This repository contains a folder - manuscript_code - which reproduces the results and figures from Khanna et al., In Review at Ecological Applications . This study has two objectives, 1) Does increased lateral connectivity resulting from floodplain inundation increase chlorophyll-a biomass? 2) Does that bump in chlorophyll-a get transported downstream? The San Francisco Estuary in California, USA, has a robust and long-term monitoring network for water quality. We integrated water temperature, chlorophyll-a, flow and floodplain inundation data from multiple sources creating a continuous dataset with fine temporal resolution spanning two decades (https://portal.edirepository.org/nis/mapbrowse?packageid=edi.1537.4). We used a consistent generalized additive mixed model (GAMM) structure across three regions: the floodplain, the mainstem of the river adjacent to the floodplain, and the section of the river downstream from both the floodplain and mainstem. We found that when the floodplain is not inundated, chlorophyll-a biomass is mainly influenced by water temperature. However, when the floodplain is laterally connected during periods of inundation, water spreads over a larger surface area in the floodplain, water velocity decreases and water temperatures increase creating favorable conditions for chlorophyll-a production. High flows during the flood pulse quickly transport chlorophyll-a downstream, flushing the estuary with food.
The diagram below shows the structure and flow of the code within this folder and how figures from the manuscript are produced:
