As high-throughput methods become more common, training undergraduates to analyze data must include having them generate informative summaries of large datasets. This flexible case study provides an opportunity for undergraduate students to become familiar with the capabilities of R programming in the context of high-throughput evolutionary data collected using macroarrays. The story line introduces a recent graduate hired at a biotech firm and tasked with analysis and visualization of changes in gene expression from 20,000 generations of the Lenski Lab’s Long-Term Evolution Experiment (LTEE). Our main character is not familiar with R and is guided by a coworker to learn about this platform. Initially this involves a step-by-step analysis of the small Iris dataset built into R which includes sepal and petal length of three species of irises. Practice calculating summary statistics and correlations, and making histograms and scatter plots, prepares the protagonist to perform similar analyses with the LTEE dataset. In the LTEE module, students analyze gene expression data from the long-term evolutionary experiments, developing their skills in manipulating and interpreting large scientific datasets through visualizations and statistical analysis. Prerequisite knowledge is basic statistics, the Central Dogma, and basic evolutionary principles. The Iris module provides hands-on experience using R programming to explore and visualize a simple dataset; it can be used independently as an introduction to R for biological data or skipped if students already have some experience with R. Both modules emphasize understanding the utility of R, rather than creation of original code. Pilot testing showed the case study was well-received by students and faculty, who described it as a clear introduction to R and appreciated the value of R for visualizing and analyzing large datasets.

This child item describes R code used to determine public supply consumptive use estimates. Consumptive use was estimated by scaling an assumed fraction of deliveries used for outdoor irrigation by spatially explicit estimates of evaporative demand using estimated domestic and commercial, industrial, and institutional deliveries from the public supply delivery machine learning model child item. This method scales public supply water service area outdoor water use by the relationship between service area gross reference evapotranspiration provided by GridMET and annual continental U.S. (CONUS) growing season maximum evapotranspiration. This relationship to climate at the CONUS scale could result in over- or under-estimation of consumptive use at public supply service areas where local variations differ from national variations in climate. This method also assumes that 50% of deliveries for total domestic and commercial, industrial, and institutional deliveries is used for outdoor purposes. This dataset is part of a larger data release using machine learning to predict public supply water use for 12-digit hydrologic units from 2000-2020. This page includes the following file: PS_ConsumptiveUse.zip - a zip file containing input datasets, scripts, and output datasets

{# 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 --------------------------------------------------------------------------------------------------------}

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 document describes the ‘vwline’ package, which provides an R interface for drawing variable-width curves. The package provides functions to draw line segments through a set of locations, or a smooth curve relative to a set of control points, with the width of the line allowed to vary along the length of the line.

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.

The South Florida Water Management District (SFWMD) and the U.S. Geological Survey have developed projected future change factors for precipitation depth-duration-frequency (DDF) curves at 174 National Oceanic and Atmospheric Administration (NOAA) Atlas 14 stations in central and south Florida. The change factors were computed as the ratio of projected future to historical extreme precipitation depths fitted to extreme precipitation data from various downscaled climate datasets using a constrained maximum likelihood (CML) approach. The change factors correspond to the period 2050-2089 (centered in the year 2070) as compared to the 1966-2005 historical period. An R script (basin_boxplot.R) is provided provided as an example on how to create a wrapper function that will automate the generation of boxplots of change factors for all AHED basins. The wrapper script sources the file create_boxplot.R and calls the function create_boxplot() one AHED basin at a time to create a figure with boxplots of change fators for all durations (1, 3, and 7 days) and return periods (5, 10, 25, 50, 100, and 200 years) evaluated as part of this project. An example is also provided in the code that shows how to generate a figure showing boxplots of change factors for a single duration and return period. A Microsoft Word file documenting code usage is also provided within this data release (Documentation_R_script_create_boxplot.docx). As described in the documentation, the R script relies on some of the Microsoft Excel spreadsheets published as part of this data release.

Complete dataset of “Film Circulation on the International Film Festival Network and the Impact on Global Film Culture”

A peer-reviewed data paper for this dataset is in review to be published in NECSUS_European Journal of Media Studies - an open access journal aiming at enhancing data transparency and reusability, and will be available from https://necsus-ejms.org/ and https://mediarep.org

Please cite this when using the dataset.

Detailed description of the dataset:

1 Film Dataset: Festival Programs

The Film Dataset consists a data scheme image file, a codebook and two dataset tables in csv format.

The codebook (csv file “1_codebook_film-dataset_festival-program”) offers a detailed description of all variables within the Film Dataset. Along with the definition of variables it lists explanations for the units of measurement, data sources, coding and information on missing data.

The csv file “1_film-dataset_festival-program_long” comprises a dataset of all films and the festivals, festival sections, and the year of the festival edition that they were sampled from. The dataset is structured in the long format, i.e. the same film can appear in several rows when it appeared in more than one sample festival. However, films are identifiable via their unique ID.

The csv file “1_film-dataset_festival-program_wide” consists of the dataset listing only unique films (n=9,348). The dataset is in the wide format, i.e. each row corresponds to a unique film, identifiable via its unique ID. For easy analysis, and since the overlap is only six percent, in this dataset the variable sample festival (fest) corresponds to the first sample festival where the film appeared. For instance, if a film was first shown at Berlinale (in February) and then at Frameline (in June of the same year), the sample festival will list “Berlinale”. This file includes information on unique and IMDb IDs, the film title, production year, length, categorization in length, production countries, regional attribution, director names, genre attribution, the festival, festival section and festival edition the film was sampled from, and information whether there is festival run information available through the IMDb data.

