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Matt Wiley and Joshua F. Wiley

Advanced R Statistical Programming

and Data Models
Analysis, Machine Learning, and Visualization
Matt Wiley
Columbia City, IN, USA

Joshua F. Wiley
Columbia City, IN, USA

Any source code or other supplementary material referenced by the

author in this book is available to readers on GitHub via the book’s
product page, located at www.​apress.​com/​9781484228715 . For more
detailed information, please visit http://​www.​apress.​com/​source-code
.

ISBN 978-1-4842-2871-5 e-ISBN 978-1-4842-2872-2

https://doi.org/10.1007/978-1-4842-2872-2

Library of Congress Control Number: 2019932986

© Matt Wiley and Joshua F. Wiley 2019

This work is subject to copyright. All rights are reserved by the

Publisher, whether the whole or part of the material is concerned,
specifically the rights of translation, reprinting, reuse of illustrations,
recitation, broadcasting, reproduction on microfilms or in any other
physical way, and transmission or information storage and retrieval,
electronic adaptation, computer software, or by similar or dissimilar
methodology now known or hereafter developed.

Trademarked names, logos, and images may appear in this book. Rather
than use a trademark symbol with every occurrence of a trademarked
name, logo, or image we use the names, logos, and images only in an
editorial fashion and to the benefit of the trademark owner, with no
intention of infringement of the trademark. The use in this publication
of trade names, trademarks, service marks, and similar terms, even if
they are not identified as such, is not to be taken as an expression of
opinion as to whether or not they are subject to proprietary rights.

While the advice and information in this book are believed to be true
and accurate at the date of publication, neither the authors nor the
editors nor the publisher can accept any legal responsibility for any
errors or omissions that may be made. The publisher makes no
warranty, express or implied, with respect to the material contained
herein.

Distributed to the book trade worldwide by Springer Science+Business

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LLC is a California LLC and the sole member (owner) is Springer
Science + Business Media Finance Inc (SSBM Finance Inc). SSBM
Finance Inc is a Delaware corporation.
Introduction
This book shows how to conduct data analysis using the popular R
language. Our goal is to provide a practical resource for conducting
advanced statistical analyses using R . As this is an advanced book, the
reader is assumed to have some background in using R , including
familiarity with general data management and the use of functions.
Because the book is primarily practical, we do not provide in-depth
theoretical or conceptual introductions to the various statistical models
discussed. However, to aid understanding and their appropriate
application, we do provide some conceptual background on each
analytic technique discussed.

Conventions
Bold lowercase letters are used to refer to a vector, for example, x . Bold
uppercase letters are used to refer to a matrix, for example, X .
Generally, the Latin alphabet is used for data and the Greek alphabet is
used for parameters. Mathematical functions are indicated with
parentheses, for example, f (·).
In the text, reference to R code or function will be in monospaced
font like this. R function names have parentheses included to
help indicate it is a function, such as mean() to indicate the mean
function in R .

Package Setup
Throughout the book, we will make use of many different R packages
that make tasks easier or provide more robust or sophisticated
graphing and analysis options.
Although not required for readers, we make use of the
checkpoint package to help ensure the book is reproducible [23]. If
you do not care about reproducibility and are happy to take your
chances that our code that worked with one version of R and packages
also works with whatever versions you have, then you can just skip
reading this section. If you want reproducibility, but do not care why or
how it works, then just create R scripts for the code for each chapter,
save them, and then run the checkpoint package at the beginning. If
you care and want to know why and how it all works, read on the next
few paragraphs.
Details on Reproducibility
The many additional packages available for R are one of its greatest
strengths. However, they also create some challenges. For example, as a
reader, suppose that on your computer, you have R v3.4.3 installed
and as part of that in January you had installed the ggplot2 package
for graphs. By default, you will have whatever version of ggplot2 was
available in January when you installed it. Now in one chapter, we tell
you that you need both the ggplot2 and cowplot packages. Because
you already had ggplot2 installed, you do not need to install it again.
However, suppose that you did not have the cowplot package
installed. So, whenever you happen to be reading that chapter, you
attempt to install the cowplot package, let’s say it’s in April. You will
now by default get the latest version of cowplot available for that
version of R as of April.
Now imagine a second reader comes along and also had R v3.4.3
but had neither the ggplot2 nor the cowplot package installed. They
also read the chapter in April, but they install both packages in April, so
they get the latest version of both packages available in April for R
v3.4.3 .
Even though both you and the other reader had the same version of
R installed, you will end up with different package versions from each
other, and likely different versions yet from whatever versions we used
to write the book.
The end result is that different people, even with the same version
of R, very likely are using different versions of different packages. This
can pose a major challenge for reproducibility. If you are reading a
book, it can be a frustration because code does not seem to work as we
said it would. If you are using code in production or for scientific
research or decision-making, nonreproducibility can pose an even
bigger challenge.
 The solution to standardize versions across people and ensure
results are fully reproducible is to control not only the version of R but
also the version of all packages. This requires a different approach to
package installation and management than the default system, which
uses the latest package versions from CRAN. The checkpoint
package is designed to solve this challenge. It does require some extra
steps and processes to use, and at first may seem a nuisance, but the
payoff is that you can be guaranteed that you are not only using the
same version of R but also the same version of all packages.
To understand how the checkpoint package works, we need a bit
more background regarding how R ’s libraries and package system
work.
Mainstream R packages are distributed through CRAN. Package
authors can submit new versions of their packages to CRAN, and CRAN
updates nightly. For some operating systems, CRAN just stores the
package source code, such as for Linux machines. For others, such as
Windows operating systems, CRAN builds precompiled package
binaries and hosts those. CRAN keeps old source code but generally not
old binary packages for long. On a local machine, when
install.packages is run, R goes online to a repository, by default
CRAN, finds the package name, downloads it, and installs it into a local
library . The local library is basically just a directory on your own
machine. R has a default location it likes to use as its local library, and
by default when you install packages, they are added to the default
library. Once a package is installed, when it is loaded or opened using
library(), R goes to its default library, finds a package with the
same name, and opens it.
The checkpoint package works by creating a new library on the
local machine, for a particular version of R for a particular date. Then it
scans all the R script files in R ’s current working directory—you can
identify this using the getwd() function—and identifies any calls to
the library() or require() functions. Then it goes and checks
whether those packages are installed in the local library. If they are not,
it goes to a snapshot of CRAN taken by another server setup to support
the checkpoint package. That way, checkpoint can install the
version of the package available from a specific date. In that way, the
checkpoint package can ensure that you have the same specific
version of R and specific version of all packages that we used when
writing the book. Or if you are trying to re-run some analysis from a
year ago, you can get the same version of those packages on a new
computer.
Assuming that you have the following code in an R script, you can
use the checkpoint package to read the R script and find the call to
library(data.table), and it will install the data.table
package, which is a great package for data management [29]. If you do
not want checkpoint to look in the current working directory, you
can specify the project path, as we do to the book in this example. You
can also change where checkpoint sets its library to another folder
location, instead of the default location, which we also do. We
accomplish both of these using variables set as part of our R project,
book_directory and checkpoint_directory . If you are using
checkpoint on your own machine, set those variables to the relevant
directories, for example, as book_directory <-
"path/to/your/directory" . Note that whatever folder you
choose, R will need read and write privileges for that folder.

library(checkpoint)
checkpoint("2018-09-28", R. version = "3.5.1",
project = book_directory,
checkpointLocation = checkpoint_directory,
scanForPackages = FALSE,
scan.rnw.with.knitr = TRUE, use.knitr = TRUE)

library(data.table)

options(
width = 70,
stringsAsFactors = FALSE,
digits = 2)

Data Setup
One of the datasets we will use throughout this book is a longitudinal
study, the Americans’ Changing Lives (ACL) [45]. This is publicly
available data and can be downloaded by going to
http://doi.org/10.3886/ICPSR04690.v7 .
The Americans’ Changing Lives (ACL) is a longitudinal study with
five waves of data, shown in Table I-1 .

