Collating for real with CollateX

Okay, let's do some serious hands-on collation. Create a new Jupyter notebook (if you don't remember how to do this, here it is the tutorial) and follow the instructions.

First of all we want to make sure that you have the latest version of CollateX. That's why we do in the Jupyter Notebook:



In [1]:

    
!pip install --upgrade collatex









    



Requirement already up-to-date: collatex in c:\users\elena\python35\lib\site-packages
Requirement already up-to-date: networkx in c:\users\elena\python35\lib\site-packages (from collatex)
Requirement already up-to-date: prettytable in c:\users\elena\python35\lib\site-packages (from collatex)
Requirement already up-to-date: decorator>=3.4.0 in c:\users\elena\python35\lib\site-packages (from networkx->collatex)

Or directly in the commandline: pip install --upgrade collatex (without the exclamation mark at the beginning of the line).

You don't need to do this every time, but make sure you do it regularly.

Next we need to tell Python that we will be needing the Python library that holds the code for CollateX…



In [2]:

    
from collatex import *

Now we're ready to make a collation object. We do this with the slightly hermetic line of code:

collation = Collation()

Here the lower case collation is the arbitrary named variable that refers to a copy (officially it is called an instance) of the CollateX collation engine. We simply tell the collation library to create a new instance by saying Collation().



In [3]:

    
collation = Collation()

Now we add some witnesses. Each witness gets a letter or name that will identify them, and for each we add the literal text of the witness to the collation object, like so…



In [4]:

    
collation.add_plain_witness( "A", "The quick brown fox jumped over the lazy dog.")
collation.add_plain_witness( "B", "The brown fox jumped over the dog." )
collation.add_plain_witness( "C", "The bad fox jumped over the lazy dog." )

And now we can let CollateX do its work of collating these witnesses and sit back for about 0.001 seconds. The result will be an alignment table, so we'll refer to the result with a variable named alignment_table.



In [5]:

    
alignment_table = collate(collation, layout='vertical', segmentation=False )

Well, that worked nicely it seems. But there's no printout, no visualization. That's okay, we can come up with a printout of the alignment table too:



In [6]:

    
print( alignment_table )









    



+--------+--------+--------+
|   A    |   B    |   C    |
+--------+--------+--------+
|  The   |  The   |  The   |
+--------+--------+--------+
| quick  |   -    |  bad   |
+--------+--------+--------+
| brown  | brown  |   -    |
+--------+--------+--------+
|  fox   |  fox   |  fox   |
+--------+--------+--------+
| jumped | jumped | jumped |
+--------+--------+--------+
|  over  |  over  |  over  |
+--------+--------+--------+
|  the   |  the   |  the   |
+--------+--------+--------+
|  lazy  |   -    |  lazy  |
+--------+--------+--------+
|  dog   |  dog   |  dog   |
+--------+--------+--------+
|   .    |   .    |   .    |
+--------+--------+--------+

Usually you will want those segments that run parallel to be collected and displayed together. Since this is what most people seem to want, CollateX does that by default. We switched this option off in the example above for a moment because the result then shows you more clearly what the underlying primary structure is that CollateX returns. But for all practicle purposes you will probabably lose that segmentation=False option. So, let's get rid of that, and collate again…



In [7]:

    
alignment_table = collate(collation, layout='vertical' )



In [8]:

    
print( alignment_table )









    



+---------------------+---------------------+---------------------+
|          A          |          B          |          C          |
+---------------------+---------------------+---------------------+
|         The         |         The         |         The         |
+---------------------+---------------------+---------------------+
|        quick        |          -          |         bad         |
+---------------------+---------------------+---------------------+
|        brown        |        brown        |          -          |
+---------------------+---------------------+---------------------+
| fox jumped over the | fox jumped over the | fox jumped over the |
+---------------------+---------------------+---------------------+
|         lazy        |          -          |         lazy        |
+---------------------+---------------------+---------------------+
|         dog.        |         dog.        |         dog.        |
+---------------------+---------------------+---------------------+

The aligment table visualization is CollateX's default way of rendering a collation result. There are various ways in which one can depict collated results of course. The output in alignment table form can be a good basis for further visualizations. CollateX can also format your collation as a variant graph. This is a visualization that lets you trace from left to right through a directed network, to follow which witness carries what readings.



In [9]:

    
graph = collate( collation, output="svg", segmentation=True )

Okay, that's all good and nice, but that's just tiny fragments—we want decent chunks of text to collate! Well, we can do that too, although it requires a little more work. Specifically for reading in text files from the file system. If we didn't do it that way, we would have to key in all the characters of each witness, and that's just a lot of unnecessary work if we have those texts already in a file. The code below uses the open command to open each text file and assign the contents to a variable with an appropriately chosen name.

The encoding="utf-8" bit is needed because you should always tell Python which encoding your data uses. This is probably the only place and time where you will use that encoding directive: when you open a (text) file.