2 Survey Dataset

The Survey Dataset consists of a data scheme image file, a codebook and two dataset tables in csv format.

The codebook “2_codebook_survey-dataset” includes coding information for both survey datasets. It lists the definition of the variables or survey questions (corresponding to Samoilova/Loist 2019), units of measurement, data source, variable type, range and coding, and information on missing data.

The csv file “2_survey-dataset_long-festivals_shared-consent” consists of a subset (n=161) of the original survey dataset (n=454), where respondents provided festival run data for films (n=206) and gave consent to share their data for research purposes. This dataset consists of the festival data in a long format, so that each row corresponds to the festival appearance of a film.

The csv file “2_survey-dataset_wide-no-festivals_shared-consent” consists of a subset (n=372) of the original dataset (n=454) of survey responses corresponding to sample films. It includes data only for those films for which respondents provided consent to share their data for research purposes. This dataset is shown in wide format of the survey data, i.e. information for each response corresponding to a film is listed in one row. This includes data on film IDs, film title, survey questions regarding completeness and availability of provided information, information on number of festival screenings, screening fees, budgets, marketing costs, market screenings, and distribution. As the file name suggests, no data on festival screenings is included in the wide format dataset.

3 IMDb & Scripts

The IMDb dataset consists of a data scheme image file, one codebook and eight datasets, all in csv format. It also includes the R scripts that we used for scraping and matching.

The codebook “3_codebook_imdb-dataset” includes information for all IMDb datasets. This includes ID information and their data source, coding and value ranges, and information on missing data.

The csv file “3_imdb-dataset_aka-titles_long” contains film title data in different languages scraped from IMDb in a long format, i.e. each row corresponds to a title in a given language.

The csv file “3_imdb-dataset_awards_long” contains film award data in a long format, i.e. each row corresponds to an award of a given film.

The csv file “3_imdb-dataset_companies_long” contains data on production and distribution companies of films. The dataset is in a long format, so that each row corresponds to a particular company of a particular film.

The csv file “3_imdb-dataset_crew_long” contains data on names and roles of crew members in a long format, i.e. each row corresponds to each crew member. The file also contains binary gender assigned to directors based on their first names using the GenderizeR application.

The csv file “3_imdb-dataset_festival-runs_long” contains festival run data scraped from IMDb in a long format, i.e. each row corresponds to the festival appearance of a given film. The dataset does not include each film screening, but the first screening of a film at a festival within a given year. The data includes festival runs up to 2019.

The csv file “3_imdb-dataset_general-info_wide” contains general information about films such as genre as defined by IMDb, languages in which a film was shown, ratings, and budget. The dataset is in wide format, so that each row corresponds to a unique film.

The csv file “3_imdb-dataset_release-info_long” contains data about non-festival release (e.g., theatrical, digital, tv, dvd/blueray). The dataset is in a long format, so that each row corresponds to a particular release of a particular film.

The csv file “3_imdb-dataset_websites_long” contains data on available websites (official websites, miscellaneous, photos, video clips). The dataset is in a long format, so that each row corresponds to a website of a particular film.

The dataset includes 8 text files containing the script for webscraping. They were written using the R-3.6.3 version for Windows.

The R script “r_1_unite_data” demonstrates the structure of the dataset, that we use in the following steps to identify, scrape, and match the film data.

The R script “r_2_scrape_matches” reads in the dataset with the film characteristics described in the “r_1_unite_data” and uses various R packages to create a search URL for each film from the core dataset on the IMDb website. The script attempts to match each film from the core dataset to IMDb records by first conducting an advanced search based on the movie title and year, and then potentially using an alternative title and a basic search if no matches are found in the advanced search. The script scrapes the title, release year, directors, running time, genre, and IMDb film URL from the first page of the suggested records from the IMDb website. The script then defines a loop that matches (including matching scores) each film in the core dataset with suggested films on the IMDb search page. Matching was done using data on directors, production year (+/- one year), and title, a fuzzy matching approach with two methods: “cosine” and “osa.” where the cosine similarity is used to match titles with a high degree of similarity, and the OSA algorithm is used to match titles that may have typos or minor variations.

The script “r_3_matching” creates a dataset with the matches for a manual check. Each pair of films (original film from the core dataset and the suggested match from the IMDb website was categorized in the following five categories: a) 100% match: perfect match on title, year, and director; b) likely good match; c) maybe match; d) unlikely match; and e) no match). The script also checks for possible doubles in the dataset and identifies them for a manual check.

The script “r_4_scraping_functions” creates a function for scraping the data from the identified matches (based on the scripts described above and manually checked). These functions are used for scraping the data in the next script.

The script “r_5a_extracting_info_sample” uses the function defined in the “r_4_scraping_functions”, in order to scrape the IMDb data for the identified matches. This script does that for the first 100 films, to check, if everything works. Scraping for the entire dataset took a few hours. Therefore, a test with a subsample of 100 films is advisable.

The script “r_5b_extracting_info_all” extracts the data for the entire dataset of the identified matches.