Table I-1 ACL Study Collection Waves

Wave Year
W1 1986
W2 1989
W3 1994
W4 2002
W5 2011

All we need is the data file in R format, which should be called

04690-0001-Data.rda . You may also find it helpful to download
the PDF documentation of the dataset for more details about the study.
After you have downloaded the data, you should extract the zip folder.
After setting up our R session and necessary libraries, we load the
data. You will need to adjust the path to wherever you saved the data
file after extracting it from the zip folder. Because it is a RDA file,
loading it loads an R object into the workspace. Next we convert to a
data table, select just the variables we are going to use for this book,
and change the variable names to be a bit more intuitive. The suffix
(e.g., “W1”) indicates which wave the variable comes from. Finally, we
convert some variables to factor class and then save the dataset using
the saveRDS() function with compression. This will allow us to read
our cleaned dataset back into R in later chapters with ease and to
assign it to any object name we wish, rather than being stuck with the
object name in the RDA file.

load ("../ICPSR_04690/DS0001/04690-0001-
Data.rda")
ls ()
 ## [1]
"book_directory" "checkpoint_directory"
## [3]
"da04690.0001" "render_apress"

acl <- as.data.table(da04690.0001)

acl <- acl[, .(
V2, V1801, V2101, V2064,
V3007, V2623, V2636, V2640,
V2000,
V2200, V2201, V2202,
V2613, V2614, V2616,
V2618, V2681,
V7007, V6623, V6636, V6640,
V6201, V6202,
V6613, V6614, V6616,
V6618, V6681
)]

setnames(acl, names(acl), c(
"ID", "Sex", "RaceEthnicity", "SESCategory",
"Employment_W1", "BMI_W1", "Smoke_W1",
"PhysActCat_W1",
"AGE_W1",
"SWL_W1", "InformalSI_W1", "FormalSI_W1",
"SelfEsteem_W1", "Mastery_W1",
"SelfEfficacy_W1",
"CESD11_W1", "NChronic12_W1",
"Employment_W2", "BMI_W2", "Smoke_W2",
"PhysActCat_W2",
"InformalSI_W2", "FormalSI_W2",
"SelfEsteem_W2", "Mastery_W2",
"SelfEfficacy_W2",
"CESD11_W2", "NChronic12_W2"
))

acl[, ID := factor(ID)]
 acl[, SESCategory := factor(SESCategory)]
acl[, SWL_W1 := SWL_W1 * -1]

saveRDS(acl, "advancedr_acl_data.RDS", compress

= "xz")
Acknowledgments
To our dear family, who may not always understand everything we
write, yet are nevertheless content to place our books on fireside
mantels and coffee tables.
Table of Contents
Chapter 1:​Univariate Data Visualization
1.​1 Distribution
Visualizing the Observed Distribution
Stacked Dot Plots and Histograms
Density Plots
Comparing the Observed Distribution with Expected
Distributions
Q-Q Plots
Density Plots
Fitting More Distributions
1.​2 Anomalous Values
1.​3 Summary
Chapter 2:​Multivariate Data Visualization
2.​1 Distribution
2.​2 Anomalous Values
2.​3 Relations Between Variables
Assessing Homogeneity of Variance
2.​4 Summary
Chapter 3:​GLM 1
3.​1 Conceptual Background
3.​2 Categorical Predictors and Dummy Coding
Two-Level Categorical Predictors
Three- or More Level Categorical Predictors
3.​3 Interactions and Moderated Effects
3.​4 Formula Interface
 3.​5 Analysis of Variance
Conceptual Background
ANOVA in R
3.​6 Linear Regression
Conceptual Background
Linear Regression in R
High-Performance Linear Regression
3.​7 Controlling for Confounds
3.​8 Case Study:​Multiple Linear Regression with Interactions
3.​9 Summary
Chapter 4:​GLM 2
4.​1 Conceptual Background
Logistic Regression
Count Regression
4.2 R Examples
Binary Logistic Regression
Ordered Logistic Regression
Multinomial Logistic Regression
Poisson and Negative Binomial Regression
4.​3 Case Study:​Multinomial Logistic Regression
4.​4 Summary
Chapter 5:​GAMs
5.​1 Conceptual Overview
Smoothing Splines
5.2 GAMs in R
Gaussian Outcomes
 Binary Outcomes
Unordered Outcomes
Count Outcomes
5.​3 Summary
Chapter 6:​ML:​Introduction
6.​1 Training and Validation Data
6.​2 Resampling and Cross-Validation
6.​3 Bootstrapping
6.​4 Parallel Processing and Random Numbers
foreach
6.​5 Summary
Chapter 7:​ML:​Unsupervised
7.​1 Data Background and Exploratory Analysis
7.​2 kmeans
7.​3 Hierarchical Clusters
7.​4 Principal Component Analysis
7.​5 Non-linear Cluster Analysis
7.​6 Summary
Chapter 8:​ML:​Supervised
8.​1 Data Preparation
One Hot Encoding
Scale and Center
Transformations
Train vs.​Validation Data
Principal Component Analysis
8.​2 Supervised Learning Models
 Support Vector Machines
Classification and Regression Trees
Random Forests
Stochastic Gradient Boosting
Multilayer Perceptron
8.​3 Summary
Chapter 9:​Missing Data
9.​1 Conceptual Background
Multiple Imputation
9.2 R Examples
Multiple Imputation with Regression
Multiple Imputation with Parallel Processing
Multiple Imputation Using Random Forests
9.​3 Case Study:​Multiple Imputation with RFs
9.​4 Summary
Chapter 10:​GLMMs:​Introduction
10.​1 Multilevel Data
Reshaping Data
Daily Dataset
10.​2 Descriptive Statistics
Basic Descriptives
Intraclass Correlation Coefficient (ICC)
10.​3 Exploration and Assumptions
Distribution and Outliers
Time Trends
Autocorrelation
 Assumptions
10.​4 Summary
Chapter 11:​GLMMs:​Linear
11.​1 Theory
Generalized Linear Mixed Models
Mixed Effects vs.​Multilevel Model Terminology
Statistical Inference
Effect Sizes
Random Intercept Model
Visualizing Random Effects
Interpreting Random Intercept Models
Random Intercept and Slope Model
Intercepts and Slopes as Outcomes
11.2 R Examples
Linear Mixed Model with Random Intercept
Linear Mixed Model with Random Intercept and Slope
11.​3 Summary
Chapter 12:​GLMMs:​Advanced
12.​1 Conceptual Background
12.​2 Logistic GLMM
Random Intercept
Random Intercept and Slope
12.​3 Poisson and Negative Binomial GLMMs
Random Intercept
Random Intercept and Slope
12.​4 Summary
Chapter 13:​Modelling IIV
13.​1 Conceptual Background
Bayesian Inference
What Is IIV?​
Intra-individual Variability as a Predictor
Software Implementation:​VARIAN
13.​2 R Examples
IIV Predicting a Continuous Outcome
13.​3 Summary
Bibliography
Index
About the Authors and About the Technical
Reviewer

About the Authors

Matt Wiley
is a tenured, associate professor of
mathematics with awards in both
mathematics education and honors
student works. He earned degrees in
pure mathematics, computer science,
and business administration through the
University of California and Texas A&M
University Systems. He serves as director
of quality enhancement at Victoria
College, facilitating comprehensive
assessment programs, key performance
indicator dashboards and one-click
reports, and data consultation for
campus stakeholders. Outside academia, he is managing partner at
Elkhart Group LLC, a statistical consultancy. With experience in
programming R , SQL , C++ , Ruby , Fortran , and JavaScript , he
has always found ways to meld his passion for writing with his joy of
logical problem solving and data science. From the boardroom to the
classroom, Matt enjoys finding dynamic ways to partner with
interdisciplinary and diverse teams to make complex ideas and projects
understandable and solvable.

Joshua F. Wiley
is a lecturer in the Monash Institute of Cognitive and Clinical
Neurosciences and School of Psychological Sciences at Monash
University. He earned his PhD from the University of California, Los
Angeles, and completed his postdoctoral training in primary care and
prevention. His research uses advanced quantitative methods to
understand the dynamics between
psychosocial factors, sleep, and other
health behaviors in relation to
psychological and physical health. He
develops or codevelops a number of R
packages including varian , a package
to conduct Bayesian scale-location
structural equation models, and
MplusAutomation , a popular package
that links R to the commercial Mplus
software, and miscellaneous functions to
explore data or speed up analysis in
JWileymisc .

