diff --git a/doc/pub/svm/html/._svm-bs000.html b/doc/pub/svm/html/._svm-bs000.html new file mode 100644 index 000000000..7785d35d9 --- /dev/null +++ b/doc/pub/svm/html/._svm-bs000.html @@ -0,0 +1,194 @@ + + + + + + + +Data Analysis and Machine Learning: Support Vector Machines + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Data Analysis and Machine Learning: Support Vector Machines

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+Morten Hjorth-Jensen [1, 2] +
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[1] Department of Physics, University of Oslo
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[2] Department of Physics and Astronomy and National Superconducting Cyclotron Laboratory, Michigan State University
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Nov 5, 2018

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+ © 1999-2018, Morten Hjorth-Jensen. Released under CC Attribution-NonCommercial 4.0 license +
+ + + + + + diff --git a/doc/pub/svm/html/._svm-bs001.html b/doc/pub/svm/html/._svm-bs001.html new file mode 100644 index 000000000..c64556007 --- /dev/null +++ b/doc/pub/svm/html/._svm-bs001.html @@ -0,0 +1,193 @@ + + + + + + + +Data Analysis and Machine Learning: Support Vector Machines + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + +

Support Vector Machines, overarching aims

+ +

+A Support Vector Machine (SVM) is a very powerful and versatile +Machine Learning model, capable of performing linear or nonlinear +classification, regression, and even outlier detection. It is one of +the most popular models in Machine Learning, and anyone interested in +Machine Learning should have it in their toolbox. SVMs are +particularly well suited for classification of complex but small-sized or +medium-sized datasets. + +

+The case with two well-separated classes only can be understood in an intuitive way in terms of lines in a two-dimensional space separating the two classes (see figure below). + +

+The basic mathematics behind the SVM is however less familiar to most of us. +It relies on the definition of hyperplanes and the +definition of a margin which separates classes (in case of +classification problems) of variables. It is also used for regression +problems. + +

+With SVMs we distinguish between hard margin and soft margins. The latter introduces a so-called softening parameter to be discussed below. +We distinguish also between linear and non-linear approaches. The latter are the most frequent ones since it is rather unlikely that we can separate classes easily by say straight lines. + +

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+ + + + +

Hyperplanes and all that

+ +

+The theory behind support vector machines (SVM hereafter) is based on +the mathematical description of so-called hyperplanes. Let us start +with a two-dimensional case. This will also allow us to introduce our +first SVM examples. These will be tailored to the case of two specific +classes, as displayed in the figure here. + +

+We assume here that our data set can be well separated into two +domains, where a straight line does the job in the separating the two +classes. Here the two classes are represented by either crosses or +circles. + +

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+ + + + +

What is a hyperplane?

+ +

+The aim of the SVM algorithm is to find a hyperplane in an \( p \)-dimensional space, where \( p \) is the number of features that distinctly classifies the data points. + +

+In a \( p \)-dimensional space, a hyperplane is what we call an affine subspace of dimension of \( p-1 \). +As an example, in two dimension, a hyperplane is simply as straight line while in three dimensions it is +a two-dimensional subspace, or stated simply, a plane. + +

+In two dimensions, with the variables \( x_1 \) and \( x_2 \), the hyperplane is defined as +$$ +b+w_1x_1+w_2x_2=0, +$$ + +where \( b \) is the intercept and \( w_1 \) and \( w_2 \) define the elements of a vector orthogonal to the line +\( b+w_1x_1+w_2x_2=0 \). +In two dimensions we define the vectors \( \hat{x} =[x1,x2] \) and \( \hat{w}=[w1,w2] \). +We can then rewrite the above equation as +$$ +\hat{w}^T\hat{x}+b=0. +$$ + +

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+ + + + +

A \( p \)-dimensional space of features

+ +

+We limit ourselves to two classes of outputs \( y_i \) and assign these classes the values \( y_i = \pm 1 \). +In a \( p \)-dimensional space of say \( p \) features we have a hyperplane defines as +$$ +b+wx_1+w_2x_2+\dots +w_px_p=0. +$$ + +If we define a +matrix \( \hat{X}=\left[\hat{x}_1,\hat{x}_2,\dots, \hat{x}_p\right] \) +of dimension \( n\times p \), where \( n \) represents the observations for each feature and each vector \( x_i \) is a column vector of the matrix \( \hat{X} \), +$$ +\hat{x}_i = \begin{bmatrix} x_{i1} \\ x_{i2} \\ \dots \\ \dots \\ x_{ip} \end{bmatrix}. +$$ + +If the above condition is not met for a given vector \( \hat{x}_i \) we have +$$ +b+w_1x_{i1}+w_2x_{i}2+\dots +w_px_{ip} >0, +$$ + +if our output \( y_i=1 \). +In this case we say that \( \hat{x}_i \) lies on one of the sides of the hyperplane and if +$$ +b+w_1x_{i1}+w_2x_{i}2+\dots +w_px_{ip} < 0, +$$ + +for the class of observations \( y_i=-1 \), +then \( \hat{x}_i \) lies on the other side. + +

+Equivalently, for the two classes of observations we have +$$ +y_i\left(b+w_1x_{i1}+w_2x_{i}2+\dots +w_px_{ip}\right) > 0. +$$ + +

+When we try to separate hyperplanes, if it exists, we can use it to construct a natural classifier: a test observation is assigned a given class depending on which side of the hyperplane it is located. + +

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+ + + + +

The two-dimensional case

+ +

+Let us try to develop our intuition about SVMs by limiting ourselves to a two-dimensional +plane. To separate the two classes of data points, there are many +possible lines (hyperplanes if you prefer a more strict naming) +that could be chosen. Our objective is to find a +plane that has the maximum margin, i.e the maximum distance between +data points of both classes. Maximizing the margin distance provides +some reinforcement so that future data points can be classified with +more confidence. + +

