The matrix has 24000 rows and columns (125 commodities x 192 regions), and is available in two versions, based on the method to allocate inputs to outputs in production processes: Z_mass (mass allocation) and Z_value (value allocation). Note that the row sums of the Z matrix (= total intermediate use by commodity) are identical in both versions. Y: the final demand matrix, denoting the consumption of all 24000 commodities by destination country and final use category. There are six final use categories (yielding 192 x 6 = 1152 columns): 1) food use, 2) other use (non-food), 3) losses, 4) stock addition, 5) balancing, and 6) unspecified. X: the total output vector of all 24000 commodities. Total output is equal to the sum of intermediate and final use by commodity. L: the Leontief inverse, computed as (I – A)-1, where A is the matrix of input coefficients derived from Z and x. Again, there are two versions, depending on the underlying version of Z (L_mass and L_value). E: environmental extensions for each of the 24000 commodities, including four resource categories: 1) primary biomass extraction (in tons), 2) land use (in hectares), 3) blue water use (in m3)., and 4) green water use (in m3). mr_sup_mass/mr_sup_value: For each allocation method (mass/value), the supply table gives the physical supply quantity of each commodity by producing process, with processes in the rows (118 processes x 192 regions = 22656 rows) and commodities in columns (24000 columns). mr_use: the use table capture the quantities of each commodity (rows) used as an input in each process (columns). A description of the included countries and commodities (i.e. the rows and columns of the Z matrix) can be found in the auxiliary file io_codes.csv. Separate lists of the country sample (including ISO3 codes and continental grouping) and commodities (including moisture content) are given in the files regions.csv and items.csv, respectively. For information on the individual processes, see auxiliary file su_codes.csv. RDS files can be opened in R. Information on how to read these files can be obtained here: https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/readRDS Except of X.rds, which contains a matrix, all variables are organized as lists, where each element contains a sparse matrix. Please note that values are always given in physical units, i.e. tonnes or head, as specified in items.csv. The suffixes value and mass only indicate the form of allocation chosen for the construction of the symmetric IO tables (for more details see Bruckner et al. 2019). Product, process and country classifications can be found in the file fabio_classifications.xlsx. Footprint results are not contained in the database but can be calculated, e.g. by using this script: https://github.com/martinbruckner/fabio_comparison/blob/master/R/fabio_footprints.R How to cite: To cite FABIO work please refer to this paper: Bruckner, M., Wood, R., Moran, D., Kuschnig, N., Wieland, H., Maus, V., Börner, J. 2019. FABIO – The Construction of the Food and Agriculture Input–Output Model. Environmental Science & Technology 53(19), 11302–11312. DOI: 10.1021/acs.est.9b03554 License: This data repository is distributed under the CC BY-NC-SA 4.0 License. You are free to share and adapt the material for non-commercial purposes using proper citation. If you remix, transform, or build upon the material, you must distribute your contributions under the same license as the original. In case you are interested in a collaboration, I am happy to receive enquiries at martin.bruckner@wu.ac.at. Known issues: The underlying FAO data have been manipulated to the minimum extent necessary. Data filling and supply-use balancing, yet, required some adaptations. These are documented in the code and are also reflected in the balancing item in the final demand matrices. For a proper use of the database, I recommend to distribute the balancing item over all other uses proportionally and to do analyses with and without balancing to illustrate uncertainties.