About the Technical Reviewer

Andrew Moskowitz
is an analytics and data science
professional in the entertainment
industry focused on understanding user
behavior, marketing attribution and
efficacy, and using advanced data science
concepts to address business problems.
He earned his PhD in quantitative
psychology at the University of
California, Los Angeles, where he
focused on hypothesis testing and mixed
effects models.
© Matt Wiley and Joshua F. Wiley 2019
Matt Wiley and Joshua F. Wiley, Advanced R Statistical Programming and Data Models
https://doi.org/10.1007/978-1-4842-2872-2_1

1. Univariate Data Visualization

Matt Wiley1 and Joshua F. Wiley1

(1) Columbia City, IN, USA

Most statistical models discussed in the rest of the book make

assumptions about the data and the best model to use for them. As data
analysts, we often must specify the distribution that we assume the
data come from. Anomalous values, also called extreme values or
outliers, may also have undue influence on the results from many
statistical models. In this chapter, we examine visual and graphical
approaches to exploring the distributions and anomalous values for
one variable at a time (i.e., univariate). The goal of this chapter is not
specifically to create beautiful or publication quality graphs nor to
show results, but rather to use graphs to understand the distribution of
a variable and identify anomalous values. This chapter focuses on
univariate data visualization, and the next chapter will employ some of
the same concepts but applied to multivariate distributions and cover
how to assess the relations between variables.

library(checkpoint)
checkpoint("2018-09-28", R.version = "3.5.1",
project = book_directory,
checkpointLocation = checkpoint_directory,
scanForPackages = FALSE,
scan.rnw.with.knitr = TRUE, use.knitr = TRUE)

library(knitr)
library(ggplot2)
library(cowplot)
library(MASS)
library(JWileymisc)
library(data.table)

options(width = 70, digits = 2)

The ggplot2 package [109] creates elegant graphs, and the
cowplot package is an add-on that makes graphs cleaner [117]. The
MASS package provides functions to test how well different
distributions fit data [98]. The JWileymisc package is maintained by
one of this text’s authors and provides miscellaneous functions that
allow us to focus on the graphics in this chapter [114]. The
data.table package will be used a lot for data management [29].

1.1 Distribution
Visualizing the Observed Distribution
Many statistical models require that the distribution of a variable be
specified. Histograms use bars to graph a distribution and are probably
the most common graph used to visualize the distribution of a single
variable. Although relatively rare, stacked dot plots are another
approach and provide a precise way to visualize the distribution of data
that shows the individual data points. Finally, density plots are also
quite common and are graphed by using a line that shows the
approximate density or amount of data falling at any given value.

Stacked Dot Plots and Histograms

Dot plots work by plotting a dot for each observed data value, and if
two dots would fall on top of each other, they are stacked up [118].
Compared to histograms or density plots, dot plots are unique in that
they actually plot the raw individual data points, rather than
aggregating or summarizing them. This makes dot plots a nice place to
start looking at the distribution or spread of a variable, particularly if
you have a relatively small number of observations.
The granular approach, plotting individual data points, is also dot
plots limitation. With even moderately large datasets (e.g., several
hundred), it becomes impractical to plot individual values. With
thousands or millions of observations, dot plots are even less effective
at visualizing the overall distribution.
We can create a plot easily using ggplot2, and the results are
shown in Figure 1-1.

ggplot(mtcars, aes(mpg)) +
geom_dotplot()

## 'stat_bindot()' using 'bins = 30'. Pick

better value with 'binwidth'.

Figure 1-1 Stacked dot plot of miles per gallon from old cars

As a brief aside, much of the code for ggplot2 follows the format
shown in the following code snippet. In our case, we wanted a dot plot,
so the geometric object, or “geom”, is a dot plot (geom_dotplot() ).
Many excellent online tutorials and books exist to learn how to use the
ggplot2 package for graphs, so we will not provide a greater
introduction to ggplot2 here. In particular, Hadley Wickham, who
develops ggplot2, has a recently updated book on the package,
ggplot2: Elegant Graphics for Data Analysis [109], which is an excellent
guide. For those who prefer less conceptual background and more of a
cookbook, we recommend the R Graphics Cookbook by Winston Chang
[20].

ggplot(the-data, aes(variable-to-plot)) +
geom_type-of-graph()
 Unlike a dot plot that plots the raw data, a histogram is a bar graph
where the height of the bar is the count of the number of values falling
within the range specified by the width of the bar. You can vary the
width of bars to control how many nearby values are aggregated and
counted in one bar. Narrower bars aggregate fewer data points and
provide a more granular view. Wider bars aggregate more and provide
a broader view. A histogram showing the distribution of sepal lengths
of flowers from the famous iris dataset is shown in Figure 1-2.

ggplot(iris, aes(Sepal.Length)) +
geom_histogram()

## 'stat_bin()' using 'bins = 30'. Pick better

value with 'binwidth'.

Figure 1-2 Histogram of sepal length from the iris data

 If you know the shape of a distribution (e.g., a normal distribution),
you can examine whether the histogram for a variable looks like the
shape of a distribution you recognize. In the case of the sepal length
data, they appear approximately normally distributed, although they
are clearly not perfect.
If data do not appear to follow the distribution we hoped for (e.g.,
normal), it is common to apply a transformation to the raw data. Again,
histograms are a useful way to examine how the distribution looks after
transformation. Figure 1-3 shows a histogram of annual Canadian lynx
trappings. From the graph we can see the variable is positively skewed
(has a long right tail).

ggplot(data.table(lynx = as.vector(lynx)),
aes(lynx)) +
geom_histogram()

## 'stat_bin()' using 'bins = 30'. Pick better

value with 'binwidth'.
Figure 1-3 Histogram of annual Canadian lynx trappings
For positive skew, a square root or log transformation can help to
reduce positive skew and make variables closer to a normal
distribution, assuming that there are no negative values. This histogram
of lynx trappings after a natural log transformation is shown in Figure
1-4.

ggplot(data.table(lynx = as.vector(lynx)),
aes(log(lynx))) +
geom_histogram()

## 'stat_bin()' using 'bins = 30'. Pick better

value with 'binwidth'.
Figure 1-4 Histogram of annual Canadian lynx trappings after a natural log
transformation

Density Plots
Another common tool to visualize the observed distribution of data is
by plotting the empirical density. The code for ggplot2 is identical to
that for histograms except that geom_histogram() is replaced with
geom_density() . The code follows and the result is shown in Figure
1-5.

ggplot(iris, aes(Sepal.Length)) +
geom_density()
Figure 1-5 This is the density plot for our sepal lengths
Empirical density plots include some degree of smoothing, because
with continuous variables, there is never going to be many observations
at any specific value (e.g., it may be that no observation has a value of
3.286, even though there are values of 3.281 and 3.292). Empirical
density plots show the overall shape of the distribution by applying
some degree of smoothing. At times it can be helpful to adjust the
degree of smooth to see a coarser (closer to the raw data) or smoother
(closer to the “distribution”) graph. Smoothing is controlled in
ggplot2 using the adjust argument. The default, which we saw in
Figure 1-5, is adjust = 1. Values less than 1 are “noisier” or have less
smoothing, while values greater than 1 increase the smoothness. We
compare and contrast noisier in Figure 1-6 vs. very smooth in Figure 1-
7.

ggplot(iris, aes(Sepal.Length)) +
geom_density(adjust = .5)
 ggplot(iris, aes(Sepal.Length)) +
geom_density(adjust = 5)

