\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_matrix
create_topolow_map()
–>
euclidean_embedding()
initial_parameter_optimization()
:
Parameter distance_matrix
renamed to
dissimilarity_matrix
distance_matrix = your_matrix
with
dissimilarity_matrix = your_matrix
run_adaptive_sampling()
: Parameter
distance_matrix
renamed to
dissimilarity_matrix
distance_matrix = your_matrix
with
dissimilarity_matrix = your_matrix
adaptive_MC_sampling()
:
distance_matrix
renamed to
dissimilarity_matrix
batch_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]]$train
take_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_mat
save_plot
changed
from TRUE
to FALSE
linewidth
instead
of deprecated size
error_calculator_comparison()
:
Parameter names changed for consistency
p_dist_mat
–>
predicted_dissimilarities
truth_matrix
–>
true_dissimilarities
input_matrix
–> input_dissimilarities
(now optional, defaults to NULL
)calculate_prediction_interval()
:
Parameter names changed for consistency
distance_matrix
–>
dissimilarity_matrix
p_dist_mat
–>
predicted_dissimilarity_matrix
long_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:
```r # Old (deprecated): result <- create_topolow_map(distance_matrix = my_matrix, # … other parameters )
result <- euclidean_embedding(dissimilarity_matrix = my_matrix, # parameter name changed # … other parameters (unchanged) )