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.

description: This dataset was developed by NREL's distributed energy systems integration group as part of a study on high penetrations of distributed solar PV [1]. It consists of hourly load data in CSV format for use with the PNNL taxonomy of distribution feeders [2]. These feeders were developed in the open source GridLAB-D modelling language [3]. In this dataset each of the load points in the taxonomy feeders is populated with hourly averaged load data from a utility in the feeder s geographical region, scaled and randomized to emulate real load profiles. For more information on the scaling and randomization process, see [1]. The taxonomy feeders are statistically representative of the various types of distribution feeders found in five geographical regions of the U.S. Efforts are underway (possibly complete) to translate these feeders into the OpenDSS modelling language. This data set consists of one large CSV file for each feeder. Within each CSV, each column represents one load bus on the feeder. The header row lists the name of the load bus. The subsequent 8760 rows represent the loads for each hour of the year. The loads were scaled and randomized using a Python script, so each load series represents only one of many possible randomizations. In the header row, "rl" = residential load and "cl" = commercial load. Commercial loads are followed by a phase letter (A, B, or C). For regions 1-3, the data is from 2009. For regions 4-5, the data is from 2000. For use in GridLAB-D, each column will need to be separated into its own CSV file without a header. The load value goes in the second column, and corresponding datetime values go in the first column, as shown in the sample file, sample_individual_load_file.csv. Only the first value in the time column needs to written as an absolute time; subsequent times may be written in relative format (i.e. "+1h", as in the sample). The load should be written in P+Qj format, as seen in the sample CSV, in units of Watts (W) and Volt-amps reactive (VAr). This dataset was derived from metered load data and hence includes only real power; reactive power can be generated by assuming an appropriate power factor. These loads were used with GridLAB-D version 2.2. Browse files in this dataset, accessible as individual files and as a single ZIP file. This dataset is approximately 242MB compressed or 475MB uncompressed. For questions about this dataset, contact andy.hoke@nrel.gov. If you find this dataset useful, please mention NREL and cite [1] in your work. References: [1] A. Hoke, R. Butler, J. Hambrick, and B. Kroposki, Steady-State Analysis of Maximum Photovoltaic Penetration Levels on Typical Distribution Feeders, IEEE Transactions on Sustainable Energy, April 2013, available at http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6357275 . [2] K. Schneider, D. P. Chassin, R. Pratt, D. Engel, and S. Thompson, Modern Grid Initiative Distribution Taxonomy Final Report, PNNL, Nov. 2008. Accessed April 27, 2012: http://www.gridlabd.org/models/feeders/taxonomy of prototypical feeders.pdf [3] K. Schneider, D. Chassin, Y. Pratt, and J. C. Fuller, Distribution power flow for smart grid technologies, IEEE/PES Power Systems Conference and Exposition, Seattle, WA, Mar. 2009, pp. 1-7, 15-18.; abstract: This dataset was developed by NREL's distributed energy systems integration group as part of a study on high penetrations of distributed solar PV [1]. It consists of hourly load data in CSV format for use with the PNNL taxonomy of distribution feeders [2]. These feeders were developed in the open source GridLAB-D modelling language [3]. In this dataset each of the load points in the taxonomy feeders is populated with hourly averaged load data from a utility in the feeder s geographical region, scaled and randomized to emulate real load profiles. For more information on the scaling and randomization process, see [1]. The taxonomy feeders are statistically representative of the various types of distribution feeders found in five geographical regions of the U.S. Efforts are underway (possibly complete) to translate these feeders into the OpenDSS modelling language. This data set consists of one large CSV file for each feeder. Within each CSV, each column represents one load bus on the feeder. The header row lists the name of the load bus. The subsequent 8760 rows represent the loads for each hour of the year. The loads were scaled and randomized using a Python script, so each load series represents only one of many possible randomizations. In the header row, "rl" = residential load and "cl" = commercial load. Commercial loads are followed by a phase letter (A, B, or C). For regions 1-3, the data is from 2009. For regions 4-5, the data is from 2000. For use in GridLAB-D, each column will need to be separated into its own CSV file without a header. The load value goes in the second column, and corresponding datetime values go in the first column, as shown in the sample file, sample_individual_load_file.csv. Only the first value in the time column needs to written as an absolute time; subsequent times may be written in relative format (i.e. "+1h", as in the sample). The load should be written in P+Qj format, as seen in the sample CSV, in units of Watts (W) and Volt-amps reactive (VAr). This dataset was derived from metered load data and hence includes only real power; reactive power can be generated by assuming an appropriate power factor. These loads were used with GridLAB-D version 2.2. Browse files in this dataset, accessible as individual files and as a single ZIP file. This dataset is approximately 242MB compressed or 475MB uncompressed. For questions about this dataset, contact andy.hoke@nrel.gov. If you find this dataset useful, please mention NREL and cite [1] in your work. References: [1] A. Hoke, R. Butler, J. Hambrick, and B. Kroposki, Steady-State Analysis of Maximum Photovoltaic Penetration Levels on Typical Distribution Feeders, IEEE Transactions on Sustainable Energy, April 2013, available at http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6357275 . [2] K. Schneider, D. P. Chassin, R. Pratt, D. Engel, and S. Thompson, Modern Grid Initiative Distribution Taxonomy Final Report, PNNL, Nov. 2008. Accessed April 27, 2012: http://www.gridlabd.org/models/feeders/taxonomy of prototypical feeders.pdf [3] K. Schneider, D. Chassin, Y. Pratt, and J. C. Fuller, Distribution power flow for smart grid technologies, IEEE/PES Power Systems Conference and Exposition, Seattle, WA, Mar. 2009, pp. 1-7, 15-18.

