Patterns in bird and pollinator occupancy and richness in a mosaic of urban office parks across scales and seasons

Urbanization is a leading cause of global biodiversity loss, yet cities can provide resources required by many species throughout the year. In recognition of this, cities around the world are adopting strategies to increase biodiversity. These efforts would benefit from a robust understanding of how natural and enhanced features in urbanized areas influence various taxa. We explored seasonal and spatial patterns in occupancy and taxonomic richness of birds and pollinators among office parks in Santa Clara County, California, USA, where natural features and commercial landscaping have generated variation in conditions across scales. We surveyed birds and insect pollinators, estimated multi-species occupancy and species richness, and found that spatial scale, season, and urban sensitivity were all important for understanding how communities occupied sites. Features at the landscape- and local-scale (i.e., distance to streams or baylands and tree canopy, shrub, or impervious cover, respect..., Study area, sites, and species
Surveys of avian and pollinator communities were conducted at 45 1-hectare sites located in 3 cities—Palo Alto, The City of Mountain View, and Sunnyvale—in the Santa Clara Valley of the south San Francisco Bay Area, California (Figure 1). This area is known colloquially as ‘Silicon Valley,’ famous for high-tech companies and start-ups. Santa Clara Valley experienced rapid urbanization in the late 20th century, with commercial and office park developments concentrated near San Francisco Bay in areas developed later than adjacent uplands due to higher groundwater levels (Grossinger et al. 2007, Beller et al. 2020). The resulting study area is a gradient mosaic of land use bounded in the north by tidal marsh mudflats and salt ponds of the Bay; moving southward through a band of semi-natural vegetation of varying quality and comprising private and protected open space, a golf course, airfield, and decommissioned landfills; and ending in the south among office ..., , # Patterns in bird and pollinator occupancy and richness in a mosaic of urban office parks across scales and seasons

## Description of the data and file structure

Scripts repository:

* 00_shared_functions: code sourced in higher-level scripts
* 01_bird_spoccupancy: code to run avian dynamic multispecies models and model predictions using R package spOccupancy.
* 02_pollinators: code to run Poisson regressions for pollinator data.
* 01_manuscript_values.R: code that extracts general values for the manuscript, including tables and plots
* 02_spatial_autocorrelation.R: spatial autocorrelation analysis for both birds and pollinators
* 03_species_probability_bar_chart_occupancy.R: code for producing appendix figure
* 04_species_probability_bar_chart_detection: code for producing appendix figure
* 05_occupancy_summary_panel.R: code for producing main text Figure 2
* 06_best_worst_site_values.R: code for producing main text Figure 3
* 07_richness_change.R: code for sum...