This readme.txt file was generated on 20220524 by Jake Ferguson Recommended citation for the data: ------------------- GENERAL INFORMATION ------------------- 1. R Code and Data Supporting: A comparison of survey method efficiency for estimating densities of Zebra Mussels (Dreissena polymorpha) 2. Author Information Principal Investigator Contact Information Name: John Fieberg Institution: Department of Fisheries, Wildlife, and Conservation Biology Address: University of Minnesota-Twin Cities Email: jfieberg [at] umn.edu Co-investigator Contact Information Name: Michael A. McCartney Institution: Minnesota Aquatic Invasive Species Research Center Address: University of Minnesota-Twin Cities Email: mmccartn [at] umn.edu Co-investigator Contact Information Name: Jake M. Ferguson Institution: School of Life Sciences Address: University of Hawaii Email: jakeferg [at] umn.edu 3. Date published or finalized for release: 4. Date of data collection: Summer 2018 5. Geographic location of data collection (where was data collected?): Lake Burgan, Lake Florida, Little Birch Lake in central Minnesota 6. Information about funding sources that supported the collection of the data: This study was funded by the Minnesota Aquatic Invasive Species Research Center with funding from the Minnesota Environmental and Natural Resources Trust Fund as recommended by the Legislative-Citizen Commission on Minnesota Resources. JF received partial support from the Minnesota Agricultural Experimental Station and the McKnight Foundation. 7. Overview of the data (abstract): Contains data for three different survey methods (quadrat, removal, and distance-removal) in three central Minnesota Lakes. R code contains methods for formatting and estimating density in all three methods. -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: Attribution-NonCommercial-ShareAlike 3.0 United States 2. Links to publications that cite or use the data: Ferguson et al. (in review) 3. Was data derived from another source? If yes, list source(s): 4. 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: Encounters - Distance.csv Short description: This file contains all field measurements for the distance survey observations. B. Filename: Encounters - Quadrats.csv Short description: This file contains all field measurements for the quadrat survey observations. C. Filename: Encounters - Removal.csv Short description: This file contains all field measurements for the removal survey observations. D. Filename: Transect datasheets.csv Short description: This file contains transect-level habitat measurement for all surveyed transects. E. Filename: DensEstCode.R Short description: This R file runs the analyses from the paper and produces several of the main manuscript figures. F. Filename: HelperFuncs.R Short description: This R file contains all the functions needed to run the density estimates. 2. Relationship between files: You need to run DensEstCode.R file, this calls functions in HelperFuncs.R which in turn calls the survey and transect data csv files. -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: 2. Methods for processing the data: The included data are the raw data. Functions in HelperFuncs.R are used to process the data for analysis. 3. Instrument- or software-specific information needed to interpret the data: R and Excel are needed to run and view the files. 4. Standards and calibration information, if appropriate: 5. Environmental/experimental conditions: 6. Describe any quality-assurance procedures performed on the data: 7. People involved with sample collection, processing, analysis and/or submission: Jake M. Ferguson, Laura Jimenez, Aislyn A. Keyes, Austen Hilding, Michael A. McCartney, Katie St. Clair, Douglas H. Johnson, John Fieberg ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Encounters - Distance.csv ----------------------------------------- 1. Number of variables: 13 2. Number of cases/rows: 371 3. Missing data codes: blanks 4. Variable List A. Name: Timestamp Description: Time that observation was entered into database B. Name: Date Description: Survey date C. Name: Lake name Description: Name of surveyed lake D. Name: Observer name Description: Name of diver that made the observation E. Name: Transect # Description: The number of the transect the detection was made on F. Name: Distance along transect (m) Description: The distance of a detection from the start of the transect G. Name: Perpendicular distance from transect (cm) Description: The distance of a detection from the transect line H. Name: Left or right of transect line? Description: The side of the transect that a detection was made I. Name: Number of mussels in cluster Description: The number of mussels in a detection event J. Name: Length of cluster (cm) Description: Approximate long dimension of cluster K. Name: Width of cluster (cm) Description: Approximate dimension of cluster perpendicular to long axis L. Name: Attached to: Description: Substrate cluster is attached to M. Name: Comments Description: Any comments the divers made during observation ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Encounters - Quadrats.csv ----------------------------------------- 1. Number of variables: 10 2. Number of cases/rows: 1049 3. Missing data codes: blanks 4. Variable List A. Name: Timestamp Description: Time that observation was entered into database B. Name: Date Description: Survey date C. Name: Lake name Description: Name of surveyed lake D. Name: Observer name Description: Name of diver that made the observation E. Name: Transect # Description: The number of the transect the detection was made on F. Name: Distance along transect (m) Description: The distance of a detection from the start of the transect G. Name: Number of mussels in quadrat Description: The number of mussels that were counted in the quadrat H. Name: Attached to: Description: Substrate mussels were attached to I. Name: Comments Description: Any comments the divers made during observation J. Name: Number of clusters in quadrat Description: The number of distinct mussel clusters in a quadrat ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Encounters - Removal.csv ----------------------------------------- 1. Number of variables: 11 2. Number of cases/rows: 382 3. Missing data codes: blanks 4. Variable List A. Name: Timestamp Description: Time that observation was entered into database B. Name: Date Description: Survey date C. Name: Lake name Description: Name of surveyed lake D. Name: Observer name Description: Name of diver that made the observation E. Name: Transect # Description: The number of the transect the detection was made on F. Name: Distance along transect (m) Description: The distance of a detection from the start of the transect G. Name: Number of mussels in cluster Description: The number of mussels in a detection event H. Name: Length of cluster (cm) Description: Approximate long dimension of cluster I. Name: Width of cluster (cm) Description: Approximate dimension of cluster perpendicular to long axis J. Name: Attached to: Description: Substrate cluster is attached to K. Name: Comments Description: Any comments the divers made during observation ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Transect datasheets.csv ----------------------------------------- 1. Number of variables: 15 2. Number of cases/rows: 120 3. Missing data codes: blanks 4. Variable List A. Name: Survey type Description: Type of survey: values are Double observer no distance (referred to as Removal survey in the manuscript), Double observer distance (referred to as a Distance survey in the manuscript), or Quadrat survey B. Name: Lake name Description: Name of surveyed lake for this transect C. Name: Date Description: Date that the transect was surveyed D. Name: Observers Description: Names of the divers that performed transect survey E. Name: Primary observer (double observer survey) Description: Name of primary observer for double observer surveys F. Name: Secondary observer (double observer survey) Description: Name of secondary observer for double observer surveys G. Name: Transect length (if transect survey) Description: The length of the transect H. Name: Transect number Description: Transects are assigned a number for each unique combination of lake and survey design I. Name: GPS latitude Description: Latitude measurement at the start of the transect J. Name: GPS longitude Description: Longitude measurement at the start of the transect K. Name: Compass bearing Description: Bearing of the transect line from the start point perpendicular to the shoreline L. Name: Setup time Description: Amount of time it took to setup the transect M. Name: Habitat time Description: Amount of time it took to perform habitat survey N. Name: Encounter time Description: Amount of time it took to perform survey and record encounters O. Name: Clarity (m) Description: Approximate distance that diver could see -------------------------------- R SESSION INFORMATION -------------------------------- > sessionInfo() R version 4.1.2 (2021-11-01) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 22.04.2 LTS Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] cowplot_1.1.1 wesanderson_0.3.6 readxl_1.3.1 forcats_0.5.1 [5] stringr_1.4.0 dplyr_1.0.8 purrr_0.3.4 readr_2.1.2 [9] tidyr_1.2.0 tibble_3.1.6 ggplot2_3.4.2 tidyverse_1.3.1 [13] lubridate_1.8.0 mrds_2.2.8 loaded via a namespace (and not attached): [1] tidyselect_1.1.2 splines_4.1.2 haven_2.4.3 [4] lattice_0.20-45 colorspace_2.0-2 vctrs_0.6.2 [7] generics_0.1.2 mgcv_1.8-39 utf8_1.2.2 [10] rlang_1.1.1 pillar_1.7.0 withr_2.5.0 [13] glue_1.6.1 DBI_1.1.2 dbplyr_2.1.1 [16] optimx_2022-4.30 modelr_0.1.8 lifecycle_1.0.3 [19] munsell_0.5.0 gtable_0.3.0 cellranger_1.1.0 [22] rvest_1.0.2 tzdb_0.2.0 parallel_4.1.2 [25] fansi_1.0.2 broom_0.7.12 Rcpp_1.0.8 [28] backports_1.4.1 scales_1.2.1 jsonlite_1.7.3 [31] truncnorm_1.0-9 fs_1.5.2 hms_1.1.1 [34] stringi_1.7.6 numDeriv_2016.8-1.1 grid_4.1.2 [37] cli_3.6.1 tools_4.1.2 magrittr_2.0.2 [40] Rsolnp_1.16 crayon_1.5.0 pkgconfig_2.0.3 [43] ellipsis_0.3.2 Matrix_1.4-0 xml2_1.3.3 [46] reprex_2.0.1 assertthat_0.2.1 httr_1.4.2 [49] rstudioapi_0.13 R6_2.5.1 nlme_3.1-155 [52] compiler_4.1.2