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Bayesian Analysis with Python

Unleash the power and flexibility of the Bayesian

framework

Osvaldo Martin

BIRMINGHAM - MUMBAI
Bayesian Analysis with Python

Copyright © 2016 Packt Publishing

All rights reserved. No part of this book may be reproduced, stored in a retrieval
system, or transmitted in any form or by any means, without the prior written
permission of the publisher, except in the case of brief quotations embedded in
critical articles or reviews.

Every effort has been made in the preparation of this book to ensure the accuracy
of the information presented. However, the information contained in this book
is sold without warranty, either express or implied. Neither the author nor Packt
Publishing, and its dealers and distributors will be held liable for any damages
caused or alleged to be caused directly or indirectly by this book.

Packt Publishing has endeavored to provide trademark information about all of the
companies and products mentioned in this book by the appropriate use of capitals.
However, Packt Publishing cannot guarantee the accuracy of this information.

First published: November 2016

Production reference: 1211116

Published by Packt Publishing Ltd.

Livery Place
35 Livery Street
Birmingham B3 2PB, UK.

ISBN 978-1-78588-380-4
www.packtpub.com
 Credits

Author Project Coordinator

Osvaldo Martin Nidhi Joshi

Reviewer Proofreader
Austin Rochford Safis Editor

Commissioning Editor Indexer

Veena Pagare Mariammal Chettiyar

Acquisition Editor Graphics

Tushar Gupta Disha Haria

Content Development Editor Production Coordinator

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Copy Editor
Safis Editing
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 About the Author

Osvaldo Martin is a researcher at The National Scientific and Technical Research

Council (CONICET), the main organization in charge of the promotion of science
and technology in Argentina. He has worked on structural bioinformatics and
computational biology problems, especially on how to validate structural protein
models. He has experience in using Markov Chain Monte Carlo methods to simulate
molecules and loves to use Python to solve data analysis problems. He has taught
courses about structural bioinformatics, Python programming, and, more recently,
Bayesian data analysis. Python and Bayesian statistics have transformed the way he
looks at science and thinks about problems in general. Osvaldo was really motivated
to write this book to help others in developing probabilistic models with Python,
regardless of their mathematical background. He is an active member of the PyMOL
community (a C/Python-based molecular viewer), and recently he has been making
small contributions to the probabilistic programming library PyMC3.

I would like to thank my wife, Romina, for her support while writing
this book and in general for her support in all my projects, specially
the unreasonable ones. I also want to thank Walter Lapadula,
Juan Manuel Alonso, and Romina Torres-Astorga for providing
invaluable feedback and suggestions on my drafts.
A special thanks goes to the core developers of PyMC3. This book
was possible only because of the dedication, love, and hard work
they have put into PyMC3. I hope this book contributes to the spread
and adoption of this great library.
 About the Reviewer

Austin Rochford is a principal data scientist at Monetate Labs, where he

develops products that allow retailers to personalize their marketing across billions
of events a year. He is a mathematician by training and is a passionate advocate of
Bayesian methods.
 www.PacktPub.com

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 Table of Contents
Preface vii
Chapter 1: Thinking Probabilistically - A Bayesian Inference Primer 1
Statistics as a form of modeling 2
Exploratory data analysis 2
Inferential statistics 3
Probabilities and uncertainty 5
Probability distributions 7
Bayes' theorem and statistical inference 10
Single parameter inference 13
The coin-flipping problem 13
The general model 14
Choosing the likelihood 14
Choosing the prior 16
Getting the posterior 18
Computing and plotting the posterior 18
Influence of the prior and how to choose one 21
Communicating a Bayesian analysis 23
Model notation and visualization 23
Summarizing the posterior 24
Highest posterior density 24
Posterior predictive checks 27
Installing the necessary Python packages 28
Summary 29
Exercises 29
Chapter 2: Programming Probabilistically – A PyMC3 Primer 31
Probabilistic programming 32
Inference engines 33
Non-Markovian methods 33
Markovian methods 36

[i]
Table of Contents

PyMC3 introduction 46
Coin-flipping, the computational approach 46
Model specification 47
Pushing the inference button 48
Diagnosing the sampling process 48
Summarizing the posterior 55
Posterior-based decisions 55
ROPE 56
Loss functions 57
Summary 58
Keep reading 58
Exercises 59
Chapter 3: Juggling with Multi-Parametric and
Hierarchical Models 61
Nuisance parameters and marginalized distributions 62
Gaussians, Gaussians, Gaussians everywhere 64
Gaussian inferences 64
Robust inferences 69
Student's t-distribution 69
Comparing groups 75
The tips dataset 76
Cohen's d 80
Probability of superiority 81
Hierarchical models 81
Shrinkage 84
Summary 88
Keep reading 88
Exercises 89
Chapter 4: Understanding and Predicting Data with Linear
Regression Models 91
Simple linear regression 92
The machine learning connection 92
The core of linear regression models 93
Linear models and high autocorrelation 100
Modifying the data before running 101
Changing the sampling method 103
Interpreting and visualizing the posterior 103
Pearson correlation coefficient 107
Pearson coefficient from a multivariate Gaussian 110
Robust linear regression 113
Hierarchical linear regression 117
Correlation, causation, and the messiness of life 124
[ ii ]
 Table of Contents

