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Joos Korstanje

Machine Learning on Geographical Data

Using Python
Introduction into Geodata with Applications and
Use Cases
Joos Korstanje
VIELS MAISONS, France

ISBN 978-1-4842-8286-1 e-ISBN 978-1-4842-8287-8

https://doi.org/10.1007/978-1-4842-8287-8

© Joos Korstanje 2022

Apress Standard

The use of general descriptive names, registered names, trademarks,

service marks, etc. in this publication does not imply, even in the
absence of a specific statement, that such names are exempt from the
relevant protective laws and regulations and therefore free for general
use.

The publisher, the authors and the editors are safe to assume that the
advice and information in this book are believed to be true and accurate
at the date of publication. Neither the publisher nor the authors or the
editors give a warranty, expressed or implied, with respect to the
material contained herein or for any errors or omissions that may have
been made. The publisher remains neutral with regard to jurisdictional
claims in published maps and institutional affiliations.

This Apress imprint is published by the registered company APress

Media, LLC, part of Springer Nature.
The registered company address is: 1 New York Plaza, New York, NY
10004, U.S.A.
Introduction
Spatial data has long been an ignored data type in general data science
and statistics courses. Yet at the same time, there is a field of spatial
analysis which is strongly developed. Due to differences in tools and
approaches, the two fields have long developed in separate
environments.
With the popularity of data in many business environments, the
importance of treating spatial data is also increasing. The goal of the
current book is to bridge the gap between data science and spatial
analysis by covering tools of both worlds and showing how to use tools
from both to answer use cases.
The book starts with a general introduction to geographical data,
including data storage formats, data types, common tools and libraries
in Python, and the like. Strong attention is paid to the specificities of
spatial data, including coordinate systems and more.
The second part of the book covers a number of methods of the field
of spatial analysis. All of this is done in Python. Even though Python is
not the most common tool in spatial analysis, the ecosystem has taken
large steps in user-friendliness and has great interoperability with
machine learning libraries. Python with its rich ecosystem of libraries
will be an important tool for spatial analysis in the near future.
The third part of the book covers multiple machine learning use
cases on spatial data. In this part of the book, you see that tools from
spatial analysis are combined with tools from machine learning and
data science to realize more advanced use cases than would be possible
in many spatial analysis tools. Specific considerations are needed for
applying machine learning to spatial data, due to the specific nature of
coordinates and other specific data formats of spatial data.

Source Code
All source code used in the book can be downloaded from
github.com/apress/machine-learning-geographic-
data-python.
Any source code or other supplementary material referenced by the
author in this book is available to readers on GitHub
(https://github.com/Apress). For more detailed information, please
visit http://www.apress.com/source-code.
Table of Contents
Part I: General Introduction
Chapter 1:​Introduction to Geodata
Reading Guide for This Book
Geodata Definitions
Cartesian Coordinates
Polar Coordinates and Degrees
The Difference with Reality
Geographic Information Systems and Common Tools
What Are Geographic Information Systems
Standard Formats of Geodata
Shapefile
Google KML File
GeoJSON
TIFF/​JPEG/​PNG
CSV/​TXT/​Excel
Overview of Python Tools for Geodata
Key Takeaways
Chapter 2:​Coordinate Systems and Projections
Coordinate Systems
Geographic Coordinate Systems
Projected Coordinate Systems
Local Coordinate Systems
Which Coordinate System to Choose
Playing Around with Some Maps
Example:​Working with Own Data
 Key Takeaways
Chapter 3:​Geodata Data Types
Vector vs.​Raster Data
Dealing with Attributes in Vector and Raster
Points
Definition of a Point
Importing an Example Point Dataset in Python
Some Basic Operations with Points
Lines
Definition of a Line
An Example Line Dataset in Python
Polygons
Definition of a Polygon
An Example Polygon Dataset in Python
Some Simple Operations with Polygons
Rasters/​Grids
Definition of a Grid or Raster
Importing a Raster Dataset in Python
Key Takeaways
Chapter 4:​Creating Maps
Mapping Using Geopandas and Matplotlib
Getting a Dataset into Python
Making a Basic Plot
Plot Title
Plot Legend
Mapping a Point Dataset with Geopandas and Matplotlib
 Concluding on Mapping with Geopandas and Matplotlib
Making a Map with Cartopy
Concluding on Mapping with Cartopy
Making a Map with Plotly
Concluding on Mapping with Plotly
Making a Map with Folium
Concluding on Mapping with Folium
Key Takeaways
Part II: GIS Operations
Chapter 5:​Clipping and Intersecting
What Is Clipping?​
A Schematic Example of Clipping
What Happens in Practice When Clipping?​
Clipping in Python
What Is Intersecting?​
What Happens in Practice When Intersecting?​
Conceptual Examples of Intersecting Geodata
Intersecting in Python
Difference Between Clipping and Intersecting
Key Takeaways
Chapter 6:​Buffers
What Are Buffers?​
A Schematic Example of Buffering
What Happens in Practice When Buffering?​
Creating Buffers in Python
Creating Buffers Around Points in Python
 Creating Buffers Around Lines in Python
Creating Buffers Around Polygons in Python
Combining Buffers and Set Operations
Key Takeaways
Chapter 7:​Merge and Dissolve
The Merge Operation
What Is a Merge?​
A Schematic Example of Merging
Merging in Python
Row-Wise Merging in Python
Attribute Join in Python
Spatial Join in Python
The Dissolve Operation
What Is the Dissolve Operation?​
Schematic Overview of the Dissolve Operation
The Dissolve Operation in Python
Key Takeaways
Chapter 8:​Erase
The Erase Operation
Schematic Overview of Spatially Erasing Points
Schematic Overview of Spatially Erasing Lines
Schematic Overview of Spatially Erasing Polygons
Erase vs.​Other Operations
Erase vs.​Deleting a Feature
Erase vs.​Clip
Erase vs.​Overlay
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 Erasing in Python
Erasing Portugal from Iberia to Obtain Spain
Erasing Points in Portugal from the Dataset
Cutting Lines to Be Only in Spain
Key Takeaways
Part III: Machine Learning and Mathematics
Chapter 9:​Interpolation
What Is Interpolation?​
Different Types of Interpolation
Linear Interpolation
Polynomial Interpolation
Nearest Neighbor Interpolation
From One-Dimensional to Spatial Interpolation
Spatial Interpolation in Python
Linear Interpolation Using Scipy Interp2d
Kriging
Linear Ordinary Kriging
Gaussian Ordinary Kriging
Exponential Ordinary Kriging
Conclusion on Interpolation Methods
Key Takeaways
Chapter 10:​Classification
Quick Intro to Machine Learning
Quick Intro to Classification
Spatial Classification Use Case
Feature Engineering with Additional Data
 Importing and Inspecting the Data
Spatial Operations for Feature Engineering
Reorganizing and Standardizing the Data
Modeling
Model Benchmarking
Key Takeaways
Chapter 11:​Regression
Introduction to Regression
Spatial Regression Use Case
Importing and Preparing Data
Iteration 1 of Data Exploration
Iteration 1 of the Model
Iteration 2 of Data Exploration
Iteration 2 of the Model
Iteration 3 of the Model
Iteration 4 of the Model
Interpretation of Iteration 4 Model
Key Takeaways
Chapter 12:​Clustering
Introduction to Unsupervised Modeling
Introduction to Clustering
Different Clustering Models
Spatial Clustering Use Case
Importing and Inspecting the Data
Cluster Model for One Person
Tuning the Clustering Model
 Applying the Model to All Data
Key Takeaways
Chapter 13:​Conclusion
What You Should Remember from This Book
Recap of Chapter 1 – Introduction to Geodata
Recap of Chapter 2 – Coordinate Systems and Projections
Recap of Chapter 3 – Geodata Data Types
Recap of Chapter 4 – Creating Maps
Recap of Chapter 5 – Clipping and Intersecting
Recap of Chapter 6 – Buffers
Recap of Chapter 7 – Merge and Dissolve
Recap of Chapter 8 – Erase
Recap of Chapter 9 – Interpolation
Recap of Chapter 10 – Classification
Recap of Chapter 11 – Regression
Recap of Chapter 12 – Clustering
Further Learning Path
Going into Specialized GIS
Specializing in Machine Learning
Remote Sensing and Image Treatment
Other Specialties
Key Takeaways
Index
About the Author
Joos Korstanje
is a data scientist, with over five years of
industry experience in developing
machine learning tools. He has a double
MSc in Applied Data Science and in
Environmental Science and has extensive
experience working with geodata use
cases. He has worked at a number of
large companies in the Netherlands and
France, developing machine learning for
a variety of tools. His experience in
writing and teaching has motivated him
to write this book on machine learning
for geodata with Python.
About the Technical Reviewer
Xiaochi Liu
is a PhD researcher and data scientist at
Macquarie University, specializing in
machine learning, explainable artificial
intelligence, spatial analysis, and their
novel application in environmental and
public health. He is a programming
enthusiast using Python and R to
conduct end-to-end data analysis. His
current research applies cutting-edge AI
technologies to untangle the causal
nexus between trace metal
contamination and human health to
develop evidence-based intervention
strategies for mitigating environmental exposure.
Part I
General Introduction
© The Author(s), under exclusive license to APress Media, LLC, part of Springer
Nature 2022
J. Korstanje, Machine Learning on Geographical Data Using Python
https://doi.org/10.1007/978-1-4842-8287-8_1

