initial import of material for public archive into git
We're creating a fresh archive because the history for our old chapter includes API keys, data files, and other material we can't share.
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code/bibliometrics/00_citation_network_analysis.py
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232
code/bibliometrics/00_citation_network_analysis.py
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# coding: utf-8
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# # Import data and get things setup
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import random
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random.seed(9001)
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# import code to write r modules and create our variable we'll write to
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import rpy2.robjects as robjects
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from rpy2.robjects import pandas2ri
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pandas2ri.activate()
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r = {}
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def remember(name, x):
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r[name] = x
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# load in modules we'll need for analysis
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import subprocess
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import csv
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from igraph import *
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import pandas as pd
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import numpy as np
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import re
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# grab the largest connected compontent with a little function
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def get_largest_component(g):
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g_components = g.components(mode="WEAK")
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max_size = max(g_components.sizes())
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for g_tmp in g_components.subgraphs():
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if g_tmp.vcount() == max_size:
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return(g_tmp)
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# look the full edgelist into igraph
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def edge_list_iter(df):
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for i, row in df.iterrows():
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yield (row['from'], row['to'])
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# list top 5 journals for each of the clusters
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def top_journals_for_clusters(clu):
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articles_tmp = pd.merge(clu, articles[['eid', 'source_title']])
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output = pd.DataFrame()
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for cid in articles_tmp['cluster'].unique():
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journal_counts = articles_tmp['source_title'][articles_tmp['cluster'] == cid].value_counts().head(5)
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tmp = pd.DataFrame({'cluster' : cid, 'count' : journal_counts })
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output = output.append(tmp)
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output = output.reset_index()
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output = output.rename(columns = {'index' : "journal"})
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return(output)
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def infomap_edgelist(g, edgelist_filename, directed=True):
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nodes_tmp = pd.DataFrame([ {'node_infomap' : v.index,
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'eid' : v['name']} for v in g.vs ])
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# write out the edgelist to an external file so we can call infomap on it
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with open("code/bibliometrics/" + edgelist_filename + ".txt", 'w') as f:
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for e in g.es:
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if e.source != e.target:
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if 'weight' in e.attributes():
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print("{}\t{}\t{}".format(e.source, e.target, e['weight']), file=f)
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else:
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print("{}\t{}".format(e.source, e.target), file=f)
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# run the external program to generate the infomap clustering
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infomap_cmdline = ["code/bibliometrics/infomap/Infomap", "code/bibliometrics/" + edgelist_filename + ".txt", "code/bibliometrics/output_dir -z --map --clu --tree"]
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if directed:
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infomap_cmdline.append("-d")
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subprocess.call(infomap_cmdline)
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# load up the clu data
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clu = pd.read_csv("code/bibliometrics/output_dir/" + edgelist_filename + ".clu",
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header=None, comment="#", delim_whitespace=True)
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clu.columns = ['node_infomap', 'cluster', 'flow']
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return pd.merge(clu, nodes_tmp, on="node_infomap")
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def write_graphml(g, clu, graphml_filename):
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clu = clu[['node_infomap', 'cluster']].sort_values('node_infomap')
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g.vs["cluster"] = clu["cluster"].tolist()
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g.write_graphml("code/bibliometrics/" + graphml_filename)
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# load article data
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articles = pd.read_csv("processed_data/abstracts.tsv", delimiter="\t")
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# # network for just the central "social media" set
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# this contains the list of all INCOMING citations to for paper in the original set
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raw_edgelist = pd.read_csv("processed_data/social_media_edgelist.txt", delimiter="\t")
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g_sm_all = Graph.TupleList([i for i in edge_list_iter(raw_edgelist)], directed=True)
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g_sm = get_largest_component(g_sm_all)
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g_sm = g_sm.simplify()
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g_sm_clu = infomap_edgelist(g_sm, "sm_edgelist_infomap", directed=True)
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g_sm_clu['cluster'].value_counts()
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write_graphml(g_sm, g_sm_clu, "g_sm.graphml")
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# # larger network that contains the incoming cites to citing articles
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# this contains the list of all INCOMING citations to everything in the original set
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# plus every INCOMING citation to every paper that cites one of those papers
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raw_edgelist_files = ["processed_data/citation_edgelist.txt",
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"processed_data/social_media_edgelist.txt"]
