In [1]:

    

from tethne.readers import wos


    

In [12]:

    

wos_corpus = wos.read('/Users/erickpeirson/Downloads/JHB from JSTOR/wos')


    

In [3]:

    

len(wos_corpus)


    

    
Out[3]:





1168

In [4]:

    

from tethne.networks import coauthors, cocitation


    

In [5]:

    

ca = coauthors(wos_corpus)


    

In [6]:

    

ca.order(), ca.size()


    

    
Out[6]:





(137, 96)

In [133]:

    

from tethne import GraphCollection


    

In [24]:

    

GCA = GraphCollection(wos_corpus, coauthors, slice_kwargs={"window_size": 4, 'step_size': 1})


    

In [25]:

    

GCA.order(), GCA.size()


    

    
Out[25]:





(137, 371)

In [138]:

    

from tethne import LDAModel, tokenize


    

In [139]:

    

wos_corpus.index_feature('abstract', tokenize=tokenize, structured=True)


    

In [140]:

    

from nltk.corpus import stopwords
stoplist = stopwords.words()


    

In [141]:

    

def apply_stoplist(f, v, c, dc):
    def number(v):
        try:
            eval(v)
            return True
        except:
            return False
                
    if f.lower() in stoplist or dc > 50 or dc < 3 or number(f) or len(f) < 4:
        return None
    return v


    

In [142]:

    

wos_corpus.features['abstract_filtered'] = wos_corpus.features['abstract'].transform(apply_stoplist)


    

In [143]:

    

model = LDAModel(wos_corpus, featureset_name='abstract_filtered')


    

In [144]:

    

model.fit(Z=50, max_iter=500)


    

In [145]:

    

model.print_topics()


    

    




Topic	Top 10 words
0  	political society popular response position sociobiology classification hand figure offered
1  	debate significant question origins great humans nuclear prominent radiation connection
2  	genetic organisms systems specific information genes provided virus gene effects
3  	project princeton medical results atomic energy primarily describes production potential
4  	theories technol status geneticists richard difference morgan reasons conducted conception
5  	questions nineteenth number taxonomy museum received systematics involved european technical
6  	authors eugenics racial eugenic present perspective diversity strong nazi rats
7  	variation developmental argued individual light processes main weismann stage weismanns
8  	heredity inheritance hereditary explain characteristics found characters distinct acquired elements
9  	plant focus examines alternative applied fundamental ideal half disciplines decades
10 	context institute postwar special japanese hybrid mexican interaction corn dynamic
11 	cell researchers material cells eventually objects chemical protein claim made
12 	german order morphology england progress interpretation attempt organic manchester conceptual
13 	argue modern idea types darwinism chicago economy shared journal decades
14 	naturalists related called discussions individuals relationships writings detailed beagle collecting
15 	forms period politics transformation turn interest understood experimentation reaction pittsburgh
16 	essay united states growth sites examining washington resources features activities
17 	synthesis hypothesis explanation view major ultimately mitchell london biol enzyme
18 	practice community professional academic relationship literature amateurs victorian liberal goals
19 	understanding developed group explores relations argued movement place essential provided
20 	techniques issues focusing biochemical technology biochemistry department ways reflected technol
21 	population understand suggests framework education concerns mayr movement models conflict
22 	public impact contributed case publication observations england fact making colonial
23 	influence personal considered contributions interactions contemporary basis moral claims workers
24 	animal animals show behavior provide methodological primate attention systematic radford
25 	historians evidence views importance laws emphasis thinking principles articles conclusions
26 	works term broader identification investigations soil published discoveries proposed chemistry
27 	including environment support today prior place interested accounts calif director
28 	methods agricultural point developed germany statistical disciplines student significance tech
29 	biol data record generation huxley sense link arizona fossil past
30 	knowledge made sexual published organisms theoretical accepted papers reception robert
31 	practices inst wallace berlin germany groups story helped contrast shaped
32 	breeding breeders practical world mendelism agricultural artificial true unit humanities
33 	mexico physiology played physiological argues physiologists culture perception discipline visual
34 	origin ideas charles form thought presented aristotles famous issue letter
35 	university institutional school national international agriculture vision europe biophysics universities
36 	process discipline darwinian revolution intellectual examination strategies professionalization investigation culture
37 	concept concepts french france notion language tradition paris giraffe physical
38 	ecology ecological local large shows controversy vegetation committee areas members
39 	based patterns elements recent explanations implications experience recognized mcclintock lineage
40 	factors studying regeneration aging path epistemic broad remained approaches marine
41 	attention central western cultural china efforts america soviet power cold
42 	account scientist generally theoretical discusses variety clements interests approach organism
43 	south environmental began change management world control conservation national africa
44 	general problems method living philosophical similar experiment canada things problem
45 	late discovery experiments cancer episode vivisection lack search biomedical blood
46 	case success established netherlands worked women colleagues make environments philosophers
47 	british coll william cambridge scholars toronto writing parts views division
48 	series book comparative lectures working anderson major establishment columbia publications
49 	view system change trees shift mechanism edition created mendelian text