Polynomial regression 126

Interpreting the parameters of a polynomial regression 129
Polynomial regression – the ultimate model? 130
Multiple linear regression 131
Confounding variables and redundant variables 135
Multicollinearity or when the correlation is too high 138
Masking effect variables 142
Adding interactions 144
The GLM module 145
Summary 146
Keep reading 146
Exercises 147
Chapter 5: Classifying Outcomes with Logistic Regression 149
Logistic regression 150
The logistic model 151
The iris dataset 152
The logistic model applied to the iris dataset 155
Making predictions 158
Multiple logistic regression 159
The boundary decision 159
Implementing the model 160
Dealing with correlated variables 162
Dealing with unbalanced classes 163
How do we solve this problem? 165
Interpreting the coefficients of a logistic regression 165
Generalized linear models 166
Softmax regression or multinomial logistic regression 167
Discriminative and generative models 171
Summary 174
Keep reading 174
Exercises 175
Chapter 6: Model Comparison 177
Occam's razor – simplicity and accuracy 178
Too many parameters leads to overfitting 179
Too few parameters leads to underfitting 181
The balance between simplicity and accuracy 182
Regularizing priors 183
Regularizing priors and hierarchical models 184
Predictive accuracy measures 185
Cross-validation 185

[ iii ]
Table of Contents

Information criteria 186

The log-likelihood and the deviance 186
Akaike information criterion 187
Deviance information criterion 188
Widely available information criterion 189
Pareto smoothed importance sampling leave-one-out cross-validation 190
Bayesian information criterion 190
Computing information criteria with PyMC3 190
A note on the reliability of WAIC and LOO computations 194
Interpreting and using information criteria measures 194
Posterior predictive checks 196
Bayes factors 197
Analogy with information criteria 199
Computing Bayes factors 199
Common problems computing Bayes factors 202
Bayes factors and information criteria 202
Summary 205
Keep reading 205
Exercises 205
Chapter 7: Mixture Models 207
Mixture models 207
How to build mixture models 209
Marginalized Gaussian mixture model 215
Mixture models and count data 216
The Poisson distribution 216
The Zero-Inflated Poisson model 218
Poisson regression and ZIP regression 220
Robust logistic regression 223
Model-based clustering 225
Fixed component clustering 227
Non-fixed component clustering 227
Continuous mixtures 228
Beta-binomial and negative binomial 228
The Student's t-distribution 229
Summary 230
Keep reading 230
Exercises 230
Chapter 8: Gaussian Processes 233
Non-parametric statistics 234
Kernel-based models 234
The Gaussian kernel 235
Kernelized linear regression 235

[ iv ]
 Table of Contents

Overfitting and priors 241

Gaussian processes 242
Building the covariance matrix 243
Sampling from a GP prior 243
Using a parameterized kernel 245
Making predictions from a GP 247
Implementing a GP using PyMC3 252
Posterior predictive checks 254
Periodic kernel 255
Summary 257
Keep reading 257
Exercises 258
Index 259

[v]
 Preface
Bayesian statistics has been around for more than 250 years now. During this time
it has enjoyed as much recognition and appreciation as disdain and contempt.
Through the last few decades it has gained more and more attention from people in
statistics and almost all other sciences, engineering, and even outside the walls of the
academic world. This revival has been possible due to theoretical and computational
developments. Modern Bayesian statistics is mostly computational statistics. The
necessity for flexible and transparent models and a more interpretation of statistical
analysis has only contributed to the trend.

Here, we will adopt a pragmatic approach to Bayesian statistics and we will not
care too much about other statistical paradigms and their relationship to Bayesian
statistics. The aim of this book is to learn about Bayesian data analysis with the help
of Python. Philosophical discussions are interesting but they have already been
undertaken elsewhere in a richer way than we can discuss in these pages.

We will take a modeling approach to statistics, we will learn to think in terms of

probabilistic models, and apply Bayes' theorem to derive the logical consequences
of our models and data. The approach will also be computational; models will
be coded using PyMC3—a great library for Bayesian statistics that hides most of
the mathematical details and computations from the user. Bayesian methods are
theoretically grounded in probability theory and hence it's no wonder that many
books about Bayesian statistics are full of mathematical formulas requiring a certain
level of mathematical sophistication. Learning the mathematical foundations of
statistics could certainly help you build better models and gain intuition about
problems, models, and results. Nevertheless, libraries, such as PyMC3 allow us to
learn and do Bayesian statistics with only a modest mathematical knowledge, as you
will be able to verify by yourself throughout this book.

[ vii ]
Preface

What this book covers

Chapter 1, Thinking Probabilistically – A Bayesian Inference Primer, tells us about
Bayes' theorem and its implications for data analysis. We then proceed to describe
the Bayesian-way of thinking and how and why probabilities are used to deal
with uncertainty. This chapter contains the foundational concepts used in the rest
of the book.

Chapter 2, Programming Probabilistically – A PyMC3 Primer, revisits the concepts from

the previous chapter, this time from a more computational perspective. The PyMC3
library is introduced and we learn how to use it to build probabilistic models, get
results by sampling from the posterior, diagnose whether the sampling was done
right, and analyze and interpret Bayesian results.