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 `

This child page contains a zipped folder which contains all of the items necessary to run load estimation using R-LOADEST to produce results that are published in U.S. Geological Survey Investigations Report 2021-XXXX [Tatge, W.S., Nustad, R.A., and Galloway, J.M., 2021, Evaluation of Salinity and Nutrient Conditions in the Heart River Basin, North Dakota, 1970-2020: U.S. Geological Survey Scientific Investigations Report 2021-XXXX, XX p]. The folder contains an allsiteinfo.table.csv file, a "datain" folder, and a "scripts" folder. The allsiteinfo.table.csv file can be used to cross reference the sites with the main report (Tatge and others, 2021). The "datain" folder contains all the input data necessary to reproduce the load estimation results. The naming convention in the "datain" folder is site_MI_rloadest or site_NUT_rloadest for either the major ion loads or the nutrient loads. The .Rdata files are used in the scripts to run the estimations and the .csv files can be used to look at the data. The "scripts" folder contains the written R scripts to produce the results of the load estimation from the main report. R-LOADEST is a software package for analyzing loads in streams and an accompanying report (Runkel and others, 2004) serves as the formal documentation for R-LOADEST. The package is a collection of functions written in R (R Development Core Team, 2019), an open source language and a general environment for statistical computing and graphics. The following system requirements are necessary for producing results: Windows 10 operating system R (version 3.4 or later; 64-bit recommended) RStudio (version 1.1.456 or later) R-LOADEST program (available at https://github.com/USGS-R/rloadest). Runkel, R.L., Crawford, C.G., and Cohn, T.A., 2004, Load Estimator (LOADEST): A FORTRAN Program for Estimating Constituent Loads in Streams and Rivers: U.S. Geological Survey Techniques and Methods Book 4, Chapter A5, 69 p., [Also available at https://pubs.usgs.gov/tm/2005/tm4A5/pdf/508final.pdf.] R Development Core Team, 2019, R—A language and environment for statistical computing: Vienna, Austria, R Foundation for Statistical Computing, accessed December 7, 2020, at https://www.r-project.org.

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/

The data represent web-scraping of hyperlinks from a selection of environmental stewardship organizations that were identified in the 2017 NYC Stewardship Mapping and Assessment Project (STEW-MAP) (USDA 2017). There are two data sets: 1) the original scrape containing all hyperlinks within the websites and associated attribute values (see "README" file); 2) a cleaned and reduced dataset formatted for network analysis. For dataset 1: Organizations were selected from from the 2017 NYC Stewardship Mapping and Assessment Project (STEW-MAP) (USDA 2017), a publicly available, spatial data set about environmental stewardship organizations working in New York City, USA (N = 719). To create a smaller and more manageable sample to analyze, all organizations that intersected (i.e., worked entirely within or overlapped) the NYC borough of Staten Island were selected for a geographically bounded sample. Only organizations with working websites and that the web scraper could access were retained for the study (n = 78). The websites were scraped between 09 and 17 June 2020 to a maximum search depth of ten using the snaWeb package (version 1.0.1, Stockton 2020) in the R computational language environment (R Core Team 2020). For dataset 2: The complete scrape results were cleaned, reduced, and formatted as a standard edge-array (node1, node2, edge attribute) for network analysis. See "READ ME" file for further details. References: R Core Team. (2020). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/. Version 4.0.3. Stockton, T. (2020). snaWeb Package: An R package for finding and building social networks for a website, version 1.0.1. USDA Forest Service. (2017). Stewardship Mapping and Assessment Project (STEW-MAP). New York City Data Set. Available online at https://www.nrs.fs.fed.us/STEW-MAP/data/. This dataset is associated with the following publication: Sayles, J., R. Furey, and M. Ten Brink. How deep to dig: effects of web-scraping search depth on hyperlink network analysis of environmental stewardship organizations. Applied Network Science. Springer Nature, New York, NY, 7: 36, (2022).

Author: Andrew J. FeltonDate: 5/5/2024

This R project contains the primary code and data (following pre-processing in python) used for data production, manipulation, visualization, and analysis and figure production for the study entitled:

"Global estimates of the storage and transit time of water through vegetation"

Please note that 'turnover' and 'transit' are used interchangeably in this project.

Data information:

The data folder contains key data sets used for analysis. In particular:

"data/turnover_from_python/updated/annual/multi_year_average/average_annual_turnover.nc" contains a global array summarizing five year (2016-2020) averages of annual transit, storage, canopy transpiration, and number of months of data. This is the core dataset for the analysis; however, each folder has much more data, including a dataset for each year of the analysis. Data are also available is separate .csv files for each land cover type. Oterh data can be found for the minimum, monthly, and seasonal transit time found in their respective folders. These data were produced using the python code found in the "supporting_code" folder given the ease of working with .nc and EASE grid in the xarray python module. R was used primarily for data visualization purposes. The remaining files in the "data" and "data/supporting_data"" folder primarily contain ground-based estimates of storage and transit found in public databases or through a literature search, but have been extensively processed and filtered here.

Code information

Python scripts can be found in the "supporting_code" folder.

Each R script in this project has a particular function:

01_start.R: This script loads the R packages used in the analysis, sets thedirectory, and imports custom functions for the project. You can also load in the main transit time (turnover) datasets here using the source() function.

02_functions.R: This script contains the custom function for this analysis, primarily to work with importing the seasonal transit data. Load this using the source() function in the 01_start.R script.

03_generate_data.R: This script is not necessary to run and is primarilyfor documentation. The main role of this code was to import and wranglethe data needed to calculate ground-based estimates of aboveground water storage.

04_annual_turnover_storage_import.R: This script imports the annual turnover andstorage data for each landcover type. You load in these data from the 01_start.R scriptusing the source() function.

05_minimum_turnover_storage_import.R: This script imports the minimum turnover andstorage data for each landcover type. Minimum is defined as the lowest monthlyestimate.You load in these data from the 01_start.R scriptusing the source() function.

06_figures_tables.R: This is the main workhouse for figure/table production and supporting analyses. This script generates the key figures and summary statistics used in the study that then get saved in the manuscript_figures folder. Note that allmaps were produced using Python code found in the "supporting_code"" folder.

Market Basket Analysis

Market basket analysis with Apriori algorithm

The retailer wants to target customers with suggestions on itemset that a customer is most likely to purchase .I was given dataset contains data of a retailer; the transaction data provides data around all the transactions that have happened over a period of time. Retailer will use result to grove in his industry and provide for customer suggestions on itemset, we be able increase customer engagement and improve customer experience and identify customer behavior. I will solve this problem with use Association Rules type of unsupervised learning technique that checks for the dependency of one data item on another data item.

