KLR_predict | R Documentation |
'KLR_predict()' is a function to predict the probability of site presence to a new list of data based on the fitted alpha parameters returned from the 'KLR()' funtion.
KLR_predict( test_data, train_data, alphas_pred, sigma, progress = TRUE, dist_metric = "euclidean" )
test_data |
- [list] Training data used to create similarity kernel matrix |
train_data |
- [list] Testing data to predict class |
alphas_pred |
- [vector] Numeric vector of alpha parameters from KLR function |
sigma |
- [scaler] Smoothing parameter for RBF kernel |
progress |
- [logical] False = no progress bar; 1 = show progress bar |
dist_metric |
[character] One of the distance methods from rdist::cdist. Default = "euclidean". see ?rdist::cdist |
This function takes a list of the 'test_data', a list of the 'train_data', a vector of the approximated alpha parameters as 'alpha_pred', a scalar value for the 'sigma' kernel hyperparameter, and a distance method (deafult = "Euclidean"). This function predicts the probability of site presence for new observations based on the training data and 'alphas' parameters. This is accomplished by building the 'k*k' kernel matrix as the similarity between the training test data then computing the inverse logit of 'k*k
- [vector] - predicted probabiity of positive class
## Not run: sim_data <- get_sim_data(site_samples = 800, N_site_bags = 75, sites_var1_mean = 80, sites_var1_sd = 10, sites_var2_mean = 5, sites_var2_sd = 2, backg_var1_mean = 100,backg_var1_sd = 20, backg_var2_mean = 6, backg_var2_sd = 3) formatted_data <- format_site_data(sim_data, N_sites=10, train_test_split=0.8, sample_fraction = 0.9, background_site_balance=1) train_data <- formatted_data[["train_data"]] train_presence <- formatted_data[["train_presence"]] test_presence <- formatted_data[["test_presence"]] ##### Logistic Mean Embedding KLR Model #### Build Kernel Matrix K <- build_K(train_data, sigma = sigma, dist_metric = dist_metric) #### Train train_log_pred <- KLR(K, train_presence, lambda, 100, 0.001, verbose = 2) #### Predict test_log_pred <- KLR_predict(test_data, train_data, dist_metric = dist_metric, train_log_pred[["alphas"]], sigma) ## End(Not run)
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