Chapter 3, Juggling with Multi-Parametric and Hierarchical Models, tells us about the
very basis of Bayesian modeling and we start adding complexity to the mix. We
learn how to build and analyze models with more than one parameter and how to
put structure into models, taking advantages of hierarchical models.

Chapter 4, Understanding and Predicting Data with Linear Regression Models, tells us
about how linear regression is a very widely used model per se and a building block
of more complex models. In this chapter, we apply linear models to solve regression
problems and how to adapt them to deal with outliers and multiple variables.

Chapter 5, Classifying Outcomes with Logistic Regression, generalizes the the linear
model from previous chapter to solve classification problems including problems
with multiple input and output variables.

Chapter 6, Model Comparison, discusses the difficulties associated with comparing

models that are common in statistics and machine learning. We will also learn a bit
of theory behind the information criteria and Bayes factors and how to use them to
compare models, including some caveats of these methods.

Chapter 7, Mixture Models, discusses how to mix simpler models to build more
complex ones. This leads us to new models and also to reinterpret models learned
in previous chapters. Problems, such as data clustering and dealing with count data,
are discussed.

Chapter 8, Gaussian Processes, closes the book by briefly discussing some more
advanced concepts related to non-parametric statistics. What kernels are, how to use
kernelized linear regression, and how to use Gaussian processes for regression are
the central themes of this chapter.