Figure 1-6 A noisy density plot

Discovering Diverse Content Through
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to the other. Here were two men whose spirits were in accord. It is easy to
think of them as sitting the candle out in converse about the winter fire, or
as sitting far into the night in silence, each finding pleasure in the mere
presence of the other. Such a relationship had grown up through the years.
They thought alike, found similar enjoyment in agricultural pursuits, and in
the many little things of common life.
‘What say you,’ wrote Jefferson just before the beginning of the much-
discussed journey, ‘to taking a wade into the country at noon? It will be
pleasant above head at least, and the party will finish by dining here.
Information that Colonel Beckwith[314] is coming to be an intimate with
you, and I presume not a desirable one, encourages me to make a
proposition which I did not venture as long as you had your agreeable
congressional society about you; that is to come and take a bed and plate
with me.... To me it will be a relief from the solitude of which I have too
much; and it will lessen your repugnance to be assured that it will not
increase my expenses an atom.... The approaching season will render this
situation more agreeable than Fifth Street, and even in the winter you will
not find it disagreeable.’[315] It required no assiduous and cunning
cultivation by Jefferson to wean Madison away from Hamilton. The
relations of the first two far antedated those of the last. Madison had agreed
with Hamilton on the necessity for a more permanent and substantial union.
They had fought together for the ratification of the Constitution, but such
were their temperamental differences that the breach which quickly
appeared was inevitable when it came to the determination of the policies of
that union. While Jefferson was still in Paris, Madison, without consulting
his friend, was foreshadowing the policy of the future Jeffersonian party in
his fight for discrimination against England in the revenue measure of the
first congressional session. He proposed discrimination between the original
creditors and the speculators before he had the opportunity to discuss the
subject with Jefferson. If there was an accord with the latter, it was due less
to the influence of one upon the other than to the similarity of their
thinking. The little man with the mild, almost shy expression, who rode out
of Philadelphia with Jefferson that spring of 1791, was much too big to
have been led around by the nose by any of his contemporaries.
As early as the spring of 1791, the names of the two were associated in
the minds of many as the prospective leaders of a party that would
challenge the purposes of the Federalists. Answering a series of articles in
the ‘Maryland Journal,’ some one advised the author of how to make his
opinions worth while. ‘Keep always before your eyes the steps by which
Jefferson and Madison have gradually ascended to their present
preëminence of fame. Like them you must devote your whole leisure to the
most useful reading. Like them you must dive into the depths of philosophy
and government.’[316] Thus they were already associated in the public
mind, and there was some whispering among the Federalist leaders when
they set forth in their carriage.
Bumping and splashing over the rough tree-lined roads those spring
days, they unquestionably discussed the political situation, but these
discussions were only the continuation of others that had been proceeding
throughout the previous fall and winter. If politics was the object of the
journey, they were both remarkably successful in covering their tracks.
There is nothing in the letter Jefferson wrote his daughter Mary to indicate
anything more than a pleasure jaunt.[317] In a letter to his other daughter,
Martha, we hear much of fishing for speckled trout, salmon, and bass, of the
strawberries in bloom, of vegetation and agricultural conditions—but
nothing of politics.[318] To his son-in-law he wrote descriptions of historic
places, of botanical objects and scenery, and of running foul of the blue law
in Vermont prohibiting traveling on Sunday.[319] The one reference to the
journey in the correspondence of Madison merely says that ‘it was a very
agreeable one, and carried us through an interesting country, new to us
both.’[320] In none of these letters do we find a single reference to politics
or politicians.
Something is made of the call of the travelers on Burr and Livingston
when in New York, and on Governor Clinton at Albany; but their conduct
would have been suspicious only if they had failed to observe the ordinary
amenities of social life in calling upon the leading public characters in the
towns through which they passed. Still we may safely surmise that they
found time while waiting for the fish to bite to exchange views on the
necessity of organizing an opposition to the Federalists. It is even possible
that out of these conversations on country roads actually sprang the
Democratic Party, but there is no evidence.