The script “r_5c_extracting_info_skipped” checks the films with missing data (where data was not scraped) and tried to extract data one more time to make sure that the errors were not caused by disruptions in the internet connection or other technical issues.

The script “r_check_logs” is used for troubleshooting and tracking the progress of all of the R scripts used. It gives information on the amount of missing values and errors.

4 Festival Library Dataset

The Festival Library Dataset consists of a data scheme image file, one codebook and one dataset, all in csv format.

The codebook (csv file “4_codebook_festival-library_dataset”) offers a detailed description of all variables within the Library Dataset. It lists the definition of variables, such as location and festival name, and festival categories, units of measurement, data sources and coding and missing data.

The csv file “4_festival-library_dataset_imdb-and-survey” contains data on all unique festivals collected from both IMDb and survey sources. This dataset appears in wide format, all information for each festival is listed in one row. This

This paper explores a unique dataset of all the SET ratings provided by students of one university in Poland at the end of the winter semester of the 2020/2021 academic year. The SET questionnaire used by this university is presented in Appendix 1. The dataset is unique for several reasons. It covers all SET surveys filled by students in all fields and levels of study offered by the university. In the period analysed, the university was entirely in the online regime amid the Covid-19 pandemic. While the expected learning outcomes formally have not been changed, the online mode of study could have affected the grading policy and could have implications for some of the studied SET biases. This Covid-19 effect is captured by econometric models and discussed in the paper. The average SET scores were matched with the characteristics of the teacher for degree, seniority, gender, and SET scores in the past six semesters; the course characteristics for time of day, day of the week, course type, course breadth, class duration, and class size; the attributes of the SET survey responses as the percentage of students providing SET feedback; and the grades of the course for the mean, standard deviation, and percentage failed. Data on course grades are also available for the previous six semesters. This rich dataset allows many of the biases reported in the literature to be tested for and new hypotheses to be formulated, as presented in the introduction section. The unit of observation or the single row in the data set is identified by three parameters: teacher unique id (j), course unique id (k) and the question number in the SET questionnaire (n ϵ {1, 2, 3, 4, 5, 6, 7, 8, 9} ). It means that for each pair (j,k), we have nine rows, one for each SET survey question, or sometimes less when students did not answer one of the SET questions at all. For example, the dependent variable SET_score_avg(j,k,n) for the triplet (j=Calculus, k=John Smith, n=2) is calculated as the average of all Likert-scale answers to question nr 2 in the SET survey distributed to all students that took the Calculus course taught by John Smith. The data set has 8,015 such observations or rows. The full list of variables or columns in the data set included in the analysis is presented in the attached filesection. Their description refers to the triplet (teacher id = j, course id = k, question number = n). When the last value of the triplet (n) is dropped, it means that the variable takes the same values for all n ϵ {1, 2, 3, 4, 5, 6, 7, 8, 9}.Two attachments:- word file with variables description- Rdata file with the data set (for R language).Appendix 1. Appendix 1. The SET questionnaire was used for this paper. Evaluation survey of the teaching staff of [university name] Please, complete the following evaluation form, which aims to assess the lecturer’s performance. Only one answer should be indicated for each question. The answers are coded in the following way: 5- I strongly agree; 4- I agree; 3- Neutral; 2- I don’t agree; 1- I strongly don’t agree. Questions 1 2 3 4 5 I learnt a lot during the course. ○ ○ ○ ○ ○ I think that the knowledge acquired during the course is very useful. ○ ○ ○ ○ ○ The professor used activities to make the class more engaging. ○ ○ ○ ○ ○ If it was possible, I would enroll for the course conducted by this lecturer again. ○ ○ ○ ○ ○ The classes started on time. ○ ○ ○ ○ ○ The lecturer always used time efficiently. ○ ○ ○ ○ ○ The lecturer delivered the class content in an understandable and efficient way. ○ ○ ○ ○ ○ The lecturer was available when we had doubts. ○ ○ ○ ○ ○ The lecturer treated all students equally regardless of their race, background and ethnicity. ○ ○

This data release contains the input-data files and R scripts associated with the analysis presented in [citation of manuscript]. The spatial extent of the data is the contiguous U.S. The input-data files include one comma separated value (csv) file of county-level data, and one csv file of city-level data. The county-level csv (“county_data.csv”) contains data for 3,109 counties. This data includes two measures of water use, descriptive information about each county, three grouping variables (climate region, urban class, and economic dependency), and contains 18 explanatory variables: proportion of population growth from 2000-2010, fraction of withdrawals from surface water, average daily water yield, mean annual maximum temperature from 1970-2010, 2005-2010 maximum temperature departure from the 40-year maximum, mean annual precipitation from 1970-2010, 2005-2010 mean precipitation departure from the 40-year mean, Gini income disparity index, percent of county population with at least some college education, Cook Partisan Voting Index, housing density, median household income, average number of people per household, median age of structures, percent of renters, percent of single family homes, percent apartments, and a numeric version of urban class. The city-level csv (city_data.csv) contains data for 83 cities. This data includes descriptive information for each city, water-use measures, one grouping variable (climate region), and 6 explanatory variables: type of water bill (increasing block rate, decreasing block rate, or uniform), average price of water bill, number of requirement-oriented water conservation policies, number of rebate-oriented water conservation policies, aridity index, and regional price parity. The R scripts construct fixed-effects and Bayesian Hierarchical regression models. The primary difference between these models relates to how they handle possible clustering in the observations that define unique water-use settings. Fixed-effects models address possible clustering in one of two ways. In a "fully pooled" fixed-effects model, any clustering by group is ignored, and a single, fixed estimate of the coefficient for each covariate is developed using all of the observations. Conversely, in an unpooled fixed-effects model, separate coefficient estimates are developed only using the observations in each group. A hierarchical model provides a compromise between these two extremes. Hierarchical models extend single-level regression to data with a nested structure, whereby the model parameters vary at different levels in the model, including a lower level that describes the actual data and an upper level that influences the values taken by parameters in the lower level. The county-level models were compared using the Watanabe-Akaike information criterion (WAIC) which is derived from the log pointwise predictive density of the models and can be shown to approximate out-of-sample predictive performance. All script files are intended to be used with R statistical software (R Core Team (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org) and Stan probabilistic modeling software (Stan Development Team. 2017. RStan: the R interface to Stan. R package version 2.16.2. http://mc-stan.org).