[ viii ]
 Another Random Document on
Scribd Without Any Related Topics
unless such decision shall be deemed to favor a fraud. But a rider or
driver thrown or taken by force from his horse or vehicle, after
having passed the winning-post, shall not be considered as having
dismounted without permission of the Judges, and if disabled may
be carried to the Judges’ stand to be weighed, and the Judges may
take the circumstances into consideration and decide accordingly.
And the riders or drivers who shall carry during the heat and bring
home with them the weights which have been approved or
announced correct and proper by the Judges, shall be subject to no
penalty for light weight in that heat; provided the Judges are
satisfied the mistake or fault was their own, and that there has been
no deception on the part of the rider or driver who shall be deficient
in weight; but all parties shall thereafter carry the required weight.
Rule 21.—Handicaps and Miscellaneous Weights.—In matches or
handicaps, where extra or lesser weights are to be carried, the
Judges shall carefully examine and ascertain before starting,
whether the riders, drivers or vehicles are of such weights as have
been agreed upon or required by the match or handicap, and
thereafter the riders and drivers shall be subject to the same
penalties and conditions as if they were to carry the weights
prescribed by the rules.
Rule 22.—When Riders and Drivers are Overweight.—If the bodily
weight of any rider or driver shall be found to exceed that which is
prescribed in the rules, or that which is required by the conditions of
the race, and the overweight shall exceed twenty pounds, it shall be
announced from the stand before the heat; and the judges shall
have power, if in their belief such extra weight was imposed on the
horse for an improper or fraudulent purpose, to substitute another
rider or driver of suitable weight; and if they believe the horse has
been prejudiced in the race by such overweight, he shall not be
allowed to start again or continue in the race, and all outside bets on
such horse shall be declared off. [See also Rule 28.]
A horse prevented by this rule from continuing in the race shall
not be distanced, but ruled out.
 Rule 23.—Length of Whips.—Riders and drivers will be allowed
whips not to exceed the following lengths: For saddle horses, 2 ft.
10 in,; sulkies, 4 ft. 8 in.; wagons, 5 ft. 10 in.; double teams, 8 ft. 6
in.; tandem teams and four-in-hand, unlimited: snappers, not longer
than three inches, will be allowed in addition to the foregoing
measurement.
Rule 24.—Judges’ Stand.—None but the Judges of the race in
progress, and their assistants, shall be allowed in the Judges’ stand
during the pendency of a heat, except members of the Board of
Appeals.
Rule 25.—Selection of Judges.—[See also Art. 13 of By-Laws.] In
every exhibition or race, over any course represented in the National
Association, each course for itself, through the proprietor or
association controlling the same, shall choose or authorize the
selection of three (3) competent Judges, for the day or race, who
shall understand the rules of the said National Association, and shall
rigidly enforce the same; and all their decisions shall be subject to
and in conformity with said rules.
Any person having any interest in, or any bet dependent upon the
result of a race, or having any interest in either of the horses
engaged therein, shall thereby be disqualified and restricted from
acting as a Judge in that race. And if any person who is thus
disqualified shall intentionally and deceptively violate this restriction,
he shall, upon conviction thereof by the Board of Appeals, be
adjudged guilty of a dishonorable act, for which he shall be expelled
from every course represented in said National Association.
Rule 26.—Authority of Judges.—The Judges of the day or race
shall have authority, while presiding, to appoint distance and patrol
judges and timers; to inflict fines and penalties, as prescribed by
these rules; to determine all questions of fact relating to the race
over which they preside; to decide respecting any matters of
difference between parties to the race, or any contingent matter
which shall arise, such as are not otherwise provided for in these
rules; but all their decisions shall be in strict conformity with the
rules, or with the principles thereof. They shall have control over the
horses about to start, and the riders or drivers and assistants of the
horses, and, in the absence of other provision in these rules, they
shall have authority to punish by a fine not exceeding $100, or by
suspension or expulsion, any such person who shall fail to obey their
orders or the rules.
Rule 27.—Distance and Patrol Judges.—In all races of heats there
shall be a Distance Judge appointed by the Judges of the race or by
those in authority, who shall remain in the distance stand during the
heats, and immediately after each heat shall repair to the Judges’
stand and report to the Judges the horse or horses that are
distanced, and all foul or improper conduct, if any has occurred
under his observation.
Patrol Judges may be similarly appointed, and it shall be their duty
to repair in like manner to the Judges’ stand, and report all foul or
improper conduct, if any has occurred under their observation.
Rule 28.—Powers and Duties of Judges.—The Judges shall be in
the stand fifteen minutes before the time for starting the race; they
shall weigh the riders or drivers, and determine the positions of the
horses, and inform each rider or driver of his place, before starting;
they may require the riders and drivers to be properly dressed; they
shall be prepared to take the time of each heat in the race, and they
may appoint some suitable person or persons to assist them in that
respect, and the time so taken shall be recorded and announced in
conformity with these rules. [See also Rules 39 and 40, and Art. 13
of By-Laws.]
The Judges shall ring the bell, or give other notice, ten minutes
previous to the time announced for the race to come off, which shall
be notice to all parties to prepare for the race at the appointed time,
when all the horses must appear at the stand, ready for the race,
and any rider or driver failing to obey this summons may be
punished by a fine not exceeding $100, or his horse may be ruled
out by the Judges and considered drawn; but in all stakes and
matches a failure to appear promptly at the appointed time shall
render the delinquent party liable to forfeit.
The result of a heat shall not be announced until the Judges are
satisfied as to the weights of the riders or drivers, and sufficient time
has elapsed to receive the reports of the Distance and Patrol Judges.
The Judges shall not notice or consider complaints of foul from
any person or persons except the Distance and Patrol Judges
appointed by themselves or by those in authority, and from owners,
riders, or drivers in the race.
If the Judges believe that a horse is being or has been “pulled,” or
has been ridden or driven in other respects improperly, with a design