Introduction

Association Rule is most used when you are planning to build association in different objects in a set. It works when you are planning to find frequent patterns in a transaction database. It can tell you what items do customers frequently buy together and it allows retailer to identify relationships between the items.

An Example of Association Rules

Assume there are 100 customers, 10 of them bought Computer Mouth, 9 bought Mat for Mouse and 8 bought both of them. - bought Computer Mouth => bought Mat for Mouse - support = P(Mouth & Mat) = 8/100 = 0.08 - confidence = support/P(Mat for Mouse) = 0.08/0.09 = 0.89 - lift = confidence/P(Computer Mouth) = 0.89/0.10 = 8.9 This just simple example. In practice, a rule needs the support of several hundred transactions, before it can be considered statistically significant, and datasets often contain thousands or millions of transactions.

Strategy

• Data Import
• Data Understanding and Exploration
• Transformation of the data – so that is ready to be consumed by the association rules algorithm
• Running association rules
• Exploring the rules generated
• Filtering the generated rules
• Visualization of Rule

Dataset Description

• File name: Assignment-1_Data
• List name: retaildata
• File format: . xlsx
• Number of Row: 522065

• Number of Attributes: 7

  • BillNo: 6-digit number assigned to each transaction. Nominal.
  • Itemname: Product name. Nominal.
  • Quantity: The quantities of each product per transaction. Numeric.
  • Date: The day and time when each transaction was generated. Numeric.
  • Price: Product price. Numeric.
  • CustomerID: 5-digit number assigned to each customer. Nominal.
  • Country: Name of the country where each customer resides. Nominal.

https://user-images.githubusercontent.com/91852182/145270162-fc53e5a3-4ad1-4d06-b0e0-228aabcf6b70.png">

Libraries in R

First, we need to load required libraries. Shortly I describe all libraries.

• arules - Provides the infrastructure for representing, manipulating and analyzing transaction data and patterns (frequent itemsets and association rules).
• arulesViz - Extends package 'arules' with various visualization. techniques for association rules and item-sets. The package also includes several interactive visualizations for rule exploration.
• tidyverse - The tidyverse is an opinionated collection of R packages designed for data science.
• readxl - Read Excel Files in R.
• plyr - Tools for Splitting, Applying and Combining Data.
• ggplot2 - A system for 'declaratively' creating graphics, based on "The Grammar of Graphics". You provide the data, tell 'ggplot2' how to map variables to aesthetics, what graphical primitives to use, and it takes care of the details.
• knitr - Dynamic Report generation in R.
• magrittr- Provides a mechanism for chaining commands with a new forward-pipe operator, %>%. This operator will forward a value, or the result of an expression, into the next function call/expression. There is flexible support for the type of right-hand side expressions.
• dplyr - A fast, consistent tool for working with data frame like objects, both in memory and out of memory.
• tidyverse - This package is designed to make it easy to install and load multiple 'tidyverse' packages in a single step.

https://user-images.githubusercontent.com/91852182/145270210-49c8e1aa-9753-431b-a8d5-99601bc76cb5.png">

Data Pre-processing

Next, we need to upload Assignment-1_Data. xlsx to R to read the dataset.Now we can see our data in R.

https://user-images.githubusercontent.com/91852182/145270229-514f0983-3bbb-4cd3-be64-980e92656a02.png"> https://user-images.githubusercontent.com/91852182/145270251-6f6f6472-8817-435c-a995-9bc4bfef10d1.png">

After we will clear our data frame, will remove missing values.

https://user-images.githubusercontent.com/91852182/145270286-05854e1a-2b6c-490e-ab30-9e99e731eacb.png">

To apply Association Rule mining, we need to convert dataframe into transaction data to make all items that are bought together in one invoice will be in ...

Database of Uniaxial Cyclic and Tensile Coupon Tests for Structural Metallic Materials

Background

This dataset contains data from monotonic and cyclic loading experiments on structural metallic materials. The materials are primarily structural steels and one iron-based shape memory alloy is also included. Summary files are included that provide an overview of the database and data from the individual experiments is also included.

The files included in the database are outlined below and the format of the files is briefly described. Additional information regarding the formatting can be found through the post-processing library (https://github.com/ahartloper/rlmtp/tree/master/protocols).

Usage

• The data is licensed through the Creative Commons Attribution 4.0 International.
• If you have used our data and are publishing your work, we ask that you please reference both:
  1. this database through its DOI, and
  2. any publication that is associated with the experiments. See the Overall_Summary and Database_References files for the associated publication references.

Included Files

• Overall_Summary_2022-08-25_v1-0-0.csv: summarises the specimen information for all experiments in the database.
• Summarized_Mechanical_Props_Campaign_2022-08-25_v1-0-0.csv: summarises the average initial yield stress and average initial elastic modulus per campaign.
• Unreduced_Data-#_v1-0-0.zip: contain the original (not downsampled) data
  • Where # is one of: 1, 2, 3, 4, 5, 6. The unreduced data is broken into separate archives because of upload limitations to Zenodo. Together they provide all the experimental data.
  • We recommend you un-zip all the folders and place them in one "Unreduced_Data" directory similar to the "Clean_Data"
  • The experimental data is provided through .csv files for each test that contain the processed data. The experiments are organised by experimental campaign and named by load protocol and specimen. A .pdf file accompanies each test showing the stress-strain graph.
  • There is a "db_tag_clean_data_map.csv" file that is used to map the database summary with the unreduced data.
  • The computed yield stresses and elastic moduli are stored in the "yield_stress" directory.
• Clean_Data_v1-0-0.zip: contains all the downsampled data
  • The experimental data is provided through .csv files for each test that contain the processed data. The experiments are organised by experimental campaign and named by load protocol and specimen. A .pdf file accompanies each test showing the stress-strain graph.
  • There is a "db_tag_clean_data_map.csv" file that is used to map the database summary with the clean data.
  • The computed yield stresses and elastic moduli are stored in the "yield_stress" directory.
• Database_References_v1-0-0.bib
  • Contains a bibtex reference for many of the experiments in the database. Corresponds to the "citekey" entry in the summary files.

