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Indices metadata - numeric bounds #894

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merged 13 commits into from
Dec 13, 2023
Merged

Indices metadata - numeric bounds #894

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78b333d
Indices: Initial metadata work to provide index bounds
shawnlaffan Dec 4, 2023
bbef148
Indices metadata bounds: use correct args
shawnlaffan Dec 4, 2023
3c620d3
Indices: Generalised bounds and distribution implementation
shawnlaffan Dec 8, 2023
1b59239
Indices: implement distribution metadata.
shawnlaffan Dec 8, 2023
857a4f5
Indices metadata: factory generation of distribution methods
shawnlaffan Dec 8, 2023
6c80b71
Indices metadata: default distribution to sequential
shawnlaffan Dec 8, 2023
a4ea6b1
Indices metadata: Add a TO_JSON method
shawnlaffan Dec 10, 2023
474394c
Indices: Add methods to get metadata as a perl hash and as JSON
shawnlaffan Dec 10, 2023
ce03253
quieten some logging
shawnlaffan Dec 10, 2023
731c3ee
Tests: remove some unreachable code
shawnlaffan Dec 10, 2023
21fe30b
Indices metadata: add index bounds
shawnlaffan Dec 10, 2023
9c4599b
Indices metadata: Fix TO_JSON method
shawnlaffan Dec 10, 2023
e104292
Indices metadata: store bounds for each index
shawnlaffan Dec 10, 2023
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62 changes: 59 additions & 3 deletions lib/Biodiverse/Indices.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@ use List::MoreUtils qw /uniq/;
use List::Util qw /sum/;
use English ( -no_match_vars );
use Ref::Util qw { :all };
use JSON::MaybeXS;

#use MRO::Compat;
use Class::Inspector;
Expand Down Expand Up @@ -96,7 +97,7 @@ sub get_calculations {

my %calculations;

my $list = Class::Inspector->methods( blessed $self);
my $list = Class::Inspector->methods( blessed $self );

foreach my $method ( grep { $_ =~ /^calc_/ } @$list ) {
next if $method =~ /calc_abc\d?$/; # skip calc_abc1,2&3
Expand Down Expand Up @@ -355,6 +356,36 @@ sub get_calculation_metadata_as_wiki {
return $html;
}

sub get_calculation_metadata {
my $self = shift;

if (!blessed $self) {
state $default_bd = Biodiverse::BaseData->new (
NAME => 'for indices',
CELL_SIZES => [1,1],
);
$self = __PACKAGE__->new (BASEDATA_REF => $default_bd);
}

my %calculations = $self->get_calculations_as_flat_hash();

my %calculation_hash;
foreach my $calc_sub ( sort keys %calculations ) {
my $ref = $self->get_metadata( sub => $calc_sub );
$calculation_hash{$calc_sub} = $ref;
}

return wantarray ? %calculation_hash : \%calculation_hash;
}

sub get_calculation_metadata_as_json {
my $self = shift;
my $metadata = $self->get_calculation_metadata;
my $json_obj = JSON::MaybeXS::JSON()->new;
$json_obj->convert_blessed(1);
return $json_obj->encode($metadata);
}

# now we have moved to github
sub get_calculation_metadata_as_markdown {
my $self = shift;
Expand Down Expand Up @@ -1303,8 +1334,7 @@ sub get_ratio_indices {
foreach my $calculations ( keys %$list ) {
my $meta = $self->get_metadata( sub => $calculations );
INDEX:
foreach my $index ( keys %{ $meta->get_indices } ) {
next INDEX if !$meta->get_index_is_ratio($index);
foreach my $index ( grep {$meta->get_index_is_ratio($_)} keys %{ $meta->get_indices } ) {
$indices{$index} = $meta->get_index_description($index);
}
}
Expand Down Expand Up @@ -1348,6 +1378,32 @@ sub index_is_divergent {
return !!$hash->{$args{index} // ''};
}

sub get_index_bounds {
my ($self, %args) = @_;
my $index = $args{index};

# return undef if !$self->index_is_scalar(index => $index);

my $index_source = $self->get_index_source(index => $index);
my $meta = $self->get_metadata( sub => $index_source );

my $bounds = $meta->get_index_bounds ($index);

return $bounds;
}

sub index_distribution_is_valid {
my $self = shift;
my %args = @_;
my $index = $args{index};

my $index_source = $self->get_index_source(index => $index);
my $meta = $self->get_metadata( sub => $index_source );

return $meta->index_distribution_is_valid ($index);
}


sub get_valid_calculations_to_run {
my $self = shift;