to prevent his winning a heat which he was evidently able to win,
and that such act was done on the part of the rider or driver for the
purpose of throwing the race, or to perpetrate or aid a fraud, they
may declare that heat void, and they shall have power to substitute
a competent and reliable rider or driver for the remainder of the
race, who shall be paid a reasonable compensation for his services,
but not to exceed $50; and any professional rider or driver who,
without good and sufficient reason, refuses to be so substituted,
may be fined, suspended, or expelled, by order of the Judges and
upon approval of the Board of Appeals; and if the result and
circumstances of the race shall confirm their belief, the rider or
driver so removed shall be expelled by the Judges. And at the close
of the race, if they are warranted under the foregoing circumstances
in deciding that such improper conduct has changed the result of the
race to the prejudice of innocent parties, they shall declare all
outside bets “off,” and if the owner or person or persons controlling
the offending horse shall be a party or parties to such fraud, he or
they, together with the horse, shall be punished by expulsion. [See
also Rules 22 and 48.]
Rule 29.—Starting and Keeping Positions.—No rider or driver shall
cause unnecessary delay after the horses are called up, either by
neglecting to prepare for the race in time, or by failing to come for
the word, or otherwise; and in scoring, if the word is not given, all
the horses in the race shall immediately turn, at the tap of the bell
or other signal given, and jog back for a fresh start. But there shall
be no recall after the starting word or signal has been given.
Provided, however, that if the Judges shall through any error give
signal of recall, after having given the word, Distance shall be waived
in that heat, except for foul riding or driving.
When the Judges are prevented from giving a fair start by a horse
or horses persistently scoring ahead of others, or being refractory, or
from any other fault of either horse, rider, or driver, it shall be their
duty, after three scorings, to select one of the contending horses, of
average speed compared with the others, and no driver shall come
up in advance of said horse before crossing the score.
No driver shall be allowed to sponge out his horse or horses
oftener than once in five times scoring.
If these requirements are not complied with on the part of any
rider or driver, the Judges may not only start the race, or give the
word without regard to the absence or position of the offending
party or parties, but the offender may be punished by a fine not
exceeding $100, or by suspension not to exceed one year.
In all cases, the starting word or signal shall be given from the
Judges’ stand, and in no instance shall a standing start be given.
When, through any fault of either horse, rider, or driver, the
Judges are prevented from giving a fair and prompt start, they shall
warn the faulty party of the penalties to which he is subject, and if
such warning is not heeded, they shall rigidly enforce said penalties.
The horse winning a heat shall take the pole (or inside position)
the succeeding heat, and all others shall take their positions in the
order assigned them in judging the last heat. When two or more
horses shall make a dead heat, the horses shall start for the
succeeding heat in the same positions they occupied at the finish of
the dead heat.
In coming out on the homestretch the foremost horse or horses
shall keep the positions first selected, or be liable to be distanced;
and the hindmost horse or horses, when there is sufficient room to
pass on the inside or anywhere on the homestretch, without
interfering with others, shall be allowed to do so, and any party
interfering to prevent him or them shall be distanced.
If a horse, in attempting to pass another on the homestretch,
should at any time cross or swerve, so as to impede the progress of
a horse behind him, he shall not be entitled to win that heat.
Although a leading horse is entitled to any part of the track,
except after selecting his position on the homestretch, he shall not
change from the right to the left, or from the inner to the outer side
of the track, during any part of the race, when another horse is so
near him that in altering his position he compels the horse behind
him to shorten his stride, or causes the rider or driver of such other
horse to pull him out of his stride; neither shall any horse, rider, or
driver, cross, jostle, or strike another horse, rider, or driver, nor
swerve or do any other thing that impedes the progress of another
horse; nor shall any horse, in passing a leading horse, take the track
of the other horse so soon after getting the lead as to cause the
horse passed to shorten his stride.
In any heat wherein there shall be a violation of any of these
restrictions, the offending horse shall not be entitled to win the heat,
and he shall be placed behind all other horses in that heat. And if
the impropriety was intentional on the part of the rider or driver, the
offending horse may be distanced, and the rider or driver shall be
suspended or expelled. [See also Rule 48.]
Rule 30.—Horses Breaking.—When any horse or horses break from
their gait in trotting or pacing, their riders or drivers shall at once
pull them to the gait in which they were to go the race, and any
party failing to comply with this requirement, if he come out ahead,
shall lose the heat, and the next best horse shall win the heat; and
whether such breaking horse come out ahead or not, all other
horses shall be placed ahead of him in that heat, and the Judges
shall have discretionary power to distance the offending horse or
horses, and the rider or driver may be punished by a fine not to
exceed $100, or by suspension not exceeding one year.
Should the rider or driver comply with this requirement, and the
horse should gain by a break, twice the distance so gained shall be
taken from him at the coming out; but this provision must not be so
construed as to shield any trotting or pacing horse from punishment
for running.
In case of any horse (in a trotting race) repeatedly breaking, or
running, or pacing, while another horse is trotting, the Judges shall
punish the horse so breaking, running, or pacing, by placing him last
in the heat, or by distancing him.
A horse breaking at or near the score shall be subject to the same
penalty as if he broke on any other part of the track.
Rule 31.—Relative to Heats and Horses Eligible to Start.—In heats,
one, two, three, or four miles, a horse not winning one heat in three,
shall not start for a fourth, unless such horse shall have made a
dead heat. In heats best three in five, a horse not winning a heat in
the first five shall not start for a sixth, unless said horse shall have
made a dead heat. But where ten or more horses start in a race,
every horse not distanced shall have the right to compete until the
race is completed—subject, however, to all other penalties in these
rules.
Rule 32.—Dead Heats.—A dead heat shall be counted in the race,