VI
 On his return to Philadelphia, Jefferson found himself the center of a
remarkable newspaper controversy. Fascinated by the beauty of Marie
Antoinette, Edmund Burke of England had written his bitter attack, not only
on the excesses of the French Revolution, but upon its democratic
principles as well. It was the fashion in those days to conceal a hate of
democracy under the cloak of a simulated horror over the crimes of the
Terrorists. Thomas Paine had replied to Burke with his brilliant and
eloquent defense of democracy, ‘The Rights of Man.’ In American circles
where democracy was anathema, and even republicanism was discussed
with cynicism, the Burke pamphlet was received with enthusiasm. It was
not until some time later that ‘The Rights of Man’ reached New York, albeit
its nature was known and there had been a keen curiosity to see it. Early in
May, Madison had promised Jefferson to secure a copy as soon as possible.
He understood that the pamphlet had been suppressed in England, and that
Paine had found it convenient to retire to Paris. ‘This,’ he wrote, ‘may
account for his not sending copies to friends in this country.’[321] At length
a single copy arrived and was loaned by its owner to Madison, who passed
it on to Jefferson. He read it with enthusiasm. Here was a spirited defense of
democracy, and of the fight the French were waging for their liberties; here
an excoriation of the prattle in high social and governmental circles of the
advantage, if not necessity, for titles of nobility. Here was not only an
answer to Burke, but to John Adams, whose ‘Discourses of Davilla’ had
been running for weeks in Fenno’s paper, and had been copied extensively
in other journals with a similar slant. Jefferson was immensely pleased.
Before he had finished with it, the owner had called upon Madison for
its return, as arrangements had been made for its publication by a
Philadelphia printer. It was agreed that Jefferson should send it directly to
the print shop, and in the transmission he wrote a brief explanation of the
delay, and added: ‘I am extremely pleased to find it will be reprinted here,
and that something is at length to be publicly said against the political
heresies which have sprung up among us. I have no doubt our citizens will
rally a second time round the standard of “Common Sense.” ’
To this note he attached so little importance that he kept no copy. With
astonishment he found that the printer had used his note as the preface, with
his name and official title as Secretary of State. The general conviction that
the word ‘heresies’ was meant to apply to the Adams papers sufficiently
indicates the popular interpretation of their trend. The storm broke.
 Major Beckwith, the British Agent, hastened to express his pained
surprise to Washington’s Secretary at the recommendation by the Secretary
of State of a pamphlet which had been suppressed in England. The secretary
was sufficiently impressed by the scandalized tone of the aristocratic
society of Philadelphia, which was usually lionizing some degenerate
members of the European nobility, to write his chief in detail. When
Randolph dined with Mrs. Washington, Lear retailed it to him, and the
suggestion was made that Jefferson should know. Thus there was something
more than a tempest in a teapot. Everywhere men were partisans of the
pamphlets of Burke or Paine, the aristocrats on one side, the democrats on
the other, the stoutest of the republicans everywhere delighted with ‘The
Rights of Man.’ This was true in even the small towns and the villages of
far places. One traveler passing through Reading was surprised to find the
two pamphlets the ‘general topic of conversation,’ and he was assured of
the delight that awaited him in the reading of Paine’s.[322] All too long had
the Americans been drugged with Fenno’s deification of the upper classes
—with John Adams’s ‘Discourses’ on the necessity of ‘distinctions’—and
here was old ‘Common Sense’ back again in the old form slashing the
aristocrats fore and aft. The press responded to the popular demand, and
everywhere ‘The Rights of Man’ was being published serially to be eagerly
read by the thousands who had not seen the pamphlet. But it was not all
one-sided. If the ‘Painites’ wrote furiously in some papers, the ‘Burkites’
were prolific in Fenno’s and a few others. In the fashionable drawing-rooms
a poll would have shown a decided preference for the defender of
aristocracy who had wept so eloquently over the woes of a frivolous Queen.
Nowhere was Burke so popular and Paine so loathed as in the home of
Adams, the Vice-President. ‘What do you think of Paine’s pamphlet?’ asked
Dr. Rush, to whom society was cooling because of his democratic
tendencies. The second official of the Republic hesitated as if for dramatic
effect, and then, solemnly laying his hand upon his heart, he answered, ‘I
detest that book and its tendency from the bottom of my heart.’ Indeed,
most of the Federalists were frankly with Burke. ‘Although Mr. Burke may
have carried his veneration for old establishments too far, and may not have
made sufficient allowance for the imperfections of human nature in the
conflict of the French Revolution,’ wrote Davie to Judge Iredell, ‘yet I think
his letter contains a sufficient amount of intelligence to have rescued him
from the undistinguishing abuse of Paine.’[323]
 With most of the Federalist leaders in sympathy with Burke, few
ventured to attack Paine in the open. Not so with Adams who was
spluttering mad over the Jefferson ‘preface.’ He was positive that the
publication of Paine’s pamphlet in this country had been instigated by his
former colleague at Paris.[324] To him the pamphlet of Paine, the ‘preface’
of Jefferson, the acclaim for both on the part of the people was but a
devilish conspiracy of Jefferson’s to pull him down. ‘More of Jefferson’s
subterranean tricks.’ And with this conviction, John Quincy Adams, the
son, then in Boston, took up a trenchant pen to write the articles of
‘Publicola’ for the ‘Centinel,’ sneering at the Jeffersonian note to the
printer, assailing Paine and democracy, and stoutly defending the
governmental forms of England. So well did he discharge his filial duty that
his articles were published in pamphlet form in England by the friends of
Burke, and many of the Federalist papers reproduced them as they
appeared.
Then the newspaper battle began in earnest. Many indignant democrats
rushed to the attack of ‘Publicola’ with all the greater zest because of the
belief that ‘Publicola’ was none other than ‘Davilla’ himself. ‘America will
not attend to this antiquated sophistry,’ wrote one, ‘whether decorated by
the gaudy ornaments of a Burke, the curious patch-work of a Parr to which
all antiquity must have contributed its prettiest rags and tatters, or the
homely ungraceful garb which has been furnished her by Mr. John
Adams.’[325] Another suggested that ‘Publicola’ would soon cease to write
since ‘the time for the new election is approaching,’ although the
‘Discourses’ might be continued without danger since ‘dullness, like the
essence of opium, sets every reader to sleep before he has passed the third
sentence.’[326] As for ‘Publicola,’ his letters were ‘being brought forward to
persuade the people that an hereditary nobility, and, of consequence, high
salaries, pomp and parade are essential to the prosperity of the country.’[327]
In Boston, where the letters were appearing, ‘Agricola’ and ‘Brutus’ began
spirited replies in the rival paper.[328] Other writers, with less grace and
force, joined in the fray. Who are to constitute our nobility, demanded
‘Republican,’ our moneyed men—the speculators? If so ‘Dukes, Lords and
Earls will swarm like insects gendered by the sun,’ and the worn-out soldier
who had been tricked out of his paper would have the satisfaction of
‘bowing most submissively to their lordships while seated in their
carriages.’[329]
But Adams was not without his defenders. ‘An American’ declared that
all the abuse was ‘designed as a political ladder by which to climb.’
Miserable creatures! ‘Ages after the tide of time has swept their names into
oblivion, the immortal deeds of Adams will shine on the brightest pages of
history.’[330] ‘The Ploughman’ indignantly resented the insinuation that
Adams had written the ‘Publicola’ letters. In truth, ‘his friends consider Dr.
Adams as being calumniated’ by having such sentiments ascribed to him.
[331] To all the ‘hornets’ that were buzzing about Adams, Fenno felt he
could be indifferent, for they had no stings. They were merely nonentities
trying to give consequence to their scribblings by appearing to be answering
the Vice-President.
Meanwhile, Jefferson was keenly enjoying the turmoil. We wish it were
possible to trace it all to his contrivance, for nothing could have served his
purpose better. To have foreseen that the writing of a few simple lines
would have awakened the militant republicanism of the country and have
aroused the democratic impulses of the inert mass would have been
complimentary to his political genius. But this is not the only instance
where a clever politician with the reputation of a magician has stumbled
forward. There is no doubt that Jefferson was astonished and embarrassed
on learning that the printer had made an unauthorized use of his personal
note. He admitted to Washington that he had Adams’s writings in mind, but
that nothing was more remote from his thoughts than of becoming ‘a
contributor before the public.’ However, he was not impressed with the
reflections on his taste. ‘Their real fear,’ he added, ‘is that this popular and
republican pamphlet ... is likely ... to wipe out all the unconstitutional
doctrines which their bellwether, Davilla, has been preaching for a twelve-
month.’[332] This explanation was enough for Knox, who wrote accordingly
to Adams,[333] but not enough for Jefferson who sent a frank explanation to
Adams with an expression of regret. In generous mood, the latter accepted
the explanation with the protestation that their old friendship was ‘still dear
to my heart,’ and that ‘there is no office I would not resign rather than give
a just occasion for one friend to desert me.’[334]
Madison, to whom Jefferson had sent a similar explanation, had assumed
that there had been a mistake or an imposition, but he could see no reason
for indignation on the part of Adams or his friends. ‘Surely,’ he wrote, ‘if it
be innocent and decent for one servant of the public to write against its
government, it cannot be very criminal or indecent in another to patronize a
written defence of the principles on which that Government is
founded.’[335]
However much Jefferson may have regretted the unauthorized use of his
letter, he rejoiced in its effect. He wrote Paine that the controversy had
awakened the people, shown the ‘monocrats’ that the silence of the masses
concerning the teachings of ‘Davilla’ did not mean that they had been
converted ‘to the doctrine of king, lords and commons,’ and that they were
‘confirmed in their good old faith.’[336] The incident had established
Jefferson in the public mind as the outstanding leader of democracy, had set
the public tongue to wagging on politics again. More was involved in the
pamphlets of Burke and Paine than differences over the French Revolution.
The keynote of Burke’s was aristocracy and privilege; that of Paine’s was
democracy and equal rights. The former was the gospel of the American
Federalists; the latter the covenant of the American Democracy. Studying
the reactions with his characteristic keenness, Jefferson was convinced that
the time was ripe to mobilize for the inevitable struggle.

VII

‘What do you think of this scrippomony?’ Jefferson wrote to Edward

Rutledge in the late summer. ‘Ships are lying idle at the wharfs, buildings
are stopped, capital withdrawn from commerce, manufactures, arts and
agriculture to be employed in gambling, and the tide of public prosperity ...
is arrested in its course.... I imagine that we shall hear that all the cash has
quitted the extremities of the nation and accumulated here.’[337] As he
wrote, Jefferson had before him the report of the craze which had just
reached him in a letter from Madison in New York. ‘Stock and scrip the
sole domestic subjects of conversation ... speculations ... carried on with
money borrowed at from two and a half per cent a month to one per cent a
week.’[338]
Men grown reckless with the frenzy of the intoxication were resorting to
fraud to rob the Government, many taking out administration papers for
deceased soldiers who had left no heirs. ‘By this knavery,’ wrote Madison
at an earlier period, ‘a prodigious sum will be unsaved by the public, and
reward the worst of its citizens.’ And suppose one of the clerks of the
account offices is not proof against the temptation?[339]
By the middle of the summer (July 10th) Bank stock had risen as much
in the market in New York as in Philadelphia with the feeling that there was
a certainty of gain. A scramble had set in ‘for so much public plunder.’ The
meticulously scrupulous Madison, with his lofty notions of official
propriety, was shocked to find ‘the members of the Legislature who were
most active in pushing this job openly grasping the emoluments.’ Schuyler,
the father-in-law of Hamilton, was to be the head of the directors of the
Bank ‘if the weight of the New York subscribers can effect it.’ Stock-
jobbing monopolized all conversation. The coffee-houses buzzed with the
gamblers.[340]
Meanwhile, from the high-placed to the ordinary scamp, men maddened,
by the money-itch, were resorting to ordinary crime to get possession of
public paper. In some places clever counterfeiters were driving through the
country under the pretext of examining securities with the idea of purchase
and cleverly exchanging the worthless for the real.[341] In the South and in
the remote parts of Maine, swindlers were scouring the woods for State
notes, lying to the uninformed and ignorant about their value, and getting
them for a song. ‘What must be the feelings of the widow and orphan,’
wrote a correspondent of a Philadelphia paper, ‘when they find themselves
thus defrauded of a great part of their little all, and that, not unlikely, the
earnings of their late husbands and fathers, who died in the service of their
country, by these pests of society who ought to be despised?’[342] But greed
knew no shame. An appalling picture: members of Congress feathering
their nest through their legislative acts, counterfeiters robbing the unwary,
common crooks stealing from the Government by posing as the
administrators of the dead, and distinguished members of the Boston Bar,
like Otis and Gore, speculating with their clients’ money without their
knowledge or consent.
So sinister was the situation that notes of warning began to appear in the
newspapers. The ‘Pennsylvania Gazette’ found that speculators had ‘turned
raving mad, and others so agitated that they appear on the borders of
insanity.’[343] Fenno tried vainly to restore sobriety to the drunk—for
Hamilton himself was shocked and not a little concerned.[344] Better be
careful about parting with Bank scrip, warned the ‘New York Daily
Advertiser.’ Efforts were being made to buy up all the scrip in the city ‘and
for this purpose a powerful combination was formed ... on Saturday night to
reduce the price.’[345] Beware of another South Sea Bubble, warned
‘Centinel’ in the same paper. ‘The National Bank stock has risen so high, so
enormously above its real value, that no two transactions in the annals of
history can be found to equal it....’[346]
From Boston came similar stories of the madness. All the while the New
York papers were publishing day-by-day quotations on the scrip.[347] By
August 15th the mania was at its height. ‘It has risen like a rocket,’ wrote an
amused scribbler. ‘Like a rocket it will burst with a crack and down drops
the rocket stick. What goes up must come down—so take care of your pate,
brother Jonathan.’[348] The craze was becoming ridiculous. The sane and
the honest looked upon it as a spectacle. Above the angry cries in the
market-place rang the laughter of the observers who kept their heads. Some
put their scoffing into verse:

‘What magic this among the people,

That swells a Maypole to a steeple?’[349]

Suddenly the bubble showed signs of bursting. A New York bank stopped
discounting for some of the speculators. Messengers hurried forth with the
ominous news, horses’ hoofs hammering the Jersey roads to Philadelphia,
where there was consternation and a falling-off in buying.[350] Pay-day had
not yet come, but it was on the way, and men began to regain their senses.
Then came the emergence of the political phase. ‘Does history afford an
instance,’ asked one observer, ‘where inequality in property, without any
adequate consideration, ever before so suddenly took place in the world? or
the basis of the power and influence of an Aristocracy was created?’[351] A
Boston paper commented significantly on the ease with which the mere
opening and closing of the galleries of Congress could serve the purposes of
speculation. ‘How easily might this be done should any member of
Congress be inclined to speculate.’[352]
Thus the talk of a ‘corrupt squadron’ in the First Congress was not the
invention of Jefferson—it was the talk of the highways and the byways, the
coffee-houses and the taverns, and we find it recurring in the
correspondence of the public men of the period. Everywhere sudden
fortunes sprang up as if by magic. There was a rumbling and grumbling in
the offing. With the people thinking more seriously of Madison’s fight for
discrimination, he began to loom along with Jefferson as a prospective
leader against the ‘system.’ With the discovery that the law had been
violated in the subscription of more than thirty shares, it was hoped that it
would ‘draw the attention of Madison ... immediately on the meeting of
Congress’ and that ‘the whole proceedings ... be declared nugatory.’[353]
Then came the election of Bank directors in the fall, and indignation
flamed when the prizes went to leaders in the Congress that had created the
Bank—to Rufus King, Samuel Johnson of North Carolina, William Smith
of South Carolina, Jeremiah Wadsworth of the ‘fast sailing vessels,’ John
Laurance of New York, William Bingham of Philadelphia, Charles Carroll
of Carrollton, George Cabot, Fisher Ames, and Thomas Willing, the partner
of Robert Morris.
Members of Congress had speculated heavily and profitably on their
knowledge of their own intent in legislation; they were owners of bank
scrip of the Bank they created, and their leaders were on the board of
directors. There was talk among the people of a ‘corrupt squadron,’ and
Jefferson did not invent the term; he found it in the street and used it.
Though Hamilton, scrupulously honest, was not involved in proceedings
that were vicious, if not corrupt, many of his lieutenants were, and that, for
the purposes of politics, made an issue.
But Hamilton was in the saddle, booted and spurred, and riding hard
toward the realization of his conception of government, followed by an
army that fairly glittered with the brilliancy of many of his field marshals,
and which was imposing in the financial, social, and cultural superiority of
the rank and file; an army that could count on the greater part of the press to
publish its orders of the day, and on the beneficiaries of its policies to fill its
campaign coffers. And it was at this juncture that Jefferson began the
mobilization of an army that would seem uncouth and ragged by
comparison. The cleavage was distinct; the ten-year war was on.
As a preliminary to the story of the struggle, it is important to know
more of the character and methods of the man who dared challenge
Hamilton’s powerful array and something of the social atmosphere in
Philadelphia where the great battles were fought.
 CHAPTER V

THOMAS JEFFERSON: A PORTRAIT

I N the personal appearance of Thomas Jefferson there was little to denote

the powerful, dominating leader and strict disciplinarian that he was.
Unlike Hamilton, he did not look the commander so much as the rather
shy philosopher. The gruff Maclay, on seeing him for the first time, was
disappointed with his slender frame, the looseness of his figure, and the ‘air
of stiffness in his manner,’ while pleased with the sunniness of his face.[354]
He was of imposing height, being more than six feet, and slender without
being thin.[355] All contemporaries who have left descriptions refer to the
long, loosely jointed limbs, and none of them convey an impression of
grace. His hair, much redder than that of Hamilton, was combed loosely
over the forehead and at the side, and tied behind. His complexion was
light, his eyes blue and usually mild in expression, his forehead broad and
high. Beneath the eyes, his face was rather broad, the cheek-bones high, the
chin noticeably long, and the mouth of generous size. The casual glance
discovered more of benevolence than force, more of subtlety than
pugnacity. Nor, in that day of lace and frills, was there anything in his garb
to proclaim him of the élite. His enemies then, and ever since, have made
too much of his loose carpet slippers and worn clothes, and the only thing
they prove is that he may have had the Lincolnian indifference to style.
Long before he made his ‘pose’ in the President’s house for the benefit of
the groundlings, we find a critic who was to be numbered among his
followers complaining because his clothes were too small for his body.[356]
The truth, no doubt, is that he dressed conventionally, because men must,
and was careless of his attire.
Certain it is that when she first met him, Mrs. Bayard Smith, who had
been unduly impressed with the Federalist references to the ‘coarseness and
vulgarity of his manners,’ was astonished at the contradiction of the
caricature by the man. ‘So meek and mild, yet dignified in his manners,
with a voice so soft and low, with a countenance so benign and intelligent’
she found him.[357] In truth there was enough dignity in his manner to
discourage the stranger on a first approach, as Tom Moore found to his
disgust. Even Mrs. Smith thought his ‘dignified and reserved air’ chill at
first;[358] and a French admirer who made a sentimental journey to
Monticello thought him somewhat cold and reserved.’[359] ‘The cold first
look he always cast upon a stranger’[360] appears too often in the
observations of his contemporaries to have been imaginary.
As some have found fault with his dress, others have criticized a
slovenly way of sitting—‘in a lounging manner, on one hip commonly, with
one of his shoulders elevated much above the other’;[361] while another—a
woman too—was charmed at the ‘free and easy manner’ in which he
accepted a proffered chair.[362] The natural deduction from the
contradictions is that he seated himself as comfortably as possible with little
regard to the picture in the pose. There is a manifest absurdity in the idea
that the man who moved familiarly in the most cultured circles of the most
polished capital in Europe could have been either impossible in dress or
boorish in manner.
But there is one unpleasant criticism of his manner that cannot be so
easily put aside—a shiftiness in his glance which bears out the charge of his
enemies that he was lacking in frankness. The most democratic member of
the first Senate, meeting him for the first time, was disappointed to find that
‘he had a rambling vacant look, and nothing of that firm collected
deportment which I expected would dignify the presence of a Secretary or
Minister.’[363] Another found that ‘when speaking he did not look at his
auditor, but cast his eyes toward the ceiling or anywhere but at the eye of
his auditor.’[364] This weakness was possibly overemphasized, for he was
notoriously shy.
Aside from this, there is abundant evidence that there was an ineffable
charm in his manner. One who objected to his ‘shifty glance’ was favorably
impressed with ‘the simplicity and sobriety’ of his deportment, and found
that while ‘he was quiet and unobtrusive ... a stranger would perceive that
he was in the presence of one who was not a common man.’[365] He was
free of the affectations of pedantry, courteous and kindly, modest and
tolerant. Thus he appeared to excellent advantage in conversation, and, with
one exception, all who knew him and have left their impressions found him
an entertaining and illuminating talker. Maclay, who was certainly not the
most competent of judges, thought his conversation ‘loose and rambling,’
and yet admitted that ‘he scattered information wherever he went, and some
even brilliant sentiments sparkled from him.’[366] It is probable that the
gout-racked radical confused conversation with set speeches, and quite as
possible that on this particular occasion, when Jefferson was meeting with a
curious senatorial committee, he was not inclined to tell all he knew.
Certainly the polished nobleman, familiar with the most intellectual
circles of Paris, who found his ‘conversation of the most agreeable kind,’
and that he possessed ‘a stock of information not inferior to that of any
other man,’ and ‘in Europe ... would hold a distinguished rank among men
of letters,’ was quite as competent a judge as the Senator from the
wilderness of Pennsylvania.[367] Among men his manner of conversation
was calm and deliberate, without the Johnsonian ex-cathedra touch, and yet
he ‘spoke like one who considered himself as entitled to deference.’[368]
Among friends, and particularly women, he appears to have been
deferential and captivating in his tactful kindness. Then when, ‘with a
manner and voice almost femininely soft and gentle,’ he ‘entered into
conversation on the commonplace topics of the day,’ at least one woman
found that ‘there was something in his manner, his countenance and voice
that at once unlocked [her] heart.’[369]
Such was the Jefferson seen superficially by his contemporaries.