+What a linear classifier attempts to accomplish is to split the +feature space into two half spaces by placing a hyperplane between the +data points. This hyperplane will be our decision boundary. All +points on one side of the plane will belong to class one and all points +on the other side of the plane will belong to the second class two. + +

+Unfortunately there are many ways in which we can place a hyperplane +to divide the data. Below is an example of two candidate hyperplanes +for our data sample. + +

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+ + + + + + diff --git a/doc/pub/svm/html/._svm-bs006.html b/doc/pub/svm/html/._svm-bs006.html new file mode 100644 index 000000000..052c816f4 --- /dev/null +++ b/doc/pub/svm/html/._svm-bs006.html @@ -0,0 +1,189 @@ + + + + + + + +Data Analysis and Machine Learning: Support Vector Machines + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + +

Getting into the details

+ +

+Let us define the function +$$ +f(x) = \hat{w}^T\hat{x}+b = 0, +$$ + +as the function that determines the line \( L \) that separates two classes (our two features), see the figure here. + +

+Any point defined by \( \hat{x}_i \) and \( \hat{x}_2 \) on the line \( L \) will satisfy \( \hat{w}^T(\hat{x}_1-\hat{x}_2)=0 \). + +

+The signed distance \( \delta \) from any point defined by a vector \( \hat{x} \) and a point \( \hat{x}_0 \) on the line \( L \) is then +$$ +\delta = \frac{1}{\vert\vert \hat{w}\vert\vert}(\hat{w}^T\hat{x}+b). +$$ + +

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+ + + + +

First attempt at a minimization approach

+ +

+How do we find the parameter \( b \) and the vector \( \hat{w} \)? What we could +do is to define a cost function which now contains the set of all +misclassified points \( M \) and attempt to minimize this function + +$$ +C(\hat{w},b) = -\sum_{i\in M} y_i(\hat{w}^T\hat{x}_i+b). +$$ + +

+We could now for example define all values \( y_i =1 \) as misclassified in case we have \( \hat{w}^T\hat{x}_i+b < 0 \) and the opposite if we have \( y_i=-1 \). Taking the derivatives gives us +$$ +\frac{\partial C}{\partial b} = -\sum_{i\in M} y_i, +$$ + +and +$$ +\frac{\partial C}{\partial \hat{w}} = -\sum_{i\in M} y_ix_i. +$$ + +

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+ + + + +

Solving the equations

+ +

+We can now use the Newton-Raphson method or gradient descent to solve the equations +$$ +b \leftarrow b +\eta \frac{\partial C}{\partial b}, +$$ + +and +$$ +\hat{w} \leftarrow \hat{w} +\eta \frac{\partial C}{\partial \hat{w}}, +$$ + +where \( \eta \) is our by now well-known learning rate. + +

+There are however problems with this approach, although it looks +pretty straightforward to implement. In case we separate our data into +two distinct classes, we may up with many possible lines, as indicated +in the figure and shown by running the following program. For small +gaps between the entries, we may also end up needing many iterations +before the solutions converge and if the data cannot be separated +properly into two distinct classes, we may not experience a converge +at all. + +

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+ +

 

 

 

+ + + + +

A better approach

+ +

+A better approach is rather to try to define a large margin between +the two classes (if they are well separated from the beginning). + +

+Thus, we wish to find a margin \( M \) with \( \hat{w} \) normalized to +\( \vert\vert \hat{w}\vert\vert =1 \) subject to the condition + +$$ +y_i(\hat{w}^T\hat{x}_i+b) \geq M \forall i=1,2,\dots, p. +$$ + +All points are thus at a signed distance from the decision boundary defined by the line \( L \). The parameters \( b \) and \( w_1 \) and \( w_2 \) define this line. + +

+We seek thus the largest value \( M \) defined by +$$ +\frac{1}{\vert \vert \hat{w}\vert\vert}y_i(\hat{w}^T\hat{x}_i+b) \geq M \forall i=1,2,\dots, n, +$$ + +or just +$$ +y_i(\hat{w}^T\hat{x}_i+b) \geq M\vert \vert \hat{w}\vert\vert \forall i. +$$ + +If we scale the equation so that \( \vert \vert \hat{w}\vert\vert = 1/M \), we have to find the minimum of +\( \hat{w}^T\hat{w}=\vert \vert \hat{w}\vert\vert \) (the norm) subject to the condition +$$ +y_i(\hat{w}^T\hat{x}_i+b) \geq 1 \forall i. +$$ + +

+We have thus defined our margin as the invers of the norm of \( \hat{w} \). We want to minimize the norm in order to have a as large as possible margin \( M \). Before we proceed, we need to remind ourselves about Lagrangian multipliers. + +

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+ +

 

 

 

+ + + + +

A quick reminder on Lagrangian multipliers

+ +

+Consider a function of three independent variables \( f(x,y,z) \) . For the function \( f \) to be an +extreme we have +$$ +df=0. +$$ + +A necessary and sufficient condition is +$$ +\frac{\partial f}{\partial x} =\frac{\partial f}{\partial y}=\frac{\partial f}{\partial z}=0, +$$ + +due to +$$ +df = \frac{\partial f}{\partial x}dx+\frac{\partial f}{\partial y}dy+\frac{\partial f}{\partial z}dz. +$$ + +In many problems the variables \( x,y,z \) are often subject to constraints (such as those above for the margin) +so that they are no longer all independent. It is possible at least in principle to use each +constraint to eliminate one variable +and to proceed with a new and smaller set of independent varables. + +

+The use of so-called Lagrangian multipliers is an alternative technique when the elimination +of variables is incovenient or undesirable. Assume that we have an equation of constraint on +the variables \( x,y,z \) +$$ +\phi(x,y,z) = 0, +$$ + + resulting in +$$ +d\phi = \frac{\partial \phi}{\partial x}dx+\frac{\partial \phi}{\partial y}dy+\frac{\partial \phi}{\partial z}dz =0. +$$ + +Now we cannot set anymore +$$ +\frac{\partial f}{\partial x} =\frac{\partial f}{\partial y}=\frac{\partial f}{\partial z}=0, +$$ + +if \( df=0 \) is wanted +because there are now only two independent variables! Assume \( x \) and \( y \) are the independent +variables. +Then \( dz \) is no longer arbitrary. + +

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+ +

 

 

 

+ + + + +

Adding the muliplier

+ +

+However, we can add to +$$ +df = \frac{\partial f}{\partial x}dx+\frac{\partial f}{\partial y}dy+\frac{\partial f}{\partial z}dz, +$$ + +a multiplum of \( d\phi \), viz. \( \lambda d\phi \), resulting in +$$ +df+\lambda d\phi = (\frac{\partial f}{\partial z}+\lambda +\frac{\partial \phi}{\partial x})dx+(\frac{\partial f}{\partial y}+\lambda\frac{\partial \phi}{\partial y})dy+ +(\frac{\partial f}{\partial z}+\lambda\frac{\partial \phi}{\partial z})dz =0. +$$ + +Our multiplier is chosen so that +$$ +\frac{\partial f}{\partial z}+\lambda\frac{\partial \phi}{\partial z} =0. +$$ + +

+We need to remember that we took \( dx \) and \( dy \) to be arbitrary and thus we must have +$$ +\frac{\partial f}{\partial x}+\lambda\frac{\partial \phi}{\partial x} =0, +$$ + +and +$$ +\frac{\partial f}{\partial y}+\lambda\frac{\partial \phi}{\partial y} =0. +$$ + +When all these equations are satisfied, \( df=0 \). We have four unknowns, \( x,y,z \) and +\( \lambda \). Actually we want only \( x,y,z \), \( \lambda \) needs not to be determined, +it is therefore often called +Lagrange's undetermined multiplier. +If we have a set of constraints \( \phi_k \) we have the equations +$$ +\frac{\partial f}{\partial x_i}+\sum_k\lambda_k\frac{\partial \phi_k}{\partial x_i} =0. +$$ + +

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+ +

 

 

 

+ + + + +

Setting up the problem

+In order to solve the above problem, we define the following Lagrangian function to be minimized +$$ +{\cal L}(\lambda,b,\hat{w})=\frac{1}{2}\hat{w}^T\hat{w}-\sum_{i=1}^n\lambda_i\left[y_i(\hat{w}^T\hat{x}_i+b)-1\right], +$$ + +where \( \lambda_i \) is a so-called Lagrange multiplier subject to the condition \( \lambda_i \geq 0 \). + +

+Taking the derivatives with respect to \( b \) and \( \hat{w} \) we obtain +$$ +\frac{\partial {\cal L}}{\partial b} = -\sum_{i} \lambda_iy_i=0, +$$ + +and +$$ +\frac{\partial {\cal L}}{\partial \hat{w}} = 0 = \hat{w}-\sum_{i} \lambda_iy_i\hat{x}_i. +$$ + +Inserting these constraints into the equation for \( {\cal L} \) we obtain +$$ +{\cal L}=\sum_i\lambda_i-\frac{1}{2}\sum_{ij}^n\lambda_i\lambda_jy_iy_j\hat{x}_i^T\hat{x}_j, +$$ + +subject to the constraints \( \lambda_i\geq 0 \) and \( \sum_i\lambda_iy_i=0 \). +We must in addition satisfy the Karush-Kuhn-Tucker (KKT) condition +$$ +\lambda_i\left[y_i(\hat{w}^T\hat{x}_i+b) -1\right] \forall i. +$$ + + +

    +
  1. If \( \lambda_i > 0 \), then \( y_i(\hat{w}^T\hat{x}_i+b)=1 \) and we say that \( x_i \) is on the boundary.
  2. +
  3. If \( y_i(\hat{w}^T\hat{x}_i+b)> 1 \), we say \( x_i \) is not on the boundary and we set \( \lambda_i=0 \).
  4. +
+ +When \( \lambda_i > 0 \), the vectors \( \hat{x}_i \) are called support vectors. They are the vectors closest to the line (or hyperplane) and define the margin \( M \). + +

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+ + + + + + diff --git a/doc/pub/svm/html/._svm-bs013.html b/doc/pub/svm/html/._svm-bs013.html new file mode 100644 index 000000000..6f16b18eb --- /dev/null +++ b/doc/pub/svm/html/._svm-bs013.html @@ -0,0 +1,187 @@ + + + + + + + +Data Analysis and Machine Learning: Support Vector Machines + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ +

 

 

 

+ + + + +

The problem to solve

+ +

+We can rewrite +$$ +{\cal L}=\sum_i\lambda_i-\frac{1}{2}\sum_{ij}^n\lambda_i\lambda_jy_iy_j\hat{x}_i^T\hat{x}_j, +$$ + +and its constraints in terms of a matrix-vector problem where we minimize w.r.t. \( \lambda \) the following problem +$$ +\frac{1}{2} \hat{\lambda}^T\begin{bmatrix} y_1y_1\hat{x}_1^T\hat{x}_1 & y_1y_2\hat{x}_1^T\hat{x}_2 & \dots & \dots & y_1y_n\hat{x}_1^T\hat{x}_n \\ +y_2y_1\hat{x}_2^T\hat{x}_1 & y_2y_2\hat{x}_2^T\hat{x}_2 & \dots & \dots & y_1y_n\hat{x}_2^T\hat{x}_n \\ +\dots & \dots & \dots & \dots & \dots \\ +\dots & \dots & \dots & \dots & \dots \\ +y_ny_1\hat{x}_n^T\hat{x}_1 & y_ny_2\hat{x}_n^T\hat{x}_2 & \dots & \dots & y_ny_n\hat{x}_n^T\hat{x}_n \\ +\end{bmatrix}\hat{\lambda}-\mathbb{1}\hat{\lambda}, +$$ + +subject to \( \hat{y}^T\hat{\lambda}=0 \). + +

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+ + + + + + diff --git a/doc/pub/svm/html/._svm-bs014.html b/doc/pub/svm/html/._svm-bs014.html new file mode 100644 index 000000000..648d0204b --- /dev/null +++ b/doc/pub/svm/html/._svm-bs014.html @@ -0,0 +1,276 @@ + + + + + + + +Data Analysis and Machine Learning: Support Vector Machines + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ +

 

 

 

+ + + + +

Examples with kernels

+ +

+ + +

from IPython.display import set_matplotlib_formats, display
+import pandas as pd
+import numpy as np
+import matplotlib.pyplot as plt
+import mglearn
+from cycler import cycler
+from sklearn.linear_model import LogisticRegression
+from sklearn.svm import LinearSVC
+from sklearn.datasets import make_blobs
+
+
+X, y = make_blobs(centers=4, random_state=8)
+y = y % 2
+
+mglearn.discrete_scatter(X[:, 0], X[:, 1], y)
+plt.xlabel("Feature 0")
+plt.ylabel("Feature 1")
+plt.show()
+
+from sklearn.svm import LinearSVC
+linear_svm = LinearSVC().fit(X, y)
+
+mglearn.plots.plot_2d_separator(linear_svm, X)
+mglearn.discrete_scatter(X[:, 0], X[:, 1], y)
+plt.xlabel("Feature 0")
+plt.ylabel("Feature 1")
+
+

+ + +

# add the squared first feature
+X_new = np.hstack([X, X[:, 1:] ** 2])
+
+
+from mpl_toolkits.mplot3d import Axes3D, axes3d
+figure = plt.figure()
+# visualize in 3D
+ax = Axes3D(figure, elev=-152, azim=-26)
+# plot first all the points with y==0, then all with y == 1
+mask = y == 0
+ax.scatter(X_new[mask, 0], X_new[mask, 1], X_new[mask, 2], c='b',
+           cmap=mglearn.cm2, s=60, edgecolor='k')
+ax.scatter(X_new[~mask, 0], X_new[~mask, 1], X_new[~mask, 2], c='r', marker='^',
+           cmap=mglearn.cm2, s=60, edgecolor='k')
+ax.set_xlabel("feature0")
+ax.set_ylabel("feature1")
+ax.set_zlabel("feature1 ** 2")
+
+

+ + +

linear_svm_3d = LinearSVC().fit(X_new, y)
+coef, intercept = linear_svm_3d.coef_.ravel(), linear_svm_3d.intercept_
+
+# show linear decision boundary
+figure = plt.figure()
+ax = Axes3D(figure, elev=-152, azim=-26)
+xx = np.linspace(X_new[:, 0].min() - 2, X_new[:, 0].max() + 2, 50)
+yy = np.linspace(X_new[:, 1].min() - 2, X_new[:, 1].max() + 2, 50)
+
+XX, YY = np.meshgrid(xx, yy)
+ZZ = (coef[0] * XX + coef[1] * YY + intercept) / -coef[2]
+ax.plot_surface(XX, YY, ZZ, rstride=8, cstride=8, alpha=0.3)
+ax.scatter(X_new[mask, 0], X_new[mask, 1], X_new[mask, 2], c='b',
+           cmap=mglearn.cm2, s=60, edgecolor='k')
+ax.scatter(X_new[~mask, 0], X_new[~mask, 1], X_new[~mask, 2], c='r', marker='^',
+           cmap=mglearn.cm2, s=60, edgecolor='k')
+
+ax.set_xlabel("feature0")
+ax.set_ylabel("feature1")
+ax.set_zlabel("feature1 ** 2")
+
+ZZ = YY ** 2
+dec = linear_svm_3d.decision_function(np.c_[XX.ravel(), YY.ravel(), ZZ.ravel()])
+plt.contourf(XX, YY, dec.reshape(XX.shape), levels=[dec.min(), 0, dec.max()],
+             cmap=mglearn.cm2, alpha=0.5)
+mglearn.discrete_scatter(X[:, 0], X[:, 1], y)
+plt.xlabel("Feature 0")
+plt.ylabel("Feature 1")
+
+

+ + +

from sklearn.svm import SVC
+X, y = mglearn.tools.make_handcrafted_dataset()                                                                  
+svm = SVC(kernel='rbf', C=10, gamma=0.1).fit(X, y)
+mglearn.plots.plot_2d_separator(svm, X, eps=.5)
+mglearn.discrete_scatter(X[:, 0], X[:, 1], y)
+# plot support vectors
+sv = svm.support_vectors_
+# class labels of support vectors are given by the sign of the dual coefficients
+sv_labels = svm.dual_coef_.ravel() > 0
+mglearn.discrete_scatter(sv[:, 0], sv[:, 1], sv_labels, s=15, markeredgewidth=3)
+plt.xlabel("Feature 0")
+plt.ylabel("Feature 1")
+
+fig, axes = plt.subplots(3, 3, figsize=(15, 10))
+
+for ax, C in zip(axes, [-1, 0, 3]):
+    for a, gamma in zip(ax, range(-1, 2)):
+        mglearn.plots.plot_svm(log_C=C, log_gamma=gamma, ax=a)
+        
+axes[0, 0].legend(["class 0", "class 1", "sv class 0", "sv class 1"],
+                  ncol=4, loc=(.9, 1.2))
+
+

+ +

+ +

+ + +
+ + + + + + + +
+ +
+ + + + + + diff --git a/doc/pub/svm/html/svm-bs.html b/doc/pub/svm/html/svm-bs.html index 05d35bb72..7785d35d9 100644 --- a/doc/pub/svm/html/svm-bs.html +++ b/doc/pub/svm/html/svm-bs.html @@ -41,9 +41,9 @@ Automatically generated HTML file from DocOnce source @@ -63,7 +66,7 @@ end of tocinfo --> + + + +``` + +The presentation markup hierarchy needs to be `.reveal > .slides > section` where the `section` represents one slide and can be repeated indefinitely. If you place multiple `section` elements inside of another `section` they will be shown as vertical slides. The first of the vertical slides is the "root" of the others (at the top), and will be included in the horizontal sequence. For example: + +```html +
+
+
Single Horizontal Slide
+
+
Vertical Slide 1
+
Vertical Slide 2
+
+
+
+``` + +### Markdown + +It's possible to write your slides using Markdown. To enable Markdown, add the `data-markdown` attribute to your `
` elements and wrap the contents in a ` +
+``` + +#### External Markdown + +You can write your content as a separate file and have reveal.js load it at runtime. Note the separator arguments which determine how slides are delimited in the external file: the `data-separator` attribute defines a regular expression for horizontal slides (defaults to `^\r?\n---\r?\n$`, a newline-bounded horizontal rule) and `data-separator-vertical` defines vertical slides (disabled by default). The `data-separator-notes` attribute is a regular expression for specifying the beginning of the current slide's speaker notes (defaults to `note:`). The `data-charset` attribute is optional and specifies which charset to use when loading the external file. + +When used locally, this feature requires that reveal.js [runs from a local web server](#full-setup). The following example customises all available options: + +```html +
+ +
+``` + +#### Element Attributes + +Special syntax (in html comment) is available for adding attributes to Markdown elements. This is useful for fragments, amongst other things. + +```html +
+ +
+``` + +#### Slide Attributes + +Special syntax (in html comment) is available for adding attributes to the slide `
` elements generated by your Markdown. + +```html +
+ +
+``` + +#### Configuring *marked* + +We use [marked](https://github.com/chjj/marked) to parse Markdown. To customise marked's rendering, you can pass in options when [configuring Reveal](#configuration): + +```javascript +Reveal.initialize({ + // Options which are passed into marked + // See https://github.com/chjj/marked#options-1 + markdown: { + smartypants: true + } +}); +``` + +### Configuration + +At the end of your page you need to initialize reveal by running the following code. Note that all config values are optional and will default as specified below. + +```javascript +Reveal.initialize({ + + // Display presentation control arrows + controls: true, + + // Help the user learn the controls by providing hints, for example by + // bouncing the down arrow when they first encounter a vertical slide + controlsTutorial: true, + + // Determines where controls appear, "edges" or "bottom-right" + controlsLayout: 'bottom-right', + + // Visibility rule for backwards navigation arrows; "faded", "hidden" + // or "visible" + controlsBackArrows: 'faded', + + // Display a presentation progress bar + progress: true, + + // Set default timing of 2 minutes per slide + defaultTiming: 120, + + // Display the page number of the current slide + slideNumber: false, + + // Push each slide change to the browser history + history: false, + + // Enable keyboard shortcuts for navigation + keyboard: true, + + // Enable the slide overview mode + overview: true, + + // Vertical centering of slides + center: true, + + // Enables touch navigation on devices with touch input + touch: true, + + // Loop the presentation + loop: false, + + // Change the presentation direction to be RTL + rtl: false, + + // Randomizes the order of slides each time the presentation loads + shuffle: false, + + // Turns fragments on and off globally + fragments: true, + + // Flags if the presentation is running in an embedded mode, + // i.e. contained within a limited portion of the screen + embedded: false, + + // Flags if we should show a help overlay when the questionmark + // key is pressed + help: true, + + // Flags if speaker notes should be visible to all viewers + showNotes: false, + + // Global override for autoplaying embedded media (video/audio/iframe) + // - null: Media will only autoplay if data-autoplay is present + // - true: All media will autoplay, regardless of individual setting + // - false: No media will autoplay, regardless of individual setting + autoPlayMedia: null, + + // Number of milliseconds between automatically proceeding to the + // next slide, disabled when set to 0, this value can be overwritten + // by using a data-autoslide attribute on your slides + autoSlide: 0, + + // Stop auto-sliding after user input + autoSlideStoppable: true, + + // Use this method for navigation when auto-sliding + autoSlideMethod: Reveal.navigateNext, + + // Enable slide navigation via mouse wheel + mouseWheel: false, + + // Hides the address bar on mobile devices + hideAddressBar: true, + + // Opens links in an iframe preview overlay + // Add `data-preview-link` and `data-preview-link="false"` to customise each link + // individually + previewLinks: false, + + // Transition style + transition: 'slide', // none/fade/slide/convex/concave/zoom + + // Transition speed + transitionSpeed: 'default', // default/fast/slow + + // Transition style for full page slide backgrounds + backgroundTransition: 'fade', // none/fade/slide/convex/concave/zoom + + // Number of slides away from the current that are visible + viewDistance: 3, + + // Parallax background image + parallaxBackgroundImage: '', // e.g. "'https://s3.amazonaws.com/hakim-static/reveal-js/reveal-parallax-1.jpg'" + + // Parallax background size + parallaxBackgroundSize: '', // CSS syntax, e.g. "2100px 900px" + + // Number of pixels to move the parallax background per slide + // - Calculated automatically unless specified + // - Set to 0 to disable movement along an axis + parallaxBackgroundHorizontal: null, + parallaxBackgroundVertical: null, + + // The display mode that will be used to show slides + display: 'block' + +}); +``` + + +The configuration can be updated after initialization using the ```configure``` method: + +```javascript +// Turn autoSlide off +Reveal.configure({ autoSlide: 0 }); + +// Start auto-sliding every 5s +Reveal.configure({ autoSlide: 5000 }); +``` + + +### Presentation Size + +All presentations have a normal size, that is the resolution at which they are authored. The framework will automatically scale presentations uniformly based on this size to ensure that everything fits on any given display or viewport. + +See below for a list of configuration options related to sizing, including default values: + +```javascript +Reveal.initialize({ + + ... + + // The "normal" size of the presentation, aspect ratio will be preserved + // when the presentation is scaled to fit different resolutions. Can be + // specified using percentage units. + width: 960, + height: 700, + + // Factor of the display size that should remain empty around the content + margin: 0.1, + + // Bounds for smallest/largest possible scale to apply to content + minScale: 0.2, + maxScale: 1.5 + +}); +``` + +If you wish to disable this behavior and do your own scaling (e.g. using media queries), try these settings: + +```javascript +Reveal.initialize({ + + ... + + width: "100%", + height: "100%", + margin: 0, + minScale: 1, + maxScale: 1 +}); +``` + +### Dependencies + +Reveal.js doesn't _rely_ on any third party scripts to work but a few optional libraries are included by default. These libraries are loaded as dependencies in the order they appear, for example: + +```javascript +Reveal.initialize({ + dependencies: [ + // Cross-browser shim that fully implements classList - https://github.com/eligrey/classList.js/ + { src: 'lib/js/classList.js', condition: function() { return !document.body.classList; } }, + + // Interpret Markdown in
elements + { src: 'plugin/markdown/marked.js', condition: function() { return !!document.querySelector( '[data-markdown]' ); } }, + { src: 'plugin/markdown/markdown.js', condition: function() { return !!document.querySelector( '[data-markdown]' ); } }, + + // Syntax highlight for elements + { src: 'plugin/highlight/highlight.js', async: true, callback: function() { hljs.initHighlightingOnLoad(); } }, + + // Zoom in and out with Alt+click + { src: 'plugin/zoom-js/zoom.js', async: true }, + + // Speaker notes + { src: 'plugin/notes/notes.js', async: true }, + + // MathJax + { src: 'plugin/math/math.js', async: true } + ] +}); +``` + +You can add your own extensions using the same syntax. The following properties are available for each dependency object: +- **src**: Path to the script to load +- **async**: [optional] Flags if the script should load after reveal.js has started, defaults to false +- **callback**: [optional] Function to execute when the script has loaded +- **condition**: [optional] Function which must return true for the script to be loaded + +To load these dependencies, reveal.js requires [head.js](http://headjs.com/) *(a script loading library)* to be loaded before reveal.js. + +### Ready Event + +A 'ready' event is fired when reveal.js has loaded all non-async dependencies and is ready to start navigating. To check if reveal.js is already 'ready' you can call `Reveal.isReady()`. + +```javascript +Reveal.addEventListener( 'ready', function( event ) { + // event.currentSlide, event.indexh, event.indexv +} ); +``` + +Note that we also add a `.ready` class to the `.reveal` element so that you can hook into this with CSS. + +### Auto-sliding + +Presentations can be configured to progress through slides automatically, without any user input. To enable this you will need to tell the framework how many milliseconds it should wait between slides: + +```javascript +// Slide every five seconds +Reveal.configure({ + autoSlide: 5000 +}); +``` +When this is turned on a control element will appear that enables users to pause and resume auto-sliding. Alternatively, sliding can be paused or resumed by pressing »a« on the keyboard. Sliding is paused automatically as soon as the user starts navigating. You can disable these controls by specifying ```autoSlideStoppable: false``` in your reveal.js config. + +You can also override the slide duration for individual slides and fragments by using the ```data-autoslide``` attribute: + +```html +
+

After 2 seconds the first fragment will be shown.

+

After 10 seconds the next fragment will be shown.

+

Now, the fragment is displayed for 2 seconds before the next slide is shown.

+
+``` + +To override the method used for navigation when auto-sliding, you can specify the ```autoSlideMethod``` setting. To only navigate along the top layer and ignore vertical slides, set this to ```Reveal.navigateRight```. + +Whenever the auto-slide mode is resumed or paused the ```autoslideresumed``` and ```autoslidepaused``` events are fired. + + +### Keyboard Bindings + +If you're unhappy with any of the default keyboard bindings you can override them using the ```keyboard``` config option: + +```javascript +Reveal.configure({ + keyboard: { + 13: 'next', // go to the next slide when the ENTER key is pressed + 27: function() {}, // do something custom when ESC is pressed + 32: null // don't do anything when SPACE is pressed (i.e. disable a reveal.js default binding) + } +}); +``` + +### Touch Navigation + +You can swipe to navigate through a presentation on any touch-enabled device. Horizontal swipes change between horizontal slides, vertical swipes change between vertical slides. If you wish to disable this you can set the `touch` config option to false when initializing reveal.js. + +If there's some part of your content that needs to remain accessible to touch events you'll need to highlight this by adding a `data-prevent-swipe` attribute to the element. One common example where this is useful is elements that need to be scrolled. + + +### Lazy Loading + +When working on presentation with a lot of media or iframe content it's important to load lazily. Lazy loading means that reveal.js will only load content for the few slides nearest to the current slide. The number of slides that are preloaded is determined by the `viewDistance` configuration option. + +To enable lazy loading all you need to do is change your "src" attributes to "data-src" as shown below. This is supported for image, video, audio and iframe elements. Lazy loaded iframes will also unload when the containing slide is no longer visible. + +```html +
+ + + +
+``` + + +### API + +The ``Reveal`` object exposes a JavaScript API for controlling navigation and reading state: + +```javascript +// Navigation +Reveal.slide( indexh, indexv, indexf ); +Reveal.left(); +Reveal.right(); +Reveal.up(); +Reveal.down(); +Reveal.prev(); +Reveal.next(); +Reveal.prevFragment(); +Reveal.nextFragment(); + +// Randomize the order of slides +Reveal.shuffle(); + +// Toggle presentation states, optionally pass true/false to force on/off +Reveal.toggleOverview(); +Reveal.togglePause(); +Reveal.toggleAutoSlide(); + +// Shows a help overlay with keyboard shortcuts, optionally pass true/false +// to force on/off +Reveal.toggleHelp(); + +// Change a config value at runtime +Reveal.configure({ controls: true }); + +// Returns the present configuration options +Reveal.getConfig(); + +// Fetch the current scale of the presentation +Reveal.getScale(); + +// Retrieves the previous and current slide elements +Reveal.getPreviousSlide(); +Reveal.getCurrentSlide(); + +Reveal.getIndices(); // { h: 0, v: 0 } } +Reveal.getPastSlideCount(); +Reveal.getProgress(); // (0 == first slide, 1 == last slide) +Reveal.getSlides(); // Array of all slides +Reveal.getTotalSlides(); // total number of slides + +// Returns the speaker notes for the current slide +Reveal.getSlideNotes(); + +// State checks +Reveal.isFirstSlide(); +Reveal.isLastSlide(); +Reveal.isOverview(); +Reveal.isPaused(); +Reveal.isAutoSliding(); +``` + +### Slide Changed Event + +A 'slidechanged' event is fired each time the slide is changed (regardless of state). The event object holds the index values of the current slide as well as a reference to the previous and current slide HTML nodes. + +Some libraries, like MathJax (see [#226](https://github.com/hakimel/reveal.js/issues/226#issuecomment-10261609)), get confused by the transforms and display states of slides. Often times, this can be fixed by calling their update or render function from this callback. + +```javascript +Reveal.addEventListener( 'slidechanged', function( event ) { + // event.previousSlide, event.currentSlide, event.indexh, event.indexv +} ); +``` + +### Presentation State + +The presentation's current state can be fetched by using the `getState` method. A state object contains all of the information required to put the presentation back as it was when `getState` was first called. Sort of like a snapshot. It's a simple object that can easily be stringified and persisted or sent over the wire. + +```javascript +Reveal.slide( 1 ); +// we're on slide 1 + +var state = Reveal.getState(); + +Reveal.slide( 3 ); +// we're on slide 3 + +Reveal.setState( state ); +// we're back on slide 1 +``` + +### Slide States + +If you set ``data-state="somestate"`` on a slide ``
``, "somestate" will be applied as a class on the document element when that slide is opened. This allows you to apply broad style changes to the page based on the active slide. + +Furthermore you can also listen to these changes in state via JavaScript: + +```javascript +Reveal.addEventListener( 'somestate', function() { + // TODO: Sprinkle magic +}, false ); +``` + +### Slide Backgrounds + +Slides are contained within a limited portion of the screen by default to allow them to fit any display and scale uniformly. You can apply full page backgrounds outside of the slide area by adding a ```data-background``` attribute to your ```
``` elements. Four different types of backgrounds are supported: color, image, video and iframe. + +#### Color Backgrounds +All CSS color formats are supported, like rgba() or hsl(). +```html +
+

Color

+
+``` + +#### Image Backgrounds +By default, background images are resized to cover the full page. Available options: + +| Attribute | Default | Description | +| :--------------------------- | :--------- | :---------- | +| data-background-image | | URL of the image to show. GIFs restart when the slide opens. | +| data-background-size | cover | See [background-size](https://developer.mozilla.org/docs/Web/CSS/background-size) on MDN. | +| data-background-position | center | See [background-position](https://developer.mozilla.org/docs/Web/CSS/background-position) on MDN. | +| data-background-repeat | no-repeat | See [background-repeat](https://developer.mozilla.org/docs/Web/CSS/background-repeat) on MDN. | +```html +
+

Image

+
+
+

This background image will be sized to 100px and repeated

+
+``` + +#### Video Backgrounds +Automatically plays a full size video behind the slide. + +| Attribute | Default | Description | +| :--------------------------- | :------ | :---------- | +| data-background-video | | A single video source, or a comma separated list of video sources. | +| data-background-video-loop | false | Flags if the video should play repeatedly. | +| data-background-video-muted | false | Flags if the audio should be muted. | +| data-background-size | cover | Use `cover` for full screen and some cropping or `contain` for letterboxing. | + +```html +
+

Video

+
+``` + +#### Iframe Backgrounds +Embeds a web page as a slide background that covers 100% of the reveal.js width and height. The iframe is in the background layer, behind your slides, and as such it's not possible to interact with it by default. To make your background interactive, you can add the `data-background-interactive` attribute. +```html +
+

Iframe

+
+``` + +#### Background Transitions +Backgrounds transition using a fade animation by default. This can be changed to a linear sliding transition by passing ```backgroundTransition: 'slide'``` to the ```Reveal.initialize()``` call. Alternatively you can set ```data-background-transition``` on any section with a background to override that specific transition. + + +### Parallax Background + +If you want to use a parallax scrolling background, set the first two config properties below when initializing reveal.js (the other two are optional). + +```javascript +Reveal.initialize({ + + // Parallax background image + parallaxBackgroundImage: '', // e.g. "https://s3.amazonaws.com/hakim-static/reveal-js/reveal-parallax-1.jpg" + + // Parallax background size + parallaxBackgroundSize: '', // CSS syntax, e.g. "2100px 900px" - currently only pixels are supported (don't use % or auto) + + // Number of pixels to move the parallax background per slide + // - Calculated automatically unless specified + // - Set to 0 to disable movement along an axis + parallaxBackgroundHorizontal: 200, + parallaxBackgroundVertical: 50 + +}); +``` + +Make sure that the background size is much bigger than screen size to allow for some scrolling. [View example](http://revealjs.com/?parallaxBackgroundImage=https%3A%2F%2Fs3.amazonaws.com%2Fhakim-static%2Freveal-js%2Freveal-parallax-1.jpg¶llaxBackgroundSize=2100px%20900px). + + + +### Slide Transitions +The global presentation transition is set using the ```transition``` config value. You can override the global transition for a specific slide by using the ```data-transition``` attribute: + +```html +
+

This slide will override the presentation transition and zoom!

+
+ +
+

Choose from three transition speeds: default, fast or slow!

+
+``` + +You can also use different in and out transitions for the same slide: + +```html +
+ The train goes on … +
+
+ and on … +
+
+ and stops. +
+
+ (Passengers entering and leaving) +
+
+ And it starts again. +
+``` + + +### Internal links + +It's easy to link between slides. The first example below targets the index of another slide whereas the second targets a slide with an ID attribute (```
```): + +```html +Link +Link +``` + +You can also add relative navigation links, similar to the built in reveal.js controls, by appending one of the following classes on any element. Note that each element is automatically given an ```enabled``` class when it's a valid navigation route based on the current slide. + +```html + + + + + + +``` + + +### Fragments +Fragments are used to highlight individual elements on a slide. Every element with the class ```fragment``` will be stepped through before moving on to the next slide. Here's an example: http://revealjs.com/#/fragments + +The default fragment style is to start out invisible and fade in. This style can be changed by appending a different class to the fragment: + +```html +
+

grow

+

shrink

+

fade-out

+

fade-up (also down, left and right!)

+

visible only once

+

blue only once

+

highlight-red

+

highlight-green

+

highlight-blue

+
+``` + +Multiple fragments can be applied to the same element sequentially by wrapping it, this will fade in the text on the first step and fade it back out on the second. + +```html +
+ + I'll fade in, then out + +
+``` + +The display order of fragments can be controlled using the ```data-fragment-index``` attribute. + +```html +
+

Appears last

+

Appears first

+

Appears second

+
+``` + +### Fragment events + +When a slide fragment is either shown or hidden reveal.js will dispatch an event. + +Some libraries, like MathJax (see #505), get confused by the initially hidden fragment elements. Often times this can be fixed by calling their update or render function from this callback. + +```javascript +Reveal.addEventListener( 'fragmentshown', function( event ) { + // event.fragment = the fragment DOM element +} ); +Reveal.addEventListener( 'fragmenthidden', function( event ) { + // event.fragment = the fragment DOM element +} ); +``` + +### Code syntax highlighting + +By default, Reveal is configured with [highlight.js](https://highlightjs.org/) for code syntax highlighting. To enable syntax highlighting, you'll have to load the highlight plugin ([plugin/highlight/highlight.js](plugin/highlight/highlight.js)) and a highlight.js CSS theme (Reveal comes packaged with the zenburn theme: [lib/css/zenburn.css](lib/css/zenburn.css)). + +Below is an example with clojure code that will be syntax highlighted. When the `data-trim` attribute is present, surrounding whitespace is automatically removed. HTML will be escaped by default. To avoid this, for example if you are using `` to call out a line of code, add the `data-noescape` attribute to the `` element. + +```html +
+

+(def lazy-fib
+  (concat
+   [0 1]
+   ((fn rfib [a b]
+        (lazy-cons (+ a b) (rfib b (+ a b)))) 0 1)))
+	
+
+``` + +### Slide number +If you would like to display the page number of the current slide you can do so using the ```slideNumber``` and ```showSlideNumber``` configuration values. + +```javascript +// Shows the slide number using default formatting +Reveal.configure({ slideNumber: true }); + +// Slide number formatting can be configured using these variables: +// "h.v": horizontal . vertical slide number (default) +// "h/v": horizontal / vertical slide number +// "c": flattened slide number +// "c/t": flattened slide number / total slides +Reveal.configure({ slideNumber: 'c/t' }); + +// Control which views the slide number displays on using the "showSlideNumber" value: +// "all": show on all views (default) +// "speaker": only show slide numbers on speaker notes view +// "print": only show slide numbers when printing to PDF +Reveal.configure({ showSlideNumber: 'speaker' }); + +``` + + +### Overview mode + +Press "Esc" or "o" keys to toggle the overview mode on and off. While you're in this mode, you can still navigate between slides, +as if you were at 1,000 feet above your presentation. The overview mode comes with a few API hooks: + +```javascript +Reveal.addEventListener( 'overviewshown', function( event ) { /* ... */ } ); +Reveal.addEventListener( 'overviewhidden', function( event ) { /* ... */ } ); + +// Toggle the overview mode programmatically +Reveal.toggleOverview(); +``` + + +### Fullscreen mode +Just press »F« on your keyboard to show your presentation in fullscreen mode. Press the »ESC« key to exit fullscreen mode. + + +### Embedded media +Add `data-autoplay` to your media element if you want it to automatically start playing when the slide is shown: + +```html + +``` + +If you want to enable or disable autoplay globally, for all embedded media, you can use the `autoPlayMedia` configuration option. If you set this to `true` ALL media will autoplay regardless of individual `data-autoplay` attributes. If you initialize with `autoPlayMedia: false` NO media will autoplay. + +Note that embedded HTML5 `