In [146]:

    

from tethne.networks.topics import topic_coupling, terms, cotopics


    

In [147]:

    

tc = topic_coupling(model)


    

In [148]:

    

tc.order(), tc.size()


    

    
Out[148]:





(299, 3599)

In [149]:

    

tr = terms(model)
tr.order(), tr.size()


    

    
Out[149]:





(1414, 24857)

In [150]:

    

ct = cotopics(model)
ct.order(), ct.size()


    

    
Out[150]:





(50, 1017)

In [151]:

    

model.M = model.Z


    

In [1]:

    

from tethne.readers import dfr


    

In [ ]:

    

dfr_corpus = dfr.read('/Users/erickpeirson/JHB/data/DfR')


    

In [ ]:

    

len(dfr_corpus)


    

In [ ]:

    

corpus.features


    

In [10]:

    

from tethne.readers import merge


    

In [13]:

    

corpus = merge(wos_corpus, dfr_corpus)


    

In [14]:

    

len(corpus)


    

    
Out[14]:





1627

In [13]:

    

corpus[('authors', ('BENNETT', 'BRETT M'))][0].__dict__


    

    
Out[13]:





{'ER': u'',
 'FX': [u'I would like to thank the outside reviewers who critiqued this article',
  u'and offered many useful comments. Jane and Libby gave invaluable advice',
  u'and constant help during the revision process. The Centre for',
  u'Environmental History and the History Program at the Australian National',
  u'University provided me with office space and an intellectual home away',
  u'from home that allowed me to revise this article for publication. I',
  u'would also like to acknowledge the Social Science Research Council and',
  u'the American Council of Learned Societies for funding my International',
  u'Dissertation Research Fellowship, which allowed me to pursue archival',
  u'research for this article in Australia, South Africa, and the United',
  u'Kingdom.'],
 'GA': u'739JW',
 'ISSN': [u'0022-5010', u'J9 J HIST BIOL'],
 'PD': u'FEB',
 'PG': 21,
 'PM': 20665086,
 'PT': u'J',
 'WC': u'Biology; History & Philosophy Of Science',
 'abstract': u'Scholars studying the globalization of Australian trees have previously emphasized the rapid natural propagation of Australian trees outside of their native habitats, believing their success to be a reversal of "ecological imperialism" from the "new world" to the "old world." This article argues that the expansion of Australian trees should not be viewed as a biological phenomenon, but as the result of a long-term attempt by powerful states and state-sponsored scientists to select and breed Australian species that could grow in a variety of climates and ecological conditions. Five non-biological factors largely determined the success of these attempts to grow Australian trees: the abundance or paucity of natural forests, state power, the amount of scientific research directed to planting Australian trees, the cost of labor, and the ability to utilize hardwood timbers and bark. This paper compares the use of Australian trees in Australia, India, and South Africa to demonstrate that biology was not the determining factor in the long-term success of many Australian genera and species. C1 Univ Western Sydney, Sch Humanities & Languages, Sydney, NSW, Australia.',
 'authorKeywords': [u'ACACIA', u'IMPERIALISM'],
 'authors_full': [(u'BENNETT', u'BRETT M')],
 'authors_init': [(u'BENNETT', u'B M')],
 'citationCount': 80,
 'citedReferences': [<tethne.classes.paper.Paper at 0x10a025fd0>,
  <tethne.classes.paper.Paper at 0x10a034090>,
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  <tethne.classes.paper.Paper at 0x10a034b90>,
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  <tethne.classes.paper.Paper at 0x10a034c10>,
  <tethne.classes.paper.Paper at 0x10a034c50>,
  <tethne.classes.paper.Paper at 0x10a034c90>,
  <tethne.classes.paper.Paper at 0x10a034cd0>,
  <tethne.classes.paper.Paper at 0x10a034d10>,
  <tethne.classes.paper.Paper at 0x10a034d50>,