1. Introduction to Geodata
Joos Korstanje1
(1) VIELS MAISONS, France

Mapmaking and analysis of the geographical environment around us have

been present in nature and human society for a long time. Human maps
are well known to all of us: they are a great way to share information
about our environment with others.
Yet communicating geographical instructions is not invented only by
the human species. Bees, for example, are well known to communicate on
food sources with their fellow hive mates. Bees do not make maps, but,
just like us, they use a clearly defined communication system.
As geodata is the topic of this book, I find it interesting to share this
out-of-the-box geodata system used by honeybees. Geodata in the bee
world has two components: distance and direction.
Honeybee distance metrics
– The round dance: A food source is present less than 50 meters from the
hive.
– The sickle dance: Food sources are present between 50 and 150 meters
from the hive.
– The waggle (a.k.a. wag-tail) dance: Food sources are over 150 meters
from the hive. In addition, the duration of the waggle dance is an
indicator of how far over 150 meters the source is located.
Honeybee direction metrics
– Although more complicated, the angle of the dance is known to be an
indicator of the angle relative to the sun that bees must follow to get to
their food source.
 – As the sun changes location throughout the day, bees will update each
other by adapting their communication dances accordingly.
The human counterpart of geographical communication works a bit
better, as we have compasses that point to the magnetic north. Those of
you who are familiar with compass use, for example, on boats, may know
that even using a compass is not a perfect solution.
The magnetic north changes much less than the position of the sun.
What is interesting though is that the magnetic north and the true north
are not located at the same exact place. The true north is a fixed location
on the globe (the so-called North Pole), but compasses are based on
magnetism and therefore point to the magnetic north: a location that
moves a little bit every year.
If you are navigating a ship with a compass, you will constantly need
to do calculations that convert your magnetic direction measurements
into true direction measurements by adding magnetic variation, which is
a value that changes depending on where you are on earth.

Reading Guide for This Book

As you will understand from these two examples, working with geodata is
a challenge. While identifying locations of points by coordinates may
appear simple, the devil really is in the details.
The goal of this book is to go over all those details while working on
example code projects in Python. This should give you the fundamental
knowledge needed to start working in the interesting domain of geodata
while avoiding mistakes. You will then discover numerous ways to
represent geodata and learn to work with tools that make working with
geodata easier.
After laying the basis, the book will become more and more advanced
by focusing on machine learning techniques for the geodata domain. As
you may expect, the specificities of the use of geodata make that a lot of
standards techniques are not applicable at all, or in other cases, they may
need specific adaptations and configurations.

Geodata Definitions
To get started, I want to cover the basics of coordinate systems in the
simplest mathematic situation: the Euclidean space. Although the world
does not respect the hypothesis made by Euclidean geometry, it is a great
entry into the deeper understanding of coordinate systems.
A two-dimensional Euclidean space is often depicted as shown in
Figure 1-1.

