This readme.md file was generated on 2021-04-20 by Jacob T. Wittman ------------------- GENERAL INFORMATION ------------------- 1. Data and code for forecasting overwintering mortality of Spathius galinae in North America 2. Author Information   Principal Investigator Contact Information         Name: Jacob T. Wittman            Institution: University of Minnesota            Email: wittm094@umn.edu   ORCID: https://orcid.org/0000-0002-2220-5598   Associate or Co-investigator Contact Information         Name: Brian H. Aukema            Institution: University of Minnesota   ORCID: https://orcid.org/0000-0003-4370-0499   Associate or Co-investigator Contact Information            Name: Jian J. Duan            Institution: United States Department of Agriculture - Agricultural Research Service                Associate or Co-investigator Contact Information            Name: Robert C. Venette            Institution: United States Department of Agriculture - Forest Service 3. Date of data collection (single date, range, approximate date):    2018-09-01 - 2020-09-01 4. Geographic location of data collection (where was data collected?):    Minnesota, USA    Delaware, USA 5. Information about funding sources that supported the collection of the data: Environmental and Natural Resources Trust Fund overseen by the Legislative Citizen's Commission on Minnesota Resources Project M.L. 2017 Chpt. 96 Subd. 06-066 --------------------- DATA & FILE OVERVIEW --------------------- 1. File List    A. Filename: data/2019_supercooling_winter/D_M_YYYY_ct_trial_ABC.csv       Short description: These .csv files contain temperatures recorded during cold tolerance assays. Each file contains the temperature recorded by up to 16 thermocouple sensors every second.                  B. Filename: data/2019_supercooling_winter/mortality_obs.xlsx       Short description: This file contains data on the fate of insects used in the supercooling cold tolerance assays also in the 2019_supercooling_winter folder. This file is cleaned by the script 01_01_clean_scp.R and the cleaned_scp_data.csv is generated.    C. Filename: data/cleaned_hobo_dat.csv       Short description: Cleaned hobo data used in analysis. Generated by scripts/02_02_hobo_dat.R        D. Filename: data/cleaned_scp_dat.csv       Short description: Data from the laboratory assays done in this study. Generated from the mortality_obs.csv by the scripts/01_01_clean_scp.R script.        E. Filename: hobo_data/*.csv       The .csv files in this directory are all temperatures and relative humidity recorded by HOBO data loggers at the sites used in the field assays of this study and in the incubators used to rear experimental insects after exposure to winter temperatures. The filename identifies the site and treatment, or the incubator the HOBO was placed in.          F. Filename: hobo_data/*.hobo       Short description: The .hobo files in this directory are the files used to generate the .csv files in this directory from the HOBO Data logger software.          G. Filename: overwintering_hobo_dat.csv       Short description: Data on *Spathius galinae* emergence and eclosion from field experiments along with summaries of HOBO recorded temperatures and relative humidity.          H. Filename: processed_rasters/na_sf_polygons.RDS       Short description: SF Polygons object containing polygons for North America.          I. Filename: processed_rasters/wc_winter_YYYY_YYYY.nc       Short description: WorldClim rasters containing minimum temperatures for the winter of October YYYY - March YYYY in parts of North America where ash are found.    L. Filename: manuscript/Wittman_etal_sgalinae_coldtolerance.Rmd     Short description: Contains code for all analyses, figures, and tables reported in the manuscript. When knit, generates a Word document containing the figures and tables.        M. Filename: scripts/01_01_clean_scp.R     Short description: Script used to clean mortality_obs.xlsx file, which contains data from the laboratory assays.        N. Filename: scripts/01_02_scp.R     Short description: Script used to generate graphs of temperatures recorded during laboratory assays. Used to identify value of supercooling point.        O. Filename: scripts/02_01_clean_overwintering.R     Short description: Very short script used to clean data from field experiments reported in this manuscript.        P. Filename: scripts/02_02_hobo_dat.R     Short description: Script used for summarizing and visualizing HOBO data recorded as part of the field experiments in this manuscript. 2. Additional related data collected that was not included in the current data package: Ash distribution rasters obtained from the US Forest Service and Natural Resources Canada were used crop and mask the minimum temperature rasters to only the distribution of ash in North America. -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: Link to publication to be added later 2. Methods for processing the data: The R scripts with "clean" in the title were used to process data. Additional processing is done in the .Rmd file in the manuscript folder. 3. Instrument- or software-specific information needed to interpret the data: R (required), Rstudio (suggested) ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: [cleaned_hobo_dat.csv] ----------------------------------------- 1. Number of variables: 6 2. Number of cases/rows: 28566 3. Missing data codes:         Code/symbol: "NA"        Definition: Missing 4. Variable List     A. Name: location        Description: Character string identifying location that HOBO recorded temperature and humidity for. Strings after underscore identify the treatment if the HOBO was in a field experiment location.     B. Name: date_time        Description: Date and time of recorded temperature or humidity. MM/DD/YYYY HH:MM format.             C. Name: temp_F     Description: Temperature in °F         D. Name: RH     Description: Relative humidity (%)         E. Name: date_time_true     Description: Date time column formatted to be read by R as a date object from the lubridate package.         F. Name: temp_C     Description: Temperature in °C.     ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: [cleaned_scp_dat.csv] ----------------------------------------- 1. Number of variables: 12 2. Number of cases/rows: 428 3. Missing data codes:         Code/symbol: "NA"        Definition: Missing 4. Variable List     A. Name: date_SC        Description: Date the supercooling assay was run.     B. Name: trial        Description: Character string to uniquely identify a trial when combined with the date_SC column.             C. Name: Channel     Description: String to identify channel that recorded the temperature for each individual insect, or if the insect was a control.         D. Name: degree_min     Description: Degrees (°C) per minute that the insect was chilled.         E. Name: temp_pulled     Description: Pre-designated lower temperature (°C) at which the insect was removed from the chiller bath.         F. Name: discolor_3day     Description: Binary variable indicating if insect was discolored (1) or normal colored (0) 3 days after assay.         G. Name: est_scp     Description. Numeric variable of the estimated supercooling point (°C) if the thermocouple recorded an exotherm.         H. Name: eclose     Description. Binary variable indicated if insect eclosed (1) or not (0).         I. Name: temp_pulled_grouped     Description: temp_pulled variable adjusted so that the minimum temperatured pulled was -32 °C. Insects were intially pre-designated to cool as low as -40 °C, however the chilling bath had issues cooling below -32 °C so no insect was cooled lower than this number.         J. Name: uid     Description: Unique numeric identifier         K. Name: trial_id     Description: Concatenated date_SC and trial columns         L. Name: degree_min_continuous     Description: Degrees (°C) per minute that the insect was chilled. Meant to be read into R as a continuous numeric variable. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: [overwintering_hobo_dat.csv] ----------------------------------------- 1. Number of variables: 28 2. Number of cases/rows: 428 3. Missing data codes:         Code/symbol: "NA"        Definition: Missing 4. Variable List     A. Name: site        Description: The site at which the insects were kept overwinter.     B. Name: treatment        Description: The treatment group for each log: Air (or above the snowline), Snow (under the snow), or Control             C. Name: tree_type     Description: String to identify tree type of log used. All logs are GA (green ash, *Fraxinus pennsylvanica*)         D. Name: log_id_number     Description: Identifier for each log         E. Name: sg_brood_id     Description: Unique ID for each *Spathius galinae* brood         F. Name: sq_count     Description: Number of *Spathius galinae* in each brood         G. Name: unemerged_larvae     Description: Number of unemerged *Spathius galinae* larvae in each brood.         H. Name: unemerged_adults     Description. Number of unemerged *Spathius galinae* adults in each brood. These individuals were considered to have successfully eclosed.         I. Name: number_emg_sg     Description: Number of *Spathius galinae* that emerged from the log.         J. Name: total_adults     Description: Total number of adults in each brood, should be the sum of unemerged_adults and number_emg_sg         K. Name: total_insects     Description: Total number of *Spathius galinae* in each brood. Should be the sum of total_adults and unemerged_larvae.         L. Name: log_uid     Description: Unique identifier for log.         M. Name: brood_uid     Description: Unique identifier for brood within log.         N. Name: prop_success     Description: Proportion of insects that successfully eclosed in each brood.         O. Name: prop_emerged     Description: Proportion of insects that successfully emerged in each brood.         Q. Name: min_temp     Description: Absolute lowest temperature (°C) recorded by the HOBO data logger assigned to each site/treatment combination over the time the logs were left outside.         R. Name: avg_min_temp     Description: Average daily minimum temperature (°C) recorded by the HOBO data logger assigned to each site/treatment combination over the time the logs were left outside.         S. Name: mean_RH     Description: Average relative humidity (%) recorded by the HOBO data logger assigned to each site/treatment combination over the time the logs were left outside.         T. Name: max_temp     Description: Absolute highest temperature (°C) recorded by the HOBO data logger assigned to each site/treatment combination over the time the logs were left outside.         U. Name: mean_temp     Description: Average temperature (°C) recorded by the HOBO data logger assigned to each site/treatment combination over the time the logs were left outside.         V. Name: sd_temp     Description: Standard deviation of temperature (°C) recorded by the HOBO data logger assigned to each site/treatment combination over the time the logs were left outside.         W. Name: min_RH     Description: Minimum relative humidity recorded by the HOBO data logger assigned to each site/treatment combination over the time the logs were left outside.         X. Name: max_RH     Description: Maximum relative humidity recorded by the HOBO data logger assigned to each site/treatment combination over the time the logs were left outside.         Z. Name: n_temp     Description: Number of temperature observations recorded by HOBO data logger. Used in calculating var_ variables.         AA. Name: var_min_temp     Description: Variation in the minimum temperature (°C) recorded by the HOBO data logger assigned to each site/treatment combination over the time the logs were left outside.         AB. Name: var_RH     Description: Variation in relative humidity (%) recorded by the HOBO data logger assigned to each site/treatment combination over the time the logs were left outside.