Remove references to empty subsampling attributes from tutorial
@@ -71,14 +71,12 @@ switzerland:
# Focal samples for country
country:
group_by: "division year month"
- seq_per_group:
max_sequences: 1500
exclude: "--exclude-where 'country!={country}'"
# Contextual samples from country's region
region:
group_by: "country year month"
seq_per_group: 20
- max_sequences:
exclude: "--exclude-where 'country={country}' 'region!={region}'"
priorities:
type: "proximity"
@@ -88,7 +86,6 @@ switzerland:
global:
group_by: "country year month"
seq_per_group: 10
- max_sequences:
exclude: "--exclude-where 'region={region}'"
priorities:
type: "proximity"
@@ -101,8 +98,6 @@ Since we set `group_by` to "division year month", all the Swiss sequences will b
Alternatively, in the `region`-level sampling, we set `seq_per_group` to 20.
This means that all the sequences from Europe (excluding Switzerland) will be divided into groups by their sampling country, month, and year (as defined by `group_by`), and then 20 sequences will taken from each group (if there are fewer than 20 in any given group, all of the samples from that group will be taken).
-Since `max_sequences` and `seq_per_group` are mutually exclusive, you should supply a blank entry for whichever you don't want to use, as shown above.
-
Now we'll look at a subsampling scheme which defines a multi-`canton` build.
Cantons are regional divisions in Switzerland - below 'country,' but above 'location' (often city-level).
In the advanced example, we'd like to be able to specify a set of neighboring 'cantons' and do focal sampling there, with contextual samples from elsewhere in the country, other countries in the region, and other regions in the world.
@@ -116,31 +111,26 @@ lac-leman:
geneva:
group_by: "year month"
seq_per_group: 300
- max_sequences:
exclude: "--exclude-where 'division!=geneva'"
vaud:
group_by: "year month"
seq_per_group: 300
- max_sequences:
exclude: "--exclude-where 'division!=vaud'"
valais:
group_by: "year month"
seq_per_group: 300
- max_sequences:
exclude: "--exclude-where 'division!=valais'"
# Contextual samples from the country
country:
group_by: "division year month"
seq_per_group: 20
- max_sequences:
exclude: "--exclude-where 'country!=switzerland'"
# Contextual samples from division's region
region:
group_by: "country year month"
seq_per_group: 10
- max_sequences:
exclude: "--exclude-where 'region!=europe'"
priorities:
type: "proximity"
@@ -150,7 +140,6 @@ lac-leman:
global:
group_by: "country year month"
seq_per_group: 5
- max_sequences:
exclude: "--exclude-where 'region=europe'"
priorities:
type: "proximity"