  <tethne.classes.paper.Paper at 0x10a034d90>,
  <tethne.classes.paper.Paper at 0x10a034dd0>,
  <tethne.classes.paper.Paper at 0x10a034e10>,
  <tethne.classes.paper.Paper at 0x10a034e90>,
  <tethne.classes.paper.Paper at 0x10a034e50>,
  <tethne.classes.paper.Paper at 0x10a034ed0>,
  <tethne.classes.paper.Paper at 0x10a034f10>,
  <tethne.classes.paper.Paper at 0x10a034f50>,
  <tethne.classes.paper.Paper at 0x10a034f90>,
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  <tethne.classes.paper.Paper at 0x10a041090>,
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  <tethne.classes.paper.Paper at 0x10a0410d0>,
  <tethne.classes.paper.Paper at 0x10a041110>,
  <tethne.classes.paper.Paper at 0x10a041150>,
  <tethne.classes.paper.Paper at 0x10a041190>,
  <tethne.classes.paper.Paper at 0x10a0411d0>,
  <tethne.classes.paper.Paper at 0x10a041210>,
  <tethne.classes.paper.Paper at 0x10a041250>,
  <tethne.classes.paper.Paper at 0x10a0412d0>,
  <tethne.classes.paper.Paper at 0x10a041290>,
  <tethne.classes.paper.Paper at 0x10a041310>,
  <tethne.classes.paper.Paper at 0x10a041350>,
  <tethne.classes.paper.Paper at 0x10a041390>,
  <tethne.classes.paper.Paper at 0x10a041410>,
  <tethne.classes.paper.Paper at 0x10a041450>,
  <tethne.classes.paper.Paper at 0x10a041490>,
  <tethne.classes.paper.Paper at 0x10a0414d0>,
  <tethne.classes.paper.Paper at 0x10a041510>,
  <tethne.classes.paper.Paper at 0x10a041590>,
  <tethne.classes.paper.Paper at 0x10a0415d0>,
  <tethne.classes.paper.Paper at 0x10a041550>,
  <tethne.classes.paper.Paper at 0x10a041610>,
  <tethne.classes.paper.Paper at 0x10a041650>,
  <tethne.classes.paper.Paper at 0x10a041690>,
  <tethne.classes.paper.Paper at 0x10a0416d0>,
  <tethne.classes.paper.Paper at 0x10a041710>,
  <tethne.classes.paper.Paper at 0x10a041750>,
  <tethne.classes.paper.Paper at 0x10a041790>,
  <tethne.classes.paper.Paper at 0x10a0417d0>,
  <tethne.classes.paper.Paper at 0x10a041810>,
  <tethne.classes.paper.Paper at 0x10a041850>,
  <tethne.classes.paper.Paper at 0x10a0418d0>,
  <tethne.classes.paper.Paper at 0x10a041890>,
  <tethne.classes.paper.Paper at 0x10a041910>,
  <tethne.classes.paper.Paper at 0x10a041950>,
  <tethne.classes.paper.Paper at 0x10a041990>,
  <tethne.classes.paper.Paper at 0x10a0419d0>,
  <tethne.classes.paper.Paper at 0x10a041a10>,
  <tethne.classes.paper.Paper at 0x10a041a50>,
  <tethne.classes.paper.Paper at 0x10a041a90>,
  <tethne.classes.paper.Paper at 0x10a041ad0>,
  <tethne.classes.paper.Paper at 0x10a041b10>,
  <tethne.classes.paper.Paper at 0x10a041b90>,
  <tethne.classes.paper.Paper at 0x10a041c10>,
  <tethne.classes.paper.Paper at 0x10a041bd0>,
  <tethne.classes.paper.Paper at 0x10a041c50>,
  <tethne.classes.paper.Paper at 0x10a041b50>,
  <tethne.classes.paper.Paper at 0x10a041c90>],
 'date': 2011,
 'documentType': u'Article',
 'doi': u'10.1007/s10739-010-9243-7',
 'emailAddress': u'utxaustinbennett@yahoo.com',
 'funding': [(u'Social Science Research Council', None),
  (u'American Council of Learned Societies', None)],
 'isoSource': u'J. Hist. Biol.',
 'issue': 1,
 'journal': u'JOURNAL OF THE HISTORY OF BIOLOGY',
 'keywordsPlus': [u'Acacia; ecological imperialism; Eucalyptus; forestry; globalization;',
  u'invasive species; plantation; silviculture'],
 'language': u'English',
 'pageEnd': 145,
 'pageStart': 125,
 'publisher': u'SPRINGER',
 'publisherAddress': u'VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS',
 'publisherCity': u'DORDRECHT',
 'reprintAddress': u'Bennett, BM (reprint author), Univ Western Sydney, Sch Humanities & Languages, Sydney, NSW, Australia.',
 'subject': [u'Life Sciences & Biomedicine - Other Topics; History & Philosophy of',
  u'Science'],
 'timesCited': [9, u'Z9 10'],
 'title': u'A Global History Of Australian Trees',
 'volume': u'44',
 'wosid': u'WOS:000288714200007'}