File Format: Downsampled Data

These are the "LP_

• The header of the first column is empty: the first column corresponds to the index of the sample point in the original (unreduced) data
• Time[s]: time in seconds since the start of the test
• e_true: true strain
• Sigma_true: true stress in MPa
• (optional) Temperature[C]: the surface temperature in degC

These data files can be easily loaded using the pandas library in Python through:

import pandas
data = pandas.read_csv(data_file, index_col=0)

The data is formatted so it can be used directly in RESSPyLab (https://github.com/AlbanoCastroSousa/RESSPyLab). Note that the column names "e_true" and "Sigma_true" were kept for backwards compatibility reasons with RESSPyLab.

File Format: Unreduced Data

These are the "LP_

• The first column is the index of each data point
• S/No: sample number recorded by the DAQ
• System Date: Date and time of sample
• Time[s]: time in seconds since the start of the test
• C_1_Force[kN]: load cell force
• C_1_Déform1[mm]: extensometer displacement
• C_1_Déplacement[mm]: cross-head displacement
• Eng_Stress[MPa]: engineering stress
• Eng_Strain[]: engineering strain
• e_true: true strain
• Sigma_true: true stress in MPa
• (optional) Temperature[C]: specimen surface temperature in degC

The data can be loaded and used similarly to the downsampled data.

File Format: Overall_Summary

The overall summary file provides data on all the test specimens in the database. The columns include:

• hidden_index: internal reference ID
• grade: material grade
• spec: specifications for the material
• source: base material for the test specimen
• id: internal name for the specimen
• lp: load protocol
• size: type of specimen (M8, M12, M20)
• gage_length_mm_: unreduced section length in mm
• avg_reduced_dia_mm_: average measured diameter for the reduced section in mm
• avg_fractured_dia_top_mm_: average measured diameter of the top fracture surface in mm
• avg_fractured_dia_bot_mm_: average measured diameter of the bottom fracture surface in mm
• fy_n_mpa_: nominal yield stress
• fu_n_mpa_: nominal ultimate stress
• t_a_deg_c_: ambient temperature in degC
• date: date of test
• investigator: person(s) who conducted the test
• location: laboratory where test was conducted
• machine: setup used to conduct test
• pid_force_k_p, pid_force_t_i, pid_force_t_d: PID parameters for force control
• pid_disp_k_p, pid_disp_t_i, pid_disp_t_d: PID parameters for displacement control
• pid_extenso_k_p, pid_extenso_t_i, pid_extenso_t_d: PID parameters for extensometer control
• citekey: reference corresponding to the Database_References.bib file
• yield_stress_mpa_: computed yield stress in MPa
• elastic_modulus_mpa_: computed elastic modulus in MPa
• fracture_strain: computed average true strain across the fracture surface
• c,si,mn,p,s,n,cu,mo,ni,cr,v,nb,ti,al,b,zr,sn,ca,h,fe: chemical compositions in units of %mass
• file: file name of corresponding clean (downsampled) stress-strain data

File Format: Summarized_Mechanical_Props_Campaign

Meant to be loaded in Python as a pandas DataFrame with multi-indexing, e.g.,

tab1 = pd.read_csv('Summarized_Mechanical_Props_Campaign_' + date + version + '.csv',
          index_col=[0, 1, 2, 3], skipinitialspace=True, header=[0, 1],
          keep_default_na=False, na_values='')

• citekey: reference in "Campaign_References.bib".
• Grade: material grade.
• Spec.: specifications (e.g., J2+N).
• Yield Stress [MPa]: initial yield stress in MPa
  • size, count, mean, coefvar: number of experiments in campaign, number of experiments in mean, mean value for campaign, coefficient of variation for campaign
• Elastic Modulus [MPa]: initial elastic modulus in MPa
  • size, count, mean, coefvar: number of experiments in campaign, number of experiments in mean, mean value for campaign, coefficient of variation for campaign

Caveats

• The files in the following directories were tested before the protocol was established. Therefore, only the true stress-strain is available for each:
  • A500
  • A992_Gr50
  • BCP325
  • BCR295
  • HYP400
  • S460NL
  • S690QL/25mm
  • S355J2_Plates/S355J2_N_25mm and S355J2_N_50mm

analyze the health and retirement study (hrs) with r the hrs is the one and only longitudinal survey of american seniors. with a panel starting its third decade, the current pool of respondents includes older folks who have been interviewed every two years as far back as 1992. unlike cross-sectional or shorter panel surveys, respondents keep responding until, well, death d o us part. paid for by the national institute on aging and administered by the university of michigan's institute for social research, if you apply for an interviewer job with them, i hope you like werther's original. figuring out how to analyze this data set might trigger your fight-or-flight synapses if you just start clicking arou nd on michigan's website. instead, read pages numbered 10-17 (pdf pages 12-19) of this introduction pdf and don't touch the data until you understand figure a-3 on that last page. if you start enjoying yourself, here's the whole book. after that, it's time to register for access to the (free) data. keep your username and password handy, you'll need it for the top of the download automation r script. next, look at this data flowchart to get an idea of why the data download page is such a righteous jungle. but wait, good news: umich recently farmed out its data management to the rand corporation, who promptly constructed a giant consolidated file with one record per respondent across the whole panel. oh so beautiful. the rand hrs files make much of the older data and syntax examples obsolete, so when you come across stuff like instructions on how to merge years, you can happily ignore them - rand has done it for you. the health and retirement study only includes noninstitutionalized adults when new respondents get added to the panel (as they were in 1992, 1993, 1998, 2004, and 2010) but once they're in, they're in - respondents have a weight of zero for interview waves when they were nursing home residents; but they're still responding and will continue to contribute to your statistics so long as you're generalizing about a population from a previous wave (for example: it's possible to compute "among all americans who were 50+ years old in 1998, x% lived in nursing homes by 2010"). my source for that 411? page 13 of the design doc. wicked. this new github repository contains five scripts: 1992 - 2010 download HRS microdata.R loop through every year and every file, download, then unzip everything in one big party impor t longitudinal RAND contributed files.R create a SQLite database (.db) on the local disk load the rand, rand-cams, and both rand-family files into the database (.db) in chunks (to prevent overloading ram) longitudinal RAND - analysis examples.R connect to the sql database created by the 'import longitudinal RAND contributed files' program create tw o database-backed complex sample survey object, using a taylor-series linearization design perform a mountain of analysis examples with wave weights from two different points in the panel import example HRS file.R load a fixed-width file using only the sas importation script directly into ram with < a href="http://blog.revolutionanalytics.com/2012/07/importing-public-data-with-sas-instructions-into-r.html">SAScii parse through the IF block at the bottom of the sas importation script, blank out a number of variables save the file as an R data file (.rda) for fast loading later replicate 2002 regression.R connect to the sql database created by the 'import longitudinal RAND contributed files' program create a database-backed complex sample survey object, using a taylor-series linearization design exactly match the final regression shown in this document provided by analysts at RAND as an update of the regression on pdf page B76 of this document . click here to view these five scripts for more detail about the health and retirement study (hrs), visit: michigan's hrs homepage rand's hrs homepage the hrs wikipedia page a running list of publications using hrs notes: exemplary work making it this far. as a reward, here's the detailed codebook for the main rand hrs file. note that rand also creates 'flat files' for every survey wave, but really, most every analysis you c an think of is possible using just the four files imported with the rand importation script above. if you must work with the non-rand files, there's an example of how to import a single hrs (umich-created) file, but if you wish to import more than one, you'll have to write some for loops yourself. confidential to sas, spss, stata, and sudaan users: a tidal wave is coming. you can get water up your nose and be dragged out to sea, or you can grab a surf board. time to transition to r. :D

