Table Of Contents

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Main Siren webpage

Parameters

Note

Siren allows to tune various parameters via an interface menu Edit ‣ Preferences.

Non-default parameters can be stored in a preferences file, e.g. via Export ‣ Export preferences.

Parameters are listed below by their label and identifier, as used respectively in the interface and in preference files, with a short explanation of the parameter, type, default value and indication of file where the parameter is defined.

The parameters that can be set through the preference interface can be mainly divided into two categories, mining parameters, that pertain to the mining algorithm, and visualization parameters, that pertain to the interactive visualizations, each split over several tabs.

Mining parameters

Mining parameters are specified here and can be set through the interface.

Quite many parameters are available for tuning, but in general only a few of them need to be adjusted. In particular, the parameters setting threshold values on the support of the queries, on the accuracy of the returned redescriptions, as well as on the type of queries, are the most important ones.

Mining: Method

Mining algorithm
mining_algo
  • Algorithm to use for mining, greedy ReReMi or based on classification trees (restrictions apply).
  • single option in {reremi, layeredtrees, splittrees, cartwheel, fim}
  • default: reremi
  • miner_confdef.xml

Mining: Queries

LHS max number of variables
max_var_s0
  • Maximum number of variables in a left-hand side query, maximum tree depth in tree-based algorithms.
  • open text
  • default: 4
  • miner_confdef.xml
RHS max number of variables
max_var_s1
  • Maximum number of variables in a right-hand side query, maximum tree depth in tree-based algorithms.
  • open text
  • default: 4
  • miner_confdef.xml

Mining: Candidate filtering

Min contribution
min_itm_c
  • Minimum contribution, number of supporting entities impacted by the addition of a literal in ReReMi or minimum node size in tree-based algorithms. Values between 0 and 1 are interpreted as ratio of the total number of entities.
  • open text
  • default: 3.0
  • miner_confdef.xml
Min support
min_itm_in
  • Minimum number of supporting entities. Values between 0 and 1 are interpreted as ratio of the total number of entities.
  • open text
  • default: 0.05
  • miner_confdef.xml
Min uncovered
min_itm_out
  • Minimum number of uncovered entities. Values between 0 and 1 are interpreted as ratio of the total number of entities.
  • open text
  • default: 0.05
  • miner_confdef.xml
Min improvement
min_impr
  • Minimum improvement score for an acceptable extension.
  • open text
  • default: 0.0
  • miner_confdef.xml
Max initial candidates
max_inits
  • Maximum number of initial candidates explored, pairs for ReReMi, initial targets for trees. -1 leads to expand all.
  • open text
  • default: 100
  • miner_confdef.xml
Initial candidates productivity
inits_productivity
  • Productivity when creating an initial pair of literals from non-Boolean variables.
  • single option in {low, medium, high}
  • default: medium
  • miner_confdef.xml
Excluded initial cand. pair types
inits_types_exclude
  • Excluded variable types in initial pairs. B, C and N stand for Boolean, Categorical and Numerical variables, respectively. Note order is simpler type first, not by sides.
  • multiple options in {BB, BC, BN, CC, CN, NN}
  • default: {}
  • miner_confdef.xml

Mining: Final filtering

Min support
min_fin_in
  • Minimum number of supporting entities, applied for final filtering. Values between 0 and 1 are interpreted as ratio of the total number of entities.
  • open text
  • default: -1.0
  • miner_confdef.xml
Min uncovered
min_fin_out
  • Minimum number of uncovered entities, applied for final filtering. Values between 0 and 1 are interpreted as ratio of the total number of entities.
  • open text
  • default: -1.0
  • miner_confdef.xml
Min accuracy
min_fin_acc
  • Minimum accuracy, applied for final filtering.
  • open text
  • default: 0.01
  • miner_confdef.xml
Max p-value
max_fin_pval
  • Maximum p-value, applied for final filtering.
  • open text
  • default: 0.01
  • miner_confdef.xml