and shall be considered a heat which is undecided only as between
the horses making it, and it shall be considered a heat that is lost by
all the other horses contending therein; and the time made in a
dead heat shall constitute a record for each horse making such dead
heat.
Whenever each of the horses making a dead heat would have
been entitled to terminate the race had he won said dead heat, they
only shall start again; and, in that case, each of the horses thus
prevented from starting shall retain his position in the award of
premiums as if said dead heat had been decided in favor of one of
the horses which made the same a “dead heat.”
A horse prevented from starting by this rule shall not be
distanced, but ruled out.
Rule 33.—Time Between Heats.—The time between heats shall be
twenty minutes for mile heats; and for mile heats best three in five,
twenty-five minutes; and for two-mile heats, thirty minutes; for
three-mile heats, thirty-five minutes; and should there be a race of
four-mile heats, the time shall be forty minutes.
After the first heat the horses shall be called five minutes prior to
the time of starting.
Rule 34.—Time Allowed in Case of Accidents.—In case of
accidents, ten minutes shall be allowed; but the Judges may allow
more time when deemed necessary and proper.
Rule 35.—Collision and Break-Down.—In case of collision and
break-down, the party causing the same, whether willfully or
otherwise, may be distanced; and if the Judges find the collision was
intentional or to aid fraud, the driver in fault shall be forthwith
suspended or expelled, and his horse shall be distanced; but, if
necessary to defeat fraud, the Judges may direct the offending horse
to start again.
No horse but the offending one shall be distanced in such a heat,
except for foul driving.
The Judges in a concluding heat, finding that a collision involved a
fraudulent object, may declare that heat void. [See also Rule 48.]
Rule 36.—Placing Horses.—A horse must win a majority of the
heats which are required by the conditions of the race to be entitled
to the purse or stake; but if a horse shall have distanced all
competitors in one heat, the race will then be concluded, and such
horse shall receive the entire purse and stakes contended for.
When more than one horse remains in the race entitled to be
placed at the finish of the last heat, the second best horse shall
receive the second premium, if there be any; and if there be any
third or fourth premium, etc., for which no horse has won and
maintained a specific place, the same shall go to the winner;
provided, that the number of premiums awarded shall not exceed
the number of horses which started in the race.
The foregoing provisions shall always apply, in such cases, unless
otherwise stated in the published conditions of the race.
In deciding the rank of horses other than the winner, as to second,
third, and fourth places, etc., to be assigned among such as remain
in the race entitled to be placed at the conclusion of the last heat
thereof, the several positions which have been assigned to each
horse so contending shall be considered as to every heat in the race
—that is, horses having won two heats, better than those winning
one; a horse that has won a heat, better than a horse only making a
dead heat; a horse winning one or two heats and making a dead
heat, better than one winning an equal number of heats but not
making a dead heat; a horse winning a heat or making a dead heat
and not distanced in the race, better than a horse that has not won
a heat or made a dead heat; a horse that has been placed “second”
twice, better than a horse that has been placed “second” only once,
etc.
When two or more horses shall be equal in the race at the
commencement of a final heat thereof, they shall rank as to each
other as they are placed in the decision of such final heat.
In case these provisions shall not give a specific decision as to
second and third money, etc., the Judges of the race are to make
the awards according to their best judgment, but in conformity with
the principles of this rule.
Rule 37.—Distances.—In races of mile heats, 80 yards shall be a
distance. In races of two-mile heats, 150 yards shall be a distance.
In races of three-mile heats, 220 yards shall be a distance. In races
of mile heats, best three in five, 100 yards shall be a distance. But if
any association or proprietor shall choose, they can provide, in heats
of not over one mile, wherein eight or more horses contend, to
increase the distance one-half, in which case such change shall be
stated in the published conditions of the race before entry.
All horses whose heads have not reached the distance-stand as
soon as the leading horse arrives at the winning-post shall be
declared distanced, except in cases otherwise provided for, or the
punishment of the leading horse by setting him back for running,
when it shall be left to the discretion of the Judges.
A distanced horse is out of the race, and if in any heat one horse
shall distance all competitors the race will then be completed, and
the winner shall be entitled to the entire purse and stakes contended
for, unless otherwise stipulated in the published conditions of the
race.
Rule 38.—Rank Between Distanced Horses.—Horses distanced in
the first heat of a race shall be equal, but horses that are distanced
in any subsequent heat shall rank as to each other in the order of
the positions to which they were entitled at the start of the heat in
which they were distanced.
Rule 39.—Time and its Record.—In every public race the time of
each heat shall be accurately taken and placed in the record, and
upon the decision of each heat the time thereof shall be publicly
announced by the Judges, except as provided in these rules
concerning those heats which are “not awarded to either of the
leading horses.”
It shall be the duty of the Judges of the race to take the time as
aforesaid, or to appoint some suitable person or persons to assist
them in that respect, and no unofficial timing shall be announced or
admitted to the record. [See also Rule 40.]
Rule 40.—Two Leading Horses to be Separately Timed.—The two
leading horses shall be separately timed, and if the heat is awarded
to either, his time only shall be announced and be a record.
In case of a dead heat, the time shall constitute a record for the
horses making the dead heat; and if for any other cause the heat is
not awarded to either of the leading horses, it shall be awarded to
the next best horse, and no time shall be given out by the Judges or
recorded against either horse; and the Judges may waive the
application of the rule in regard to distance in that heat, except for
foul riding or driving.
Rule 41.—Suppression of Time.—In any public race, if there shall
be any intentional suppression or misrepresentation in either the
record or the announcement of the time of any heat in the race,
procured through any connivance, or collusive arrangement, or
understanding between the proprietor or Judges or Timers and the
owner of the winning horse or his driver or other authorized agent, it