In [10]:

    
collation = Collation()
witness_1859 = open( "../fixtures/Darwin/txt/darwin1859_par1.txt", encoding='utf-8' ).read()
witness_1860 = open( "../fixtures/Darwin/txt/darwin1860_par1.txt", encoding='utf-8' ).read()
witness_1861 = open( "../fixtures/Darwin/txt/darwin1861_par1.txt", encoding='utf-8' ).read()
witness_1866 = open( "../fixtures/Darwin/txt/darwin1866_par1.txt", encoding='utf-8' ).read()
witness_1869 = open( "../fixtures/Darwin/txt/darwin1869_par1.txt", encoding='utf-8' ).read()
witness_1872 = open( "../fixtures/Darwin/txt/darwin1872_par1.txt", encoding='utf-8' ).read()
collation.add_plain_witness( "1859", witness_1859 )
collation.add_plain_witness( "1860", witness_1860 )
collation.add_plain_witness( "1861", witness_1861 )
collation.add_plain_witness( "1866", witness_1866 )
collation.add_plain_witness( "1869", witness_1869 )
collation.add_plain_witness( "1872", witness_1872 )

Now let's check if these witnesses actually contain some text by printing a few of them.



In [11]:

    
print( witness_1859 )









    



WHEN we look to the individuals of the same variety or sub-variety of our older cultivated plants and animals, one of the first points which strikes us, is, that they generally differ much more from each other, than do the individuals of any one species or variety in a state of nature. When we reflect on the vast diversity of the plants and animals which have been cultivated, and which have varied during all ages under the most different climates and treatment, I think we are driven to conclude that this greater variability is simply due to our domestic productions having been raised under conditions of life not so uniform as, and somewhat different from, those to which the parent-species have been exposed under nature. There is, also, I think, some probability in the view propounded by Andrew Knight, that this variability may be partly connected with excess of food. It seems pretty clear that organic beings must be exposed during several generations to the new conditions of life to cause any appreciable amount of variation; and that when the organisation has once begun to vary, it generally continues to vary for many generations. No case is on record of a variable being ceasing to be variable under cultivation. Our oldest cultivated plants, such as wheat, still often yield new varieties: our oldest domesticated animals are still capable of rapid improvement or modification.



In [12]:

    
print( witness_1860 )









    



WHEN we look to the individuals of the same variety or sub-variety of our older cultivated plants and animals, one of the first points which strikes us, is, that they generally differ more from each other than do the individuals of any one species or variety in a state of nature. When we reflect on the vast diversity of the plants and animals which have been cultivated, and which have varied during all ages under the most different climates and treatment, I think we are driven to conclude that this great variability is simply due to our domestic productions having been raised under conditions of life not so uniform as, and somewhat different from, those to which the parent-species have been exposed under nature. There is also, I think, some probability in the view propounded by Andrew Knight, that this variability may be partly connected with excess of food. It seems pretty clear that organic beings must be exposed during several generations to the new conditions of life to cause any appreciable amount of variation; and that when the organisation has once begun to vary, it generally continues to vary for many generations. No case is on record of a variable being ceasing to be variable under cultivation. Our oldest cultivated plants, such as wheat, still often yield new varieties: our oldest domesticated animals are still capable of rapid improvement or modification.

And now let's collate those witnesses and let's put the result up as an HTML-formatted alignment table…



In [13]:

    
alignment_table = collate(collation, layout='vertical', output='html')









    





    
        1859
        1860
        1861
        1866
        1869
        1872
    
    
        -
        -
        -
        Causes of
Variability.
        Causes of
Variability.
        Causes of
Variability.
    
    
        WHEN we
        WHEN we
        WHEN we
        WHEN we
        WHEN we
        WHEN we
    
    
        look to
        look to
        look to
        look to
        compare
        compare
    
    
        the individuals of
the same variety or
sub-variety of our
older cultivated
plants and animals,
one of the first
points which strikes
us
        the individuals of
the same variety or
sub-variety of our
older cultivated
plants and animals,
one of the first
points which strikes
us
        the individuals of
the same variety or
sub-variety of our
older cultivated
plants and animals,
one of the first
points which strikes
us
        the individuals of
the same variety or
sub-variety of our
older cultivated
plants and animals,
one of the first
points which strikes
us
        the individuals of
the same variety or
sub-variety of our
older cultivated
plants and animals,
one of the first
points which strikes
us
        the individuals of
the same variety or
sub-variety of our
older cultivated
plants and animals,
one of the first
points which strikes
us
    
    
        ,
        ,
        ,
        ,
        -
        -
    
    
        is, that they
generally differ
        is, that they
generally differ
        is, that they
generally differ
        is, that they
generally differ
        is, that they
generally differ
        is, that they
generally differ
    
    
        much
        -
        -
        -
        -
        -
    
    
        more
        more
        more
        more
        -
        more
    
    
        from each other
        from each other
        from each other
        from each other
        from each other
        from each other
    
    
        ,
        -
        -
        -
        more
        -
    
    
        than do the
individuals of any
one species or
variety in a state
of nature.
        than do the
individuals of any
one species or
variety in a state
of nature.
        than do the
individuals of any
one species or
variety in a state
of nature.
        than do the
individuals of any
one species or
variety in a state
of nature.
        than do the
individuals of any
one species or
variety in a state
of nature.
        than do the
individuals of any
one species or
variety in a state
of nature.
    
    
        When
        When
        When
        When
        And if
        And if
    
    
        we reflect on the
vast diversity of
the plants and
animals which have
been cultivated, and
which have varied
during all ages
under the most
different climates
and treatment,
        we reflect on the
vast diversity of
the plants and
animals which have
been cultivated, and
which have varied
during all ages
under the most
different climates
and treatment,
        we reflect on the
vast diversity of
the plants and
animals which have
been cultivated, and
which have varied
during all ages
under the most
different climates
and treatment,
        we reflect on the
vast diversity of
the plants and
animals which have
been cultivated, and
which have varied
during all ages
under the most
different climates
and treatment,
        we reflect on the
vast diversity of
the plants and
animals which have
been cultivated, and
which have varied
during all ages
under the most
different climates
and treatment,
        we reflect on the
vast diversity of
the plants and
animals which have
been cultivated, and
which have varied
during all ages
under the most
different climates
and treatment,
    
    
        I think
        I think
        I think
        I think
        -
        -
    
    
        we are driven to
conclude that this
        we are driven to
conclude that this
        we are driven to
conclude that this
        we are driven to
conclude that this
        we are driven to
conclude that this
        we are driven to
conclude that this
    
    
        greater
        great
        great
        great
        great
        great
    
    
        variability is
        variability is
        variability is
        variability is
        variability is
        variability is
    
    
        simply
        simply
        simply
        simply
        -
        -
    
    
        due to our domestic
productions having
been raised under
conditions of life
not so uniform as,
and somewhat
different from,
those to which the
parent-species
        due to our domestic
productions having
been raised under
conditions of life
not so uniform as,
and somewhat
different from,
those to which the
parent-species
        due to our domestic
productions having
been raised under
conditions of life
not so uniform as,
and somewhat
different from,
those to which the
parent-species
        due to our domestic
productions having
been raised under
conditions of life
not so uniform as,
and somewhat
different from,
those to which the
parent-species
        due to our domestic
productions having
been raised under
conditions of life
not so uniform as,
and somewhat
different from,
those to which the
parent-species
        due to our domestic
productions having
been raised under
conditions of life
not so uniform as,
and somewhat
different from,
those to which the
parent-species
    
    
        have
        have
        have
        have
        had
        had
    
    
        been exposed under
nature. There is
        been exposed under
nature. There is
        been exposed under
nature. There is
        been exposed under
nature. There is
        been exposed under
nature. There is
        been exposed under
nature. There is
    
    
        ,
        -
        -
        -
        -
        ,
    
    
        also
        also
        also
        also
        also
        also
    
    
        , I think
        , I think
        , I think
        , I think
        , I think
        -
    
    
        , some probability
in the view
propounded by Andrew
Knight, that this
variability may be
partly connected
with excess of food.
It seems
        , some probability
in the view
propounded by Andrew
Knight, that this
variability may be
partly connected
with excess of food.
It seems
        , some probability
in the view
propounded by Andrew
Knight, that this
variability may be
partly connected
with excess of food.
It seems
        , some probability
in the view
propounded by Andrew
Knight, that this
variability may be
partly connected
with excess of food.
It seems
        , some probability
in the view
propounded by Andrew
Knight, that this
variability may be
partly connected
with excess of food.
It seems
        , some probability
in the view
propounded by Andrew
Knight, that this
variability may be
partly connected
with excess of food.
It seems
    
    
        pretty
        pretty
        pretty
        pretty
        -
        -
    
    
        clear that organic
beings must be
exposed during
several generations
to
        clear that organic
beings must be
exposed during
several generations
to
        clear that organic
beings must be
exposed during
several generations
to
        clear that organic
beings must be
exposed during
several generations
to
        clear that organic
beings must be
exposed during
several generations
to
        clear that organic
beings must be
exposed during
several generations
to
    
    
        the
        the
        the
        the
        -
        -
    
    
        new
        new
        new
        new
        new
        new
    
    
        conditions of life
        conditions of life
        conditions of life
        conditions of life
        conditions
        conditions
    
    
        to cause any
        to cause any
        to cause any
        to cause any
        to cause any
        to cause any
    
    
        appreciable
        appreciable
        appreciable
        appreciable
        appreciable
        great
    
    
        amount of variation;
and that
        amount of variation;
and that
        amount of variation;
and that
        amount of variation;
and that
        amount of variation;
and that
        amount of variation;
and that
    
    
        -
        -
        -
        ,
        ,
        ,
    
    
        when the
organisation has
once begun to vary,
it generally
        when the
organisation has
once begun to vary,
it generally
        when the
organisation has
once begun to vary,
it generally
        when the
organisation has
once begun to vary,
it generally
        when the
organisation has
once begun to vary,
it generally
        when the
organisation has
once begun to vary,
it generally
    
    
        continues
        continues
        continues
        continues
        con- tinues
        continues
    
    
        to vary
        to vary
        to vary
        to vary
        varying
        varying
    
    
        for many
generations. No case
is on record of a
variable
        for many
generations. No case
is on record of a
variable
        for many
generations. No case
is on record of a
variable
        for many
generations. No case
is on record of a
variable
        for many
generations. No case
is on record of a
variable
        for many
generations. No case
is on record of a
variable
    
    
        being
        being
        being
        being
        organism
        organism
    
    
        ceasing
        ceasing
        ceasing
        ceasing
        ceasing
        ceasing
    
    
        to be variable
        to be variable
        to be variable
        to be variable
        to vary
        to vary
    
    
        under cultivation.
Our oldest
cultivated plants,
such as wheat, still
        under cultivation.
Our oldest
cultivated plants,
such as wheat, still
        under cultivation.
Our oldest
cultivated plants,
such as wheat, still
        under cultivation.
Our oldest
cultivated plants,
such as wheat, still
        under cultivation.
Our oldest
cultivated plants,
such as wheat, still
        under cultivation.
Our oldest
cultivated plants,
such as wheat, still
    
    
        often
        often
        often
        often
        -
        -
    
    
        yield new varieties:
our oldest
domesticated animals
are still capable of
rapid improvement or
modification.
        yield new varieties:
our oldest
domesticated animals
are still capable of
rapid improvement or
modification.
        yield new varieties:
our oldest
domesticated animals
are still capable of
rapid improvement or
modification.
        yield new varieties:
our oldest
domesticated animals
are still capable of
rapid improvement or
modification.
        yield new varieties:
our oldest
domesticated animals
are still capable of
rapid improvement or
modification.
        yield new varieties:
our oldest
domesticated animals
are still capable of
rapid improvement or
modification.

Hmm… that is still a little hard to read. Wouldn't it be nice if we got a hint where the actual differences are? Sure, try…



In [14]:

    
alignment_table = collate(collation, layout='vertical', output='html2')









    





 
  1859
  1860
  1861
  1866
  1869
  1872
 
 
  -
  -
  -
  Causes of
Variability.
  Causes of
Variability.
  Causes of
Variability.
 
 
  WHEN we
  WHEN we
  WHEN we
  WHEN we
  WHEN we
  WHEN we
 
 
  look to
  look to
  look to
  look to
  compare
  compare
 
 
  the individuals of
the same variety or
sub-variety of our
older cultivated
plants and animals,
one of the first
points which strikes
us
  the individuals of
the same variety or
sub-variety of our
older cultivated
plants and animals,
one of the first
points which strikes
us
  the individuals of
the same variety or
sub-variety of our
older cultivated
plants and animals,
one of the first
points which strikes
us
  the individuals of
the same variety or
sub-variety of our
older cultivated
plants and animals,
one of the first
points which strikes
us
  the individuals of
the same variety or
sub-variety of our
older cultivated
plants and animals,
one of the first
points which strikes
us
  the individuals of
the same variety or
sub-variety of our
older cultivated
plants and animals,
one of the first
points which strikes
us
 
 
  ,
  ,
  ,
  ,
  -
  -
 
 
  is, that they
generally differ
  is, that they
generally differ
  is, that they
generally differ
  is, that they
generally differ
  is, that they
generally differ
  is, that they
generally differ
 
 
  much
  -
  -
  -
  -
  -
 
 
  more
  more
  more
  more
  -
  more
 
 
  from each other
  from each other
  from each other
  from each other
  from each other
  from each other
 
 
  ,
  -
  -
  -
  more
  -
 
 
  than do the
individuals of any
one species or
variety in a state
of nature.
  than do the
individuals of any
one species or
variety in a state
of nature.
  than do the
individuals of any
one species or
variety in a state
of nature.
  than do the
individuals of any
one species or
variety in a state
of nature.
  than do the
individuals of any
one species or
variety in a state
of nature.
  than do the
individuals of any
one species or
variety in a state
of nature.
 
 
  When
  When
  When
  When
  And if
  And if
 
 
  we reflect on the
vast diversity of
the plants and
animals which have
been cultivated, and
which have varied
during all ages
under the most
different climates
and treatment,
  we reflect on the
vast diversity of
the plants and
animals which have
been cultivated, and
which have varied
during all ages
under the most
different climates
and treatment,
  we reflect on the
vast diversity of
the plants and
animals which have
been cultivated, and
which have varied
during all ages
under the most
different climates
and treatment,
  we reflect on the
vast diversity of
the plants and
animals which have
been cultivated, and
which have varied
during all ages
under the most
different climates
and treatment,
  we reflect on the
vast diversity of
the plants and
animals which have
been cultivated, and
which have varied
during all ages
under the most
different climates
and treatment,
  we reflect on the
vast diversity of
the plants and
animals which have
been cultivated, and
which have varied
during all ages
under the most
different climates
and treatment,
 
 
  I think
  I think
  I think
  I think
  -
  -
 
 
  we are driven to
conclude that this
  we are driven to
conclude that this
  we are driven to
conclude that this
  we are driven to
conclude that this
  we are driven to
conclude that this
  we are driven to
conclude that this
 
 
  greater
  great
  great
  great
  great
  great
 
 
  variability is
  variability is
  variability is
  variability is
  variability is
  variability is
 
 
  simply
  simply
  simply
  simply
  -
  -
 
 
  due to our domestic
productions having
been raised under
conditions of life
not so uniform as,
and somewhat
different from,
those to which the
parent-species
  due to our domestic
productions having
been raised under
conditions of life
not so uniform as,
and somewhat
different from,
those to which the
parent-species
  due to our domestic
productions having
been raised under
conditions of life
not so uniform as,
and somewhat
different from,
those to which the
parent-species
  due to our domestic
productions having
been raised under
conditions of life
not so uniform as,
and somewhat
different from,
those to which the
parent-species
  due to our domestic
productions having
been raised under
conditions of life
not so uniform as,
and somewhat
different from,
those to which the
parent-species
  due to our domestic
productions having
been raised under
conditions of life
not so uniform as,
and somewhat
different from,
those to which the
parent-species
 
 
  have
  have
  have
  have
  had
  had
 
 
  been exposed under
nature. There is
  been exposed under
nature. There is
  been exposed under
nature. There is
  been exposed under
nature. There is
  been exposed under
nature. There is
  been exposed under
nature. There is
 
 
  ,
  -
  -
  -
  -
  ,
 
 
  also
  also
  also
  also
  also
  also
 
 
  , I think
  , I think
  , I think
  , I think
  , I think
  -
 
 
  , some probability
in the view
propounded by Andrew
Knight, that this
variability may be
partly connected
with excess of food.
It seems
  , some probability
in the view
propounded by Andrew
Knight, that this
variability may be
partly connected
with excess of food.
It seems
  , some probability
in the view
propounded by Andrew
Knight, that this
variability may be
partly connected
with excess of food.
It seems
  , some probability
in the view
propounded by Andrew
Knight, that this
variability may be
partly connected
with excess of food.
It seems
  , some probability
in the view
propounded by Andrew
Knight, that this
variability may be
partly connected
with excess of food.
It seems
  , some probability
in the view
propounded by Andrew
Knight, that this
variability may be
partly connected
with excess of food.
It seems
 
 
  pretty
  pretty
  pretty
  pretty
  -
  -
 
 
  clear that organic
beings must be
exposed during
several generations
to
  clear that organic
beings must be
exposed during
several generations
to
  clear that organic
beings must be
exposed during
several generations
to
  clear that organic
beings must be
exposed during
several generations
to
  clear that organic
beings must be
exposed during
several generations
to
  clear that organic
beings must be
exposed during
several generations
to
 
 
  the
  the
  the
  the
  -
  -
 
 
  new
  new
  new
  new
  new
  new
 
 
  conditions of life
  conditions of life
  conditions of life
  conditions of life
  conditions
  conditions
 
 
  to cause any
  to cause any
  to cause any
  to cause any
  to cause any
  to cause any
 
 
  appreciable
  appreciable
  appreciable
  appreciable
  appreciable
  great
 
 
  amount of variation;
and that
  amount of variation;
and that
  amount of variation;
and that
  amount of variation;
and that
  amount of variation;
and that
  amount of variation;
and that
 
 
  -
  -
  -
  ,
  ,
  ,
 
 
  when the
organisation has
once begun to vary,
it generally
  when the
organisation has
once begun to vary,
it generally
  when the
organisation has
once begun to vary,
it generally
  when the
organisation has
once begun to vary,
it generally
  when the
organisation has
once begun to vary,
it generally
  when the
organisation has
once begun to vary,
it generally
 
 
  continues
  continues
  continues
  continues
  con- tinues
  continues
 
 
  to vary
  to vary
  to vary
  to vary
  varying
  varying
 
 
  for many
generations. No case
is on record of a
variable
  for many
generations. No case
is on record of a
variable
  for many
generations. No case
is on record of a
variable
  for many
generations. No case
is on record of a
variable
  for many
generations. No case
is on record of a
variable
  for many
generations. No case
is on record of a
variable
 
 
  being
  being
  being
  being
  organism
  organism
 
 
  ceasing
  ceasing
  ceasing
  ceasing
  ceasing
  ceasing
 
 
  to be variable
  to be variable
  to be variable
  to be variable
  to vary
  to vary
 
 
  under cultivation.
Our oldest
cultivated plants,
such as wheat, still
  under cultivation.
Our oldest
cultivated plants,
such as wheat, still
  under cultivation.
Our oldest
cultivated plants,
such as wheat, still
  under cultivation.
Our oldest
cultivated plants,
such as wheat, still
  under cultivation.
Our oldest
cultivated plants,
such as wheat, still
  under cultivation.
Our oldest
cultivated plants,
such as wheat, still
 
 
  often
  often
  often
  often
  -
  -
 
 
  yield new varieties:
our oldest
domesticated animals
are still capable of
rapid improvement or
modification.
  yield new varieties:
our oldest
domesticated animals
are still capable of
rapid improvement or
modification.
  yield new varieties:
our oldest
domesticated animals
are still capable of
rapid improvement or
modification.
  yield new varieties:
our oldest
domesticated animals
are still capable of
rapid improvement or
modification.
  yield new varieties:
our oldest
domesticated animals
are still capable of
rapid improvement or
modification.
  yield new varieties:
our oldest
domesticated animals
are still capable of
rapid improvement or
modification.

And finally, we can also generate the variant graph for this collation…



In [15]:

    
graph = collate( collation, output="svg" )

Note: you may have noticed that if you run the cells in an IPython notebook in order, they know about one another. For this reason, in the end of this tutorial we could produce different outputs using the information typed into the previous cells. When you open a notebook, remember to run the cells in order or to "run all cells" (from the menu Cell), otherwise you may get an error message.



In [ ]:

1859	1860	1861	1866	1869	1872
-	-	-	Causes of Variability.	Causes of Variability.	Causes of Variability.
WHEN we	WHEN we	WHEN we	WHEN we	WHEN we	WHEN we
look to	look to	look to	look to	compare	compare
the individuals of the same variety or sub-variety of our older cultivated plants and animals, one of the first points which strikes us	the individuals of the same variety or sub-variety of our older cultivated plants and animals, one of the first points which strikes us	the individuals of the same variety or sub-variety of our older cultivated plants and animals, one of the first points which strikes us	the individuals of the same variety or sub-variety of our older cultivated plants and animals, one of the first points which strikes us	the individuals of the same variety or sub-variety of our older cultivated plants and animals, one of the first points which strikes us	the individuals of the same variety or sub-variety of our older cultivated plants and animals, one of the first points which strikes us
,	,	,	,	-	-
is, that they generally differ	is, that they generally differ	is, that they generally differ	is, that they generally differ	is, that they generally differ	is, that they generally differ
much	-	-	-	-	-
more	more	more	more	-	more
from each other	from each other	from each other	from each other	from each other	from each other
,	-	-	-	more	-
than do the individuals of any one species or variety in a state of nature.	than do the individuals of any one species or variety in a state of nature.	than do the individuals of any one species or variety in a state of nature.	than do the individuals of any one species or variety in a state of nature.	than do the individuals of any one species or variety in a state of nature.	than do the individuals of any one species or variety in a state of nature.
When	When	When	When	And if	And if
we reflect on the vast diversity of the plants and animals which have been cultivated, and which have varied during all ages under the most different climates and treatment,	we reflect on the vast diversity of the plants and animals which have been cultivated, and which have varied during all ages under the most different climates and treatment,	we reflect on the vast diversity of the plants and animals which have been cultivated, and which have varied during all ages under the most different climates and treatment,	we reflect on the vast diversity of the plants and animals which have been cultivated, and which have varied during all ages under the most different climates and treatment,	we reflect on the vast diversity of the plants and animals which have been cultivated, and which have varied during all ages under the most different climates and treatment,	we reflect on the vast diversity of the plants and animals which have been cultivated, and which have varied during all ages under the most different climates and treatment,
I think	I think	I think	I think	-	-
we are driven to conclude that this	we are driven to conclude that this	we are driven to conclude that this	we are driven to conclude that this	we are driven to conclude that this	we are driven to conclude that this
greater	great	great	great	great	great
variability is	variability is	variability is	variability is	variability is	variability is
simply	simply	simply	simply	-	-
due to our domestic productions having been raised under conditions of life not so uniform as, and somewhat different from, those to which the parent-species	due to our domestic productions having been raised under conditions of life not so uniform as, and somewhat different from, those to which the parent-species	due to our domestic productions having been raised under conditions of life not so uniform as, and somewhat different from, those to which the parent-species	due to our domestic productions having been raised under conditions of life not so uniform as, and somewhat different from, those to which the parent-species	due to our domestic productions having been raised under conditions of life not so uniform as, and somewhat different from, those to which the parent-species	due to our domestic productions having been raised under conditions of life not so uniform as, and somewhat different from, those to which the parent-species
have	have	have	have	had	had
been exposed under nature. There is	been exposed under nature. There is	been exposed under nature. There is	been exposed under nature. There is	been exposed under nature. There is	been exposed under nature. There is
,	-	-	-	-	,
also	also	also	also	also	also
, I think	, I think	, I think	, I think	, I think	-
, some probability in the view propounded by Andrew Knight, that this variability may be partly connected with excess of food. It seems	, some probability in the view propounded by Andrew Knight, that this variability may be partly connected with excess of food. It seems	, some probability in the view propounded by Andrew Knight, that this variability may be partly connected with excess of food. It seems	, some probability in the view propounded by Andrew Knight, that this variability may be partly connected with excess of food. It seems	, some probability in the view propounded by Andrew Knight, that this variability may be partly connected with excess of food. It seems	, some probability in the view propounded by Andrew Knight, that this variability may be partly connected with excess of food. It seems
pretty	pretty	pretty	pretty	-	-
clear that organic beings must be exposed during several generations to	clear that organic beings must be exposed during several generations to	clear that organic beings must be exposed during several generations to	clear that organic beings must be exposed during several generations to	clear that organic beings must be exposed during several generations to	clear that organic beings must be exposed during several generations to
the	the	the	the	-	-
new	new	new	new	new	new
conditions of life	conditions of life	conditions of life	conditions of life	conditions	conditions
to cause any	to cause any	to cause any	to cause any	to cause any	to cause any
appreciable	appreciable	appreciable	appreciable	appreciable	great
amount of variation; and that	amount of variation; and that	amount of variation; and that	amount of variation; and that	amount of variation; and that	amount of variation; and that
-	-	-	,	,	,
when the organisation has once begun to vary, it generally	when the organisation has once begun to vary, it generally	when the organisation has once begun to vary, it generally	when the organisation has once begun to vary, it generally	when the organisation has once begun to vary, it generally	when the organisation has once begun to vary, it generally
continues	continues	continues	continues	con- tinues	continues
to vary	to vary	to vary	to vary	varying	varying
for many generations. No case is on record of a variable	for many generations. No case is on record of a variable	for many generations. No case is on record of a variable	for many generations. No case is on record of a variable	for many generations. No case is on record of a variable	for many generations. No case is on record of a variable
being	being	being	being	organism	organism
ceasing	ceasing	ceasing	ceasing	ceasing	ceasing
to be variable	to be variable	to be variable	to be variable	to vary	to vary
under cultivation. Our oldest cultivated plants, such as wheat, still	under cultivation. Our oldest cultivated plants, such as wheat, still	under cultivation. Our oldest cultivated plants, such as wheat, still	under cultivation. Our oldest cultivated plants, such as wheat, still	under cultivation. Our oldest cultivated plants, such as wheat, still	under cultivation. Our oldest cultivated plants, such as wheat, still
often	often	often	often	-	-
yield new varieties: our oldest domesticated animals are still capable of rapid improvement or modification.	yield new varieties: our oldest domesticated animals are still capable of rapid improvement or modification.	yield new varieties: our oldest domesticated animals are still capable of rapid improvement or modification.	yield new varieties: our oldest domesticated animals are still capable of rapid improvement or modification.	yield new varieties: our oldest domesticated animals are still capable of rapid improvement or modification.	yield new varieties: our oldest domesticated animals are still capable of rapid improvement or modification.

1859	1860	1861	1866	1869	1872
-	-	-	Causes of Variability.	Causes of Variability.	Causes of Variability.
WHEN we	WHEN we	WHEN we	WHEN we	WHEN we	WHEN we
look to	look to	look to	look to	compare	compare
the individuals of the same variety or sub-variety of our older cultivated plants and animals, one of the first points which strikes us	the individuals of the same variety or sub-variety of our older cultivated plants and animals, one of the first points which strikes us	the individuals of the same variety or sub-variety of our older cultivated plants and animals, one of the first points which strikes us	the individuals of the same variety or sub-variety of our older cultivated plants and animals, one of the first points which strikes us	the individuals of the same variety or sub-variety of our older cultivated plants and animals, one of the first points which strikes us	the individuals of the same variety or sub-variety of our older cultivated plants and animals, one of the first points which strikes us
,	,	,	,	-	-
is, that they generally differ	is, that they generally differ	is, that they generally differ	is, that they generally differ	is, that they generally differ	is, that they generally differ
much	-	-	-	-	-
more	more	more	more	-	more
from each other	from each other	from each other	from each other	from each other	from each other
,	-	-	-	more	-
than do the individuals of any one species or variety in a state of nature.	than do the individuals of any one species or variety in a state of nature.	than do the individuals of any one species or variety in a state of nature.	than do the individuals of any one species or variety in a state of nature.	than do the individuals of any one species or variety in a state of nature.	than do the individuals of any one species or variety in a state of nature.
When	When	When	When	And if	And if
we reflect on the vast diversity of the plants and animals which have been cultivated, and which have varied during all ages under the most different climates and treatment,	we reflect on the vast diversity of the plants and animals which have been cultivated, and which have varied during all ages under the most different climates and treatment,	we reflect on the vast diversity of the plants and animals which have been cultivated, and which have varied during all ages under the most different climates and treatment,	we reflect on the vast diversity of the plants and animals which have been cultivated, and which have varied during all ages under the most different climates and treatment,	we reflect on the vast diversity of the plants and animals which have been cultivated, and which have varied during all ages under the most different climates and treatment,	we reflect on the vast diversity of the plants and animals which have been cultivated, and which have varied during all ages under the most different climates and treatment,
I think	I think	I think	I think	-	-
we are driven to conclude that this	we are driven to conclude that this	we are driven to conclude that this	we are driven to conclude that this	we are driven to conclude that this	we are driven to conclude that this
greater	great	great	great	great	great
variability is	variability is	variability is	variability is	variability is	variability is
simply	simply	simply	simply	-	-
due to our domestic productions having been raised under conditions of life not so uniform as, and somewhat different from, those to which the parent-species	due to our domestic productions having been raised under conditions of life not so uniform as, and somewhat different from, those to which the parent-species	due to our domestic productions having been raised under conditions of life not so uniform as, and somewhat different from, those to which the parent-species	due to our domestic productions having been raised under conditions of life not so uniform as, and somewhat different from, those to which the parent-species	due to our domestic productions having been raised under conditions of life not so uniform as, and somewhat different from, those to which the parent-species	due to our domestic productions having been raised under conditions of life not so uniform as, and somewhat different from, those to which the parent-species
have	have	have	have	had	had
been exposed under nature. There is	been exposed under nature. There is	been exposed under nature. There is	been exposed under nature. There is	been exposed under nature. There is	been exposed under nature. There is
,	-	-	-	-	,
also	also	also	also	also	also
, I think	, I think	, I think	, I think	, I think	-
, some probability in the view propounded by Andrew Knight, that this variability may be partly connected with excess of food. It seems	, some probability in the view propounded by Andrew Knight, that this variability may be partly connected with excess of food. It seems	, some probability in the view propounded by Andrew Knight, that this variability may be partly connected with excess of food. It seems	, some probability in the view propounded by Andrew Knight, that this variability may be partly connected with excess of food. It seems	, some probability in the view propounded by Andrew Knight, that this variability may be partly connected with excess of food. It seems	, some probability in the view propounded by Andrew Knight, that this variability may be partly connected with excess of food. It seems
pretty	pretty	pretty	pretty	-	-
clear that organic beings must be exposed during several generations to	clear that organic beings must be exposed during several generations to	clear that organic beings must be exposed during several generations to	clear that organic beings must be exposed during several generations to	clear that organic beings must be exposed during several generations to	clear that organic beings must be exposed during several generations to
the	the	the	the	-	-
new	new	new	new	new	new
conditions of life	conditions of life	conditions of life	conditions of life	conditions	conditions
to cause any	to cause any	to cause any	to cause any	to cause any	to cause any
appreciable	appreciable	appreciable	appreciable	appreciable	great
amount of variation; and that	amount of variation; and that	amount of variation; and that	amount of variation; and that	amount of variation; and that	amount of variation; and that
-	-	-	,	,	,
when the organisation has once begun to vary, it generally	when the organisation has once begun to vary, it generally	when the organisation has once begun to vary, it generally	when the organisation has once begun to vary, it generally	when the organisation has once begun to vary, it generally	when the organisation has once begun to vary, it generally
continues	continues	continues	continues	con- tinues	continues
to vary	to vary	to vary	to vary	varying	varying
for many generations. No case is on record of a variable	for many generations. No case is on record of a variable	for many generations. No case is on record of a variable	for many generations. No case is on record of a variable	for many generations. No case is on record of a variable	for many generations. No case is on record of a variable
being	being	being	being	organism	organism
ceasing	ceasing	ceasing	ceasing	ceasing	ceasing
to be variable	to be variable	to be variable	to be variable	to vary	to vary
under cultivation. Our oldest cultivated plants, such as wheat, still	under cultivation. Our oldest cultivated plants, such as wheat, still	under cultivation. Our oldest cultivated plants, such as wheat, still	under cultivation. Our oldest cultivated plants, such as wheat, still	under cultivation. Our oldest cultivated plants, such as wheat, still	under cultivation. Our oldest cultivated plants, such as wheat, still
often	often	often	often	-	-
yield new varieties: our oldest domesticated animals are still capable of rapid improvement or modification.	yield new varieties: our oldest domesticated animals are still capable of rapid improvement or modification.	yield new varieties: our oldest domesticated animals are still capable of rapid improvement or modification.	yield new varieties: our oldest domesticated animals are still capable of rapid improvement or modification.	yield new varieties: our oldest domesticated animals are still capable of rapid improvement or modification.	yield new varieties: our oldest domesticated animals are still capable of rapid improvement or modification.