This text files aims to explain the procedure to perform both the data handling and the analyses in the paper: Description of the files: 1. Datasets PhenoAsreml.txt contains the observed values for the phenotypes described in the paper PhenoAsreml_scaled.txt contains the scaled (mean of zero and standard deviation of one) of the same phenotypes. THIS DATASET IS USED FOR BIVARIATE ANALYSES WITH 2x2 STRATA PhenoAsreml_scaledLong.txt contains the same information, organized differently because the dataset is reshaped from wide to long format. PhenoAsreml_scaledLong_3x3strata.txt contains the information for BackFat and BodyWeight, THIS DATASET IS USED FOR BIVARIATE ANALYSES WITH 3x3 STRATA PhenoAsreml_scaledLong_3x2strata.txt contains the information for BackFat and Adiponectin, THIS DATASET IS USED FOR BIVARIATE ANALYSES WITH 3x2 STRATA. It is only an example of dataset that needs to be generated in order to obtain all the results presented in the paper BEDERE_2023_Data_PedigreeHens.txt is the pedigree file (individual/sire/dam) traced back over 5 generations 2. Codes and parameter files BEDERE_2023_RScript_handlingdata_Long.R is an R code to reshape PhenoAsreml_scaled into PhenoAsreml_scaledLong and to subset it to generate PhenoAsreml_scaledLong_3x3strata for instance BEDERE_2023_ASREMLScript_bivariate_2x2strata.as (as well as ...3x2strata.as and ...3x3strata.as) are ASReml parameter files used to state the data, model specification and post-hoc calculation to ASReml Please, note that some variance components have been fixed in some analyses when the algorithm was struggling to converge. BEDERE_2023_RScript_BartlettTest.R is an R code to perform the Bartlett test. 2. Results examples Some output files of ASReml are provided to give an example of results for each type of bivariate analysis. The .asr file is the log of the program, explaining how the program ran The .res file is describing the residuals The .pvc file describes the variance components and provides the genetic parameters with their associated standard errors.

The data.gov.au Dataset Ontology is an OWL ontology designed to describe the characteristics of datasets published on data.gov.au.\r \r The ontology contains elements which describe the publication, update, origin, governance, spatial and temporal coverage and other contextual information about the dataset. The ontology also covers aspects of organisational custodianship and governance.\r \r By using this ontology to describe datasets on data.gov.au publishers increase discoverability and enable the consumption of this information in other applications/systems as Linked Data. It further enables decentralised publishing of catalogs and facilitates federated dataset search across sites, e.g. in datasets that are published by the States.\r \r Other publishers of Linked Data may make assertions about data published using this ontology, e.g. they may publish information about the use of the dataset in other applications.

