Add data, link notebooks internally, reduce resolution of figures.

Fix #9, fix #18
blab · Aug 7, 2017 · 75972be · 75972be
1 parent ff7db19
commit 75972be
Show file tree

Hide file tree

Showing 14 changed files with 357 additions and 274 deletions.
diff --git a/data/phylo/CFML_results.zip b/data/phylo/CFML_results.zip
diff --git a/data/phylo/frag_skygrid.zip b/data/phylo/frag_skygrid.zip
diff --git a/data/phylo/sequences.zip b/data/phylo/sequences.zip
diff --git a/data/phylo/skygrid.zip b/data/phylo/skygrid.zip
diff --git a/data/phylo/structured-coalescent-2fragments.zip b/data/phylo/structured-coalescent-2fragments.zip
diff --git a/data/phylo/structured-coalescent-prior.zip b/data/phylo/structured-coalescent-prior.zip
diff --git a/data/phylo/structured-coalescent.zip b/data/phylo/structured-coalescent.zip
diff --git a/figures/mers_chain.png b/figures/mers_chain.png
diff --git a/figures/mers_fragments.png b/figures/mers_fragments.png
diff --git a/figures/mers_recombinant_features.png b/figures/mers_recombinant_features.png
diff --git a/scripts/MERS.2_epi.ipynb b/scripts/MERS.2_epi.ipynb
@@ -465,7 +465,7 @@
    ],
    "source": [
     "data={1:{},2:{},3:{}} ## levels of bias\n",
-    "\n",
+    "## this bit of the notebook uses \n",
     "for f in os.listdir('/Users/evogytis/Dropbox/Jupyter_notebooks/MCMC/'):\n",
     "    #print f\n",
     "    if '_1' in f:\n",
@@ -1102,9 +1102,9 @@
     "mpl.colorbar.ColorbarBase(cb, cmap=cmap,ticks=np.linspace(0.5,1.1,7),norm=norm)\n",
     "cb.tick_params(size=5,labelsize=20)\n",
     "cb.set_ylabel('R$_{0}$')\n",
-    "# plt.savefig('/Users/evogytis/Documents/structured-mers/figures/mers_epi.png',dpi=300,bbox_inches='tight') ## save to file\n",
-    "# plt.savefig('/Users/evogytis/Documents/structured-mers/figures/mers_epi_4000c.png',dpi=300,bbox_inches='tight')\n",
-    "#plt.savefig('/Users/evogytis/Documents/structured-mers/figures/mers_epi.pdf',dpi=300,bbox_inches='tight')\n",
+    "# plt.savefig('./../figures/mers_epi.png',dpi=300,bbox_inches='tight') ## save to file\n",
+    "# plt.savefig('./../figures/mers_epi_4000c.png',dpi=300,bbox_inches='tight')\n",
+    "#plt.savefig('./../figures/mers_epi.pdf',dpi=300,bbox_inches='tight')\n",
     "plt.show()"
    ]
   },

diff --git a/scripts/MERS.2_posterior.ipynb b/scripts/MERS.2_posterior.ipynb
diff --git a/scripts/MERS.2_recombination.ipynb b/scripts/MERS.2_recombination.ipynb
diff --git a/scripts/MERS.2_trees.ipynb b/scripts/MERS.2_trees.ipynb