Expand Down
28 changes: 20 additions & 8 deletions lib/Biodiverse/Indices/Endemism.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@ sub get_metadata_calc_endemism_central_normalised {
calc_elements_used
}],
uses_nbr_lists => 1, # how many sets of lists it must have
distribution => 'nonnegative',
indices => {
ENDC_CWE_NORM => {
description => 'Corrected weighted endemism normalised by groups',
Expand Down Expand Up @@ -72,16 +73,18 @@ sub get_metadata_calc_endemism_whole_normalised {
uses_nbr_lists => 1, # how many sets of lists it must have
indices => {
ENDW_CWE_NORM => {
description => 'Corrected weighted endemism normalised by groups',
formula => [
description => 'Corrected weighted endemism normalised by groups',
formula => [
'= \frac{ENDW\_CWE}{EL\_COUNT\_ALL}',
],
distribution => 'unit_interval',
},
ENDW_WE_NORM => {
description => 'Weighted endemism normalised by groups',
formula => [
'= \frac{ENDW\_WE}{EL\_COUNT\_ALL}',
],
distribution => 'nonnegative',
},
},
); # add to if needed
Expand Down Expand Up @@ -153,13 +156,15 @@ sub get_metadata_calc_endemism_central {
pre_calc => [qw /_calc_endemism_central/],
reference => $ref,
uses_nbr_lists => 1, # how many sets of lists it must have
distribution => 'nonnegative',
indices => {
ENDC_CWE => {
description => 'Corrected weighted endemism',
lumper => 0,
formula => [
'= \frac{ENDC\_WE}{ENDC\_RICHNESS}',
],
distribution => 'unit_interval',
},
ENDC_WE => {
description => 'Weighted endemism',
Expand Down Expand Up @@ -547,12 +552,14 @@ sub get_metadata_calc_endemism_whole {
type => 'Endemism',
pre_calc => '_calc_endemism_whole',
uses_nbr_lists => 1, # how many sets of lists it must have
distribution => 'nonnegative',
indices => {
ENDW_CWE => {
description => 'Corrected weighted endemism',
formula => [
'= \frac{ENDW\_WE}{ENDW\_RICHNESS}',
],
distribution => 'unit_interval',
},
ENDW_WE => {
description => 'Weighted endemism',
Expand Down Expand Up @@ -597,7 +604,7 @@ sub get_metadata_calc_endemism_whole {
't',
' across the data set (the number of groups it is found in, '
. 'unless the range is specified at import).'
]
],
},
},
);
Expand Down Expand Up @@ -771,12 +778,13 @@ sub get_metadata_calc_endemism_absolute_lists {
type => 'Endemism',
pre_calc => ['_calc_endemism_absolute'],
uses_nbr_lists => 1, # how many sets of lists it must have
distribution => 'nonnegative',
indices => {
END_ABS1_LIST => {
END_ABS1_LIST => {
description => 'List of labels entirely endemic to neighbour set 1',
type => 'list',
},
END_ABS2_LIST => {
END_ABS2_LIST => {
description => 'List of labels entirely endemic to neighbour set 1',
type => 'list',
},
Expand Down Expand Up @@ -811,6 +819,7 @@ sub get_metadata_calc_endemism_absolute {
type => 'Endemism',
pre_calc => ['_calc_endemism_absolute'],
uses_nbr_lists => 1, # how many sets of lists it must have
distribution => 'nonnegative',
indices => {
END_ABS1 => {
description => 'Count of labels entirely endemic to neighbour set 1',
Expand All @@ -822,13 +831,16 @@ sub get_metadata_calc_endemism_absolute {
description => 'Count of labels entirely endemic to neighbour sets 1 and 2 combined',
},
END_ABS1_P => {
description => 'Proportion of labels entirely endemic to neighbour set 1',
description => 'Proportion of labels entirely endemic to neighbour set 1',
distribution => 'unit_interval',
},
END_ABS2_P => {
description => 'Proportion of labels entirely endemic to neighbour set 2',
description => 'Proportion of labels entirely endemic to neighbour set 2',
distribution => 'unit_interval',
},
END_ABS_ALL_P => {
description => 'Proportion of labels entirely endemic to neighbour sets 1 and 2 combined',
description => 'Proportion of labels entirely endemic to neighbour sets 1 and 2 combined',\
distribution => 'unit_interval',
},
},
); # add to if needed
Expand Down
2 changes: 1 addition & 1 deletion lib/Biodiverse/Indices/GroupProperties.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -344,7 +344,7 @@ sub get_metadata_calc_gpprop_gistar {
GPPROP_GISTAR_LIST => {
description => 'List of Gi* scores',
type => 'list',
is_zscore => 1,
distribution => 'zscore',
},
},
);
Expand Down
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