To get the consumption model from Section 3.1, one needs load execute the file consumption_data.R. Load the data for the 3 Phases ./data/CONSUMPTION/PL1.csv, PL2.csv, PL3.csv, transform the data and build the model (starting line 225). The final consumption data can be found in one file for each year in ./data/CONSUMPTION/MEGA_CONS_list.Rdata To get the results for the optimization problem, one needs to execute the file analyze_data.R. It provides the functions to compare production and consumption data, and to optimize for the different values (PV, MBC,). To reproduce the figures one needs to execute the file visualize_results.R. It provides the functions to reproduce the figures. To calculate the solar radiation that is needed in the Section Production Data, follow file calculate_total_radiation.R. To reproduce the radiation data from from ERA5, that can be found in data.zip, do the following steps: 1. ERA5 - download the reanalysis datasets as GRIB file. For FDIR select "Total sky direct solar radiation at surface", for GHI select "Surface solar radiation downwards", and for ALBEDO select "Forecast albedo". 2. convert GRIB to csv with the file era5toGRID.sh 3. convert the csv file to the data that is used in this paper with the file convert_year_to_grid.R

To get the consumption model from Section 3.1, one needs load execute the file consumption_data.R. Load the data for the 3 Phases ./data/CONSUMPTION/PL1.csv, PL2.csv, PL3.csv, transform the data and build the model (starting line 225). The final consumption data can be found in one file for each year in ./data/CONSUMPTION/MEGA_CONS_list.Rdata

To get the results for the optimization problem, one needs to execute the file analyze_data.R. It provides the functions to compare production and consumption data, and to optimize for the different values (PV, MBC,).

To reproduce the figures one needs to execute the file visualize_results.R. It provides the functions to reproduce the figures.

To calculate the solar radiation that is needed in the Section Production Data, follow file calculate_total_radiation.R.

To reproduce the radiation data from from ERA5, that can be found in data.zip, do the following steps: 1. ERA5 - download the reanalysis datasets as GRIB file. For FDIR select "Total sky direct solar radiation at surface", for GHI select "Surface solar radiation downwards", and for ALBEDO select "Forecast albedo". 2. convert GRIB to csv with the file era5toGRID.sh 3. convert the csv file to the data that is used in this paper with the file convert_year_to_grid.R

Overview

This dataset is the repository for the following paper submitted to Data in Brief:

Kempf, M. A dataset to model Levantine landcover and land-use change connected to climate change, the Arab Spring and COVID-19. Data in Brief (submitted: December 2023).

The Data in Brief article contains the supplement information and is the related data paper to:

Kempf, M. Climate change, the Arab Spring, and COVID-19 - Impacts on landcover transformations in the Levant. Journal of Arid Environments (revision submitted: December 2023).

Description/abstract

The Levant region is highly vulnerable to climate change, experiencing prolonged heat waves that have led to societal crises and population displacement. Since 2010, the area has been marked by socio-political turmoil, including the Syrian civil war and currently the escalation of the so-called Israeli-Palestinian Conflict, which strained neighbouring countries like Jordan due to the influx of Syrian refugees and increases population vulnerability to governmental decision-making. Jordan, in particular, has seen rapid population growth and significant changes in land-use and infrastructure, leading to over-exploitation of the landscape through irrigation and construction. This dataset uses climate data, satellite imagery, and land cover information to illustrate the substantial increase in construction activity and highlights the intricate relationship between climate change predictions and current socio-political developments in the Levant.

Folder structure

The main folder after download contains all data, in which the following subfolders are stored are stored as zipped files:

“code” stores the above described 9 code chunks to read, extract, process, analyse, and visualize the data.

“MODIS_merged” contains the 16-days, 250 m resolution NDVI imagery merged from three tiles (h20v05, h21v05, h21v06) and cropped to the study area, n=510, covering January 2001 to December 2022 and including January and February 2023.

“mask” contains a single shapefile, which is the merged product of administrative boundaries, including Jordan, Lebanon, Israel, Syria, and Palestine (“MERGED_LEVANT.shp”).

“yield_productivity” contains .csv files of yield information for all countries listed above.

“population” contains two files with the same name but different format. The .csv file is for processing and plotting in R. The .ods file is for enhanced visualization of population dynamics in the Levant (Socio_cultural_political_development_database_FAO2023.ods).

“GLDAS” stores the raw data of the NASA Global Land Data Assimilation System datasets that can be read, extracted (variable name), and processed using code “8_GLDAS_read_extract_trend” from the respective folder. One folder contains data from 1975-2022 and a second the additional January and February 2023 data.

“built_up” contains the landcover and built-up change data from 1975 to 2022. This folder is subdivided into two subfolder which contain the raw data and the already processed data. “raw_data” contains the unprocessed datasets and “derived_data” stores the cropped built_up datasets at 5 year intervals, e.g., “Levant_built_up_1975.tif”.