II

Those who prefer to think of Jefferson as an aristocrat, born to the

purple, who departed from the paths of his fathers, refer only to the
maternal ancestry. The American founder of this branch of the family liked
to think of himself as the descendant of gentlemen of title and of the half-
brother of Queen Mary. Jefferson preferred to dismiss this claim on the
aristocracy with the statement that his mother’s family traced ‘their
pedigree far back in England and Scotland, to which let every one ascribe
the faith and merit he chooses.’ From the Randolphs he probably inherited
his love of beauty, his fondness for luxury, but they failed utterly to transmit
to him any aristocratic notions of government. There was a reason—his
father was a middle-class farmer, and it was from him and his early
environment that he received his earliest and most lasting political
impressions.
This father was no ordinary man. Physically a giant, he was big in mind
and strong in character. By the light of the log fire in the evenings, he was
wont to read Shakespeare, Swift, and Addison to his family. An ardent
Whig with advanced democratic ideas, he as a magistrate manifested
sympathy for the plain people.[370] His thousand acres at Shadwell were in
the wilderness and on the frontier, and his son was as much a Westerner in
his boyhood as is the boy of Idaho to-day, for the West is a relative term.
This Western boy at the most impressionable age was sent to school in
Louisa County, which was then the hot-bed of radical democracy and
Presbyterian dissent. The natives about him were in buckskin breeches and
Indian moccasins, and, with no coat over their rough hunting shirts, they
covered their heads with coon-skin caps. It was a long cry from the polished
circles of Boston, New York, and Philadelphia to this typical Western scene;
if one was the East, the other was the West. The small proprietor farmers
lived in crude cabins, and theirs was the hard lot of the pioneer. Thus
Jefferson’s training was that of the Westerner.[371]
The boy was father to the man. When he entered college at
Williamsburg, he found himself in the headquarters of the aristocracy, for
there, at the capital, the lords of the land had their winter homes where
lavish hospitality was displayed. Into this society Jefferson was thrown, and
he moved therein as to the manor born—at heart a Western man with
Eastern polish.[372] It was not for nothing that there was Randolph blood in
his veins.
Even as he moved among the hard-drinking, fox-hunting imitators of the
English squires, his sympathies were enlisted in the growing democratic
movement of the small farmers among the upper rivers, the tobacco-
growers, the hunters and trappers of the Alleghany slopes. The western
counties, then the western frontier, had been populated by the Scotch-Irish
and Germans—earnest, hard-working, hard-thinking men, who wrestled
with nature as with their consciences, built churches in the woods, and
school-houses in the clearing. These men were democrats, and their cause
became the cause of Jefferson even while he was in college. Volumes have
been written to explain Jefferson, but it was reserved for Professor William
E. Dodd to do it in a paragraph:
 It is not difficult ... to see how the great principle of Jefferson’s life—
absolute faith in democracy—came to him. He was the product of the first
West in American history; he grew up with men who ruled their country
well, who fought the Indians valiantly.... Jefferson loved his backwoods
neighbors, and he, in turn, was loved by them.[373]
If in college he was confirming his faith in democracy, born of his
schooling in the land of the small farmers, he was burnishing his weapons
for the fight. It is significant that he disliked Blackstone and liked Coke
because he found the former a teacher of Toryism and the latter a reflector of
the philosophy of the Whigs. His training in the law was thorough, for he
studied under George Wythe, with whom both Marshall and Clay received
their legal schooling. The friendship of Professor Small encouraged his
natural spirit of toleration and investigation; and at the ‘palace’ of Francis
Fauquier, the gay and brilliant royal governor—‘a gentleman of the school
of Louis XV translated into England by Charles II, and into English by Lord
Chesterfield’[374] he formed his literary tastes and learned the virtues of
literary style. Thus assiduous in his studies, reasonably circumspect in his
morals, and profiting immeasurably by contact with superior minds, he was
receiving an intensive preparation for his future labors. In the seclusion of
his room he communed with Coke and Milton, Harrington and Locke, and
the time was to come when his most notable literary production was to
disclose, in word and phrase, the influence of the latter. Locke, not
Rousseau, was the well from which he drew; and there is no sillier assertion
in history than that his democracy was born of association with the men of
the French Revolution.

