The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.
\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.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.