This readme.txt file was generated on 11June2024 by Mike Verhoeven Recommended citation for the data: Timothy S. Mitchell, Michael R. Verhoeven, Ashley L. Darst, Cate Patterson, Emilie C. Snell-Rood. (2024). Complete data and statistical code for: Seeding roadsides is necessary but not sufficient for restoring native floral communities. ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset Complete data and statistical code for: Seeding roadsides is necessary but not sufficient for restoring native floral communities 2. Author Information Principal Investigator Contact Information Name: Timothy S. Mitchell Institution: University of Minnesota - Dept. of Ecology, Evolution, and Behavior Address: 140 Gortner Lab, 1479 Gortner Ave, Saint Paul, MN 55108 Email: mitc0713@umn.edu ORCID: 0000-0002-7136-769X Associate or Co-investigator Contact Information Name: Michael R. Verhoeven Institution: University of Minnesota - Dept. of Fisheries, Wildlife, and Conservation Biology Address: 135A Skok Hall, 2003 Upper Buford Circle Email: verh0064@umn.edu ORCID: 0000-0002-6340-9490 Associate or Co-investigator Contact Information Name: Ashley L. Darst Institution: University of Minnesota - Dept. of Ecology, Evolution, and Behavior Address: 140 Gortner Lab, 1479 Gortner Ave, Saint Paul, MN 55108 Email: darstash000@gmail.com ORCID: 0000-0002-5625-7724 Associate or Co-investigator Contact Information Name: Cate Patterson Institution: University of Minnesota - Dept. of Ecology, Evolution, and Behavior Address: 140 Gortner Lab, 1479 Gortner Ave, Saint Paul, MN 55108 Email:pattersonc@carleton.edu ORCID: Associate or Co-investigator Contact Information Name: Emilie C. Snell-Rood Institution: University of Minnesota - Dept. of Ecology, Evolution, and Behavior Address: 140 Gortner Lab, 1479 Gortner Ave, Saint Paul, MN 55108 Email: emilies@umn.edu ORCID: 0000-0002-2972-5895 3. Date published or finalized for release: 11June2024 4. Date of data collection (single date, range, approximate date): 28May2021 through 23Aug2021 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 for data collection was provided by the Minnesota Department of Transportation 7. Overview of the data (abstract): These data were collected in support of a Minnesota Department of Transportation funded study evaluating roadside plantings. The goal of our study was understand how roadside pollinator forage is affected by planting pollinator-friendly seed mixes in roadsides in Minnesota, USA. We used a field study of mixed-age roadside plantings to assess this flower diversity in roadsides planted with status quo non-native seed mixes to those planted with pollinator friendly, native seed mixes. We found that while these native seed mixes did increase the abundance of native flowers, the roadsides' flower communities of native and non-native seedmixes converged through time to grass dominated and unplanted colonizing species. This repository contains the complete datasets as a comma-separated-value files and Program R code necessary to replicate the data prep, exploration, analysis, and visualizations presented in the manuscript. -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: CC0 1.0 Universal 2. Links to publications that cite or use the data: 1. Mitchell, Timothy; Verhoeven, Michael; Darst, Ashley; Patterson, Cate; Snell-Rood, Emilie. (2024). Seeding roadsides is necessary but not sufficient for restoring native floral communities. [Accepted at: Ecological Solutions and Evidence] 2. Ashley L. Darst, Timothy S. Mitchell, Michael R. Verhoeven, Elaine Evans, Luke Tonsfeldt, Savannah Kjaer, Emilie C. Snell-Rood. (2024). Diversity of bumble bees and butterflies in Minnesota roadsides depends on floral diversity and abundance but not floral native status. Insect Conservation and Diversity. https://doi.org/10.1111/icad.12739 3. Mitchell, Timothy; Verhoeven, Michael; Darst, Ashley; Evans, Elaine;Cariveau, Dan; Snell-Rood, Emilie. 