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\value documentation
describing the output’s class, structure, and meaning.\dontrun{} wrappers have been removed5. Slower examples are
now wrapped in \donttest{} as appropriate.The wizard function Euclidify was added to run all the
workflow needed to get the main output automatically.
create_topolow_map() is now deprecated in favor of
euclidean_embedding(). The old function will be removed in
version 3.0.0.
distance_matrix –>
dissimilarity_matrixcreate_topolow_map() –>
euclidean_embedding()initial_parameter_optimization():
Parameter distance_matrix renamed to
dissimilarity_matrix
distance_matrix = your_matrix with
dissimilarity_matrix = your_matrixrun_adaptive_sampling(): Parameter
distance_matrix renamed to
dissimilarity_matrix
distance_matrix = your_matrix with
dissimilarity_matrix = your_matrixadaptive_MC_sampling():
distance_matrix renamed to
dissimilarity_matrixbatch_size from
adaptive_MC_sampling(); its value had no effect in the
processes anywaynum_parallel_jobs from
run_adaptive_sampling; set max_cores to define
the number of cores and parallel jobsdistance_matrix = your_matrix with
dissimilarity_matrix = your_matrix and remove
batch_size argumentscreate_cv_folds(): Parameter names and
return structure changed
truth_matrix –>
dissimilarity_matrix, no_noise_truth –>
ground_truth_matrix$truth, $train) instead of indexed
elementsresult[[1]][[1]] to result[[1]]$truth,
result[[1]][[2]] to result[[1]]$traintake_log parameter in clean_data() is
deprecated
analyze_network_structure(): Parameter
distance_matrix renamed to
dissimilarity_matrix for consistency with other
functionscalculate_diagnostics(): Return class
changed from topolow_amcs_diagnostics to
topolow_diagnostics for naming consistencyplot_network_structure(): Removed
aesthetic_config and layout_config parameters
width,
height, dpi parametersscatterplot_fitted_vs_true():
Parameter names updated for consistency
distance_matrix –>
dissimilarity_matrix, p_dist_mat –>
p_dissimilarity_matsave_plot changed
from TRUE to FALSElinewidth instead
of deprecated sizeerror_calculator_comparison():
Parameter names changed for consistency
p_dist_mat –>
predicted_dissimilaritiestruth_matrix –>
true_dissimilaritiesinput_matrix –> input_dissimilarities
(now optional, defaults to NULL)calculate_prediction_interval():
Parameter names changed for consistency
distance_matrix –>
dissimilarity_matrixp_dist_mat –>
predicted_dissimilarity_matrixlong_to_matrix was renamed to
titers_list_to_matrix since it is specific to viral titer
data processing.process_antigenic_data accepts a data frame as
input, instead of the previous form of a file path.process_antigenic_data, is_titer became
is_similarity for clearity for broader audience. Parameter
id_prefix was removed.euclidean_embedding() function with enhanced
performance and features:
parameter_sensitivity function to use modern
ggplot2 syntaxsize parameter with
linewidth in plotscreate_cv_folds()input_dissimilarities parameter now optional in
error_calculator_comparison()initial_parameter_optimization saves/returns the
parameters in log scale, consistent with other functioncreate_topolow_map() deprecated, issues
warningcreate_topolow_map() will be
removedTo update your code:
# Old (deprecated):
result <- create_topolow_map(distance_matrix = my_matrix,
# ... other parameters
)
# New (recommended):
result <- euclidean_embedding(dissimilarity_matrix = my_matrix, # parameter name changed
# ... other parameters (unchanged)
)Included figures in the vignette.
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