Publications by Beni Stocker
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Overview The package ingestr provides functions to extract (ingest) point data (given longitude, latitude, and required dates) from large global files or remote data servers and create time series at user-specified temporal resolution. This can be done for a set of sites at once, given a data frame containing the meta info for each site (see data...
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Essential functions Conductivity as a function of water potential The conductivity of an infinitesimally short xylem element can be described as a function of the water potential (\(\Psi\)), declining to half at a level \(\Psi_{50}\). \[ k(\Psi) = 0.5 ^ {\left( \Psi / \Psi_{50} \right) ^ b} \] Plotted with different shape parameter values \(b\)....
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Description You will investigate the apparent depression of photosynthesis rates in temperate and boreal forests in spring and after cold winters - a phenomenon that has been overlooked in global models. By combining remote sensing data, eddy covariance flux measurements, and modelling, you will find new solutions to an important challenge. Ecosy...
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Theory The P-model predicts an optimal ratio of \(c_i : c_a\), termed as \(\chi\), that balances the costs associated with maintaining the transpiration (\(E\)) stream and the carboxylation capacity \(V_{\text{cmax}}\). It can therefore be used to simulate the acclimation of the photosynthetic machinery to its environment - a mechanism that happe...
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Example Simulation settings Manually select some sites from which we’re going to use the data for evaluation and calibration. mysites <- c("BE-Vie", "DE-Tha", "DK-Sor", "FI-Hyy", "IT-Col", "NL-Loo", "US-MMS", "US-WCr", "US-UMB", "US-Syv", "DE-Hai", "IT-MBo", "US-GLE", "FR-Fon", "NL-Hor", "US-UMd", "AU-Dry", "DE-Obe", "IT-Tor", "US-Wi4") Create...
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LUE calculations
Evaluate light use efficiency. Daily data Gather data and create one nice data frame with daily data. if (!exists("out_eval_ORG")) load("./calib_results/out_eval_ORG.Rdata") if (!exists("out_eval_FULL")) load("./calib_results/out_eval_FULL.Rdata") load("~/eval_pmodel/data/obs_eval_NT_WITHFORCING.Rdata") mc <- 12.0107 # molecular mass of carbon...
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Motivation The P-model predicts the “acclimated” response of photosynthetic parameters (Vcmax, Jmax, “average” ci:ca) to the environment and reflects the acclimation process by balanced investments to maintaining the photosynthetic apparatus and transpiration stream (essentially a trade-off between the capacities of light-harvesting and d...
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Motivation The P-model predicts the “acclimated” response of photosynthetic parameters (Vcmax, Jmax, “average” ci:ca) to the environment and reflects the acclimation process by balanced investments to maintaining the photosynthetic apparatus and transpiration stream (essentially a trade-off between the capacities of light-harvesting and d...
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The rbeni package contains a set of functions that let you do standard tasks working with NetCDF files on one line and let you quickly convert the contents of a NetCDF file into a tidy data frame (tibble). Here is a demonstration example. Read Load the package and read the contents of one NetCDF file. library(rbeni) library(tidyverse) # depends...
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Site selection and meta data mysites <- "efg" Required meta information is specified for each site (in rows) and a number of variables: lat for latitude (decimal degrees) lon for longitude (decimal degrees) - this is only used for data ingestion but not for the P-model simulation with rsofun. elv for elevation (m a.s.l.) year_start and year_end ...
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