Code structure

1_MODIS_NDVI_hdf_file_extraction.R

This is the first code chunk that refers to the extraction of MODIS data from .hdf file format. The following packages must be installed and the raw data must be downloaded using a simple mass downloader, e.g., from google chrome. Packages: terra. Download MODIS data from after registration from: https://lpdaac.usgs.gov/products/mod13q1v061/ or https://search.earthdata.nasa.gov/search (MODIS/Terra Vegetation Indices 16-Day L3 Global 250m SIN Grid V061, last accessed, 09th of October 2023). The code reads a list of files, extracts the NDVI, and saves each file to a single .tif-file with the indication “NDVI”. Because the study area is quite large, we have to load three different (spatially) time series and merge them later. Note that the time series are temporally consistent.

2_MERGE_MODIS_tiles.R

In this code, we load and merge the three different stacks to produce large and consistent time series of NDVI imagery across the study area. We further use the package gtools to load the files in (1, 2, 3, 4, 5, 6, etc.). Here, we have three stacks from which we merge the first two (stack 1, stack 2) and store them. We then merge this stack with stack 3. We produce single files named NDVI_final_*consecutivenumber*.tif. Before saving the final output of single merged files, create a folder called “merged” and set the working directory to this folder, e.g., setwd("your directory_MODIS/merged").

3_CROP_MODIS_merged_tiles.R

Now we want to crop the derived MODIS tiles to our study area. We are using a mask, which is provided as .shp file in the repository, named "MERGED_LEVANT.shp". We load the merged .tif files and crop the stack with the vector. Saving to individual files, we name them “NDVI_merged_clip_*consecutivenumber*.tif. We now produced single cropped NDVI time series data from MODIS. The repository provides the already clipped and merged NDVI datasets.

4_TREND_analysis_NDVI.R

Now, we want to perform trend analysis from the derived data. The data we load is tricky as it contains 16-days return period across a year for the period of 22 years. Growing season sums contain MAM (March-May), JJA (June-August), and SON (September-November). December is represented as a single file, which means that the period DJF (December-February) is represented by 5 images instead of 6. For the last DJF period (December 2022), the data from January and February 2023 can be added. The code selects the respective images from the stack, depending on which period is under consideration. From these stacks, individual annually resolved growing season sums are generated and the slope is calculated. We can then extract the p-values of the trend and characterize all values with high confidence level (0.05). Using the ggplot2 package and the melt function from reshape2 package, we can create a plot of the reclassified NDVI trends together with a local smoother (LOESS) of value 0.3.To increase comparability and understand the amplitude of the trends, z-scores were calculated and plotted, which show the deviation of the values from the mean. This has been done for the NDVI values as well as the GLDAS climate variables as a normalization technique.

5_BUILT_UP_change_raster.R

Let us look at the landcover changes now. We are working with the terra package and get raster data from here: https://ghsl.jrc.ec.europa.eu/download.php?ds=bu (last accessed 03. March 2023, 100 m resolution, global coverage). Here, one can download the temporal coverage that is aimed for and reclassify it using the code after cropping to the individual study area. Here, I summed up different raster to characterize the built-up change in continuous values between 1975 and 2022.

6_POPULATION_numbers_plot.R

For this plot, one needs to load the .csv-file “Socio_cultural_political_development_database_FAO2023.csv” from the repository. The ggplot script provided produces the desired plot with all countries under consideration.

7_YIELD_plot.R

In this section, we are using the country productivity from the supplement in the repository “yield_productivity” (e.g., "Jordan_yield.csv". Each of the single country yield datasets is plotted in a ggplot and combined using the patchwork package in R.

8_GLDAS_read_extract_trend

The last code provides the basis for the trend analysis of the climate variables used in the paper. The raw data can be accessed https://disc.gsfc.nasa.gov/datasets?keywords=GLDAS%20Noah%20Land%20Surface%20Model%20L4%20monthly&page=1 (last accessed 9th of October 2023). The raw data comes in .nc file format and various variables can be extracted using the [“^a variable name”] command from the spatraster collection. Each time you run the code, this variable name must be adjusted to meet the requirements for the variables (see this link for abbreviations: https://disc.gsfc.nasa.gov/datasets/GLDAS_CLSM025_D_2.0/summary, last accessed 09th of October 2023; or the respective code chunk when reading a .nc file with the ncdf4 package in R) or run print(nc) from the code or use names(the spatraster collection). Choosing one variable, the code uses the MERGED_LEVANT.shp mask from the repository to crop and mask the data to the outline of the study area.From the processed data, trend analysis are conducted and z-scores were calculated following the code described above. However, annual trends require the frequency of the time series analysis to be set to value = 12. Regarding, e.g., rainfall, which is measured as annual sums and not means, the chunk r.sum=r.sum/12 has to be removed or set to r.sum=r.sum/1 to avoid calculating annual mean values (see other variables). Seasonal subset can be calculated as described in the code. Here, 3-month subsets were chosen for growing seasons, e.g. March-May (MAM), June-July (JJA), September-November (SON), and DJF (December-February, including Jan/Feb of the consecutive year).From the data, mean values of 48 consecutive years are calculated and trend analysis are performed as describe above. In the same way, p-values are extracted and 95 % confidence level values are marked with dots on the raster plot. This analysis can be performed with a much longer time series, other variables, ad different spatial extent across the globe due to the availability of the GLDAS variables.

(9_workflow_diagramme) this simple code can be used to plot a workflow diagram and is detached from the actual analysis.

Conceptualization, Methodology, Software, Validation, Formal analysis, Investigation, Resources, Data Curation, Writing - Original Draft, Writing - Review & Editing, Visualization, Supervision, Project administration, and Funding acquisition: Michael

STEAD Subsample Dataset for CDiffSD Training

Overview

This dataset is a subsampled version of the STEAD dataset, specifically tailored for training our CDiffSD model (Cold Diffusion for Seismic Denoising). It consists of four HDF5 files, each saved in a format that requires Python's `h5py` method for opening.