Figure 1-1 A two-dimensional Euclidean space. Image by author

Cartesian Coordinates
To locate points in the Euclidean space, we can use the Cartesian
coordinate system. This coordinate system specifies each point uniquely
by a pair of numerical coordinates. For example, look at the coordinate
system in Figure 1-2, in which two points are located: a square and a
triangle.
The square is located at x = 2 and y = 1 (horizontal axis). The triangle
is located at x = -2 and y = -1.
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Figure 1-2 Two points in a coordinate system. Image by author
The point where the x and y axes meet is called the Origin, and
distances are measured from there. Cartesian coordinates are among the
most well-known coordinate system and work easily and intuitively in the
Euclidean space.

Polar Coordinates and Degrees

A commonly used alternative to Cartesian coordinates is the polar
coordinate system. In the polar system, one starts by defining one point as
the pole. From this pole starts the polar axis. The graphic in Figure 1-3
shows the idea.
Figure 1-3 The polar system. Image by author
In this schematic drawing, the star is designated as the pole, and the
thick black line to the right is chosen as the polar axis. This system is
quite different from the Cartesian system but still allows us to identify the
exact same points: just in a different way.
The points are identified by two components: an angle with respect to
the polar axis and a distance. The square that used to be referred to as
Cartesian coordinate (2,1) can be referred to by an angle from the polar
axis and a distance.
This is shown in Figure 1-4.
Random documents with unrelated
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FIRST AND THIRD BOOKS
OF

THE EPIDEMICS.
 THE EPIDEMICS.
BOOK I.
THE ARGUMENT.

The ancient physicians commonly used the term Epidemic in the

same sense as it is understood now, that is to say, as applying to
any disease which attacks a multitude of persons in a locality at any
particular period. This, as will be seen in our annotations below, is
nearly the definition which Galen gives of it; and it is generally used
by Hippocrates, in the first and third books of the “Epidemics,” in
pretty much the same sense as it is used by our great modern
authority on epidemics, Sydenham. But, although this be the strict
sense in which the ancient authorities use the term, it must be borne
in mind that, as applied to the whole seven books of the “Epidemics,”
it must be taken in a much wider signification; for there are many
things treated of in them to which the term epidemic can by no
means be thus applied, such as surgical cases, fragments of
anatomical descriptions, philosophical speculations, empirical
remedies, general reflections on various topics, and so forth. In fact,
the work entitled “The Books of Epidemics” can be viewed in no
other light than as an Adversaria, or Memorandum Book, in which is
collected a variety of isolated facts and detached observations, to
serve as the materials for more elaborate and finished works on
professional subjects. Indeed, Galen does not hesitate to give it as
his opinion, that some of the most celebrated of our author’s
productions, such as the “Aphorisms” and “Prognostics,” are in a
great measure made up from the materials originally laid up in this
capacious repertory of observations;[602] and, with regard to the
former of these works, there is no person familiarly acquainted with it
but must admit the truth of Galen’s remark. But, respecting the other,
although it must be obvious, upon a comparison of them, that there
is a close connection between it and the “Epidemics,” there can be
no doubt that, in composing the “Prognostics,” Hippocrates availed
himself of other materials ready prepared for his use, in the
“Prorrhetics” and “Coan Prænotions” of his predecessors, the
Asclepiadæ;[603] so that, of all his admired productions, it, perhaps,
is the one which has the least pretension to any originality of matter.
If it be thought strange that the term epidemics should have been
applied to a work composed of such heterogeneous materials, I
would remark, in explanation, that, although the subject-matters of
which it consists are not all of this nature, the most valuable portion
of them refers to epidemics, and it is not to be wondered at that the
whole collection should have got its appellation from the most
prominent subject to which it relates.

I shall now proceed to give a succinct analysis of the various

subjects which are contained in the First and Third Books of the
“Epidemics.”
The first book opens with a description of the leading phenomena
of a certain season, which is called the First Constitution; it was
southerly, coldish, rainy, clouded and misty, with some intervals of
drought. The most noted diseases of spring in this constitution were
causus and an epidemical parotitis. But the most important subject
which is handled under this head, is an epidemic phthisis, of which a
very interesting description is given.
The Second Constitution is described as being northerly and
humid; humid ophthalmies, dysenteries, and diarrhœas are
described among the prevailing diseases of the season; but the most
marked affection which is said to have occurred in this constitution,
is a continual fever of a serious character, which did not come to a
crisis until after it had run a long course. It is described as passing
off by deposits, and principally by dropsies, and an affection of the
urinary organs. One cannot help being struck with the remark which
Hippocrates makes, that he never knew a case prove fatal in which
the strangury supervened. The directions as to the treatment he
condenses into one general rule, which well deserves to be
engraved in letters of gold, that “the aim of the physician should be
to do good to his patient, or, at least, to do no harm.” The description
of this constitution concludes with some general reflections on the
prognostics in causus and phrenitis.
The Third Constitution is described as being of a very variable
character; winter stormy, spring rainy, summer hot, autumn cold and
dry. The ardent fevers (or causi) began early in the season, but did
not assume a fatal character until autumn. This disease came to a
crisis in four modes—by an epistaxis, by a copious flow of urine, by a
deposit, or by an alvine discharge. In women, there was also
sometimes a crisis by menstruation.
The Fourth Constitution is one which, by Galen and the other
authorities, has been entitled the pestilential, and has attracted great
attention, as being supposed to have derived its peculiar characters
from the great Plague which prevailed during the Peloponnesian war,
and which is described in so interesting a manner by Thucydides.
Galen, not only in his Commentary, but in various other parts of his
works, advocates this opinion, and it will be seen from what is stated
in our annotations, that there is in reality a striking resemblance
between the features of the plague, as delineated by Thucydides,
and the epidemical diseases which are noticed by Hippocrates as
having prevailed during this constitution. Of all the diseases here
described the most remarkable is the erysipelas, which, although not
of a very fatal character, was still of a formidable nature, as it
frequently terminated in gangrene. Causus, phrenitis, and anthrax
are also described as being common under this constitution. The last
of these being a well-known symptom of the Oriental plague, it has
naturally excited a good deal of speculation to determine whether or
not our author here refers to the glandular plague. See our remarks
on Epidem. III.

