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"gdgtBay" offers an accessible opportuntiy to calibrate and predict brGDGT distributions to/with climate conditions. The function runs on the Bayesia Model-Building Interface, Bambi (Capretto et al., 2022), which sits above the Bayesian statistical modelling package, PyMC (Salvatier et al., 2016). In the combination, the user can select and modify all bayesian parameters such as prior distributions, sampling methods (see bambi and PyMC packages for further informatio). Each step of the multi-bayesian approach, as outlined by Dearing Crampton-Flood et al. (2020), is labelled below. The user has the option to run a calibration model (predictor_data defulat: none) or calibrate and then predict results (provide the predictor data of interest; e.g., MBT'5me values). Calibration model - Outputs the results of the the second bayes as well as a figure depicting the true vs. estimated predictand values. To select, use predictor_data default (None). - Useful for exploring the model and testing parameters prior to predicting values. Prediction model - Outputs the original predictor_data dataframe with two appended columns, the mean and standard deviation of the predicted values. Variable descriptions: • gdgt - Name ofindex or fractional abundance of interest. If predicting, ensure that predictor_data is lablled accordingly. • clim - Name of predictand. Must be in data • data - Calibration dataset - must inculde 'gdgt' and 'clim'. Must be in the pandas dataframe format. • bayes_summary - Summary of first bayesian method results. defaults to show. • figurepath - Pathway to save location of figures • user_priors - If true, user can alter priors in function. If false, bambi will select priors. • bayes_1_figure - Figure of posterior predictive ouput from first bayes application. useful for assessing model applicability. Defaults to show and save. • true_est_figure - Figure showing true predicted values (x axis) vs estimated values (y axis). Default to show. Only works for calibraiton-only applications. • regression_fig - Figure showing bayesian regression model (blue) as well as OLS regression model (fuchsia) and calibratio data (black). • chains - Number of Markov chains to run. _# denotes # instance of Bayes. Default as none to have bambi select. See bambi documentation for more details. • draws - Number of draws from sampling method. _# denotes # instance of Bayes. Default as none to have bambi select. See bambi documentation for more details. • cores - Number of cores for CPU to run. _# denotes # instance of Bayes. Default as none to have bambi select. See bambi documentation for more details. • tune - Number of samples used to tune predictio model (second Bayes instance). Default as none to have bambi select. See bambi documentation for more details. • predictor_data - Optional dataset cotaining predictor (gdgt) data that from which the user wants to estimate some climate variable (clim). Must be a pandas dataframe with the predictor column labelled with the same name as 'gdgt' variables. Feel free to include any other informatio in this dataframe - the prediction model appends the mean and standard deviation of predicted values onto the end of the predictor_data dataframe. Function depedencies: • Bambi • PyMC • sklearn • numpy • pandas • matplotlib """
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Implementation of bayesian linear regression for calibrating brGDGT indices to climate conditions
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