handwriter (development version)

handwriter 3.2.0

The new function plot_cluster_centers() creates a plot of the clusters centers from a cluster template. The cluster centers are displayed as orange shapes. The function also plots all graphs in each cluster as grey shapes with 5% transparency to depict the variability of graph shapes within each cluster.
The new function plotGraphs() plots every graph in a document processed with processDocument().

Fixed bug in processDocument() when the writing in the document is a single connected component, such as a single word written in cursive. Previously, the output of processDocument() for this kind of document was formatted incorrectly.
Fixed bug in get_credible_intervals() and plot_credible_intervals() where the model writers were numbered sequentially. Now these functions use the writer IDs.
Fixed bug in format_template_data() where the function coerced writer IDs to integers even if the writer IDs contained characters.
Fixed bug in get_clusters_batch() where the function would stall but not return an error message if a document had a graph with a large number of edges (paths). Now the function ignores graphs with more than 30 edges.
Fixed bug in fit_model() where the function saves the same data in two separate files: “model_clusters.rds” and “all_clusters.rds”. The argument ‘save_master_file’ was added to get_clusters_batch(). If TRUE, a data frame of all cluster assignments, “all_clusters.rds”, will be saved. The default is FALSE.

The functions fit_model() and analyze_questioned_documents() now allow writer IDs that contain numbers and letters.

Increased the speed of processHandwriting() by changing the function to process a handwritten document in sections instead of all at once. Nodes created by processHandwriting() in version 3.1.0 might differ slightly in placement from previous versions.
Fixed bugs in fit_model() and analyze_questioned_documents() introduced by the changes to process_batch_list() in version 3.0.0.

Major reductions made to the memory required by process_batch_list() so it can now process paragraph length documents from the CSAFE Handwriting Database on machines with 8 GB of RAM.
process_batch_list() now skips to the next document if an error is returned while trying to process a document. A log file records the document name(s) and error message(s) of any problem documents. If the user reruns process_batch_list() they now have the option to either try a second time to process problem documents or skip them entirely.
New function get_clusters_batch() calculates cluster assignments of all files in a directory.

Fix initializer warning with arma::vec. Apparently different versions of gcc were raising warnings with the assignment of values in neighbors. The recommended fix was to use an initializer list.

fit_model() allows the user to fit a statistical model to known handwriting samples collected from a closed-set of persons.
analyze_questioned_documents() in conjunction with a model created by fit_model() allows a user to calculate the posterior probability that each known writer in the model is the writer of the questioned document(s). analyze_questioned_documents() only works when the questioned document(s) had to have been written by one of the model writers. This function must NOT be used if someone other than one of the model writers could written the questioned document(s) as it could yield misleading results.

processDocument() is a new wrapper function that runs readPNGBinary(), thinImage(), and processHandwriting() so the user doesn’t need to run these functions individually.
plotImage(), plotImageThinned(), and plotNodes now only need one input, a document processed with processDocument()
processHandwriting() no longer crashes when the input writing is a single letter or word
read_and_process() superseded in favor of processDocument()
extractGraphs() superseded in favor of process_batch_dir()