In [14]:

    

from tethne.readers import merge


    

In [15]:

    

combined = Corpus(merge(corpus.papers, dfr_corpus_combined))


    

In [21]:

    

combined.indexed_papers


    

    
Out[21]:





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In [16]:

    

def merge(P1, P2, fields=['ayjid']):
    """
    Combines two lists (P1 and P2) of :class:`.Paper` instances into a single
    list, and attempts to merge papers with matching fields. Where there are
    conflicts, values from :class:`.Paper` in P1 will be preferred.

    Parameters
    ----------
    P1 : list
        A list of :class:`.Paper` instances.
    P2 : list
        A list of :class:`.Paper` instances.
    fields : list
        Fields used to identify matching :class:`.Paper`

    Returns
    -------
    combined : list
        A list of :class:`.Paper` instances.

    Examples
    --------

    .. code-block:: python

       >>> import tethne.readers as rd
       >>> P1 = rd.wos.read("/Path/to/data1.txt")
       >>> P2 = rd.dfr.read("/Path/to/DfR")
       >>> papers = rd.merge(P1, P2, ['ayjid'])
    """

    combined = []
    del_P1 = []
    del_P2 = []

    for x in xrange(len(P1)):
        p_1 = P1[x]
        for y in xrange(len(P2)):
            p_2 = P2[y]
            match = True
            for field in fields:
                if hasattr(p_1, field) and hasattr(p_2, field):
                    if getattr(p_1, field) != getattr(p_2, field):
                        match = False
                        break

            if match:   # Add values first from P2 paper, then from P1 paper.
                new_p = Paper()
                for key, value in p_2.__dict__.items():
                    if value != '' and value is not None:
                        new_p[key] = value
                for key, value in p_1.__dict__.items():
                    if value != '' and value is not None:
                        new_p[key] = value

                del_P1.append(x)    # Flag for deletion.
                del_P2.append(y)

                combined.append(new_p)

    for x in xrange(len(P1)):
        if x not in del_P1:
            combined.append(P1[x])
    for x in xrange(len(P2)):
        if x not in del_P2:
            combined.append(P2[x])

    return combined


    

In [17]:

    

from tethne import Paper


    

In [ ]: