Collating with CollateX

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


In [1]:
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. The instruction tells Python to create a new instance of a Collation() object and call it collation.


In [3]:
collation = Collation()
collation


Out[3]:
<collatex.core_classes.Collation at 0x10a96d128>

Now we add some witnesses to the collation object "collation". Each witness gets a letter or name (siglum) that will identify it, and for each we add the literal text of the witness to the collation object:


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." )

The object "collation" now holds three witnesses. We now tell CollateX to collate the witnesses in the object "collation", create a table to visualize the results, and orient the table vertically. We’ve created a variable called alignment_table to hold the CollateX output. We’ll discuss the Segmentation parameter later.


In [5]:
alignment_table = collate(collation, layout='vertical', segmentation=False )

When we tell CollateX to create a plain text table to hold the output, it isn’t rendered by default (other CollateX output formats are), so we have to print() it in order to see it:


In [18]:
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 we want to group our output instead of rendering each token-level set in separate cells. You can tell CollateX to construct those groups by setting the value of the segmentation parameter to True—or by not specifying a value at all, since the default behavior is equal to the True value. We switched this option off in the example above to show that CollateX is aware of the individual token alignments, but in most cases you’ll want to leave segmentation on. When we collate again with segmentation, we see the default grouping:


In [6]:
alignment_table = collate(collation, layout='vertical' )

In [7]:
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, but other supported output formats are html, html2 (color-coded HTML), xml (a generic XML that can be processed further with XSLT), tei (also somewhat generic, but based on parallel segmentation), and svg. SVG outputs a variant graph, which shows the variation as a directed graph.


In [8]:
graph = collate( collation, output="svg", segmentation=True )


%3 1 bad Sigla bad C 8 fox jumped over the Sigla fox jumped over the C, A, B 1->8 C 2 The Sigla The C, A, B 2->1 C 6 brown Sigla brown A, B 2->6 B 9 quick Sigla quick A 2->9 A 3 3 4 4 4->2 A, B, C 5 dog. Sigla dog. C, A, B 5->3 A, B, C 6->8 A, B 7 lazy Sigla lazy C, A 7->5 A, C 8->5 B 8->7 A, C 9->6 A

We can perform the same operation with files that we read from the file system. Note that we specify encoding="utf-8".


In [9]:
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 [10]:
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 [11]:
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 [25]:
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 [26]:
graph = collate( collation, output="svg" )


