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-## Incremental network construction using `hivnetworkcsv`
-
-> Sergei L Kosakovsky Pond (spond@temple.edu)
-
-> 2020-01-09 v.1
-
-For cases when a transmission network is built periodically from surveillance data, with a subsequent network (network `T`, for today) being (for the most part, see below) an expansion of a previous network (netwotk `Y`, for yesterday), `hivnetworkcsv` provides a **previous network** mode, which accomplishes the following, **assuming the `-j` (JSON output) option is selected**
-
-1. Clusters in network `T` are matched, whenever practical, with clusters in network `Y`, so that _consistent_ cluster naming is maintained.
-2. Clusters in network `T` are **annotated** to explain how they compare to clusters in network `Y`. Annotation options for cluster `c` in network `T` are (see examples below). The annotation information is stored in the output JSON dictionary under the key `Cluster description`
- 1. `existing` : cluster `c` is identical to a cluster in network `Y` 2. `expanded` : cluster `c` expands (adds node to) a cluster in network `Y`; this also includes the case of a contraction if some nodes were deleted from network `Y`. 3. `merged` : cluster `c` merges two or more clusters from network `Y`, and possibly adds/removes nodes from them; example
- 4. `new`: cluster `c` consists of nodes that did not appear in clusters of network `Y`; this also includes the case when a cluster in network `Y` split into two more more smaller clusters in network `T`.
-3. Nodes in network `T` are **annotated** to explain how they relate to nodes in network `Y` (that these attributes are **not** mututally exclusive)
- 1. `new_node` : this node does not appear in network `Y`
- 2. `new_cluster` : this node belongs to a cluster in network `T` which has no match in cluster `Y`
- 3. `moved_clusters`: this node was present in network `Y`, is present in network `T`, but moved to a different cluster
- 4. *no attribute*: this node was present in network `Y`, is present in network `T`, and remains in the matched cluster
-4. Edges in network `T` are **annotated** to explain how they relate to Edges in network `Y`
- 1. `added-to-prior`: an edge in network `T` was not present in network `Y`.
-
-### Example
-
-The `Y` (original) network is created by calling
-
-```
-hivnetworkcsv -t 0.015 -f plain -j -i tests/incremental/original.csv
--O tests/incremental/original.json
-```
-
-It consists of **5** clusters, with node names reflecting which cluster they belong to (e.g. `A1` belongs to cluster `1`)
-
-**Figure 1** The existing network.
-
-
-
-The `N` network is created in the incremental mode by calling.
-
-```
-hivnetworkcsv -t 0.015 -f plain -j -i tests/incremental/modified.csv \
--P tests/incremental/original.json -O tests/incremental/modified.json
-```
-
-> This example adds **and** removes nodes to the existing network
-
-
-The following diagnostic messages are written to `stderr`
-
-```
-[WARNING] Removed 2 nodes from the previous network, E2, A1
-Cluster 1 matches previous cluster 1
-Cluster 2 matches previous cluster 1
-[WARNING] Cluster 1 from the existing network is mapped to multiple new clusters / singletons (nodes E1, F1)
-Cluster 3 MERGES 3, 4, None
-Cluster 4 matches previous cluster 2
-[WARNING] Incostistent singletons, nodes previously clustered became unclustered ({4})
-Cluster 5 matches previous cluster 5
-Cluster 6 is a new cluster
-Added 4 edges compared to the prior network
-```
-
-**Figure 2** The updated network.
-
-
-
-**Figure 3** The changes from `Y` to `T`.
-
-
-
-1. Cluster `1` split in two clusters because node `A1` was deleted. The larger remaining cluster (3 nodes) inherited the cluster name (`1`), and the second remaining cluster (2 nodes, E1 and F1) was given a new name (`7`) and the nodes in that cluster were labeled as `moved`. In the output JSON this is annotated with 2. Cluster `2` lost one node (E2) due to deletion
-3. Clusters `3` added a node (`E3`) and merged with cluster `4` through a link between the new node in cluster `4` (E4), and cluster `3`. Cluster `3` also lost a node because the link between `B4` and `D4` was removed from network `T` (e.g., because the sequence for `D3` was revised). The resulting merged cluster inherited the ID of cluster `3`; because the existing clusters were of the same size and had to date information, the cluster with the lexicographically lowest node name (`A3`) inherited the name. Note, that cluster ID `4` has been retired, and will not appear in subsequent networks.
-4. Cluster `5` is unchanged.
-5. Cluster `6` is new, i.e., none of its nodes were clustered in network `Y`.
-
-
-### Additional information in JSON
-
-Relevant sections of the output JSON are shown below
-
-```
-"Cluster description": {
- "1": {
- "type": "extended",
- "size": 3,
- "old_size": 6
- },
- "2": {
- "type": "extended",
- "size": 4,
- "old_size": 5
- },
- "3": {
- "type": "merged",
- "size": 9,
- "old_clusters": [
- 3,
- 4
- ],
- "sizes": [
- 4,
- 4
- ],
- "old_size": 8,
- "new_nodes": 2
- },
- "5": {
- "type": "existing"
- },
- "6": {
- "type": "new",
- "size": 2,
- "new_nodes": 2
- },
- "7": {
- "type": "new",
- "size": 2,
- "moved": 2
- }
- },
-...
-
-"Nodes" : [
-...
- {
- "id": "A6",
- "cluster": 6,
- "attributes": [
- "new_node",
- "new_cluster"
- ]
- },
-...
- {
- "id": "F1",
- "cluster": 7,
- "attributes": [
- "moved_clusters",
- "new_cluster"
- ]
- },
-...