Mining: Additional filtering

Max Area Overlap
max_overlap_area
  • Two redescriptions whose area overlap is beyond this ratio are considered redundant.
  • open text
  • default: 0.5
  • miner_confdef.xml
Max Rows Overlap
max_overlap_rows
  • Two redescriptions whose row overlap is beyond this ratio are considered redundant.
  • open text
  • default: 0.5
  • miner_confdef.xml

Mining adv.: Process

Nb processes
nb_processes
  • Maximum number of mining processes to use in parallel.
  • open text
  • default: 1
  • miner_confdef.xml
Log verbosity
verbosity
  • Verbosity of the mining process output.
  • range in [0, 10]
  • default: 4
  • miner_confdef.xml
Debug checks
debug_checks
  • For debugging, double check counts.
  • yes/no
  • default: no
  • miner_confdef.xml

Mining adv.: Other common parameters

Batch output
batch_out
  • Maximum number of redescriptions returned from an expansion batch.
  • open text
  • default: 1
  • miner_confdef.xml
Min total number of variables
min_fin_var
  • Maximum number of variables per redescription, applied for final filtering.
  • open text
  • default: 2
  • miner_confdef.xml
Weight Inside
in_weight
  • Weight for entities inside selected area (only applies when such an area is specified).
  • open text
  • default: 10
  • miner_confdef.xml
Weight Outside
out_weight
  • Weight for entities outside selected area (only applies when such an area is specified).
  • open text
  • default: 1
  • miner_confdef.xml
Var group compatibility
var_compat
  • Fixes whether group ids should differ or match for variables to be considered compatible (gid=-1 is universally compatible).
  • single option in {differ, match}
  • default: differ
  • miner_confdef.xml
p-value formula
method_pval
  • Formula used for computing the p-value.
  • single option in {marg, supp, over}
  • default: marg
  • miner_confdef.xml
Missing values belief
parts_type
  • Type of Jaccard index, determines how to consider missing values when computing support statistics.
  • single option in {rejective, optimistic, pessimistic, positive, negative, basic, exclu}
  • default: rejective
  • miner_confdef.xml

Mining adv.: Tree-based algorithms

Max rounds in CartWheel
max_rounds
  • Maximum number of alternations in CartWheel algorithm.
  • open text
  • default: 10
  • miner_confdef.xml
Split criterion
split_criterion
  • Score used to evaluate splits during decision tree induction.
  • single option in {gini, entropy}
  • default: gini
  • miner_confdef.xml

Mining adv.: Splittrees variant

Init depth
splittrees_init_depth
  • Maximum tree depth for the split in the first round.
  • open text
  • default: 1
  • miner_confdef.xml
Update target
splittrees_update_target
  • Update the target between tree growing rounds.
  • yes/no
  • default: no
  • miner_confdef.xml
Both sides change
splittrees_both_sides_change
  • Require both sides to be different in successive tree growing rounds.
  • yes/no
  • default: no
  • miner_confdef.xml
Dynamic side
splittrees_dyn_side
  • Choose the side on which to grow the tree first depending on the source of the target (else always start with RHS).
  • yes/no
  • default: yes
  • miner_confdef.xml