%3 1 1 3 WHEN we Sigla WHEN we 1859, 1860, 1861, 1866, 1869, 1872 1->3 1859, 1860, 1861 46 Causes of Variability. Sigla Causes of Variability. 1866, 1869, 1872 1->46 1866, 1869, 1872 2 2 4 look to Sigla look to 1859, 1860, 1861, 1866 3->4 1859, 1860, 1861, 1866 48 compare Sigla compare 1869, 1872 3->48 1869, 1872 5 the individuals of the same variety or sub- variety of our older cultivated plants and animals, one of the first points which strikes us Sigla the individuals of the same variety or sub-variety of our older cultivated plants and animals, one of the first points which strikes us 1859, 1860, 1861, 1866 the individuals of the same variety or sub-variety of our older cultivated plants and animals, one of the first points which strikes us 1869, 1872 4->5 1859, 1860, 1861, 1866 6 , Sigla , 1859, 1860, 1861, 1866 5->6 1859, 1860, 1861, 1866 7 is, that they generally differ Sigla is, that they generally differ 1859, 1860, 1861, 1866, 1869, 1872 5->7 1869, 1872 6->7 1859, 1860, 1861, 1866 8 much Sigla much 1859 7->8 1859 9 more Sigla more 1859, 1860, 1861, 1866, 1872 7->9 1860, 1861, 1866, 1872 10 from each other Sigla from each other 1859 from each other 1860, 1861, 1866, 1869, 1872 7->10 1869 8->9 1859 9->10 1859, 1860, 1861, 1866, 1872 11 , Sigla , 1859 10->11 1859 12 than do the individuals of any one species or variety in a state of nature. Sigla than do the individuals of any one species or variety in a state of nature. 1859, 1860, 1861, 1866, 1869, 1872 10->12 1860, 1861, 1866, 1872 49 more Sigla more 1869 10->49 1869 11->12 1859 13 When Sigla When 1859, 1860, 1861, 1866 12->13 1859, 1860, 1861, 1866 50 And if Sigla And if 1869, 1872 12->50 1869, 1872 14 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, Sigla 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, 1859, 1860, 1861, 1866, 1869, 1872 13->14 1859, 1860, 1861, 1866 15 I think Sigla I think 1859, 1860, 1861, 1866 14->15 1859, 1860, 1861, 1866 16 we are driven to conclude that this Sigla we are driven to conclude that this 1859, 1860, 1861, 1866, 1869, 1872 14->16 1869, 1872 15->16 1859, 1860, 1861, 1866 17 greater Sigla greater 1859 16->17 1859 45 great Sigla great 1860, 1861, 1866, 1869, 1872 16->45 1860, 1861, 1866, 1869, 1872 18 variability is Sigla variability is 1859, 1860, 1861, 1866, 1869, 1872 17->18 1859 19 simply Sigla simply 1859, 1860, 1861, 1866 18->19 1859, 1860, 1861, 1866 20 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 Sigla 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 1859, 1860, 1861, 1866, 1869, 1872 18->20 1869, 1872 19->20 1859, 1860, 1861, 1866 21 have Sigla have 1859, 1860, 1861, 1866 20->21 1859, 1860, 1861, 1866 51 had Sigla had 1869, 1872 20->51 1869, 1872 22 been exposed under nature. There is Sigla been exposed under nature. There is 1859, 1872 been exposed under nature. There is 1860, 1861, 1866, 1869 21->22 1859, 1860, 1861, 1866 23 , Sigla , 1859, 1872 22->23 1859, 1872 24 also Sigla also 1859, 1860, 1861, 1866, 1869, 1872 22->24 1860, 1861, 1866, 1869 23->24 1859, 1872 25 , I think Sigla , I think 1859, 1860, 1861, 1866, 1869 24->25 1859, 1860, 1861, 1866, 1869 26 , some probability in the view propounded by Andrew Knight, that this variability may be partly connected with excess of food. It seems Sigla , some probability in the view propounded by Andrew Knight, that this variability may be partly connected with excess of food. It seems 1859, 1860, 1861, 1866, 1869, 1872 24->26 1872 25->26 1859, 1860, 1861, 1866, 1869 27 pretty Sigla pretty 1859, 1860, 1861, 1866 26->27 1859, 1860, 1861, 1866 28 clear that organic beings must be exposed during several generations to Sigla clear that organic beings must be exposed during several generations to 1859, 1860, 1861, 1866, 1869, 1872 26->28 1869, 1872 27->28 1859, 1860, 1861, 1866 29 the Sigla the 1859, 1860, 1861, 1866 28->29 1859, 1860, 1861, 1866 30 new Sigla new 1859, 1860, 1861, 1866, 1869, 1872 28->30 1869, 1872 29->30 1859, 1860, 1861, 1866 31 conditions of life Sigla conditions of life 1859, 1860, 1861, 1866 30->31 1859, 1860, 1861, 1866 52 conditions Sigla conditions 1869, 1872 30->52 1869, 1872 32 to cause any Sigla to cause any 1859, 1860, 1861, 1866, 1869, 1872 31->32 1859, 1860, 1861, 1866 33 appreciable Sigla appreciable 1859, 1860, 1861, 1866, 1869 32->33 1859, 1860, 1861, 1866, 1869 57 great Sigla great 1872 32->57 1872 34 amount of variation; and that Sigla amount of variation; and that 1866, 1869, 1872 amount of variation; and that 1859, 1860, 1861 33->34 1859, 1860, 1861, 1866, 1869 35 when the organisation has once begun to vary, it generally Sigla when the organisation has once begun to vary, it generally 1859, 1860, 1861, 1866, 1869, 1872 34->35 1859, 1860, 1861 47 , Sigla , 1866, 1869, 1872 34->47 1866, 1869, 1872 36 continues Sigla continues 1859, 1860, 1861, 1866, 1872 35->36 1859, 1860, 1861, 1866, 1872 53 con- tinues Sigla con- tinues 1869 35->53 1869 37 to vary Sigla to vary 1859, 1860, 1861, 1866 36->37 1859, 1860, 1861, 1866 54 varying Sigla varying 1869, 1872 36->54 1872 38 for many generations. No case is on record of a variable Sigla for many generations. No case is on record of a variable 1859, 1860, 1861, 1866, 1869, 1872 37->38 1859, 1860, 1861, 1866 39 being Sigla being 1859, 1860, 1861, 1866 38->39 1859, 1860, 1861, 1866 55 organism Sigla organism 1869, 1872 38->55 1869, 1872 40 ceasing Sigla ceasing 1859, 1860, 1861, 1866, 1869, 1872 39->40 1859, 1860, 1861, 1866 41 to be variable Sigla to be variable 1859, 1860, 1861, 1866 40->41 1859, 1860, 1861, 1866 56 to vary Sigla to vary 1869, 1872 40->56 1869, 1872 42 under cultivation. Our oldest cultivated plants, such as wheat, still Sigla under cultivation. Our oldest cultivated plants, such as wheat, still 1859, 1860, 1861, 1866, 1869, 1872 41->42 1859, 1860, 1861, 1866 43 often Sigla often 1859, 1860, 1861, 1866 42->43 1859, 1860, 1861, 1866 44 yield new varieties: our oldest domesticated animals are still capable of rapid improvement or modification. Sigla yield new varieties: our oldest domesticated animals are still capable of rapid improvement or modification. 1859, 1860, 1861, 1866, 1869, 1872 42->44 1869, 1872 43->44 1859, 1860, 1861, 1866 44->2 1859, 1860, 1861, 1866, 1869, 1872 45->18 1860, 1861, 1866, 1869, 1872 46->3 1866, 1869, 1872 47->35 1866, 1869, 1872 48->5 1869, 1872 49->12 1869 50->14 1869, 1872 51->22 1869, 1872 52->32 1869, 1872 53->54 1869 54->38 1869, 1872 55->40 1869, 1872 56->42 1869, 1872 57->34 1872

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.


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