AWC to 60cm is one of 18 attributes of soils chosen to underpin the land suitability assessment of the Roper River Water Resource Assessment (ROWRA) through the digital soil mapping process (DSM). AWC (available water capacity) indicates the ability of a soil to retain and supply water for plant growth. This AWC raster data represents a modelled dataset of AWC to 60cm (mm of water to 60cm of soil depth) and is derived from analysed site data, spline calculations and environmental covariates. AWC is a parameter used in land suitability assessments for rainfed cropping and for water use efficiency in irrigated land uses. This raster data provides improved soil information used to underpin and identify opportunities and promote detailed investigation for a range of sustainable regional development options and was created within the ‘Land Suitability’ activity of the CSIRO ROWRA. A companion dataset and statistics reflecting reliability of this data are also provided and can be found described in the lineage section of this metadata record. Processing information is supplied in ranger R scripts and attributes were modelled using a Random Forest approach. The DSM process is described in the CSIRO ROWRA published report ‘Soils and land suitability for the Roper catchment, Northern Territory’. A technical report from the CSIRO Roper River Water Resource Assessment to the Government of Australia. The Roper River Water Resource Assessment provides a comprehensive overview and integrated evaluation of the feasibility of aquaculture and agriculture development in the Roper catchment NT as well as the ecological, social and cultural (indigenous water values, rights and aspirations) impacts of development. Lineage: This AWC to 60cm dataset has been generated from a range of inputs and processing steps. Following is an overview. For more information refer to the CSIRO ROWRA published reports and in particular ' Soils and land suitability for the Roper catchment, Northern Territory’. A technical report from the CSIRO Roper River Water Resource Assessment to the Government of Australia. 1. Collated existing data (relating to: soils, climate, topography, natural resources, remotely sensed, of various formats: reports, spatial vector, spatial raster etc). 2. Selection of additional soil and land attribute site data locations by a conditioned Latin hypercube statistical sampling method applied across the covariate data space. 3. Fieldwork was carried out to collect new attribute data, soil samples for analysis and build an understanding of geomorphology and landscape processes. 4. Database analysis was performed to extract the data to specific selection criteria required for the attribute to be modelled. 5. The R statistical programming environment was used for the attribute computing. Models were built from selected input data and covariate data using predictive learning from a Random Forest approach implemented in the ranger R package. 6. Create AWC to 60cm Digital Soil Mapping (DSM) attribute raster dataset. DSM data is a geo-referenced dataset, generated from field observations and laboratory data, coupled with environmental covariate data through quantitative relationships. It applies pedometrics - the use of mathematical and statistical models that combine information from soil observations with information contained in correlated environmental variables, remote sensing images and some geophysical measurements. 7. Companion predicted reliability data was produced from the 500 individual Random Forest attribute models created. 8. QA Quality assessment of this DSM attribute data was conducted by three methods. Method 1: Statistical (quantitative) method of the model and input data. Testing the quality of the DSM models was carried out using data withheld from model computations and expressed as OOB and R squared results, giving an estimate of the reliability of the model predictions. These results are supplied. Method 2: Statistical (quantitative) assessment of the spatial attribute output data presented as a raster of the attributes “reliability”. This used the 500 individual trees of the attributes RF models to generate 500 datasets of the attribute to estimate model reliability for each attribute. For continuous attributes the method for estimating reliability is the Coefficient of Variation. This data is supplied. Method 3: Collecting independent external validation site data combined with on-ground expert (qualitative) examination of outputs during validation field trips. Across each of the study areas a two week validation field trip was conducted using a new validation site set which was produced by a random sampling design based on conditioned Latin Hypercube sampling using the reliability data of the attribute. The modelled DSM attribute value was assessed against the actual on-ground value. These results are published in the report cited in this metadata record.

The data collected by Spire from its 100 satellites launched into Low Earth Orbit (LEO) has a diverse range of applications, from analysis of global trade patterns and commodity flows to aircraft routing to weather forecasting. The data also provides interesting research opportunities on topics as varied as ocean currents and GNSS-based planetary boundary layer height. The following products can be requested: GNSS Polarimetric Radio Occultation (STRATOS) Novel Polarimetric Radio Occultation (PRO) measurements collected by three Spire satellites are available over 15 May 2023 to 30 November 2023. PRO differ from regular RO (described below) in that the H and V polarizations of the signal are available, as opposed to only Right-Handed Circularly Polarized (RHCP) signals in regular RO. The differential phase shift between H and V correlates with the presence of hydrometeors (ice crystals, rain, snow, etc.). When combined, the H and V information provides the same information on atmospheric thermodynamic properties as RO: temperature, humidity, and pressure, based on the signal’s bending angle. Various levels of the products are provided. GNSS Reflectometry (STRATOS) GNSS Reflectometry (GNSS-R) is a technique to measure Earth’s surface properties using reflections of GNSS signals in the form of a bistatic radar. Spire collects two types of GNSS-R data: Near-Nadir incidence LHCP reflections collected by the Spire GNSS-R satellites, and Grazing-Angle GNSS-R (i.e., low elevation angle) RHCP reflections collected by the Spire GNSS-RO satellites. The Near-Nadir GNSS-R collects DDM (Delay Doppler Map) reflectivity measurements. These are used to compute ocean wind / wave conditions and soil moisture over land. The Grazing-Angle GNSS-R collects 50 Hz reflectivity and additionally carrier phase observations. These are used for altimetry and characterization of smooth surfaces (such as ice and inland water). Derived Level 1 and Level 2 products are available, as well as some special Level 0 raw intermediate frequency (IF) data. Historical grazing angle GNSS-R data are available from May 2019 to the present, while near-nadir GNSS-R data are available from December 2020 to the present. Name Temporal coverage Spatial coverage Description Data format and content Application Polarimetric Radio Occultation (PRO) measurements 15 May 2023 to 30 November 2023 Global PRO measurements observe the properties of GNSS signals as they pass through by Earth's atmosphere, similar to regular RO measurements. The polarization state of the signals is recorded separately for H and V polarizations to provide information on the anisotropy of hydrometeors along the propagation path leoOrb.sp3. This file contains the estimated position, velocity and receiver clock error of a given Spire satellite after processing of the POD observation file proObs. Level 0 - Raw open loop carrier phase measurements at 50 Hz sampling for both linear polarization components (horizontal and vertical) of the occulted GNSS signal. h(v)(c)atmPhs. Level 1B - Atmospheric excess phase delay computed for each individual linear polarization component (hatmPhs, vatmPhs) and for the combined (“H” + “V”) signal (catmPhs). Also contains values for signal-to-noise ratio, transmitter and receiver positions and open loop model information. polPhs. Level 1C - Combines the information from the hatmPhs and vatmPhs files while removing phase continuities due to phase wrapping and navigation bit modulation. patmPrf. Level 2 - Bending angle, dry refractivity, and dry temperature as a function of mean sea level altitude and impact parameter derived from the “combined” excess phase delay (catmPhs) PRO measurements add a sensitivity to ice and precipitation content alongside the traditional RO measurements of the atmospheric temperature, pressure, and water vapor. Near-Nadir GNSS Reflectometry (NN GNSS-R) measurements 25 January-2024 to 24 July 2024 Global Tracks of surface reflections as observed by the near-nadir pointing GNSS-R antennas, based on Delay Doppler Maps (DDMs). gbrRCS.nc. Level 1B - Along-track calibrated bistatic radar cross-sections measured by Spire conventional GNSS-R satellites. gbrNRCS.nc. Level 1B - Along-track calibrated bistatic and normalized radar cross-sections measured by Spire conventional GNSS-R satellites. gbrSSM.nc. Level 2 - Along-track SNR, reflectivity, and retrievals of soil moisture (and associated uncertainties) and probability of frozen ground. gbrOcn.nc. Level 2 - Along-track retrievals of mean square slope (MSS) of the sea surface, wind speed, sigma0, and associated uncertainties. NN GNSS-R measurements are used to measure ocean surface winds and characterize land surfaces for applications such as soil moisture, freeze/thaw monitoring, flooding detection, inland water body delineation, sea ice classification, etc. Grazing angle GNSS Reflectometry (GA GNSS-R) measurements 25 January 2024 to 24 July 2024 Global Tracks of surface reflections as observed by the limb-facing RO antennas, based on open-loop tracking outputs: 50 Hz collections of accumulated I/Q observations grzRfl.nc. Level 1B - Along-track SNR, reflectivity, phase delay (with respect to an open loop model) and low-level observables and bistatic radar geometries such as receiver, specular reflection, and the transmitter locations. grzIce.nc. Level 2 - Along-track water vs sea ice classification, along with sea ice type classification. grzAlt.nc. Level 2 - Along-track phase-delay, ionosphere-corrected altimetry, tropospheric delay, and ancillary models (mean sea surface, tides). GA GNSS-R measurements are used to 1) characterize land surfaces for applications such as sea ice classification, freeze/thaw monitoring, inland water body detection and delineation, etc., and 2) measure relative altimetry with dm-level precision for inland water bodies, river slopes, sea ice freeboard, etc., but also water vapor characterization from delay based on tropospheric delays. Additionally, the following products (better detailed in the ToA) can be requested but the acceptance is not guaranteed and shall be evaluated on a case-by-case basis: Other STRATOS measurements: profiles of the Earth’s atmosphere and ionosphere, from December 2018 ADS-B Data Stream: monthly subscription to global ADS-B satellite data, available from December 2018 AIS messages: AIS messages observed from Spire satellites (S-AIS) and terrestrial from partner sensor stations (T-AIS), monthly subscription available from June 2016 The products are available as part of the Spire provision with worldwide coverage. All details about the data provision, data access conditions and quota assignment procedure are described in the Terms of Applicability.

This report describes several R packages that allow HTML content to be rendered as part of an R plot. The core package is called 'layoutEngine', but that package requires a "backend" package to perform HTML layout calculations. Three example backends are demonstrated: 'layoutEngineCSSBox', 'layoutEnginePhantomJS', and 'layoutEngineDOM'. We also introduce two new font packages, 'gyre' and 'courier'.

This dataset contains simulated datasets, empirical data, and R scripts described in the paper: “Li, Q. and Kou, X. (2021) WiBB: An integrated method for quantifying the relative importance of predictive variables. Ecography (DOI: 10.1111/ecog.05651)”.

A fundamental goal of scientific research is to identify the underlying variables that govern crucial processes of a system. Here we proposed a new index, WiBB, which integrates the merits of several existing methods: a model-weighting method from information theory (Wi), a standardized regression coefficient method measured by ß* (B), and bootstrap resampling technique (B). We applied the WiBB in simulated datasets with known correlation structures, for both linear models (LM) and generalized linear models (GLM), to evaluate its performance. We also applied two other methods, relative sum of wight (SWi), and standardized beta (ß*), to evaluate their performance in comparison with the WiBB method on ranking predictor importances under various scenarios. We also applied it to an empirical dataset in a plant genus Mimulus to select bioclimatic predictors of species’ presence across the landscape. Results in the simulated datasets showed that the WiBB method outperformed the ß* and SWi methods in scenarios with small and large sample sizes, respectively, and that the bootstrap resampling technique significantly improved the discriminant ability. When testing WiBB in the empirical dataset with GLM, it sensibly identified four important predictors with high credibility out of six candidates in modeling geographical distributions of 71 Mimulus species. This integrated index has great advantages in evaluating predictor importance and hence reducing the dimensionality of data, without losing interpretive power. The simplicity of calculation of the new metric over more sophisticated statistical procedures, makes it a handy method in the statistical toolbox.