ReReMi: Queries

Single side OR
single_side_or
  • Restrict use of disjunction to only one side.
  • yes/no
  • default: yes
  • miner_confdef.xml
Multi categories
multi_cats
  • Allow combining multiple categories of a categorical variable.
  • yes/no
  • default: no
  • miner_confdef.xml
Conditional
add_condition
  • Allow making conditional redescriptions, if suitable data is provided.
  • yes/no
  • default: no
  • miner_confdef.xml
LHS Literals Bool
neg_query_s0_1
  • Types of literals allowed in the left-hand side queries for Boolean literals.
  • multiple options in {positive, negative}
  • default: {positive}
  • miner_confdef.xml
LHS Literals Cat
neg_query_s0_2
  • Types of literals allowed in the left-hand side queries for categorical literals.
  • multiple options in {positive, negative}
  • default: {positive}
  • miner_confdef.xml
LHS Literals Num
neg_query_s0_3
  • Types of literals allowed in the left-hand side queries for numerical literals.
  • multiple options in {positive, negative}
  • default: {positive}
  • miner_confdef.xml
LHS Operators
ops_query_s0
  • Type of operators allowed in the left-hand side queries.
  • multiple options in {conjunction, disjunction}
  • default: {conjunction, disjunction}
  • miner_confdef.xml
RHS Literals Bool
neg_query_s1_1
  • Types of literals allowed in the right-hand side queries for Boolean literals.
  • multiple options in {positive, negative}
  • default: {positive}
  • miner_confdef.xml
RHS Literals Cat
neg_query_s1_2
  • Types of literals allowed in the right-hand side queries for categorical literals.
  • multiple options in {positive, negative}
  • default: {positive}
  • miner_confdef.xml
RHS Literals Num
neg_query_s1_3
  • Types of literals allowed in the right-hand side queries for numerical literals.
  • multiple options in {positive, negative}
  • default: {positive}
  • miner_confdef.xml
RHS Operators
ops_query_s1
  • Type of operators allowed in the right-hand side queries.
  • multiple options in {conjunction, disjunction}
  • default: {conjunction, disjunction}
  • miner_confdef.xml

ReReMi: Initial pairs

Init min score
init_minscore
  • Minimum score for an initial candidate to be considered.
  • open text
  • default: 0.01
  • miner_confdef.xml
Pairs-expand balance
pe_balance
  • Balance between generating initial pairs and expanding them (0 means generating all pairs first).
  • range in [0, 10]
  • default: 4
  • miner_confdef.xml
Expansion order
pair_sel
  • Order in which the initial pairs are processed, either overall next best score or alternating between side considering next best variables in turn.
  • single option in {overall, alternate}
  • default: alternate
  • miner_confdef.xml

ReReMi exp.: Candidate expansion

Accuracy improvement coefficient
score.impacc
  • Coefficient of the accuracy improvement for scoring extension candidates.
  • open text
  • default: 1.0
  • miner_confdef.xml
Relative Accurracy improvement coefficient
score.rel_impacc
  • Coefficient of the relative accuracy improvement for scoring extension candidates.
  • open text
  • default: 0.0
  • miner_confdef.xml
Redescription p-value coefficient
score.pval_red
  • Coefficient of the redescription p-value for scoring extension candidates. Negative values are interpreted as a threshold weighted by p-value factor.
  • open text
  • default: 0.01
  • miner_confdef.xml
Query p-value coefficient
score.pval_query
  • Coefficient of the query p-value for scoring extension candidates. Negative values are interpreted as a threshold weighted by p-value factor.
  • open text
  • default: 0.01
  • miner_confdef.xml
p-value factor
score.pval_fact
  • Weight for p-value in case of using thresholds for scoring extension candidates.
  • open text
  • default: 1.0
  • miner_confdef.xml
Batch capacity
batch_cap
  • Maximum number of candidates expanded at each step of the search.
  • open text
  • default: 4
  • miner_confdef.xml
Amnesic
amnesic
  • Not amnesic means the algorithm remembers previously generated redescriptions and avoid generating them again.
  • yes/no
  • default: no
  • miner_confdef.xml

ReReMi exp.: Numerical attributes discretization

Max number segments
max_seg
  • Maximum number of segments, i.e. distinct values for a numerical variable.
  • open text
  • default: 20
  • miner_confdef.xml
Lower tail aggregate
lower_tail_agg
  • Threshold for the lower tail, when aggregating keeping only extreme values.
  • open text
  • default: 0.0
  • miner_confdef.xml
Upper tail aggregate
upper_tail_agg
  • Threshold for the upper tail, when aggregating keeping only extreme values.
  • open text
  • default: 0.0
  • miner_confdef.xml
Max aggregation
max_agg
  • Maximum number of buckets aggregated together.
  • open text
  • default: 15
  • miner_confdef.xml
Max product buckets
max_prodbuckets
  • Maximum product of the number of buckets on either side.
  • open text
  • default: 5000
  • miner_confdef.xml

Visualization parameters

Visualization parameters are specified here and can be set through the interface. For instance, they allows to modify the appearance of the maps, choose the colors of the different support subsets, etc.