III

Long before there were levelers in France, Jefferson was a leveler in

Virginia; and because he was a leveler in Virginia, the reactionaries who
resented his reforms were afterward to charge his democracy to the influence
of the levelers of Paris. His democracy was inherent, in part inherited from a
pioneer father. His dislike of the aristocratic system amounted to a prejudice,
and he could not bear the novels of Scott because of his detestation of the
institutions of medieval times.[375] Having written the Declaration of
Independence in the house of a bricklayer, he declined a reëlection to
Congress to enter the House of Burgesses in Virginia to revamp the
institutions of the State along democratic lines. When he finished his work
there, he had made himself one of the foremost democrats of all times—and
the French Revolution was still in the distance.
The Virginia system had been made for caste society; the landed
aristocracy were as much a caste as that in England—minus the titles. They
had the same love of land, the same obsession that the alienation of any part
of their possessions was treason to the family. Through the system of entail,
the lands and slaves of the aristocracy could be passed on down through the
generations, proof against the extravagance and inefficiency of the owners
and the attacks of creditors. The law of primogeniture was designed to serve
the same general end of preventing the disruption of the great estates. With a
fine audacity, Jefferson sallied forth quite gayly to attack them both. Even
Henry thought this was radicalism gone mad. Pendleton was more hurt than
outraged. The aristocratic members of his mother’s family looked upon him
as a matricide. Undaunted by the hate engendered, he put his hand to the
plough and kept it there until he had ploughed the field and prepared it for a
democratic harvest. His friend Pendleton begged a compromise on
primogeniture giving the eldest son a double share of the land. ‘Yes,’ replied
the leveler, ‘when he can eat twice the allowance of food and do double the
allowance of work.’ It was his purpose to eradicate ‘every fibre of ancient or
future aristocracy.’[376] The outraged landed aristocracy never forgave him.
He was the first American to invite the hate of a class, and from the
beginning he turned his back on the aristocracy and made his appeal to the
middle-class yeomanry.[377] All this was behind him when he went to Paris
before the Revolution there began. There the tall, slender American in the
elegant house on the Grande Route des Champs Elysées, with its extensive
gardens and court, was an impressive figure. ‘You replace Doctor Franklin, I
hear,’ said Vergennes, the Minister of Foreign Affairs. ‘I succeed him,’
Jefferson replied; ‘nobody could replace him.’ There could have been no
more ingratiating reply, for his predecessor had been greatly admired and
loved.
No one could have found the conversation of the salons and dinner tables
more congenial. His manners were those of a man of the world, and he
shared the French fondness for speculative talk, and the French knack of
spicing gravity with frivolity. Even his table tastes were similar. He ate
sparingly and preferred the light wines. Both his natural hospitality and his
respect for the dignity of his position spread the reputation of his lavish
table; and while he gave no great parties, gay and frequent dinners were the
rule. Lafayette ran in and out constantly; members of the diplomatic set
found Jefferson’s house an agreeable meeting-place; the young French
officers who had served in America liked his company, and De la Tude, the
wit, who had served thirty-five years in prison for writing an epigram on
Pompadour, enlivened many an evening with his reminiscences. American
tourists were captivated by his civilities, introductions to celebrities,
itineraries for profitable trips. Like Franklin before him, he charmed the
beautiful women of the court with his wit and humor, and the eloquence of
his conversation. He loved the promenades and shops, and was constantly
alert for something unusual to send his friends at home—rare books for
Madison, Monroe, and Wythe, a portable table for Madison, an artistic lamp
for Lee. And yet he was far from an elegant idler, and his days were
laboriously passed; mornings at his office, afternoons given to country
walks, evenings to society, art, music. He found time for elaborate and
illuminating reports that are models in diplomatic literature and which
exacted tribute from even John Marshall. Feeling frequently the need of
absolute seclusion for his work, he had rooms in the Carthusian Monastery
on Mount Calvary where silence was enjoined outside the rooms, but where
he had the privileges of the garden.
‘I am much pleased with the people of this country,’ he wrote a lady. ‘The
roughness of the human mind is so thoroughly rubbed off with them, that it
seems one might glide through a whole life without a jostle.’[378] And in
another letter, the same impression: ‘Here it seems a man might pass a life
without encountering a single rudeness.’[379] But if he loved the society of
Paris, he was not, like Morris, seduced into an acceptance of its system. His
passion for democracy did not permit him to judge the happiness of a nation
by the luxuries of the court and aristocracy. He struck out into the country to
judge for himself of the condition of the peasants, looked into the pots on the
fire to see what they ate, felt their beds to see if they were comfortable. He
inquired into the wages and the working conditions of the artisans of the
cities—and his conclusions were unavoidable, of course. ‘It is a fact,’ he
wrote, ‘in spite of the mildness of their governors, the people are ground to
powder by their form of government. Of twenty million people supposed to
be in France, I am of opinion there are nineteen million more wretched,
more accursed in every circumstance of human existence than the most
conspicuously wretched individual in the whole United States.’[380] And to
another: ‘I find the general fate of humanity here most deplorable. The truth
of Voltaire’s observation offers itself perpetually, that every man here is
either the hammer or the anvil.’[381] He was shocked by a system that
dedicated the sons of peasants as cannon fodder in remote wars precipitated
by the whims of a prostitute; that winked at the debauchery of their wives
and daughters; that gave men to the Bastile for the expression of a criticism;
that crushed the people with intolerable taxation to sustain the luxury of a
few; that forced the poor to live on food not fit for a stray dog in a city
slums, and which awed the masses into submission to such conditions by the
bayonets of the soldiery. This was the France of which he thought in the day
when his sympathy with the Revolution was to damn him with the
Federalists’ taunt of ‘Jacobin’ and ‘anarchist.’
Such being his observations and views, he rejoiced in the popular
awakening in the dawning days of the Revolution. Witnessing the meeting of
the Assembly of the Notables, a fascinated spectator of the razing of the
Bastile, listening, deeply moved, to the audacious eloquence of Mirabeau, he
wrote, with the joy of the reformer, to Washington that ‘the French nation
has been awakened by our Revolution.’ It was in those days that Gouverneur
Morris, the friend of Hamilton, was accustomed to drop in on Jefferson for a
chat on the situation, and their friendly disagreements were soon to appear in
a party division in America. ‘He and I differ,’ wrote Morris in his diary, ‘in
our system of politics. He with all the leaders of liberty here is desirous of
annihilating distinctions of order.’[382] And yet he was not hostile to the
King or the monarchy. He hoped for reforms, freely granted. Louis he found
‘irascible, rude, very limited in his understanding,’ with ‘no mistress,’ but
governed too much by the Queen—‘devoted to pleasure and expense, and
not remarkable for any other vices or virtues.’[383] As the storm-clouds
lowered and the easy-going monarch remained inert, he became less tolerant.
‘The King, long in the habit of drowning his cares in wine, plunges deeper
and deeper. The Queen cries but sins on. The Count d’Artois is
detested.’[384] And a month later: ‘The King goes for nothing. He hunts one
half the day, is drunk the other, and signs whatever he is bid.’[385]
As the future Terrorists ascended from the cellars and descended from the
garrets, and occasional riots gave premonitory signs of the bloody days
ahead, he reported to Jay that the rioting was the work of the ‘abandoned
banditti of Paris,’ and had no ‘professed connection with the great national
reformation going on.’[386]
All this time he was being constantly consulted by Lafayette and the
moderate leaders who were to become the members of the attractive but
unfortunate party of the Gironde. They even met at his dinner table to make
plans, without notifying him of their intent, and his voluntary explanation to
the Minister was received with the expression of a hope that he might be
able to assist in an accommodation of differences. He did, in fact, propose a
plan, which, had it been accepted, might have saved the monarchy. It was his
suggestion that Louis step forward with a charter in his hands, granting
liberty of the person, of conscience, of the press, a trial by jury, an annual
legislature with the power of taxation, and with a ministry responsible to the
people.[387] These associations and these views are conclusive as to the
absurdity that he was permeated with the theories of Jacobinism and brought
them back to the United States. He was the same kind of Jacobin as
Lafayette. His interest was the interest in democracy and popular rights that
he had taken with him when he sailed for Europe. Mirabeau was still
laboring to save the monarchy with reforms when Jefferson returned to
America on leave.

IV

Jefferson was a humanitarian ahead of his time. His humanity spoke

above the passions of the Revolution in his letter to Patrick Henry against
the mistreatment of the German prisoners. ‘Is an enemy so execrable,’ he
wrote, ‘that though in captivity his wishes and comforts are to be
disregarded and even crossed? I think not. It is for the benefit of mankind to
mitigate the horrors of war as much as possible.’[388] These captives,
interned near Monticello, came to love the master on the hill for his efforts
to lighten the burdens of their captivity.[389] A little later, in the Virginia
Legislature, we find him opposing the death penalty except for treason and
murder, and the policy of working convicts on the highways and canals.
‘Exhibited as a public spectacle,’ he wrote, ‘with shaved heads and mean
clothing, working on the highroads produced in the criminals such a
prostration of self-respect, as, instead of reforming, plunged them into the
most desperate and hardened depravity.’[390] It was novel then to hear men
speaking of reform instead of punishment.
 That this humanitarian impulse was not confined to people at a distance is
shown in his relations to his own servants, both the employees and the
slaves. A woman of fashion commented on ‘the most perfect servants at the
White House’ during his eight years there and the significant circumstance
that ‘none left.’[391] But we must turn to his relations with his slaves to find
him at his best. One picture will suffice. It is on the occasion of his return to
Monticello from his French mission. At the foot of the hill all the slaves in
their gaudiest attire are assembled to greet him. The carriage appears down
the road. The slaves, laughing, shouting, rush forward to welcome him,
unhitch the horses to draw the carriage up the steep hill, some pulling, some
pushing, and others huddled in a dark mass close around the vehicle. Some
kiss his hands, others his feet, and it is long after he reaches the house before
he is permitted to enter. This was long before the day when correspondents
with cameras pursued public men and demonstrations were staged.[392] Here
was a master who loved his slaves.
Nor can there be any possible doubt as to his hostility to slavery. One of
the features of his Virginia reforms was abolition. While he failed, he never
doubted that ultimately the chains would fall. ‘Nothing is more certainly
written in the book of fate than that these people are to be free’ he wrote in
his ‘Autobiography.’[393] A little later, referring to his strictures on slavery
in his ‘Notes on Virginia,’ he expressed a desire to get them to the young
men in the colleges. ‘It is to them I look, to the rising generation, and not to
the one now in power, for these great reformations.’[394] Declining
membership in a society for abolition in France on the ground that his
official status would make improper a demonstration against an institution
his own people were retaining, he said that ‘it is decent of me to avoid too
public a demonstration of my wishes to see it [slavery] abolished.’[395]
Without any of this evidence, his hostility to slavery would be irrefutably
established by the Ordinance of the Northwest Territory, in the handwriting
of Jefferson in the archives of the Nation, prohibiting slavery in any of the
States that might be carved therefrom after the year 1800.

Such is the persistency of falsehood that Jefferson has come down to us

vaguely as an atheist and an enemy of the Christian religion. Since this
charge is to play a part in the political story we are about to tell, it calls for
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