shall be deemed fraudulent. And any horse winning a heat or
making a dead heat wherein there was such a fraudulent
suppression of time, together with the parties implicated in the
fraud, shall by operation of the rules be thenceforth expelled.
Rule 42.—A Public Race.—Any contest for purse, premium, stake,
or wager, on any course, and in the presence of a Judge or Judges,
shall constitute a public race.
Rule 43.—When Time Becomes a Bar.—Time made at fairs and on
any track, whether short or not, shall constitute a bar, the same as if
made over a track that was full measurement.
Rule 44.—When Time shall not be a Bar.—Time made under the
saddle, as well as time made when two or more horses are
harnessed together, shall constitute a record for races of the same
character, but shall not be a bar for races of a different character.
Rule 45.—Complaints by Riders or Drivers.—All complaints by
riders or drivers, of any foul riding or driving, or other misconduct,
must be made at the termination of the heat, and before the rider or
driver dismounts or leaves his vehicle.
Rule 46.—Decorum.—If any owner, trainer, rider, driver, or
attendant of a horse, or any other person, use improper language to
the officers of the course or the Judges in a race, or be guilty of any
improper conduct, the person or persons so offending shall be
punished by a fine not exceeding $100, or by suspension or
expulsion. [See also Rule 48.]
Rule 47.—Loud Shouting.—Any rider or driver guilty of loud
shouting, or making other improper noise, or of making improper
use of the whip during the pendency of a heat, shall be punished by
a fine not to exceed $25, or by suspension during the meeting. [See
also Rule 48.]
Rule 48.—Fouls.—If any act or thing shall be done by any owner,
rider, driver, or their horse or horses, during any race or in
connection therewith, which these rules define or warrant the
Judges in deciding to be fraudulent or foul, and if no special
provision is made in these rules to meet the case, the Judges shall
have power to punish the offender by fine not to exceed $100, or by
suspension or expulsion. And in any case of foul riding or driving
they shall distance the offending horse, unless they believe such a
decision will favor a fraud.
The term “foul” shall be construed to apply to riding or driving
contrary to rule, to any act of a fraudulent nature, and to any
unprincipled conduct such as tends to debase the character of the
trotting turf in the estimation of the public. [See also Rules 28, 29,
35, 46 and 47.]
Rule 49.—Fines.—All persons who shall have been fined under
these rules, unless they pay the fines imposed in full on the day of
assessment, shall be suspended until they are so paid or deposited
with the Treasurer of the National Association.
All fines which shall be paid to the association or proprietor on
whose grounds they were imposed, shall by them be reported and
paid to the Treasurer of said National Association.
Rule 50.—No Compromise of Penalties.—In no case shall there be
any compromise in the manner of punishment prescribed in the
rules, but the same shall be strictly enforced.
Rule 51.—Suspensions and Expulsions.—Whenever the penalty of
suspension is prescribed in these rules, if applied to a horse, it shall
be construed to mean a disqualification during the time of
suspension to enter or compete in any race to be performed on the
course of the association or proprietor; and if applied to a person, it
shall be construed to mean a conditional withholding of all right or
privilege to make an entry, or to ride, drive, train, or assist on the
course and grounds of the association or proprietor.
If no limit is fixed in an order of suspension and none is defined in
the rule applicable to the case, the punishment shall be considered
as limited to the season in which the order was issued.
Whenever the penalty of expulsion is prescribed in these rules, it
shall be construed to mean unconditional exclusion and
disqualification from any participation in the privileges and uses of
the course and grounds of the association or proprietor.
No penalty of expulsion shall be removed or modified, except by
the order or upon the approval of the Board of Appeals.
Whenever either of these penalties has been imposed on any
horse or person, on the grounds of any association or proprietor
holding membership in said National Association, written or printed
notice thereof shall immediately be forwarded to the Secretary of
said National Association, stating the offense and the character of
punishment, who shall at once transmit the information to each
associated course or member; and thereupon the offender thus
punished shall suffer the same penalty and disqualification with each
and every association and proprietor holding membership in said
National Association.
Rule 52.—Right of Appeal.—Any person who has been subjected
to the penalty of suspension, or a fine, by the decision of the Judges
of a race, can appeal from such decision to the association or
proprietor upon whose grounds the penalty was imposed, and from
their decision can appeal to the Board of Appeals; provided, that
where the penalty was a fine, it shall have been previously paid.
All decisions and rulings of the Judges of any race, and of the
several associations and proprietors belonging to said National
Association, may be appealed to the Board of Appeals, and shall be
subject to review by said Board, upon facts and questions involving
the proper interpretation and application of these rules, and their
decisions shall be final; provided, that parties to be affected thereby,
shall be notified as the Board shall direct, of a time and place when
such appeal will be acted on by the Board.
Provided further, if the appeal relate to the decision of a race,
immediate notice shall have been given to the Judges of the race, of
the intention so to appeal. Notices of all other appeals must be given
within one week from the announcement of the decisions appealed.
Any person who shall appeal from any order suspending him or his
horse for non-payment of entrance money or a fine, may deposit the
amount claimed with the Treasurer of said National Association, who
may thereupon issue a certificate or notice temporarily reinstating or
relieving the party and his horse from such penalty, subject to the
final action of the Board of Appeals.
Rule 53.—Age of a Horse—How Reckoned.—The age of a horse
shall be reckoned from the first day of January of the year of foaling.
Rule 54.—Colts and Fillies Equally Eligible to Enter.—All colts and
fillies shall be eligible alike to all premiums and stakes for animals of
their age, unless specially excluded by the conditions imposed.
Rule 55.—A Green Horse.—A green horse is one that has never
trotted or paced for premiums or money either double or single.
Rule 56.—Races made and “No Hour Named.”—All races shall be
started at 3 o’clock p. m., from the 1st day of April to the 15th day of
September, and after that date at 2 o’clock p. m., until the season
closes, unless otherwise provided.