Views: Vizualizations

Intab grid rows
intab_nbr
  • Number of rows of the grid for visualizations in the tab.
  • open text
  • default: 1
  • views_confdef.xml
Intab grid cols
intab_nbc
  • Number of columns of the grid for visualizations in the tab.
  • open text
  • default: 2
  • views_confdef.xml
Dot size
dot_size
  • Size of the dots in points.
  • range in [0.0, 10.0]
  • default: 3.0
  • views_confdef.xml
Font size
plot_fontsize
  • Font size used in plots for ticks, etc.
  • range in [0, 100]
  • default: 12
  • views_confdef.xml
Details level
details_level
  • Level of details for plotting the parallel coordinates.
  • range in [0, 100]
  • default: 50
  • views_confdef.xml
Max emph lbls
max_emphlbl
  • More that this number of entities selected at once will not get individual labels.
  • range in [-1, 20]
  • default: 5
  • views_confdef.xml
Dot shape
dot_shape
  • Shape of the dots
  • single option in {s, o, p, h, 8, ., ,, *, +, x}
  • default: s
  • views_confdef.xml
Transparency off
alpha_off
  • Turn transparency off.
  • yes/no
  • default: no
  • views_confdef.xml
Add stamp
add_stamp
  • Stamp redescription above the figure.
  • yes/no
  • default: no
  • views_confdef.xml
Detailed missing
miss_details
  • Show details of different missing values.
  • yes/no
  • default: yes
  • views_confdef.xml
Draw uncovered
draw_delta
  • Draw uncovered entities (map)
  • yes/no
  • default: yes
  • views_confdef.xml
Click entities
click_entities
  • Show details entities labels on click.
  • yes/no
  • default: yes
  • views_confdef.xml
Hover entities
hover_entities
  • Show details entities labels on hover.
  • yes/no
  • default: no
  • views_confdef.xml
Hover coordinates
hover_coords
  • Show coordinates on hover.
  • yes/no
  • default: no
  • views_confdef.xml
Show literals contribution
literals_contrib
  • Show contribution of literals (PaCo)
  • yes/no
  • default: no
  • views_confdef.xml

Colors: Colors

Custom cluster colors
custom_ccmap
  • Custom colors for plotting clusters (matplotlib cmap name, list or dictionnary of hexadecimal colors).
  • open text
  • default:
  • views_confdef.xml
Color LHS
color_l
  • Color for plotting the LHS support.
  • color #RRGGBB
  • default: #fc5864
  • views_confdef.xml
Color RHS
color_r
  • Color for plotting the RHS support.
  • color #RRGGBB
  • default: #74a8f6
  • views_confdef.xml
Color Intersection
color_i
  • Color for plotting the intersection support.
  • color #RRGGBB
  • default: #662a8d
  • views_confdef.xml
Color Uncovered
color_o
  • Color for plotting the uncovered entities.
  • color #RRGGBB
  • default: #e6e6e6
  • views_confdef.xml
Color Highlight
color_h
  • Color for highlighting entities.
  • color #RRGGBB
  • default: #ffff00
  • views_confdef.xml

List views: Vizualizations

Max nb. clusters
max_clus
  • Maximum number of clusters in similarity list view.
  • open text
  • default: 20
  • views_confdef.xml
Values for blocks
blocks_disp_values
  • Property to use as value for blocks.
  • single option in {fractions, percentages, counts}
  • default: fractions
  • views_confdef.xml
Re-order r.ids for blocks
blocks_reorder_rids
  • Reorder redescriptions for blocks.
  • yes/no
  • default: yes
  • views_confdef.xml
Show r.ids for blocks
blocks_show_rids
  • Show redescriptions ids for blocks.
  • yes/no
  • default: yes
  • views_confdef.xml
Show values for blocks
blocks_show_values
  • Show values for blocks.
  • yes/no
  • default: no
  • views_confdef.xml
Draw selection block
blocks_show_emph
  • Draw special block for selection.
  • yes/no
  • default: yes
  • views_confdef.xml
Support parts
supp_part_clus
  • Support parts to use in computing clusters.
  • multiple options in {Exx, Exo, Eox, Eoo}
  • default: {Exx}
  • views_confdef.xml
Missing support parts
miss_part_clus
  • Missing support parts to use in computing clusters.
  • multiple options in {Exm, Emx, Eom, Emo, Emm}
  • default: {}
  • views_confdef.xml