Dataset Files

The dataset includes the following files:

• train: Used for both training and validation phases (with validation train split). Contains earthquake ground truth traces.
• noise_train: Used for both training and validation phases. Contains noise used to contaminate the traces.
• test: Used for the testing phase, structured similarly to train.
• noise_test: Used for the testing phase, contains noise data for testing.

Each file is structured to support the training and evaluation of seismic denoising models.

Data

The HDF5 files named noise contain two main datasets:

• traces: This dataset includes N number of events, with each event being 6000 in size, representing the length of the traces. Each trace is organized into three channels in the following order: E (East-West), N (North-South), Z (Vertical).
• metadata: This dataset contains the names of the traces for each event.

Similarly, the train and test files, which contain earthquake data, include the same traces and metadata datasets, but also feature two additional datasets:

• p_arrival: Contains the arrival indices of P-waves, expressed in counts.
• s_arrival: Contains the arrival indices of S-waves, also expressed in counts.

Usage

To load these files in a Python environment, use the following approach:

```python

import h5py
import numpy as np

# Open the HDF5 file in read mode
with h5py.File('train_noise.hdf5', 'r') as file:
# Print all the main keys in the file
print("Keys in the HDF5 file:", list(file.keys()))

if 'traces' in file:
# Access the dataset
data = file['traces'][:10] # Load the first 10 traces

if 'metadata' in file:
# Access the dataset
trace_name = file['metadata'][:10] # Load the first 10 metadata entries```

Ensure that the path to the file is correctly specified relative to your Python script.

Requirements

To use this dataset, ensure you have Python installed along with the Pandas library, which can be installed via pip if not already available:

```bash
pip install numpy
pip install h5py
```

R code used in the manuscript: Net carbon sequestration implications of intensified timber harvest in northeastern U.S. forests

Abstract:

U.S. forests, particularly in the eastern states, provide an important offset to greenhouse gas (GHG) emissions. Some have proposed that forest-based natural climate solutions can be strengthened via a number of strategies, including increases in production of forest biomass energy. We used output from a forest dynamics model [SORTIE-ND] in combination with a greenhouse gas accounting tool [ForGATE] to estimate the carbon consequences of current and intensified timber harvest regimes in the northeastern U.S. We considered a range of carbon pools including forest ecosystem pools, forest product pools, and waste pools, along with different scenarios of feedstock production for biomass energy. The business as usual (BAU) scenario, which represents current harvest practices derived from analysis of U.S. Forest Service Forest Inventory and Analysis data, sequestered more net CO2 equivalents than any of the intensified harvest and feedstock utilization scenarios over the next decade, the most important time period for combatting climate change. Increasing the intensity of timber harvest increased total emissions and reduced landscape average forest carbon stocks, resulting in reduced net carbon sequestration relative to current harvest regimes. Net carbon sequestration “parity points,” where the regional cumulative net carbon sequestration from alternate intensified harvest scenarios converge with and then exceed the business as usual baseline, ranged from 12 to 40 years. A “no harvest” scenario provides an estimate of an upper bound on forest carbon sequestration in the region given the expected successional dynamics of the region’s forests, but ignores leakage. Regional net carbon sequestration is primarily influenced by (i) the harvest regime and amount of forest biomass removal, (ii) the degree to which bioenergy displaces fossil fuel use, and (iii) the proportion of biomass diverted to energy feedstocks versus wood products.

File list:

Carbon ForGATE.R - this is the main file – takes input from the “load data.R” code and calculates all of the terms in the carbon sequestration model. All the rest of the files are called as source code from within this file.

Constants and initializations.R – contains constants and initializes all dynamic variables for a new run of the model.

Default decay rates.R – contains default decay rates for various carbon pools.

Feedstock utilization scenarios.R – defines the proportions of harvested biomass used as different types of biomass energy feedstocks in the various scenarios available in the model.

Load data.R – code to load the SORTIE-ND output Rdata objects generated by Brown et al. (2018).

Product transfer coefficients.R – coefficients that define the flow of carbon between the various harvested wood products pools.

Scenario graphs.R – code to generate graphs at the end of a model run.

R codes for the linear and generalized linear mixed model analyses presented in the study "Self-fertilization does not lead to inbreeding depression in Typha parent species or hybrids" by Rock, Whitehead et al.

Y prefix for each data file corresponds with the year the data was collected (Y1 = first year of the study, 2020; Y2 = 2021)

Column info: Mating_Type = Cross: the type of hand pollination conducted: Outbred = hand outcross; Inbred = hand self-pollination * Taxonomic_Group = Taxa: Taxonomic ID for the maternal parent used in the hand pollination
Sample_Name = ID: code for the plant ID; leading numbers refer to the population/site of origin; first letter in the code refers to the taxon (A = anguistifolia etc.); "1M" refers to hand outcross*; "0Z" refers to hand self pollinations*; numbers following the dash is the maternal parent plant used in the hand pollination) Box: the wooden frame in which plants were grown Number: location of the transplanted plant in the wetland
Row: the row in which plants were transplanted Seed_Set_Count = Seedset: the number of seeds per 0.5 g fruit tissue Germination_Count = Germination: the number of germinated seeds following 10 days of immersion in water Weight: mass (in g) of the sample of seeds used for the estimation of Seedset Height: the height (cm) of tallest leaf per genet Biomass: above-ground dry mass of the genet (all ramets combined) Ramet: the number of ramets per genet

• For the file Y2_CommonGarden.csv the association between the ID codes and the cross type were mixed up and Cross:Inbred actually refers to a hand outcross pollinationsl Cross:Outbred actually refers to hand self pollinations

Data and code from our experiment examining the transmission of native Drosophila viruses, between and across species, and costs in terms of lifespan and offspring production to Drosophila melanogaster.Description of the data and file structureFor the figures in the main text, use the details below (files to load are also detailed in code comments) to re-run analyses and re-make figures;Fig. 1 - load exp_exp_transmission_vial_data.csv, and exp_exper_exposure_infected_dat.csv and run the code in transmission_prevalence.RFig. 2 - load EE_virus_w_fec_overtime_and_male_off_analysis.csv, and run the code in mortality_w_viral_infection.RFig. 3 - load EE_virus_w_fec_overtime_and_male_off_analysis.csv, and run the code in lifespan_models_and_plots.R (code also makes table S4, and Fig. S4, S5 and S8)Fig. 4 - load EE_virus_w_fec_overtime_and_male_off_analysis.csv, and run the code in lifetime_offspring_production_models_and_plots.R (code also makes table S5, S6, and S9, and Fig. S1, S7, S9, and S15)Code/SoftwareThe included R files can be used to re-run all models in the paper, and re-make all figures (including supplementary figures and tables). The script section outlines allow you to jump to particular figures or tables if needed. All analyses were run in R version 4.3.2, with all packages needed listed at the top of each script.If you'd prefer not to re-run models or want to inspect our run outputs, load the Rdata files into the scripts to look at the exact model runs desribed in the paper.The shell script included is for the analysis of public datasets downloaded from the SRA. To re-run this analysis you will need to download these datasets (which we provide details of in the supplementary methods), and re-run the script in a linux environment. We provide the output from this script (mapped reads across host genes and viruses) to make the heatmap produced in the paper (in the SRA_transmission_mapping_analyses.R file).

Open data: Visual load does not decrease the auditory steady state response to 40-Hz amplitude-modulated tones The main results files are saved separately: - ASSR_study1.html: R output of the main analyses- ASSR_study1_subset_subjects.html: R output of the main analyses- ASSR_study2.html: R output of the main analyses The studies were preregistered:Study 1: https://doi.org/10.17605/OSF.IO/UYJVAStudy 2: https://doi.org/10.17605/OSF.IO/JVMFD DATA & FILE OVERVIEW File List:The files contain the raw data, scripts, and results of main and supplementary analyses of two electroencephalography (EEG) studies (Study1, Study2). Links to the hardware and software are provided under methodological information. ASSR_study1_experiment_scripts.zip: contains the Python files to run the experiment. ASSR_study1_rawdata.zip: contains raw datafiles for each subject - data_EEG: EEG data in bdf format (generated by Biosemi)- data_log: logfiles of the EEG session (generated by Python)- data_WMC: logfiles of the working memory capacity task (generated by Python) ASSR_study1_EEG_scripts.zip: Python-MNE scripts to process the EEG data ASSR_study1_EEG_preprocessed.zip: Preprocessed EEG data from Python-MNE ASSR_study1_analysis_scripts.zip: R scripts to analyze the data together with the main datafiles. The main files in the folder are: - ASSR_study1.html: R output of the main analyses- ASSR_study1_subset_subjects.html: R output of the main analyses but after excluding five subjects who were excluded because of stricter, preregistered artifact rejection criteria ASSR_study1_figures.zip: contains all figures and tables that are created by Python-MNE and R. ASSR_study2_experiment_scripts.zip: contains the Python files to run the experiment ASSR_study2_rawdata.zip: contains raw datafiles for each subject - data_EEG: EEG data in bdf format (generated by Biosemi)- data_log: logfiles of the EEG session (generated by Python)- data_WMC: logfiles of the working memory capacity task (generated by Python) ASSR_study2_EEG_scripts.zip: Python-MNE scripts to process the EEG data ASSR_study2_EEG_preprocessed.zip: Preprocessed EEG data from Python-MNE ASSR_study2_analysis_scripts.zip: R scripts to analyze the data together with the main datafiles. The main files in the folder are: - ASSR_study2.html: R output of the main analyses- ASSR_compare_performance_between_studies.html: R output of analyses that compare behavioral performance between study 1 and study 2. ASSR_study2_figures.zip: contains all figures and tables that are created by Python-MNE and R. Instrument- or software-specific information needed to interpret the data:MNE-Python (Gramfort A., et al., 2013): https://mne.tools/stable/index.html#Rstudio used with R (R Core Team, 2016): https://rstudio.com/products/rstudio/Wiens, S. (2017). Aladins Bayes Factor in R (Version 3). https://www.doi.org/10.17045/sthlmuni.4981154.v3

################################################################################################## THE FILES HAVE BEEN CREATED BY SZILÁRD ERHART FOR A RESEARCH: ERHART (2021): ESG RATINGS OF GENERAL # STOCK EXCHANGE INDICES, INTERNATIONAL REVIEW OF FINANCIAL ANALYSIS# USERS OF THE FILES AGREE TO QUOTE THE ABOVE PAPER# THE PYTHON SCRIPT (PYTHONESG_ERHART.TXT) HELPS USERS TO GET TICKERS BY STOCK EXCHANGES AND EXTRACT ESG SCORES FOR THE UNDERLYING STOCKS FROM YAHOO FINANCE.# THE R SCRIPT (ESG_UA.TXT) HELPS TO REPLICATE THE MONTE CARLO EXPERIMENT DETAILED IN THE STUDY.# THE EXPORT_ALL CSV CONTAINS THE DOWNLOADED ESG DATA (SCORES, CONTROVERSIES, ETC) ORGANIZED BY STOCKS AND EXCHANGES.############################################################################################################################################################################################################### DISCLAIMER # The author takes no responsibility for the timeliness, accuracy, completeness or quality of the information provided. # The author is in no event liable for damages of any kind incurred or suffered as a result of the use or non-use of the # information presented or the use of defective or incomplete information. # The contents are subject to confirmation and not binding. # The author expressly reserves the right to alter, amend, whole and in part, # without prior notice or to discontinue publication for a period of time or even completely. ###########################################################################################################################################READ ME############################################################# BEFORE USING THE MONTE CARLO SIMULATIONS SCRIPT: # (1) COPY THE goascores.csv and goalscores_alt.csv FILES ONTO YOUR ON COMPUTER DRIVE. THE TWO FILES ARE IDENTICAL.# (2) SET THE EXACT FILE LOCATION INFORMATION IN THE 'Read in data' SECTION OF THE MONTE CARLO SCRIPT AND FOR THE OUTPUT FILES AT THE END OF THE SCRIPT# (3) LOAD MISC TOOLS AND MATRIXSTATS IN YOUR R APPLICATION# (4) RUN THE CODE.####################################READ ME

The Meike_data_raw.csv file is used to load the data in R. The Meike_Thesis_Code.R file is the R code to prepare the data and obtain the descriptive statistics.The Meike_data_for_Jasp.csv file is the (in R) prepared and cleaned data for the analyses in Jasp.