Rule 57.—Race made and no Distance Specified.—When a race is
made and no distance specified, it shall be restricted to the following
distances, viz.: One mile and repeat; mile heats, best 3 in 5; two
miles and repeat, or three miles and repeat, and may be performed
in harness to wagon, or under the saddle.
 Rule 58.—Race made to “Go as they Please.”—When a race is
made to go as they please, it shall be construed that the
performance shall be in harness, to wagon, or under the saddle; but
after the race is commenced no change shall be made in the mode
of going, and the race shall be deemed to have commenced when
the horses appear on the track.
Rule 59.—Race made to go “in Harness.”—When a race is made to
go in harness, it shall be construed to mean that the performance
shall be to a sulky.
Rule 60.—Matches made against Time.—When a horse is matched
against time, it shall be proper to allow any other horse to
accompany him in the performance, but not to be harnessed with or
in any way attached to him.
In matches made against time, the parties making the match shall
be entitled to three trials, unless expressly stipulated to the contrary,
which trials shall be had on the same day—the time between trials
to be the same as the time between heats in similar distances.
Rule 61.—Horses sold with Engagements.—The seller of a horse
sold with his engagements has not the power of striking him out.
In case of private sale, the written acknowledgment of the parties
that the horse was sold with engagements, is necessary to entitle
the buyer to the benefit of this rule.
A true copy from the record.
D. F. LONGSTREET. Secretary.
 GENERAL INDEX.
Page.
Autobiography, 11
Bits Used in Educating Horses Addicted to Bad Habits:
To prevent a horse getting his tongue over the
bit, 251
Lolling the tongue, 251
Cure a horse sucking wind, 252
Dead mouth, 253
Cure a side-reiner, 253
Cattle, Education of:
To educate a cow not to kick while being milked, 327
To educate a cow to give down her milk, 331
Practical result of educating cows to give down
milk, 335
To educate cattle to lead behind a wagon, 339
System of educating steers, 428
Directions for Feeding and Fitting the Horse, 451
Dogs, Education of:
To roll a barrel, 411
To fire a gun, 411
To pass between your legs, 415
To jump through hoops, 415
To stand on chairs, 416
Dunbar System of Horseshoeing, etc., 445
Educating the Horse, System of:
New method of haltering a vicious or wild colt, 161
Teaching the words “Come here”, 165
How to lay a horse down, 169
How to get a horse up that throws himself, 173
To educate a colt not to be afraid of his heels, 177
To educate a colt to drive before being
harnessed, 181
How to educate a colt to move his body when he
moves his head, 185
Improved method of bitting colts, 189
Educating a horse to ride, 193
Instructions to ride the colt, 197
To halter-break and hitch a colt in the stall, 201
To educate the horse not to kick at you when
entering the stall, 205
To educate the horse that kicks or paws in the
stable, 209
To prevent a horse from getting cast in the stall, 213
To educate a colt to lead behind a wagon, 217
To educate a horse that is bad to catch, 221
To educate a horse not to rear, 225
To educate and prevent a horse from cribbing, 229
To educate and break a halter-puller, 233
To educate a horse not to kick when the rein gets
under his tail, 237
Another method of educating a kicking horse, 241
To harden a tender-mouthed horse, 244
To educate the horse bad to groom, 247
Hugging the pole, 248
Luggers on the bit, 248
To educate horses not to fear objects while
driving, 257
First lesson in educating horses not to fear an
umbrella, 261
Second lesson in educating horses not to fear an
umbrella, 265
 Horse bad to bridle, 262
To educate a single-footed horse to trot square, 269
To educate a pacing horse to trot, 273
To educate a horse to trot fast, 277
To educate a horse not to kick while in shafts, 281
To educate and infuse life into a lazy horse, 287
To educate a balky horse to draw in double
harness, 295
An easy method of starting a balky horse, 291
To educate a horse not to kick while being shod, 299
To educate a horse while standing bad to shoe, 303
Double hitch educating bridle, 307
A boon for the blacksmith, 311
To educate a horse not to be afraid of the cars, 315
To educate a horse to back at the word of
command, 319
To educate horses or cattle not to jump fences, 323
To educate a tender-mouthed horse to pull on
the bit, 343
To educate horses not to fear a buffalo robe—
illustration and instructions found between
pages, 344 and 345
To educate and make a horse bad to catch, 399
Fast Horses, Record of, 513
History of the Horse, 141
Intelligence of Animals, 345
Miscellaneous:
The only practical way of administering medicine
to a horse, 423
To tell a horse’s age, 425
New method to tell the age, 426
Sure method of producing a rapid growth in
horses’ hoofs, 444
 Corns and their treatment, 459
Ferren’s steel horseshoe, 362
Hoof-expanding shoe for contracted feet, 362
Recipes—Many Never Before Published:
An excellent liniment for sprains, splints or curbs, 270
A remedy for heaves, 324
A sure cure for worms in horses, 336
A cure for colic or gripes, 328
Cure for spavin, 408
Cure for windgalls, 408
Cure for colic, 419
Cure for heaves—never before published, 336
Diuretic drops, 284
Treatment of wounds, 266
To prevent horses being teased by flies, 304
An English stable liniment, 266
Liniment for contracted hoof, 296
For inflammation of the lungs, 324
To cure the scratches in the shortest time ever
known, 392
To cure distemper, 404
To cure hide-bound, 404
To cure inflamed swellings or lame shoulders, 408
Ring bone remedy, 270
Remedy for botts, 266
Another cure for spavin, 424
A valuable liniment for sweeny, 316
Ointment for bruises, scratches, saddle galls, etc., 296
Nerve and bone liniment, 274
Sure cure for poll-evil and fistula, 274
To cure influenza, 496
Condition powders, 498
Glanders, 499
 Lock-jaw, 503
To distinguish between distemper and glanders, 504
Chronic cough, 505
Treatment for Rheumatism, 505
Founder remedy, 506
Horse ointment, 506
Magic liniment, 507
French paste for bone spavin, 508
How to clean and oil harness, 509
Physic Ball, 510
To scatter poll-evil, 511
Healing salve for abrasion and cuts, 511
Wash for foul ulcers, 512
Antispasmodic tincture, 512
Shoeing, A Treatise on, 431
To prevent horses interfering, 441
To prevent overreaching, 443
Trick Horses:
To educate a horse to mount a pedestal, 367
To make a horse waltz, 368
To walk on his hind-feet, 371
To teach to say “No”, 372
To teach to go lame, 376
To teach to be vicious, 379
To teach to push a vehicle, 375
To teach to laugh, 380
To teach to walk on his knees, 383
To teach to drive a boy off a pedestal, 387
To teach to make a bow, 388
To teach to shake hands, 388
To teach to sit down, 391
To teach to bore for oil, 395
To teach to walk upright, 396
 To teach to take handkerchief from his side, 403
To teach to kiss a boy, 407
Rules Trotting Course, Revised, 521
*** END OF THE PROJECT GUTENBERG EBOOK THE HORSE'S
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