Maps elems.: Elements

Map background opacity
map_back_alpha
  • Opacity of the background image.
  • range in [0, 100]
  • default: 100
  • views_confdef.xml
Map background scale
map_back_scale
  • Scale of the background image.
  • range in [0, 100]
  • default: 100
  • views_confdef.xml
Map background
map_back
  • Background to use for the map (only with Basemap, not with Cartopy).
  • single option in {none, shaded relief, etopo relief, NASA Blue Marble}
  • default: none
  • views_confdef.xml
Overlay
map_lines_overlay
  • Overlay map lines on top of other plot elements.
  • yes/no
  • default: no
  • views_confdef.xml
Polygons
map_poly
  • Use polygons to represent entities on the map
  • yes/no
  • default: yes
  • views_confdef.xml
Map natural areas
map_elem_area
  • Map natural areas to paint.
  • multiple options in {seas, continents, lakes}
  • default: {seas}
  • views_confdef.xml
Map natural elements
map_elem_natural
  • Map natural elements to draw.
  • multiple options in {coasts, rivers}
  • default: {coasts}
  • views_confdef.xml
Map geopolitic elements
map_elem_geop
  • Map geopolitic borders to paint.
  • multiple options in {countries, states}
  • default: {countries}
  • views_confdef.xml
Map imaginary circles
map_elem_circ
  • Map imaginary circles to draw.
  • multiple options in {parallels, meridians}
  • default: {}
  • views_confdef.xml
Line color
line_color
  • Color for drawing map lines.
  • color #RRGGBB
  • default: #808080
  • views_confdef.xml
Sea color
sea_color
  • Color for filling water bodies in maps.
  • color #RRGGBB
  • default: #f9fcff
  • views_confdef.xml
Land color
land_color
  • Color for filling land areas in maps.
  • color #RRGGBB
  • default: #ffffff
  • views_confdef.xml

Maps proj.: Projection

Left corner longitude
llon
  • Map boundary’s left corner longitude.
  • range in [-180.0, 181.0]
  • default: 181.0
  • views_confdef.xml
Right corner longitude
ulon
  • Map boundary’s right corner longitude.
  • range in [-180.0, 181.0]
  • default: 181.0
  • views_confdef.xml
Lower corner latitude
llat
  • Map boundary’s lower corner latitude.
  • range in [-180.0, 181.0]
  • default: 181.0
  • views_confdef.xml
Upper corner latitude
ulat
  • Map boundary’s upper corner latitude.
  • range in [-180.0, 181.0]
  • default: 181.0
  • views_confdef.xml
Resolution
map_resolution
  • Resolution of the map elements.
  • single option in {crude, low, intermediate, high, full}
  • default: crude
  • views_confdef.xml
Projection
map_proj
  • Projection to use for the map.
  • single option in {none, Plate Carree, Transverse Mercator, Mercator, Lambert Cylindrical, Lambert Conformal, Lambert Azimuthal Equal Area, Miller, Rotated Pole, Gnomonic, Stereographic, North Polar Stereo, South Polar Stereo, Orthographic, Mollweide, Robinson, Interrupted Goode Homolosine, Geostationary, Albers Equal Area, Azimuthal Equidistant, Sinusoidal}
  • default: Miller
  • views_confdef.xml

Other parameters

It is possible to adjust the parameters through the interface then export them to a file. In particular, a template can be generated and exported which can be used to run the ReReMi mining algorithm from the command line, after filling in input/output parameters, which are specified here.

Further parameters pertain to randomization, cross-fold tests, server parameters, etc.

File Names: Data Input

LHS data filename
LHS_data
  • Complete filename for the left hand side data.
  • open text
  • default:
  • inout_confdef.xml
RHS data filename
RHS_data
  • Complete filename for the right hand side data.
  • open text
  • default:
  • inout_confdef.xml
Data repertory
data_rep
  • Repertory where the data files are stored.
  • open text
  • default: __TMP_DIR__
  • inout_confdef.xml
LHS data basename
data_l
  • Basename of the file containing the left hand side data.
  • open text
  • default: left
  • inout_confdef.xml
RHS data basename
data_r
  • Basename of the file containing the right hand side data.
  • open text
  • default: right
  • inout_confdef.xml
LHS data extension
ext_l
  • Extension of the file containing the left hand side data.
  • open text
  • default: .csv
  • inout_confdef.xml
RHS data extension
ext_r
  • Extension of the file containing the right hand side data.
  • open text
  • default: .csv
  • inout_confdef.xml
NA representation
NA_str
  • String representation for missing values (CSV format).
  • open text
  • default: nan
  • inout_confdef.xml
Delimiter
delim_in
  • Field delimiter (CSV format).
  • single option in {(auto), TAB, ;, ,, SPC}
  • default: (auto)
  • inout_confdef.xml
Time year first
time_yearfirst
  • Whether to interpret the first value in an ambiguous 3-integer date as the year (dateutils).
  • single option in {(auto), yes, no}
  • default: (auto)
  • inout_confdef.xml
Time day first
time_dayfirst
  • Whether to interpret the first value in an ambiguous 3-integer date as the day (dateutils).
  • single option in {(auto), yes, no}
  • default: (auto)
  • inout_confdef.xml

File Names: Results Output

Results repertory
result_rep
  • Repertory where to save the results.
  • open text
  • default: __TMP_DIR__
  • inout_confdef.xml
Results data filename
out_base
  • Name of the file where to store the results.
  • open text
  • default: results
  • inout_confdef.xml
Queries extension
ext_queries
  • Extension of the file where to save the queries.
  • open text
  • default: .queries
  • inout_confdef.xml
Supports extension
ext_support
  • Extension of the file where to save the supports.
  • open text
  • default: .supports
  • inout_confdef.xml
Log data extension
ext_log
  • Extension of the file where to save log traces.
  • open text
  • default: .txt
  • inout_confdef.xml
Queries filename
queries_file
  • Complete filename for the queries.
  • open text
  • default:
  • inout_confdef.xml
Named queries filename
queries_named_file
  • Complete filename for the queries with variable names.
  • open text
  • default:
  • inout_confdef.xml
Support filename
support_file
  • Complete filename for the support.
  • open text
  • default:
  • inout_confdef.xml

Advanced: File Names

Series ID
series_id
  • Series ID to replace __SID__ in filenames.
  • open text
  • default:
  • inout_confdef.xml
Logfile
logfile
  • File to log. + means generate filename from queries output file. - means stdout.
  • open text
  • default: -
  • inout_confdef.xml
Pairs store filename
pairs_store
  • Name of the file where to store initial pairs.
  • open text
  • default:
  • inout_confdef.xml
Alternate queries
queries_alternate
  • Alternate filename or suffix for the queries, for post-processing.
  • open text
  • default:
  • inout_confdef.xml

Advanced: Extra

Mask for LHS variables
mask_vars_LHS
  • Mask for enabling or disabling LHS variables, overriding any info in the data file.
  • open text
  • default:
  • inout_confdef.xml
Mask for RHS variables
mask_vars_RHS
  • Mask for enabling or disabling RHS variables, overriding any info in the data file.
  • open text
  • default:
  • inout_confdef.xml
Mask for rows
mask_rows
  • Mask for enabling or disabling rows, overriding any info in the data file.
  • open text
  • default:
  • inout_confdef.xml
Extensions repertory
extensions_rep
  • Repertory where extension data files are stored.
  • open text
  • default: __TMP_DIR__
  • inout_confdef.xml
Extensions data filenames
extensions_names
  • Keys and names of the extension data files.
  • open text
  • default:
  • inout_confdef.xml
Files defining reds fields
fields_rdefs
  • Files defining extra redescriptions fields.
  • open text
  • default:
  • inout_confdef.xml
Files defining vars fields
fields_vdefs
  • Files defining extra variables fields.
  • open text
  • default:
  • inout_confdef.xml
Files defining reds actions
actions_rdefs
  • Files defining extra redescriptions actions.
  • open text
  • default:
  • inout_confdef.xml
Activated extensions
activated_extensions
  • Data extensions to activate.
  • multiple options in {(auto), geoplus}
  • default: {}
  • inout_confdef.xml