In these books it is remarkable that phthisis is treated of as a

febrile disease, and in particular as supervening upon attacks of the
semitertian. There seems reason to suppose that our author means
to describe a hectic fever succeeding to intermittents, which had
caused organic derangement of the internal viscera, more especially
of the liver and spleen. See Paulus Ægineta, Book II., 32.
In the first book, fourteen cases of disease are related, and in the
beginning of the third twelve, and sixteen in the end; thus making
forty-two in all. It is worthy of remark, that in twenty-five of these the
result was fatal. There is every reason, then, to suppose that they
were selected for a purpose, but what that purpose was cannot now
be easily determined. The most natural would, no doubt, have been
to illustrate, by examples, the forms of the different diseases which
are described as occurring during the Constitutions previously
described. But there seems to be little or no reason to suppose that
this is the object for which they are related. In proof of this, I may
mention that there is not in the collection a single case of the
epidemical erysipelas which is described as having been the
prevailing disease during the fourth Constitution. Indeed it must
strike everybody, who reads them carefully, as a singular feature in
these cases, that the lineaments of a particular disease are seldom
to be recognized, and this perhaps may be regarded as a proof of
the faithfulness with which they have been copied from nature. In
short, we here recognize the features of disease in the concrete, and
not in the abstract. And is not this what we should expect in all true
copies from Nature? How often does the candid physician find
himself forced honestly to admit that he is at a loss what name to
give to the combination of morbid actions which he is called upon to
treat! The common herd of mankind would seem to fancy, as in
Nature there are certain types of all animal and vegetable
substances, and the botanist has no difficulty in classing such a
plant, for example, as the conium maculatum; and the natural
historian can readily pronounce that such a bird is the alcedo Ispida;
that the physician, in like manner, upon examining the characteristic
features of any case, should have no difficulty in pronouncing that it
is pleuritis, for example, or pneumonia, or the like. But how often
does it happen, that the complaint in question is an aggregate of
symptoms, produced by peculiarities of constitution, and incidental
circumstances, which, taken together, constitute an ensemble which
does not well admit of being referred to any one of the general forms
of disease described in our nosological systems? Now, I say the
most wonderful feature in the cases related by Hippocrates, is that
they are descriptive of the symptoms observed in certain diseased
individuals, instead of being, what most modern cases are,
symptoms drawn to correspond with certain ideal forms of disease.
What, in my opinion, likewise adds very much to the value of these
cases is, that (as Galen somewhere remarks in his Commentary) the
author never aimed to make his Books of Epidemics a work on
Therapeutics, and hence, in noting morbid phenomena, his mind in
not warped by any particular hypothesis, nor by any selfish interest,
in order to place some favorite mode of practice, advocated by
himself, in a favorable light. May I be permitted here to remark, that
the reader will be much struck with our author’s admirable talent for
describing the phenomena of disease as they are actually presented
to us, if he will compare the case related by him in these two books
with those of almost any modern authority whatever;—for example,
with those related by the late Dr. James Hamilton, in his celebrated
work on Purgative Medicines. In the latter, you look in vain for the
strongly-marked features which present themselves in all the cases
related by our author,—for a description of the condition of the
hypochondriac region,—of the state of the animal heat in the
extremities,—of the minute characters of the alvine and urinary
discharges,—of the respiration,—of the patients’ position in bed,—
and many other symptoms, which are invariably noticed by
Hippocrates. And what reasonable person will venture to deny, that
the symptoms I have just now mentioned are most important
features in every febrile disease, and that no one can be said to
have a sufficient view of such a case, who does not take these into
account? To confine our attention at present to only one of these
symptoms,—can it ever be a matter of indifference what are the
physical characters of so important an excretion as the urine? that is
to say, whether the grosser particles of it, which usually fall to the
bottom, be present in the urine or not? Yet in all the seventeen cases
related in the modern work just now referred to, the characters of the
urine are not given in a single instance. And although the object of
the writer is to enforce his own peculiar views, as to the utility of
purgative medicines in this disease, he scarcely ever gives the
minute characters of the alvine discharges, as is uniformly the case
with Hippocrates; or if they are noticed at all, it is in so confused a
manner that the reader is at a loss to determine whether they are
produced by the disease, or by the medicines which have been
administered. For the issue of the case no obvious cause is stated,
but the reader is expected to draw the conclusion that, as purgatives
were freely given, and a considerable proportion of the cases did
well,—(agreeably to the hackneyed rule, post quod, ergo propter
quod,)—the purgatives brought about the fortunate result. Had the
cases been fully and circumstantially detailed, it might have been
found that, as in those related by Hippocrates, recovery was
preceded by a critical discharge of urine, accompanied with a
copious sediment; and then the more probable inference would have
been, that the amendment was referable to it, and not to the
purgative medicines which were administered. It is, I regret to say, a
notable example of the want of logical training in the education of
professional men, in the present age, that inferences regarding a
peculiar method of practice were allowed to be founded upon
narratives of observations so defective and one-sided as those I
refer to.