-
- {
- "id": "E4",
- "cluster": 3,
- "attributes": [
- "new_node"
- ]
- },
-...
-],
-
-"Edges" : [
- ...
- {
- "source": 7,
- "target": 8,
- "directed": false,
- "length": 0.01,
- "support": 0,
- "removed": false,
- "sequences": [
- "D3",
- "E3"
- ],
- "attributes": [
- "BULK",
- "added-to-prior"
- ]
- }
- ...
-]
-
-```
-
diff --git a/docs/subclusters.md b/docs/subclusters.md
deleted file mode 100644
index 442a44b..0000000
--- a/docs/subclusters.md
+++ /dev/null
@@ -1,149 +0,0 @@
-## Subcluster construction using `hivnetworkcsv`
-
-> Sergei L Kosakovsky Pond (spond@temple.edu)
-
-> 2020-01-09 v.1
-
-Starting with version `0.6`, `hivnetworkcsv` allows the specification of multiple, comma-separated distance thresholds via the `-t` argument. This functionality permits inference of **nested** networks at different distance thresholds, i.e., the computation of subclusters of more "closely" linked nodes within clusters defined at a more permissive distance threshold.
-
-> ###This feature only affects runs where the JSON output (`-j` option) is specified.
-
-To illustrate this feature, we will use the dataset `tests/subclusters/pirc.csv` which is a distance file constructed from `tests/subclusters/pirc.msa` -- sequences from [PMID 24901437](https://www.ncbi.nlm.nih.gov/pubmed/24901437).
-
-Build the network, extracting date information from sequence names, and limiting the network to sequences from up to year 2009
-
-```
-hivnetworkcsv -j -i tests/subclusters/pirc.csv -t 0.02,0.01,0.005 -f regexp \
--p 0 "^([^|]+)\|([0-9]+)" -p 0 "^([^|]+)\|([0-9]+)" --before 20090101 \
--O tests/subclusters/pirc-2009.json
-```
-
-`stderr` output reports high level diagnostics.
-
-```
-At threshold 0.01 there were 77 subclusters
-At threshold 0.005 there were 54 subclusters
-```
-
-
-This command builds the transmission network using the maximal thershold specified in the `-t` argument (0.02), and then creates further annotation of networks at 0.01 and 0.005 that are contained in the larger network. By construction, using the same input data, network at a **lower** distance threshold will be a subset of the netwotk inferred at a higher threshold.
-
-Additional annotation in the JSON file takes the following form.
-
-1. A record in the `Settings` object
-"Settings": {
- "threshold": 0.02,
- "edge-filtering": null,
- "contaminants": null,
- "compact_json": false,
- "created": "2020-01-09T22:10:33.833333+00:00",
- "additional thresholds": [
- 0.01,
- 0.005
- ]
- }
-
-2. A dictionary `Subclusters` which, for each threshold, reports clusters at that thershold. A cluster record is of the form
-"ID" : [node1 index, node2 index, ... nodek index]
-
where `node_index` entries index into the `Node` array, also a part of the JSON output. For example,
-"Subclusters": {
- "0.01": {
- "2.1": [
- 24,
- 25,
- 26,
- 27,
- 28,
- 29,
- 30,
- 31,
- 32,
- 33,
- 34,
- 35,
- 36,
- 37,
- 38,
- 39,
- 40,
- 41,
- 42
- ],
- "19.1": [
- 135,
- 137
- ],
- "3.1": [
- 43,
- 44,
- 45,
- 46,
- 47,
- 48,
- 49,
- 50
- ],
- ...
-
- 3. Individual node records in the `Node` array which belong to subclusters, are annotated as follows
- {
- "id": "KJ723207",
- "cluster": 9,
- "subcluster": [
- [
- 0.01,
- "9.2"
- ],
- [
- 0.005,
- "9.2"
- ]
- ]
- ...
- }
- This node, in addition to belonging to cluster `9` at `t=0.02`, belongs to cluster `9.2` (a part of the larger cluster `9`) at both of the smaller thresholds.
-{
- "id": "KJ723391",
- "cluster": 14,
- "baseline": [
- 2002,
- 1,
- 1,
- 0,
- 0,
- 0,
- 1,
- 1,
- -1
- ],
- "subcluster": [
- [
- 0.01,
- "14.1"
- ]
- ]
- }
- This node belongs to cluster `14` at `t=0.02`, cluster `14.1` at `t=0.01`, and no cluster at `t=0.005`
-
-## Combining subcluster construction with incremental network building.
-
-(See `incremental.md` for background on incremental construction).
-
-When `-P` option is provided with `-t` and multiple thresholds, `hivnetworkcsv` will attempt to map subclusters from the current network to the subclusters from the previous network. The rule for matching subclusters is as follows.
-
-If the current network has a subcluster, `C`, at distance threshold, `t`, **and** the previous network has a subcluster `Cp` at the same distance thereshold, then `C` will be matched with `Cp` *if and only if*
-
-0. The subclusters each belong to the respective matched clusters.
-1. The interesection of `C` and `Cp` is non-empty (i.e. **some** of the nodes from `C` are in `Cp`).
-2. The intersection of `C` with any other previous network subcluster from the same cluster is empty, i.e. `C` does not overlap with any other existing subclusters.
-3. `Cp` does not overlap with any current network subclusters other that `C`
-
-For example,
-
-```
-hivnetworkcsv -i tests/subclusters/pirc.csv -t 0.02,0.01,0.005 \
--f regexp -p 0 "^([^|]+)\|([0-9]+)" -p 0 "^([^|]+)\|([0-9]+)" \
--P tests/subclusters/pirc-2009.json -j -O tests/subclusters/pirc.json
-```
-
-