Network: Work client

Results delay
results_delay
  • Delay between results checks by the client, in seconds.
  • open text
  • default: 5
  • network_confdef.xml

Network: Work server

Workserver IP
workserver_ip
  • IP adress of the server executing the computational tasks or local for local computations.
  • open text
  • default: local
  • network_confdef.xml
Workserver Port
workserver_port
  • Listening port of the server executing the computational tasks.
  • open text
  • default: 55444
  • network_confdef.xml
Workserver Key
workserver_authkey
  • Authentification key on the server executing the computational tasks.
  • open text
  • default: sesame
  • network_confdef.xml
Client Id
workserver_clientid
  • Client ID to reconnect on the server.
  • open text
  • default: 0
  • network_confdef.xml

Extensions: geoplus

H grid percentile
hgrid_percentile
  • Percentile to determine grid height.
  • range in [0.0, 100.0]
  • default: 90.0
  • dataext_confdef.xml
W grid percentile
wgrid_percentile
  • Factor to multiply grid width.
  • range in [0.0, 100.0]
  • default: 90.0
  • dataext_confdef.xml
Distance type
dst_type
  • Distance to use when computing the grid
  • single option in {globe, flat}
  • default: globe
  • dataext_confdef.xml
Draw tighter borders
after_cut
  • Draw tighter border between distant sites.
  • yes/no
  • default: yes
  • dataext_confdef.xml

Folds: Automatic splits

Strips direction
coo_dim
  • Coordinate to cut the strips along (-1 and -2 for cut along longitudes and latitudes, respectively).
  • open text
  • default: -1
  • folds_confdef.xml
Granularity
grain
  • Granularity of the cut (lower means narrower strips).
  • open text
  • default: 1.0
  • folds_confdef.xml
Variable
folds_col
  • Name of the variable to use for splitting the data into subsets.
  • open text
  • default:
  • folds_confdef.xml
Nb folds
nb_folds
  • Number of parts the data should be split into.
  • range in [2, 20]
  • default: 5
  • folds_confdef.xml

Randomization: Data Input

Traits data filename
traits_data
  • Complete filename for the traits data.
  • open text
  • default:
  • rnd_confdef.xml
Traits data basename
data_t
  • Basename of the file containing the traits data.
  • open text
  • default:
  • rnd_confdef.xml
Traits data extension
ext_t
  • Extension of the file containing the traits data.
  • open text
  • default: .csv
  • rnd_confdef.xml
Name count variable
count_vname
  • Name for the variable that stores occurrence counts.
  • open text
  • default: COUNTS
  • rnd_confdef.xml
Selection redescription
select_red
  • Redescription used to select data rows.
  • open text
  • default:
  • rnd_confdef.xml
Agg. precision
agg_prec
  • Precision of aggregated data.
  • open text
  • default: -1
  • rnd_confdef.xml

Randomization: Series

Randomization serie size
rnd_series_size
  • Number of runs per randomization series.
  • open text
  • default: 10
  • rnd_confdef.xml
Randomization seed
rnd_seed
  • Seed for the random number generator.
  • open text
  • default: -1
  • rnd_confdef.xml
Randomization meth.
rnd_meth
  • Randomization method used to generate data.
  • multiple options in {none, permute_RHS, permute_LHS, permute_traits, shuffle_traits, swaprnd_occs}
  • default: {none}
  • rnd_confdef.xml