I cannot quit the present subject of discussion, without saying a

few words in reference to what must strike the reader as a singular
feature in the cases related in the books of the Epidemics; I mean
the general omission of any mention of treatment. The reader will
find in our annotations various remarks of Galen on this head, from
which he will learn that the Great Commentator inclines to the
opinion, that in all these cases the usual routine of practice was
followed, but that no mention is made of medicines, unless when
there was some deviation from the established rules. For example, in
a certain febrile case, it is stated that the patient was bled on the
eighth day, and Galen contends that venesection is noticed in this
instance, merely because it was contrary to the established rule of
not bleeding after the fourth day; for that if the practice had been in
accordance with the general rule, it would not have been noticed at
all. Now it must be admitted, that this supposition is by no means
improbable, and that examples of this usage are not wanting, even in
the modern literature of medicine. To give an example, which just
occurs to me; in not a few of the cases of cerebral disease related by
Dr. Abercrombie, in his work “On the Brain,” there is no allusion
whatever to remedies, although no one, who recollects the vigorous
system of treatment then pursued by the profession in “Modern
Athens,” will doubt for a moment that they must have been applied.
As this eminent authority, then, when he believed that the treatment
had no perceptible effect on the course which the disease ran,
thought himself warranted in omitting all mention of it, it might be
supposed, in like manner, that Hippocrates may have passed over
the remedies applied, from some such motive or consideration. But
another reason for the absence of remedies in these Reports may be
readily supposed. May not Hippocrates have been at first quite
undecided what was the proper plan of treatment to be adopted in
those cases, and thought it the wisest course to attempt nothing
rashly, but to be for a season the quiet spectator of the course which
the diseases in question were naturally disposed to run, before
attempting to interfere in the struggle between morbific agents with
which he was imperfectly acquainted, and their great physician, as
he held Nature to be?[604] And however much the advocates for a
bold system of treating diseases may be disposed to deride this
expectant method, which Asclepiades contemptuously denominated
“the contemplation of death,”[605] it does not want the sanction of a
name which is second only to Hippocrates in the literature of
epidemical fevers. Sydenham admits, that with all the diligence
which he had applied to the study of these diseases, he was always
greatly puzzled what plan of treatment to adopt at the first breaking
out of a new epidemic, and that it was only “ingenti adhibita cautela
intentisque animi nervis,” that he could make up his mind what
course of treatment to adopt in such an emergency. Need it be
wondered at, then, that two thousand years earlier the modest mind
of our great author should have hesitated for a time, before deciding
how to act under similar circumstances? I must own, therefore, that I
have long inclined to the opinion, that, distracted with the conflicting
plans of treatment adopted by his contemporaries, Hippocrates at
first did little or nothing in the treatment of epidemical fevers, and
that it was only after a patient study of their symptoms, and many
cautious trials, that he ventured to lay down those excellent rules of
treatment which he has described so admirably in his work “On
Regimen in Acute Diseases.” This, however, is merely my individual
opinion, and the reader must receive it as such.
M. Littré, in the Argument prefixed to his translation of the
Epidemics, enters very fully into the discussion of the question
regarding the nature of the diseases which are treated of in the
course of this work. This is a task, however, which I deem it
superfluous to undertake at any length, as I have stated my opinions
on this subject in the Commentaries on the Second Book of Paulus
Ægineta, and after maturely weighing what has been elicited by
subsequent inquirers, I find no cause to retract any of the opinions
which are there advanced. That the causus of Hippocrates, and the
other ancient authorities, was not the typhus of the more temperate
parts of Europe, but a bilious fever, of the remittent type, must be
quite apparent to every person at all acquainted with the medical
literature of febrile diseases. M. Littré’s researches lead him to
exactly the same conclusion, and much deference is due to his
judgment in this case, as it must be admitted that a French physician
is now very favorably situated for contrasting the diseases of
temperate and hot climates, owing to the familiar intercourse which
at present subsists between Paris and Algiers. Of all the materials
which he has collected from the observations of French physicians in
Algeria, the most interesting are those which he draws from a work
on Fevers, by M. Maillot. The description which is there given of “la
fièvre algide,” is so striking, and is so much calculated to illustrate
the nature of the fevers which are treated of in this work of
Hippocrates, that I shall not scruple to quote it entire.
“La fièvre algide (dit M. Maillot) n’est pas généralement, comme
on le dit, la prolongation indéfinie du stade de froid; je l’ai vue
rarement débuter de la sorte. Il y a même entre ces deux états une
contraste frappante. Dans le premier stade des fièvres
intermittentes, la sensation du froid est hors de toute proportion avec
l’abaissement réel de la température de la peau, tandis que, dans la
fièvre algide, le froid n’est pas perçu par le malade, alors que la
peau est glacée. C’est ordinairement pendant la réaction que
commencent les symptômes qui la caractérisent; souvent ils
surviennent tout à coup au milieu d’une réaction qui paraissait
franche. Au trouble de la circulation succède en peu d’instants et
presque sans transition le ralentissement du pouls, qui devient
bientôt très rare, fuit sous le doigt et disparaît; l’abaissement de la
température du corps va vite et suit la progression promptement
décroissante de la circulation; les extrémitiés, la face, le torse, se
refroidissent successivement; l’abdomen seul conserve encore
quelque temps un peu de chaleur; le contact de la peau donne la
sensation de froid que procure le marbre. Les lèvres sont
décolorées, l’haleine froide, la voix cassée, les battemens du cœur
rares, incomplets, appréciables seulement par l’auscultation; les
facultés intellectuelles sont intactes, et le malade se complaît dans
cet état de repos, surtout lorsqu’il succède à une fièvre violente, la
physionomie est sans mobilité, l’impassibilité la plus grande est
peinte sur son visage; ses traits sont morts. La marche de cette
fièvre est très insidieuse; il n’est peut-être personne, dont elle n’ait
surpris la vigilance, avant d’être familiarisé avec l’observation des
accidens de cette nature, on prend souvent pour une très grande
amélioration due aux déplétions sanguines, le calme qui succède
aux accidents inflammatoires; et plus d’une fois, dans de semblables
circonstances, on n’a été détrompé que par la mort soudaine du
malade. Toutes les fois qu’à une réaction plus on moins forte, on
verra succéder tout à coup un ralentissement du pouls, avec pâleur
de la langue et décoloration des lèvres, on ne devra hésiter à
diagnostiquer une fièvre algide. La temporisation ici donne la mort,
en quelques heures. Dans quelques cas très rares, j’ai cependant vu
cet état algide se prolonger trois ou quatre jours. Le malade expire
en conservant toutes ses facultés intellectuelles,[606] il s’éteint
comme par un arrêt de l’innervation. Lorsque la mort n’est pas le
terme de cet état morbide si grave, le pouls se relève; la peau
reprend sa chaleur naturelle; quelquefois alors la réaction détermine
une irritation de l’encéphale ou des voies digestives; mais rarement
elle est assez intense pour qu’on soit obligé de la combattre par des
déplétions sanguines.”[607] I shall add a remark, which M. Littré gives
on the same authority: “J’ai tenu à mentionner ici l’impression
qu’éprouva M. Maillot au début de sa pratique en Algérie, et qui est
si instructive; car, aller subitement de France exercer la médecine
dans un pays chaud, ou lire les observations d’Hippocrate, c’est tout
