diff --git a/README.md b/README.md index d5b9a51..d0b5b9d 100644 --- a/README.md +++ b/README.md @@ -158,10 +158,15 @@ for generating them, is also included. #### Host/Parasite * **gopher-louse** Hafner, M.S. & Nadler, S.A. 1988. *Phylogenetic trees support the coevolution of parasites and their hosts.* Nature 332: 258-259) -* **dove-louse** Dale H. Clayton, Sarah E. Bush, Brad M. Goates, and Kevin P. Johnson. 2003. *Host defense reinforces host–parasite cospeciation.* PNAS. +* **dove-louse** Dale H. Clayton, Sarah E. Bush, Brad M. Goates, and Kevin P. Johnson. 2003. *Host defense reinforces host–parasite cospeciation.* PNAS. #### Plant/Pollinator (visitor) interactions +These were originally collected by Enrico Rezende *et al.* : + +> Enrico L. Rezende, Jessica E. Lavabre, Paulo R. GuimarĂ£es, Pedro Jordano & Jordi Bascompte +"[Non-random coextinctions in phylogenetically structured mutualistic networks](http://www.nature.com/nature/journal/v448/n7156/abs/nature05956.html)," *Nature*, 2007 + * **arr1** Arroyo, M.T.K., R. Primack & J.J. Armesto. 1982. *Community studies in pollination ecology in the high temperate Andes of central Chile. I. Pollination mechanisms and altitudinal variation.* Amer. J. Bot. 69:82-97. * **arr2** Arroyo, M.T.K., R. Primack & J.J. Armesto. 1982. *Community studies in pollination ecology in the high temperate Andes of central Chile. I. Pollination mechanisms and altitudinal variation.* Amer. J. Bot. 69:82-97. * **arr3** Arroyo, M.T.K., R. Primack & J.J. Armesto. 1982. *Community studies in pollination ecology in the high temperate Andes of central Chile. I. Pollination mechanisms and altitudinal variation.* Amer. J. Bot. 69:82-97. diff --git a/data/dove-louse/dove-louse.ipynb b/data/dove-louse/dove-louse.ipynb index 5b922ca..89c0e8c 100644 --- a/data/dove-louse/dove-louse.ipynb +++ b/data/dove-louse/dove-louse.ipynb @@ -1169,7 +1169,11 @@ " fasta = Entrez.efetch( db='nucleotide', id=ntid, rettype='fasta', retmode='text' ).read()\n", " louse_dna = parse( StringIO( fasta ), 'fasta' ).next()\n", " print louse_dna.description\n", - " louse_records.append( louse_dna )" + " louse_records.append( louse_dna )\n", + "\n", + "AF279704:AF279743\n", + "AF278608:AF278643\n", + "AY151003:AY151026" ] }, { diff --git a/data/sedge-smut/sedge-smut.ipynb b/data/sedge-smut/sedge-smut.ipynb index 594244c..d33e0ac 100644 --- a/data/sedge-smut/sedge-smut.ipynb +++ b/data/sedge-smut/sedge-smut.ipynb @@ -12,6 +12,8 @@ "Cospeciation or host-shift speciation?*](http://www.amjbot.org/content/102/7/1108.full),\n", "by Marcial Escudero.\n", "\n", + "> Escudero, Marcial. \"Phylogenetic congruence of parasitic smut fungi (*Anthracoidea*, Anthracoideaceae) and their host plants (*Carex*, Cyperaceae): Cospeciation or host-shift speciation?.\" *American journal of botany* 102.7 (2015): 1108-1114.\n", + "\n", "### Required software\n", "\n", "Python packages (available through pip) :\n", @@ -1440,7 +1442,7 @@ }, { "cell_type": "code", - "execution_count": 19, + "execution_count": 30, "metadata": { "collapsed": true }, @@ -1492,7 +1494,7 @@ }, { "cell_type": "code", - "execution_count": 20, + "execution_count": 31, "metadata": { "collapsed": false }, @@ -1612,7 +1614,7 @@ }, { "cell_type": "code", - "execution_count": 21, + "execution_count": 32, "metadata": { "collapsed": false }, @@ -1633,7 +1635,7 @@ }, { "cell_type": "code", - "execution_count": 22, + "execution_count": 33, "metadata": { "collapsed": true }, @@ -1652,7 +1654,7 @@ }, { "cell_type": "code", - "execution_count": 23, + "execution_count": 34, "metadata": { "collapsed": false }, @@ -1714,7 +1716,7 @@ }, { "cell_type": "code", - "execution_count": 24, + "execution_count": 35, "metadata": { "collapsed": true }, @@ -1727,7 +1729,7 @@ }, { "cell_type": "code", - "execution_count": 25, + "execution_count": 36, "metadata": { "collapsed": false }, @@ -3160,7 +3162,7 @@ "[39 rows x 27 columns]" ] }, - "execution_count": 25, + "execution_count": 36, "metadata": {}, "output_type": "execute_result" } @@ -3193,7 +3195,7 @@ }, { "cell_type": "code", - "execution_count": 26, + "execution_count": 37, "metadata": { "collapsed": false }, @@ -3205,7 +3207,7 @@ "" ] }, - "execution_count": 26, + "execution_count": 37, "metadata": {}, "output_type": "execute_result" } @@ -3242,7 +3244,7 @@ }, { "cell_type": "code", - "execution_count": 27, + "execution_count": 38, "metadata": { "collapsed": false }, @@ -3254,7 +3256,7 @@ "" ] }, - "execution_count": 27, + "execution_count": 38, "metadata": {}, "output_type": "execute_result" } @@ -3301,7 +3303,7 @@ }, { "cell_type": "code", - "execution_count": 28, + "execution_count": 39, "metadata": { "collapsed": false }, @@ -3317,7 +3319,7 @@ }, { "cell_type": "code", - "execution_count": 29, + "execution_count": 40, "metadata": { "collapsed": false }, @@ -3328,7 +3330,7 @@ "(0, 130)" ] }, - "execution_count": 29, + "execution_count": 40, "metadata": {}, "output_type": "execute_result" }, @@ -3336,7 +3338,7 @@ "data": { "image/png": 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"text/plain": [ - "" + "" ] }, "metadata": { diff --git a/setup.cfg b/setup.cfg new file mode 100644 index 0000000..b88034e --- /dev/null +++ b/setup.cfg @@ -0,0 +1,2 @@ +[metadata] +description-file = README.md diff --git a/setup.py b/setup.py index e9c3676..c0a2aba 100755 --- a/setup.py +++ b/setup.py @@ -12,6 +12,7 @@ author_email='ryneches@ucdavis.edu', license='BSD', packages=['SuchTree'], + download_url='https://github.com/ryneches/SuchTree/archive/0.1.tar.gz', install_requires=[ 'scipy>=0.18', 'numpy',