------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset Seasonal influence on detection probabilities for multiple aquatic invasive species using environmental DNA 2. Author Information Principal Investigator Contact Information Name: Christopher Rounds Institution: UMNTC Department of Fisheries, Wildlife and Conservation Biology Email: round060@umn.edu Orcid: 0000-0003-1346-5707 Associate or Co-investigator Contact Information Name: Todd W Arnold Institution: UMNTC Department of Fisheries, Wildlife and Conservation Biology Orcid: 0000-0002-7920-772X Associate or Co-investigator Contact Information Name: Chan Lan Chun Institution: Natural Resources Research Institute: NRRI Email: chun0157@d.umn.edu Associate or Co-investigator Contact Information Name: Josh Dumke Institution: Natural Resources Research Institute: NRRI Associate or Co-investigator Contact Information Name: Anna Totsch Institution: Natural Resources Research Institute: NRRI Associate or Co-investigator Contact Information Name: Adelle Keppers Institution: Natural Resources Research Institute: NRRI Associate or Co-investigator Contact Information Name: Katarina Edbald Institution: Natural Resources Research Institute: NRRI Associate or Co-investigator Contact Information Name: Samantha García Institution: University of Illinois Urbana-Champaign Associate or Co-investigator Contact Information Name: Eric R Larson Institution: University of Illinois Urbana-Champaign Email: erlarson@illinois.edu Associate or Co-investigator Contact Information Name: Jenna KR Nelson Institution: UMNTC Department of Fisheries, Wildlife and Conservation Biology Orcid: 0000-0003-2960-8485 Associate or Co-investigator Contact Information Name: Gretchen JA Hansen Institution: UMNTC Department of Fisheries, Wildlife and Conservation Biology Email: ghasen@umn.edu Orcid: 0000-0003-0241-7048 3. Date published or finalized for release: 4. Date of data collection (single date, range, approximate date) 2021-04-01 to 2022-11-01 5. Geographic location of data collection (where was data collected?): Minnesota, USA 6. Information about funding sources that supported the collection of the data: Funding was provided by the Minnesota Aquatic Invasive Species Research Center (MAISRC) -------------------------- SHARING/ACCESS INFORMATION -------------------------- Terms of Use: Data Repository for the U of Minnesota (DRUM) By using these files, users agree to the Terms of Use. https://conservancy.umn.edu/pages/drum/policies/#terms-of-use --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: data Short description: folder containing data to be used in the occupancy model. B. Filename: models Short description: folder containing model output (in the form of an .rds) output from the file model_code.rmd. Due to the long time required to run the model we recommend reading in this file instead of running the model. C. Filename: MAISRC_eDNA_analysis.Rproj Short description: R Project file created to help project management. D. Filename: model_code.rmd Short description: R Markdown file where clean eDNA data is read in, the model is created and ran and results are explored. E. Filename: eDNA_occ.txt Short description: text file with the JAGS code that is used in the occupancy model. 2. Relationship between files: model_code.rmd reads in the data from the data folder, prepares the data to be used in the occupancy model and outputs the occupancy model (modelW4species.gof.rds) in the models folder. -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: eDNA samples were collected from surface waters in lakes, filtered, extracted and amplified using species specific qPCR. 2. Methods for processing the data: 3. Instrument- or software-specific information needed to interpret the data: 4. Describe any quality-assurance procedures performed on the data: Data was assured to be in a consistent format using a quality control script with no erroneous inputs 5. People involved with sample collection, processing, analysis and/or submission: Christopher Rounds, Chan Lan Chun, Anna Totsch, Katarina Edbald, Samantha García 6. Session Info for R session (sessionsessionInfo()) R version 4.1.2 (2021-11-01) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 22621) Matrix products: default locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] jagsUI_1.5.2 MCMCvis_0.15.5 cowplot_1.1.1 wiqid_0.3.3 [5] HDInterval_0.2.4 mcmcOutput_0.1.3 lubridate_1.9.3 forcats_1.0.0 [9] stringr_1.5.0 dplyr_1.1.3 purrr_1.0.1 readr_2.1.4 [13] tidyr_1.3.0 tibble_3.2.1 ggplot2_3.4.1 tidyverse_2.0.0.9000 loaded via a namespace (and not attached): [1] pillar_1.9.0 compiler_4.1.2 tools_4.1.2 digest_0.6.29 timechange_0.2.0 [6] evaluate_0.23 lifecycle_1.0.3 gtable_0.3.1 lattice_0.20-45 pkgconfig_2.0.3 [11] rlang_1.1.2 cli_3.6.1 rstudioapi_0.15.0 yaml_2.2.1 parallel_4.1.2 [16] xfun_0.39 fastmap_1.1.0 coda_0.19-4 withr_2.5.2 knitr_1.39 [21] rjags_4-13 hms_1.1.3 generics_0.1.2 vctrs_0.6.1 grid_4.1.2 [26] tidyselect_1.2.0 glue_1.6.2 R6_2.5.1 fansi_1.0.3 rmarkdown_2.13 [31] tzdb_0.2.0 magrittr_2.0.3 scales_1.2.1 htmltools_0.5.4 MASS_7.3-54 [36] colorspace_2.0-3 utf8_1.2.2 stringi_1.7.8 munsell_0.5.0 truncnorm_1.0-8 ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: platewise_4species.csv ----------------------------------------- This CSV file is contzined in the data folder 1. Number of columns: 49 2. Number of cases/rows: 4090 3. Missing data codes: NA 4. Variable List Name: UID Description: The unique identifier for the sample. The first three letters correspond to one of the 20 lakes sampled. The next number is the temporal visit that the sample corresponds to (can be 1-5) and the last two numbers are the sample number (can be 01, 02, 03...10). Name: sample Description: Number 1-10 indicating which the sample location. Each sample for a specific lake is the same regardless of visit number. Ex: sample 1 from BDG is at the boat launch for all visits. Name: visit_number Description: Number 1-5 that indicates which of the visitis the sample is from. Visit 1 happened first within a year with visit 5 being last. Name: target Description: The species that the