un: l’impression est la même, le changement de scène est aussi
grand.”[608]
I cannot help remarking in this place, however, that it appears to
me singular, that M. Littré should represent the febris algida as being
confined to southern climates, and should speak of it as being
unknown in Paris; for, at all events, there seems to be no doubt that
it prevails in a more northerly region, namely, in Holland. It is thus
described by the celebrated Franciscus de le Boe (or Sylvius), who
was professor of practical medicine at Leyden about the middle of
the 17th century: “Febres algidæ observantur nonnunquam, non
tantum frigore præsertim, sed frigore tantum molestæ: adeo ut
aliquando et frequentius levis, aliquando et rarius nullus sequatur
calor. Tales, etiam semper algidas in Nosocomio academico
habuimus ita manifestas, ut non tantum incipiente, atque
augescente, sed etiam vigente et déclinante, imò cessante
paroxysmo, id est, semper tum suo, tum adstantium, tum medicorum
sensu moleste ubique frigerent, nunquam teperent, minus calerent
ullibi ægri. Suntque hæ algidæ graviores semper forsan
quotidianæ.”[609] The febris algida is also named “rigor without heat,”
by the Greek authorities, and “frigus quod non calefit” by the
Arabians, who, like Sylvius, as quoted above, regard it as a variety of
the quotidian intermittent. See Paulus Ægineta, Book II., 26.
M. Littré[610] quotes the remark of an excellent English authority
on fever, J. Johnson,[611] that it is singular the effects of marsh
effluvia should have escaped the observation of Hippocrates, more
especially as the remittent and intermittent fevers, of which he treats
so fully, are mostly derived from this source. Now I must say, that I
am not aware of there being any passages in the works of
Hippocrates where the effects of marsh effluvia in engendering such
fevers are distinctly noticed; but if Hippocrates was ignorant of this
fact, in the etiology of fevers, it was well known to Galen, as may be
seen on reference to his very interesting work “On the Difference of
Fevers.”[612] The Arabians also were familiar with the fact. See
Avicenna, iv., 1, 2, 1.
In the treatise “On Airs,” which, although not admitted by us into
the list of genuine works, has considerable pretension to be so
regarded, the causes of fever are treated of with great precision, and
there the pestilential fevers are said to derive their origin from
miasma, but whether or not under this term be included marsh
effluvia, cannot be determined. But perhaps a better reason might be
assigned for there being little or no allusion to malaria in the works of
Hippocrates, namely, that after all, this was not the cause of the
epidemical diseases which he describes. The following extract from
a work of very high authority on fever is well deserving of
consideration in this place: “A question has arisen as to whether or
not the inflammatory states of fever, in warm countries, are caused
by malaria, or by the other causes now instanced (excess of heat,
etc.). There can be no doubt that malaria very frequently produces in
the plethoric, young, and robust, who have recently arrived in a hot
climate, fever of an inflammatory and continued kind; but it must also
be conceded that this fever chiefly occurs, even in persons thus
constituted, during the dry season, and at times and in places where
the existence of malaria is doubtful, or, at least, by no means proved.
It is notoriously admitted that the inflammatory states of continued
fever, in both the East and West Indies, appear among those
soldiers, sailors, and civilians, who have not been long in a warm
country, and who have not suffered from disease since their arrival;
and that they take place chiefly during the dry and warm seasons,
and in situations where the usual affects of malaria are never
observed. This is the result of the experience of Jackson, Annesley,
Boyle, Twining, Conwell, and the other experienced practitioners in
warm countries. It agrees with my own observations, and is even
admitted by Dr. Fergusson, who has gone much further than any one
else in assigning malaria as the cause of intertropical fevers.”[613] I
may mention, moreover, that Hippocrates and his contemporaries
were evidently not ignorant of the fact, that the atmosphere in the
vicinity of marshes and large rivers is unwholesome to the
inhabitants of warm climates. See De Diæta, ii, 2.
The following are part of the conclusions which M. Littré draws
from his investigations into the nature of the fevers described by
Hippocrates. I quote them as being strongly confirmatory of the
opinions delivered by me in the Commentary on the Second Book of
Paulus Ægineta.
“Les fièvres décrites dans les Epidémies d’Hippocrate différent
de nos fièvres continués.
“Les fièvres décrites dans les Epidémies ont, dans leur
apparence générale, une similitude très grande avec celles des pays
chauds.
“La similitude n’est pas moins grande dans les détails que dans
l’ensemble.
“Dans les unes comme dans les autres les hypochondres sont
pour un tiers des cas, le siége d’une manifestation toute spéciale.
“Dans les unes comme dans les autres, il y a une forte tendence
ou réfroidissement du corps, à la sueur froide et à la lividité des
extrémités.”
On almost all the other diseases treated of in these books, M.
Littré’s opinions, in like manner, exactly coincide with those delivered
by me in the above-mentioned work. Thus he arrives at the
conclusion, that the Phrenitis and Lethargus of Hippocrates were
varieties of the Causus. Compare Paulus Ægineta, Book III., 6, 9.
He refers them to les fièvres pernicieuses comateuses pseudo-
continués et les fièvres pernicieuses dolorantes pseudo-continués of
M. Maillot. It would appear from the extracts which he quotes from a
work of M. Roux, on the Diseases of Morea, that a similar tendency
to pass into phrenitis and lethargy is still observable in the land of
Greece. The fevers of the East Indies also, as described by Dr.
Twining,[614] appear to partake very much of the same character. In
a word, the conclusions to which a patient study of modern
authorities on the subject have brought me amount to this; that the
fevers described by Hippocrates in his “Epidemics,” are exactly the
same as those which are now described as still prevailing in the land
of Greece: that they correspond very well with those described by
Cleghorn as occurring in Majorca; differ but little from those
described by Pringle, Monro, and Sylvius, as happening in the Low
Countries, and differ from those described by Twining, as happening
in Bengal, only in a few particulars.
From the analysis of their contents given above it will readily be
understood that the subject-matters of these two books are not
arranged methodically. Indeed it is quite obvious from the nature of
the work that the matters which are treated of in it had never been
methodized by the author. Certainly then, as proposed by Desmair,
[615] it would be a much more natural arrangement to give the four
Constitutions of the season first, and then to give the forty-two cases
together. But the present arrangement being of old standing, no
editor has thought himself warranted to depart from it.
There are two important professional subjects of which it may
appear surprising that there is no mention in the “Books of the
Epidemics,” I mean sphygmology and contagion. Galen repeatedly
declares it as his opinion, that Hippocrates paid no attention to the
characters of the arterial pulse, and that the subject was not at all
studied until after his time; and as far as I can see there is no ground
for calling in question this opinion of Galen. Herophilus, in fact, would
appear to have been the first person that made any progress in this
study. It is more remarkable that Hippocrates should omit all allusion
to the other subject, more especially as the contagiousness of
certain diseases would appear to have been the popular belief of his
age. Thus his contemporary, Thucydides, in describing the plague,
expresses himself in such terms as puts it beyond a doubt that he
regarded the disease as being of a contagious nature. And another
contemporary, Isocrates, makes such observations on a certain case
of empyema, by which he evidently means phthisis pulmonalis, as to
show that it also was regarded as being communicable.[616] How the
omission is to be accounted for I do not know, but certain it is that
not the least reference to contagion, in any shape, is to be found in
any of the Hippocratic treatises.
 BOOK I.—OF THE EPIDEMICS.