Methods To simulate independent datasets (size = 1000), we adopted Galipaud et al.’s approach (2014) with custom modifications of the data.simulation function, which used the multiple normal distribution function rmvnorm in R package mvtnorm(v1.0-5, Genz et al. 2016). Each dataset was simulated with a preset correlation structure between a response variable (y) and four predictors(x1, x2, x3, x4). The first three (genuine) predictors were set to be strongly, moderately, and weakly correlated with the response variable, respectively (denoted by large, medium, small Pearson correlation coefficients, r), while the correlation between the response and the last (spurious) predictor was set to be zero. We simulated datasets with three levels of differences of correlation coefficients of consecutive predictors, where ∆r = 0.1, 0.2, 0.3, respectively. These three levels of ∆r resulted in three correlation structures between the response and four predictors: (0.3, 0.2, 0.1, 0.0), (0.6, 0.4, 0.2, 0.0), and (0.8, 0.6, 0.3, 0.0), respectively. We repeated the simulation procedure 200 times for each of three preset correlation structures (600 datasets in total), for LM fitting later. For GLM fitting, we modified the simulation procedures with additional steps, in which we converted the continuous response into binary data O (e.g., occurrence data having 0 for absence and 1 for presence). We tested the WiBB method, along with two other methods, relative sum of wight (SWi), and standardized beta (ß*), to evaluate the ability to correctly rank predictor importances under various scenarios. The empirical dataset of 71 Mimulus species was collected by their occurrence coordinates and correponding values extracted from climatic layers from WorldClim dataset (www.worldclim.org), and we applied the WiBB method to infer important predictors for their geographical distributions.

A collection of datasets and python scripts for extraction and analysis of isograms (and some palindromes and tautonyms) from corpus-based word-lists, specifically Google Ngram and the British National Corpus (BNC).Below follows a brief description, first, of the included datasets and, second, of the included scripts.1. DatasetsThe data from English Google Ngrams and the BNC is available in two formats: as a plain text CSV file and as a SQLite3 database.1.1 CSV formatThe CSV files for each dataset actually come in two parts: one labelled ".csv" and one ".totals". The ".csv" contains the actual extracted data, and the ".totals" file contains some basic summary statistics about the ".csv" dataset with the same name.The CSV files contain one row per data point, with the colums separated by a single tab stop. There are no labels at the top of the files. Each line has the following columns, in this order (the labels below are what I use in the database, which has an identical structure, see section below):

Label Data type Description

isogramy int The order of isogramy, e.g. "2" is a second order isogram

length int The length of the word in letters

word text The actual word/isogram in ASCII

source_pos text The Part of Speech tag from the original corpus

count int Token count (total number of occurences)

vol_count int Volume count (number of different sources which contain the word)

count_per_million int Token count per million words

vol_count_as_percent int Volume count as percentage of the total number of volumes

is_palindrome bool Whether the word is a palindrome (1) or not (0)

is_tautonym bool Whether the word is a tautonym (1) or not (0)

The ".totals" files have a slightly different format, with one row per data point, where the first column is the label and the second column is the associated value. The ".totals" files contain the following data:

Label

Data type

Description

!total_1grams

int

The total number of words in the corpus

!total_volumes

int

The total number of volumes (individual sources) in the corpus

!total_isograms

int

The total number of isograms found in the corpus (before compacting)

!total_palindromes

int

How many of the isograms found are palindromes

!total_tautonyms

int

How many of the isograms found are tautonyms

The CSV files are mainly useful for further automated data processing. For working with the data set directly (e.g. to do statistics or cross-check entries), I would recommend using the database format described below.1.2 SQLite database formatOn the other hand, the SQLite database combines the data from all four of the plain text files, and adds various useful combinations of the two datasets, namely:• Compacted versions of each dataset, where identical headwords are combined into a single entry.• A combined compacted dataset, combining and compacting the data from both Ngrams and the BNC.• An intersected dataset, which contains only those words which are found in both the Ngrams and the BNC dataset.The intersected dataset is by far the least noisy, but is missing some real isograms, too.The columns/layout of each of the tables in the database is identical to that described for the CSV/.totals files above.To get an idea of the various ways the database can be queried for various bits of data see the R script described below, which computes statistics based on the SQLite database.2. ScriptsThere are three scripts: one for tiding Ngram and BNC word lists and extracting isograms, one to create a neat SQLite database from the output, and one to compute some basic statistics from the data. The first script can be run using Python 3, the second script can be run using SQLite 3 from the command line, and the third script can be run in R/RStudio (R version 3).2.1 Source dataThe scripts were written to work with word lists from Google Ngram and the BNC, which can be obtained from http://storage.googleapis.com/books/ngrams/books/datasetsv2.html and [https://www.kilgarriff.co.uk/bnc-readme.html], (download all.al.gz).For Ngram the script expects the path to the directory containing the various files, for BNC the direct path to the *.gz file.2.2 Data preparationBefore processing proper, the word lists need to be tidied to exclude superfluous material and some of the most obvious noise. This will also bring them into a uniform format.Tidying and reformatting can be done by running one of the following commands:python isograms.py --ngrams --indir=INDIR --outfile=OUTFILEpython isograms.py --bnc --indir=INFILE --outfile=OUTFILEReplace INDIR/INFILE with the input directory or filename and OUTFILE with the filename for the tidied and reformatted output.2.3 Isogram ExtractionAfter preparing the data as above, isograms can be extracted from by running the following command on the reformatted and tidied files:python isograms.py --batch --infile=INFILE --outfile=OUTFILEHere INFILE should refer the the output from the previosu data cleaning process. Please note that the script will actually write two output files, one named OUTFILE with a word list of all the isograms and their associated frequency data, and one named "OUTFILE.totals" with very basic summary statistics.2.4 Creating a SQLite3 databaseThe output data from the above step can be easily collated into a SQLite3 database which allows for easy querying of the data directly for specific properties. The database can be created by following these steps:1. Make sure the files with the Ngrams and BNC data are named “ngrams-isograms.csv” and “bnc-isograms.csv” respectively. (The script assumes you have both of them, if you only want to load one, just create an empty file for the other one).2. Copy the “create-database.sql” script into the same directory as the two data files.3. On the command line, go to the directory where the files and the SQL script are. 4. Type: sqlite3 isograms.db 5. This will create a database called “isograms.db”.See the section 1 for a basic descript of the output data and how to work with the database.2.5 Statistical processingThe repository includes an R script (R version 3) named “statistics.r” that computes a number of statistics about the distribution of isograms by length, frequency, contextual diversity, etc. This can be used as a starting point for running your own stats. It uses RSQLite to access the SQLite database version of the data described above.