2022. Cost-effective Roadside Revegetation Methods to Support Insect Pollinators. Local Road Research Board, Minnesota Department of Transportation, Office of Research & Innovation, 2022-08-01. https://rosap.ntl.bts.gov/view/dot/65582 4. Ashley L. Darst, Michael R. Verhoeven, Timothy S. Mitchell, Elaine Evans, Luke Tonsfeldt, Savannah Kjaer, Emilie C. Snell-Rood. (2024). Complete data and statistical code for: Diversity of bumble bees and butterflies in Minnesota roadsides depends on floral diversity and abundance but not floral native status. https://doi.org/10.13020/021p-qh16 3. Was data derived from another source? No. 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: plants_data_analysis.R Short description: R code to conduct analyses and generate figures from associated manuscript. Approximate runtime 10 minutes with prebuilt model results, OR 8 hours with mvabund model refits. B. Filename: plants_taxo_key_status.csv Short description: Plant codes key, inlcudes species latin binomials and common names and native/introduced statuses C. Filename: seedmix_matrix.csv Short description: Describes the species that are included in each coded seedmix D. Filename: site_attributes.csv Short description: Attributes of sites used in this study, specifically includes the soil compaction and composition data E. Filename: veg_occurrences.csv Short description: Data for observations of flowers in the study sites. Presented as frequency of presence in quadrats sampled in each site. F. Filename: anovaresults_A2.RData Short description: model results from a preliminary model. Included for speed of re-running code G. Filename: modelcomparison_A2.RData Short description: model results from a preliminary model. Included for speed of re-running code H. Filename: summaryresults_A2.RData Short description: model results from a preliminary model. Included for speed of re-running code I. Filename: anovaresults_B.RData Short description: model results from a final model. Included for speed of re-running code J. Filename: modelcomparison_B.RData Short description: model results from a final model. Included for speed of re-running code K. Filename: summaryresults_B.RData Short description: model results from a final model. Included for speed of re-running code 2. Relationship between files: "plants_data_anlaysis.R" will import data and run analyses and generate graphics used in the analysis. The RData files included will be read in and contain the results of mvabund models (they can also be rebuilt by un commenting the necessary lines in the R script, but this will take considerable time). -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: See companion manuscript for detailed methods. 2. Methods for processing the data: The data presented in the file veg_occurences.csv represent plant observation data after minimal processing (corrected some misspellings, cleaned up data types, etc. -- code for this porcessing is available upon request from authors at the project github: https://github.com/mrverhoeven/TeamDitch) 3. Instrument- or software-specific information needed to interpret the data: None 4. Standards and calibration information, if appropriate: The companion manuscript should be referenced for detail, but the plant observations ae presence/absence at the 1 meter^2 resolution. 5. Environmental/experimental conditions: See companion manuscript and MNDOT report. 6. Describe any quality-assurance procedures performed on the data: See companion manuscript. No significant taxonomic/identification QA was performed, and the plant species identifications are presented with this caveat. 7. People involved with sample collection, processing, analysis and/or submission: Work was performed by all authors of the repository. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: plants_taxo_key_status.csv ----------------------------------------- 1. Number of variables: 6 2. Number of cases/rows: 131 3. Missing data codes: "" [blank] in the "Minnesota Native?" field indicates nativity unknown for that observation 4. Variable List A. Name: Code Description: short code that was used for species on fieldsheets B. Name: Species Name Description: latin binomial name for taxa, if not species, spp. suffix is included C. Name: Common Name Description: common or colloquial name for the species, note these are often ambigious D. Name: Minnesota Native? Description: status of the taxa in MN, if known E. Name: grass/flower Description: is the species observed a grass or a flower. Note that the reason this category exists is because our study ONLY identified in the quadrat 1:flowers in bloom, and 2: a few key grasses when seedheads were present (the grass ID was as-requested from MNDOT advisory team) F. Name: Taxon Description: taxon code with underscores, written to match to the "taxon" variable in the veg_occurrences.csv file ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: seedmix_matrix.csv ----------------------------------------- 1. Number of variables: 15 2. Number of cases/rows: 79 3. Missing data codes: NA indicates a seedmix (cols D.-O.) does not contain a species Code/symbol Definition 4. Variable List A. Name: CommonNme Description: common or colloquial name for the species, note these are often ambigious B. Name: ScientificName Description: latin binomial name for taxa, if not species, spp. suffix is included C. Name: Grass/Forb Description: is the species a grass or a forb D.-O. Name: [Seedmix ID Number] (e.g., 33-261) Description: Column anme is an identification number assigned to a commercially available seedmix. Matches the "Seed_mix" field in the site_attributes.csv dataset. Each row in these fields indicates if a species is included (1) or not included (NA) in that mix. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: site_attributes.csv ----------------------------------------- 1. Number of variables: 21 2. Number of cases/rows: 63 3. Missing data codes: NA Data missing or unavailable "" [blank] indicates no data for that record (e.g., seedmix unknown for typ sites) Code/symbol Definition 4. Variable List A. Name: Project Description: an integer assigned to each "project" within the study. A project number is unique a each construction project that the study evaluated for seedmix use outcomes. B. Name: V3 Description: extraneous column. contains no data. C. Name: Year Description: year that site was planted B. Name: County Description: Name of county in Minnesota where site is located B. Name: SP_CP Description: Source of information on planting/seedmixes. Usually a numbers & dashes code associated with a construction blueprint from the road construction project B. Name: Site Description: Site name (concatenates project number and planting/seedmix type) B. Name: pene1 Description: soil penetration value 1 B. Name: pene2 Description: soil penetration value 2 B. Name: pene3 Description: soil penetration value 3 B. Name: %soilmoisture Description: proportional content moisture in soil of site B. Name: Total Clay Description: soil clay content B. Name: Total Silt Description: soil silt content B. Name: Total Sand Description: soil sand content B. Name: Lat Description: Latitude of site centroid. decimal degrees B. Name: Lon Description: Longitude of site centroid. decimal degrees B. Name: Seed_mix Description: identification number for seedmix used. B. Name: Fertilizer Description: fertilizer used on the site, if known/discernable to research team B. Name: Other Description: other methods of planting/maintenance that were used at the site B. Name: Notes Description: other notes about the site B. Name: area_m2 Description: area of site in units of square meters B. Name: soil_pene_mean Description: mean of threee soil penetration measurements ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: veg_occurrences.csv ----------------------------------------- 1. Number of variables: 10 2. Number of cases/rows: 12,748 3. Missing data codes: "" [blank] - in the notes field indicates no notes for that observation 4. Variable List A. Name: dataentry Description: person who entered data from field sheets to digital tabular format; (anonymized to A,B,C for privacy) B. Name: date Description: date of plant observation. formatted as YYYY-MM-DD C. Name: project Description: an integer assigned to each "project" within the study. A project number is unique a each construction project that the study evaluated for seedmix use outcomes. D. Name: site Description: name of site where plant observation was made (concatenates "project" and "trt" fields) E. Name: trt Description: type of site, see companion manuscript for more detail typ = typical ditch, seedmix used is unknown nat = native sowed ditch, seedmix used was a native plants mix non = non-native sowed ditch, seedmix used was a non-native plants mix F. Name: surveyor Description: names of surveyors; (anonymized to A,B,C,D,E,F for privacy) G. Name: quadrat Description: number assigned to the quadrat within each site and date combination H. Name: notes Description: notes about the conditions in the quadrat made by the surveyor I. Name: taxon Description: name of taxa at resolution reported by surveyor, with latin binomials separated by undercores (if not to species level, then _spp suffix) J. Name: pres Description: indicator variable for taxon present in quadrat (used in wide reshape for pres/abs matrix) ------------------------------------------------- R Session Information ------------------------------------------------- R version 4.3.2 (2023-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 11 x64 (build 22631) Matrix products: default locale: [1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 [3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C [5] LC_TIME=English_United States.utf8 time zone: America/Chicago tzcode source: internal attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] cowplot_1.1.3 ggnewscale_0.4.10 ggpubr_0.6.0 lmerTest_3.1-3 nlme_3.1-163 sjPlot_2.8.15 [7] vegan_2.6-4 lattice_0.21-9 permute_0.9-7 rstanarm_2.32.1 Rcpp_1.0.12 effects_4.2-2 [13] carData_3.0-5 ggeffects_1.4.0 epiDisplay_3.5.0.2 nnet_7.3-19 MASS_7.3-60 survival_3.5-7 [19] foreign_0.8-85 broom_1.0.5 lme4_1.1-35.1 glmm_1.4.4 doParallel_1.0.17 iterators_1.0.14 [25] foreach_1.5.2 Matrix_1.6-5 mvtnorm_1.2-4 trust_0.1-8 mvabund_4.2.1 stringr_1.5.1 [31] ggplot2_3.5.0 data.table_1.14.0 loaded via a namespace (and not attached): [1] shinythemes_1.2.0 splines_4.3.2 later_1.3.2 tibble_3.2.1 datawizard_0.9.1 [6] xts_0.13.2 lifecycle_1.0.4 rstatix_0.7.2 StanHeaders_2.32.5 insight_0.19.8 [11] crosstalk_1.2.1 backports_1.4.1 survey_4.4-2 magrittr_2.0.3 httpuv_1.6.14 [16] pkgbuild_1.4.3 DBI_1.2.1 minqa_1.2.6 RColorBrewer_1.1-3 multcomp_1.4-25 [21] abind_1.4-5 purrr_1.0.2 itertools_0.1-3 TH.data_1.1-2 tensorA_0.36.2.1 [26] sandwich_3.1-0 inline_0.3.19 tweedie_2.3.5 performance_0.10.9 codetools_0.2-19 [31] DT_0.32 tidyselect_1.2.0 bayesplot_1.11.1 farver_2.1.1 effectsize_0.8.6 [36] matrixStats_1.2.0 stats4_4.3.2 base64enc_0.1-3 jsonlite_1.8.8 ellipsis_0.3.2 [41] emmeans_1.10.0 tools_4.3.2 glue_1.7.0 gridExtra_2.3 xfun_0.41 [46] mgcv_1.9-0 distributional_0.4.0 dplyr_1.1.4 loo_2.6.0 withr_3.0.0 [51] numDeriv_2016.8-1.1 fastmap_1.1.1 mitools_2.4 boot_1.3-28.1 fansi_1.0.6 [56] shinyjs_2.1.0 digest_0.6.34 R6_2.5.1 mime_0.12 estimability_1.5 [61] colorspace_2.1-0 gtools_3.9.5 markdown_1.12 threejs_0.3.3 utf8_1.2.4 [66] tidyr_1.3.1 generics_0.1.3 htmlwidgets_1.6.4 parameters_0.21.5 pkgconfig_2.0.3 [71] dygraphs_1.1.1.6 gtable_0.3.4 htmltools_0.5.7 scales_1.3.0 posterior_1.5.0 [76] snakecase_0.11.1 knitr_1.45 rstudioapi_0.15.0 reshape2_1.4.4 coda_0.19-4.1 [81] checkmate_2.3.1 curl_5.2.0 nloptr_2.0.3 zoo_1.8-12 sjlabelled_1.2.0 [86] miniUI_0.1.1.1 pillar_1.9.0 grid_4.3.2 vctrs_0.6.5 shinystan_2.6.0 [91] promises_1.2.1 car_3.1-2 xtable_1.8-4 cluster_2.1.4 cli_3.6.2 [96] compiler_4.3.2 rlang_1.1.3 crayon_1.5.2 rstantools_2.4.0 ggsignif_0.6.4 [101] modelr_0.1.11 labeling_0.4.3 plyr_1.8.9 sjmisc_2.8.9 forcats_1.0.0 [106] stringi_1.8.3 rstan_2.32.5 QuickJSR_1.1.3 munsell_0.5.0 colourpicker_1.3.0 [111] bayestestR_0.13.2 V8_4.4.2 sjstats_0.18.2 hms_1.1.3 statmod_1.5.0 [116] shiny_1.8.0 haven_2.5.4 igraph_2.0.2 RcppParallel_5.1.7