JOURNAL PUBLICATION CITATION: Frank A. Fogarty, Jian D.L. Yen, Erica Fleishman, Rahel Sollmann, and Alison Ke. Multiple-region, N-mixture community models to assess associations of riparian area, fragmentation, and species richness. Ecological Applications. Multiyear_model_code.R Model code used to fit multiple-year model. Data S1 Riparian land-cover and bird data used to fit multiple year model. Data S2 Model outputs from riparian obligate single and multiple year models, and all species single year model. Author(s) [of the material provided in DataS1.zip] Frank A. Fogarty Humboldt State University Arcata, California, USA fogartyfa@gmail.com Jian D.L. Yen Arthur Rylah Institute for Environmental Research Victoria, Australia Erica Fleishman Oregon State University Corvallis, Oregon, USA Rahel Sollmann University of California, Davis Davis, California, USA Alison Ke University of California, Davis Davis, California, USA File list Multiyear_model_code.R DataS1.zip bird_data.RDS cov_data.RDS DataS2.zip All-species model results.csv Multiple-year, riparian-obligate model results.csv Single-year, riparian obligate model results.csv Description Multiyear_model_code.R – This is the code used to fit the multiyear MNCM used in this manuscript. See comments in code file and manuscript for further details. bird_data.RDS R data file of multidimensional array containing multiyear bird data. Dimensions are as follows: 1) Four letter species code (Pyle and DeSante 2020), 2) Canyon name, 3) Point number, 4) Visit identifier. "V1" is visit 1, "V2" is visit 2, and "V3" is visit 3, 5) Year cov_data.RDS R data file of covariate data. Cov1 is total woody riparian area, Cov2 is total meadow riparian area, Cov3 is woody riparian area nLSI, Cov4 is total woody riparian area squared, Cov5 is total meadow riparian area squared, Cov6 is woody riparian area nLSI squared All-species model results.csv - S is species richness on the natural scale, indexed by canyon. mu.p and sig.p are hyperparameters for detection probability on the logit scale. mu.lam.comm and sig.lam.comm are hyperparameters for abundance on the log scale. sig.random is the hyperparameter for the random effect for canyon in the abundance process on the log scale. p is detection probability on the natural scale, indexed by species. mu.omega is the intercept of the community process on the logit scale. beta.omega1 is the coefficient for woody riparian area in the community process on the logit scale. beta.omega2 is the coefficient for wet meadow area in the community process on the logit scale. beta.omega3 is the coefficient for woody riparian normalized landscape shape index (nLSI) in the community process on the logit scale. beta.omega4 is the coefficient for (woody riparian area)2 in the community process on the logit scale. beta.omega5 is the coefficient for (wet meadow area)2 in the community process on the logit scale. beta.omega6 is the coefficient for (woody riparian nLSI)2 in the community process on the logit scale. mu.lam is the intercept of the abundance process indexed by species on the log scale. Phi is the mean availability at the canyon level, indexed by species. Species order is alphabetical by four-letter code (Pyle and DeSante 2020) and canyon order is alphabetical. Multiple-year, riparian-obligate model results.csv - S is species richness on the natural scale, indexed by canyon. mu.p and sig.p are hyperparameters for detection probability on the logit scale. mu.lam.comm and sig.lam.comm are hyperparameters for abundance on the log scale. sig.random is the hyperparameter for the random effect of canyon in the abundance process on the log scale. sig.random.year is the is the hyperparameter for the random effect for canyon in the abundance process on the log scale. p is detection probability on the natural scale, indexed by species. mu.omega is the intercept of the community process on the logit scale. beta.omega1 is the coefficient for woody riparian area in the community process on the logit scale. beta.omega2 is the coefficient for wet meadow area in the community process on the logit scale. beta.omega3 is the coefficient for woody riparian normalized landscape shape index (nLSI) in the community process on the logit scale. beta.omega4 is the coefficient for (woody riparian area)2 in the community process on the logit scale. beta.omega5 is the coefficient for (wet meadow area)2 in the community process on the logit scale. beta.omega6 is the coefficient for (woody riparian nLSI)2 in the community process on the logit scale. mu.lam is the intercept of the abundance process indexed by species on the log scale. Phi is the mean availability at the canyon level, indexed by species. Species order is alphabetical by four-letter code (Pyle and DeSante 2020) and canyon order is alphabetical. Single-year, riparian obligate model results.csv – S is species richness on the natural scale, indexed by canyon. mu.p and sig.p are hyperparameters for detection probability on the logit scale. mu.lam.comm and sig.lam.comm are hyperparameters for abundance on the log scale. sig.random is the hyperparameter for the random effect of canyon in the abundance process on the log scale. p is detection probability on the natural scale, indexed by species. mu.omega is the intercept of the community process on the logit scale. beta.omega1 is the coefficient for woody riparian area in the community process on the logit scale. beta.omega2 is the coefficient for wet meadow area in the community process on the logit scale. beta.omega3 is the coefficient for woody riparian normalized landscape shape index (nLSI) in the community process on the logit scale. beta.omega4 is the coefficient for (woody riparian area)2 in the community process on the logit scale. beta.omega5 is the coefficient for (wet meadow area)2 in the community process on the logit scale. beta.omega6 is the coefficient for (woody riparian nLSI)2 in the community process on the logit scale. mu.lam is the intercept of the abundance process indexed by species on the log scale. Phi is the mean availability at the canyon level, indexed by species. Species order is alphabetical by four-letter code (Pyle and DeSante 2020) and canyon order is alphabetical. Pyle, P. and D. F. SeSante. (2020). Four-letter (english name) and six-letter (scientific name) alpha codes for 2158 bird species (and 108 non-species taxa) in accordance with the 61st AOU Supplement (2020), sorted taxonomically. Institute for Bird Populations. www.birdpop.org