Sec. I.—Constitution First.

1. In Thasus,[617] about the autumnal equinox, and under the

Pleiades,[618] the rains were abundant, constant, and soft, with
southerly winds; the winter southerly, the northerly winds faint,
droughts; on the whole, the winter having the character of spring.
The spring was southerly, cool, rains small in quantity. Summer, for
the most part, cloudy, no rain, the Etesian winds, rare and small,
blew in an irregular manner. The whole constitution of the season
being thus inclined to the southerly, and with droughts early in the
spring, from the preceding opposite and northerly state, ardent
fevers occurred in a few instances, and these very mild, being rarely
attended with hemorrhage, and never proving fatal.[619] Swellings
appeared about the ears, in many on either side, and in the greatest
number on both sides, being unaccompanied by fever so as not to
confine the patient to bed; in all cases they disappeared without
giving trouble, neither did any of them come to suppuration, as is
common in swellings from other causes. They were of a lax, large,
diffused character, without inflammation or pain, and they went away
without any critical sign. They seized children, adults, and mostly
those who were engaged in the exercises of the palestra and
gymnasium, but seldom attacked women. Many had dry coughs
without expectoration, and accompanied with hoarseness of voice. In
some instances earlier, and in others later, inflammations with pain
seized sometimes one of the testicles, and sometimes both;[620]
some of these cases were accompanied with fever and some not;
the greater part of these were attended with much suffering. In other
respects they were free of disease, so as not to require medical
assistance.[621]
2. Early in the beginning of spring, and through the summer, and
towards winter, many of those who had been long gradually
declining, took to bed with symptoms of phthisis; in many cases
formerly of a doubtful character the disease then became confirmed;
in these the constitution inclined to the phthisical.[622] Many, and, in
fact, the most of them, died; and of those confined to bed, I do not
know if a single individual survived for any considerable time; they
died more suddenly than is common in such cases. But other
diseases, of a protracted character, and attended with fever, were
well supported, and did not prove fatal: of these we will give a
description afterwards. Consumption was the most considerable of
the diseases which then prevailed, and the only one which proved
fatal to many persons. Most of them were affected by these diseases
in the following manner: fevers accompanied with rigors, of the
continual type, acute, having no complete intermissions, but of the
form of the semitertians, being milder the one day, and the next
having an exacerbation, and increasing in violence; constant sweats,
but not diffused over the whole body; extremities very cold, and
warmed with difficulty; bowels disordered, with bilious, scanty,
unmixed, thin, pungent, and frequent dejections. The urine was thin,
colourless, unconcocted, or thick, with a deficient sediment, not
settling favorably, but casting down a crude and unseasonable
sediment. Sputa small, dense, concocted, but brought up rarely and
with difficulty; and in those who encountered the most violent
symptoms there was no concoction at all, but they continued
throughout spitting crude matters. Their fauces, in most of them,
were painful from first to last, having redness with inflammation;
defluxions thin, small and acrid; they were soon wasted and became
worse, having no appetite for any kind of food throughout; no thirst;
most persons delirious when near death. So much concerning the
phthisical affections.[623]
3. In the course of the summer and autumn many fevers of the
continual type, but not violent;[624] they attacked persons who had
been long indisposed, but who were otherwise not in an
uncomfortable state. In most cases the bowels were disordered in a
very moderate degree, and they did not suffer thereby in any manner
worth mentioning; the urine was generally well coloured, clear, thin,
and after a time becoming concocted near the crisis. They had not
much cough, nor was it troublesome; they were not deficient in
appetite, for it was necessary to give them food, (on the whole,
persons labouring under phthisis were not affected in the usual
manner).[625] They were affected with fevers, rigors, and deficient
sweats, with varied and irregular paroxysms, in general not
intermitting, but having exacerbations in the tertian form. The earliest
crisis which occurred was about the twentieth day, in most about the
fortieth, and in many about the eightieth. But there were cases in
which it did not leave them thus at all, but in an irregular manner, and
without any crisis; in most of these the fevers, after a brief interval,
relapsed again; and from these relapses they came to a crisis in the
same periods; but in many they were prolonged so that the disease
was not gone at the approach of winter. Of all those which are
described under this constitution, the phthisical diseases alone were
of a fatal character; for in all the others the patients bore up well, and
did not die of the other fevers.[626]
Sec. II.—Constitution Second.