qPCR is targeting. Can be Either Common carp, Rusty Crayfish, Spiny water flea or Zebra mussel. Name: pcr_1 Description: The presence or absence based on qPCR of subsamble 1 of the target species at the UID. One indicates amplification above the limit of detection assesed using Klymus et al. 2019 with plate specific qPCR standards. Zero indicates no amplification or amplification below the limit of detection. Name: pcr_2 Description: The presence or absence based on qPCR of subsamle 2 of the target species at the UID. One indicates amplification above the limit of detection assesed using Klymus et al. 2019 with plate specific qPCR standards. Zero indicates no amplification or amplification below the limit of detection. Name: pcr_1 Description: The presence or absence based on qPCR of subsample 3 of the target species at the UID. One indicates amplification above the limit of detection assesed using Klymus et al. 2019 with plate specific qPCR standards. Zero indicates no amplification or amplification below the limit of detection. Name: launch Description: Boolean variable indicating if the sample was taken at a public boat launch. Name: depth_m Description: The depth in m at a specific sampling location within a lake. Name: Code Description: The three digit code unique to each lake used in this study. Name: visit_site Description: The site number (1-10) that is specific to an area within a lake. Site 1 is at the same location for the 5 sampling events for an individual lake. Name: Lake Description: lake name that the sample is taken from. Name: DOW Description: The Minnesota Department of Natural Resources Waterbodies lake identifier (unique ID for each lake). Name: Lat Description: Latitiude of the centroid of the lake (WGS1984). Name: Long Description: Longitude of the centroid of the lake (WGS1984). Name: ZM Description: Known occupancy of the lake for zebra mussels. One means the species is know to be in the lake and zero means the lake is not know to contain the species. Name: SWF Description: Known occupancy of the lake for spiny waterflea. One means the species is know to be in the lake and zero means the lake is not know to contain the species. Name: CC Description: Known occupancy of the lake for common carp. One means the species is know to be in the lake and zero means the lake is not know to contain the species. Name: RC Description: Known occupancy of the lake for rusty crayfish. One means the species is know to be in the lake and zero means the lake is not know to contain the species. Name: area_acres Description: The surface area in acres of a lake. Name: littoral_area_acres Description: The area of the lake in acres that is less than 15 feet deep. Name: max_depth_ft Description: the maximum depth of the lake in feet. Name: perimeter_miles Description: the perimeter of the lake in miles. Name: mean_depth_ft Description: the mean depth of the lake in feet. If the mean depth for a lake is unknown it is NA. Name: year_infested_zm Description: the year the lake was listed as infested with Zebra Mussels (NA if the lake is not known to be infested). Name: year_infested_swf Description: the year the lake was listed as infested with Spiny Waterflea (NA if the lake is not known to be infested). Name: SDI Description: Lake Shoreline Development Index. Name: Date Description: Date the sampling occured (YYYY-MM-DD). Name: Temp_C Description: The temperature of the surface of the lake at the deepest point in the lake at the Date in degrees Celsius. Name: DO_mgL Description: the dissolved oxygen at the surface of the lake at the deepest point in the lake in mg/L. Name: cond Description: the specific conductance at the surface of the lake at the deepest point in the lake in µS/cm. Name: pH Description: the pH at the surface of the lake at the deepest point in the lake. Name: Clarity_m Description: The Secchi depth of the lake in the deepest point in m for a given date. Name: stratified Description: boolean indication of if the lake is within 1 degree C at the surface and the deepest point of the lake. Name: strat_zm Description: the depth in m of the lake where the surface is greater than 1 degree than C warmer . Name: percent_mixed Description: the percent of the water column where the lake is stratified. Name: contaminated Description: binary variable for if the the qPCR plate the sample was ran on is contaminated. One indicates potential contamination. Contaminated samples were not used in the analysis. Name: numdetection Description: binary variable indicting if there was a detection in any of thw sub samples pcr_1, pcr_2 or pcr_3. One means there was at least one detection. Name: julian_day Description: day of year the sample was taken. January 1st is 1, December 31st is 365. Name: lake_site Description: string combination of lake_code and site. Name: log_depth_m Description: the log transformed site depth in m. Name: log_depth_s Description: the standardized and logged site depth. Standardizations are taken to have mean zero and standard deviation of one. Name: jday_s Description: the standardized julian day of sampling. Standardizations are taken to have mean zero and standard deviation of one. Name: clarity_s Description: the standardized lake-visit specific Secchi depth. Standardizations are taken to have mean zero and standard deviation of one. Name: lake.size_s Description: the standardized lake surface area. Standardizations are taken to have mean zero and standard deviation of one. Name: strat.depth_s Description: the standardized depth the surface is 1 degree C warmer than a depth. Standardizations are taken to have mean zero and standard deviation of one. Name: conductivity_s Description: the standardized lake surface conductivity. Standardizations are taken to have mean zero and standard deviation of one. Name: temp_s Description: the standardized lake surface temperature. Standardizations are taken to have mean zero and standard deviation of one. Name: pH_s Description: the standardized pH at the surface of the lake at the deepest point in the lake. Standardizations are taken to have mean zero and standard deviation of one.