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combo_raw_edgelist = pd.concat([pd.read_csv(x, delimiter="\t") for x in raw_edgelist_files])
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g_full_all = Graph.TupleList([i for i in edge_list_iter(combo_raw_edgelist)], directed=True)
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g_full = get_largest_component(g_full_all)
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g_full = g_full.simplify()
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g_full_clu = infomap_edgelist(g_full, "citation_edglist_infomap", directed=True)
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g_full_clu['cluster'].value_counts()
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top_journals_for_clusters(g_full_clu)
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write_graphml(g_full, g_full_clu, "g_full.graphml")
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# # create the meta-network of connections between clusters
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edgelist_tmp = pd.merge(raw_edgelist, g_sm_clu[["eid", "cluster"]], how="inner", left_on="to", right_on="eid")
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edgelist_tmp = edgelist_tmp.rename(columns={'cluster' : 'to_cluster'})
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edgelist_tmp.drop('eid', 1, inplace=True)
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edgelist_tmp = pd.merge(edgelist_tmp, g_sm_clu[["eid", "cluster"]], how="inner", left_on="from", right_on="eid")
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edgelist_tmp = edgelist_tmp.rename(columns={"cluster" : 'from_cluster'})
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edgelist_tmp.drop('eid', 1, inplace=True)
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edgelist_tmp = edgelist_tmp[["to_cluster", "from_cluster"]]
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edgelist_tmp = edgelist_tmp[edgelist_tmp["to_cluster"] != edgelist_tmp["from_cluster"]]
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cluster_edgelist = pd.crosstab(edgelist_tmp["to_cluster"], edgelist_tmp["from_cluster"])
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cluster_edgelist["to_cluster"] = cluster_edgelist.index
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cluster_edgelist = pd.melt(cluster_edgelist, id_vars=["to_cluster"])
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cluster_edgelist = cluster_edgelist[cluster_edgelist['to_cluster'] != cluster_edgelist['from_cluster']]
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remember("cluster_edgelist", cluster_edgelist)
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top_clusters = g_sm_clu["cluster"].value_counts().head(6).index
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# write the edgelist for the total number of clusters (currently 1-6)
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cluster_edgelist_output = cluster_edgelist[(cluster_edgelist["to_cluster"].isin(top_clusters)) &
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(cluster_edgelist["from_cluster"].isin(top_clusters))]
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cluster_edgelist_output = cluster_edgelist_output[cluster_edgelist_output["value"] > 0]
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g_cluster = Graph.TupleList([tuple(x) for x in cluster_edgelist_output[["from_cluster", "to_cluster"]].values], directed=True)
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g_cluster.es["weight"] = cluster_edgelist_output["value"].tolist()
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# assign the number of total articles as an attribute for each node
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g_cluster.vs["papers"] = g_sm_clu["cluster"].value_counts()[[x["name"] for x in g_cluster.vs]].tolist()
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g_cluster.write_graphml("code/bibliometrics/clusters.graphml")
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# # create network stats for tables (overall and within clusters)
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def create_network_stats(g):
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network_stats = pd.DataFrame({'eid' : g.vs['name'],
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'eig_cent' : g.eigenvector_centrality(),
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'indegree' : g.indegree(),
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'betweenness' : g.betweenness()})
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network_stats = pd.merge(network_stats,
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articles[['eid', 'title', 'source_title']],
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how="inner")
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return network_stats
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network_stats = create_network_stats(g_full)
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network_stats.sort_values("indegree", ascending=False).head(4)
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network_stats.sort_values("eig_cent", ascending=False).head(4)
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network_stats.sort_values("betweenness", ascending=False).head(4)
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# # things to store
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remember('total_articles', articles.shape[0])
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# total number of citations in the sm dataset
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remember('sm_citations', raw_edgelist.shape[0])
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remember('sm_citing', len(raw_edgelist["from"].unique()))
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# the number of articles in the original dataset that have any INCOMING citations
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remember('sm_cited', len(raw_edgelist["to"].unique()))
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# total number of citations in the sm dataset
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remember('all_citations', combo_raw_edgelist.shape[0])
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remember('all_citing', len(combo_raw_edgelist["from"].unique()))
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# the number of articles in the original dataset that have any INCOMING citations
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remember('all_cited', len(combo_raw_edgelist["to"].unique()))
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remember('g_sm_clusters', g_sm_clu[["eid", "cluster"]])
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sorted(r.keys())
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#save the r function to rdata file
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def save_to_r(r_dict, filename="output.RData"):
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for var_name, x in r.items():
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var_name = var_name.replace('_', '.')
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if type(x) == np.int64:
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x = np.asscalar(x)
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if type(x) == pd.DataFrame:
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rx = pandas2ri.py2ri(x)
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else:
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rx = x
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robjects.r.assign(var_name, x)
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# create a new variable called in R
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robjects.r("r <- sapply(ls(), function (x) {eval(parse(text=x))})")
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robjects.r('save("r", file="{}")'.format(filename))
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robjects.r("rm(list=ls())")
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save_to_r(r, "paper/data/network_data.RData")
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