1. In Thasus, early in autumn, the winter suddenly set in rainy

before the usual time, with much northerly and southerly winds.
These things all continued so during the season of the Pleiades, and
until their setting.[627] The winter was northerly, the rains frequent, in
torrents, and large, with snow, but with a frequent mixture of fair
weather. These things were all so, but the setting in of the cold was
not much out of season. After the winter solstice, and at the time
when the zephyr usually begins to blow, severe winterly storms out
of season, with much northerly wind, snow, continued and copious
rains; the sky tempestuous and clouded; these things were
protracted, and did not remit until the equinox. The spring was cold,
northerly, rainy, and clouded; the summer was not very sultry, the
Etesian winds blew constant, but quickly afterwards, about the rising
of Arcturus, there were again many rains with north winds. The
whole season being wet, cold, and northerly, people were, for the
most part, healthy during winter; but early in the spring very many,
indeed, the greater part, were valetudinary. At first ophthalmies set
in, with rheums, pains, unconcocted discharges, small concretions,
generally breaking with difficulty, in most instances they relapsed,
and they did not cease until late in autumn.[628] During summer and
autumn there were dysenteric affections, attacks of tenesmus and
lientery, bilious diarrhœa, with thin, copious, undigested, and acrid
dejections, and sometimes with watery stools; many had copious
defluxions, with pain, of a bilious, watery, slimy, purulent nature,
attended with strangury, not connected with disease of the kidneys,
but one complaint succeeding the other; vomitings of bile, phlegm,
and undigested food, sweats, in all cases a redundance of humors.
In many instances these complaints were unattended with fever, and
did not prevent the patients from walking about, but some cases
were febrile, as will be described. In some all those described below
occurred with pain. During autumn, and at the commencement of
winter, there were phthisical complaints, continual fevers; and, in a
few cases, ardent; some diurnal, others nocturnal, semitertians, true
tertians, quartans, irregular fevers. All the fevers which are described
attacked great numbers. The ardent fevers attacked the smallest
numbers, and the patients suffered the least from them, for there
were no hemorrhages, except a few and to a small amount, nor was
there delirium; all the other complaints were slight; in these the
crises were regular, in most instances, with the intermittents, in
seventeen days; and I know no instance of a person dying of
causus, nor becoming phrenitic.[629] The tertians were more
numerous than the ardent fevers, and attended with more pain;[630]
but these all had four periods in regular succession from the first
attack, and they had a complete crisis in seven, without a relapse in
any instance. The quartans attacked many at first, in the form of
regular quartans, but in no few cases a transition from other fevers
and diseases into quartans took place; they were protracted, as is
wont with them, indeed, more so than usual. Quotidian, nocturnal,
and wandering fevers attacked many persons, some of whom
continued to keep up, and others were confined to bed. In most
instances these fevers were prolonged under the Pleiades and till
winter. Many persons, and more especially children, had convulsions
from the commencement;[631] and they had fever, and the
convulsions supervened upon the fevers; in most cases they were
protracted, but free from danger, unless in those who were in a
deadly state from other complaints. Those fevers which were
continual in the main, and with no intermissions, but having
exacerbations in the tertian form,[632] there being remissions the one
day and exacerbations the next, were the most violent of all those
which occurred at that time, and the most protracted, and occurring
with the greatest pains, beginning mildly, always on the whole
increasing, and being exacerbated, and always turning worse,
having small remissions, and after an abatement having more violent
paroxysms, and growing worse, for the most part, on the critical
days. Rigors, in all cases, took place in an irregular and uncertain
manner, very rare and weak in them, but greater in all other fevers;
frequent sweats, but most seldom in them, bringing no alleviation,
but, on the contrary, doing mischief. Much cold of the extremities in
them, and these were warmed with difficulty. Insomnolency, for the
most part, especially in these fevers, and again a disposition to
coma. The bowels, in all diseases, were disordered, and in a bad
state, but worst of all in these. The urine, in most of them, was either
thin and crude, yellow, and after a time with slight symptoms of
concoction in a critical form, or having the proper thickness, but
muddy, and neither settling nor subsiding; or having small and bad,
and crude sediments; these being the worst of all. Coughs attended
these fevers, but I cannot state that any harm or good ever resulted
from the cough. The most of these were protracted and troublesome,
went on in a very disorderly and irregular form, and, for the most
part, did not end in a crisis, either in the fatal cases or in the others;
for if it left some of them for a season it soon returned again. In a few
instances the fever terminated with a crisis; in the earliest of these
about the eightieth day, and some of these relapsed, so that most of
them were not free from the fever during the winter; but the fever left
most of them without a crisis, and these things happened alike to
those who recovered and to those who did not. There being much
want of crisis and much variety as to these diseases, the greatest
and worst symptom attended the most of them, namely, a loathing of
all articles of food, more especially with those who had otherwise
fatal symptoms; but they were not unseasonably thirsty in such
fevers. After a length of time, with much suffering and great wasting,
abscesses were formed in these cases, either unusually large, so
that the patients could not support them, or unusually small, so that
they did no good, but soon relapsed and speedily got worse. The
diseases which attacked them were in the form of dysenteries,
tenesmus, lientery, and fluxes; but, in some cases, there were
dropsies, with or without these complaints. Whatever attacked them
violently speedily cut them off, or again, did them no good. Small
rashes, and not corresponding to the violence of the disease, and
quickly disappearing, or swellings occurred about the ears, which
were not resolved, and brought on no crisis.[633] In some they were
determined to the joints, and especially to the hip-joint, terminating
critically with a few, and quickly again increasing to its original habit.
Persons died of all these diseases, but mostly of these fevers, and
especially infants just weaned, and older children, until eight or ten
years of age, and those before puberty. These things occurred to
those affected with the complaints described above, and to many
persons at first without them. The only favorable symptom, and the
greatest of those which occurred, and what saved most of those who
were in the greatest dangers, was the conversion of it to a strangury,
and when, in addition to this, abscesses were formed.[634] The
strangury attacked, most especially, persons of the ages I have
mentioned, but it also occurred in many others, both of those who
were not confined to bed and those who were. There was a speedy
and great change in all these cases. For the bowels, if they
happened previously to have watery discharges of a bad character,
became regular, they got an appetite for food, and the fevers were
mild afterwards. But, with regard to the strangury itself, the
symptoms were protracted and painful. Their urine was copious,
thick, of various characters, red, mixed with pus, and was passed
with pain. These all recovered, and I did not see a single instance of
death among them.
5.[635] With regard to the dangers of these cases, one must
always attend to the seasonable concoction of all the evacuations,
and to the favorable and critical abscesses. The concoctions indicate
a speedy crisis and recovery of health; crude and undigested
evacuations, and those which are converted into bad abscesses,
indicate either want of crisis, or pains, or prolongation of the disease,
or death, or relapses; which of these it is to be must be determined
from other circumstances. The physician must be able to tell the