These data describe the catch and biological data from 363 bottom-set gill-net lifts distributed throughout Lake Michigan (including main basin and Green Bay) between April and November in 1930–1932. Data collected from the R/V Fulmar were recorded in notebooks and are now archived at the U.S. Geological Survey’s Great Lakes Science Center. Each lift included 1–7 gangs of linen gill nets. Each gang comprised 3–5 panels each having a length of 155 m, a height of 1.5 m, and a (stretch-)mesh size of either 60, 64, 67, 70, or 76 mm. The digitization of the Fulmar data notebooks was started in the late 1990s and finished in this study.

Abstract The dataset was derived by the Bioregional Assessment Programme from multiple datasets. The source dataset is identified in the Lineage field in this metadata statement. The processes undertaken to produce this derived dataset are described in the History field in this metadata statement. The dataset consists of an excel spreadsheet and shapefile representing the locations of simulation nodes used in the AWRA-R model. Some of the nodes correspond to gauging station locations or dam …Show full descriptionAbstract The dataset was derived by the Bioregional Assessment Programme from multiple datasets. The source dataset is identified in the Lineage field in this metadata statement. The processes undertaken to produce this derived dataset are described in the History field in this metadata statement. The dataset consists of an excel spreadsheet and shapefile representing the locations of simulation nodes used in the AWRA-R model. Some of the nodes correspond to gauging station locations or dam locations whereas other locations represent river confluences or catchment outlets which have no gauging. These are marked as "Dummy". Purpose Locations are used as pour points in oder to define reach areas for river system modelling. Dataset History Subset of data for the Hunter that was extracted from the Bureau of Meteorology's hydstra system and includes all gauges where data has been received from the lead water agency of each jurisdiction. Simulation nodes were added in locations in which the model will provide simulated streamflow. There are 3 files that have been extracted from the Hydstra database to aid in identifying sites in each bioregion and the type of data collected from each on. These data were used to determine the simulation node locations where model outputs were generated. The 3 files contained within the source dataset used for this determination are: Site - lists all sites available in Hydstra from data providers. The data provider is listed in the #Station as _xxx. For example, sites in NSW are _77, QLD are _66. Some sites do not have locational information and will not be able to be plotted. Period - the period table lists all the variables that are recorded at each site and the period of record. Variable - the variable table shows variable codes and names which can be linked to the period table. Relevant location information and other data were extracted to construct the spreadsheet and shapefile within this dataset. Dataset Citation Bioregional Assessment Programme (XXXX) HUN AWRA-R simulation nodes v01. Bioregional Assessment Derived Dataset. Viewed 13 March 2019, http://data.bioregionalassessments.gov.au/dataset/fda20928-d486-49d2-b362-e860c1918b06. Dataset Ancestors Derived From National Surface Water sites Hydstra

This dataset contains four zipped subfolders: code, data, final_figures, and model_summary. code: This folder contains the R-scripts used to wrangle and analyze the data. 1_Data_Input.R is the initial data wrangling file that compiles and ensures the data is ready for analysis. 2_Clim_Win.R is the file used to perform the climate window analysis. 3_Divorce_Analysis.R is the file used to perform all of the analyses regarding divorce. 4_Reproduction_Analysis.R is the file used to perform all of the analysis regarding reproductive success. data: This folder contains all the data used in the manuscript and some additional data used during data exploration. The following files are important for the final manuscript. climwinfig.xlsx is the data resulting from the climate window analysis used to create the climate window analysis plot. partnership_data_20230113.xlsx is the main dataset used for all model analyses. There is a seperate README file in this folder that explains all the variables used in the manuscript. raw_status_data_20221101.xlsx is the data file containing the breeding statuses of the individuals during the study period which is used in conjunction with sys_Pedigree_Combined.xlsx (genetic pedigree file) to assess genetic offspring. tblNestInfo.xlsx is the data file containing information regarding the number of nests in every given year. tblGenParentageDetails is the data file containing the parentage data required to assign co-breeders. tblWeather.xlsx is the data file containing the rainfall data for each given month in each given year. tblInsectSamplingCounts.xlsx, tblInsectSamplingCountsRaw.xlsx, tblVegLeafSizes.xlsx, and tblInsectSamplingDetails.xlsx are data files containing information on insect abundance in every given year (not used in final manuscript). final_figures: Contains the figures used in the manuscript which are created using the previously described data and R-scripts. model_summary: Contains all of the statistical model summaries that are used as tables in the manuscript, which are created using the previously described data and R-scripts.