Index
A
- abline() function / Overlay a regression line on a scatterplot
- AdaBoost
- used, for combining classification tree models / Using AdaBoost to combine classification tree models, How to do it..., How it works...
- adjacency matrices
- Adjusted R-squared value / How it works...
- apply function
- used, for processing entire rows or columns / Processing entire rows or columns using the apply function, How it works...
- using, on three-dimensional array / Using apply on a three-dimensional array
- auto.arima function / How it works...
- automated ARIMA model
B
C
- cache option / There's more...
- cases, with missing values
- removing / Removing cases with missing values, How it works...
- cases with NA, eliminating / Eliminating cases with NA for selected variables
- no missing values cases, searching / Finding cases that have no missing values
- specific values, converting to NA / Converting specific values to NA
- NA values, excluding from computations / Excluding NA values from computations
- categorical variables
- dummies, creating / Creating dummies for categorical variables, How it works...
- selecting, for dummy creation / Choosing which variables to create dummies for
- charts
- creating, for comparison / Getting ready, How to do it...
- creating, to visualize causality / Creating charts that help visualize a possible causality, How to do it..., See also…
- charts, creating for comparison
- about / Creating charts that facilitate comparisons, How to do it...
- base plotting system, using / Using base plotting system
- ggplot2, using / Using ggplot2, How it works...
- boxplots, creating with ggplot2 / Creating boxplots with ggplot2
- classification
- Random Forest models, using / Using random forest models for classification, How to do it..., How it works...
- SVM, using / Getting ready, How to do it..., How it works...
- Naive Bayes approach, using / Getting ready, How it works...
- KNN approach, using / Getting ready, How it works...
- neural networks, using / Using neural networks for classification, Getting ready, How it works...
- linear discriminant function analysis, using / Getting ready, How to do it..., There's more...
- logistic regression, using / Getting ready, How to do it..., How it works...
- classification tree models
- combining, with AdaBoost / Using AdaBoost to combine classification tree models, How to do it..., How it works...
- classification trees
- building / Building, plotting, and evaluating – classification trees, How to do it..., How it works...
- plotting / Getting ready, How to do it..., How it works...
- evaluating / Getting ready, How to do it..., How it works...
- raw probabilities, computing / Computing raw probabilities
- creating / Create the ROC Chart
- cluster analysis
- about / Introduction
- performing, with K-means clustering / Performing cluster analysis using K-means clustering, How to do it..., How it works...
- performing, with hierarchical clustering / Performing cluster analysis using hierarchical clustering, Getting ready, How to do it..., How it works...
- Coordinate Reference System (CRS) / How it works...
- coordinates function / How it works...
- createDataPartition() function / How it works...
- CSV files
- data, reading from / Getting ready
- column delimiters, handling / Handling different column delimiters
- column headers/variable names, handling / Handling column headers/variable names
- missing values, handling / Handling missing values
- strings, reading as characters / Reading strings as characters and not as factors
- data, reading directly from website / Reading data directly from a website
- cut function / How it works...
D
- data
- reading, from CSV files / Getting ready
- reading, from fixed width formatted files / Reading data from fixed-width formatted files, Files with headers
- reading, from R files / Getting ready, How to do it...
- reading, from R libraries / Getting ready, How it works...
- reading, from MySQL / Reading data from relational databases – MySQL
- reading, from relational databases / Reading data from relational databases – MySQL, Getting ready
- reading, from NoSQL database / Reading data from NoSQL databases – MongoDB, How it works...
- reading, from MongoDB / Reading data from NoSQL databases – MongoDB, How it works...
- data frames
- data, normalizing / Normalizing or standardizing data in a data frame, How it works...
- data, standardizing / Normalizing or standardizing data in a data frame, How it works...
- several variables, standardizing / Standardizing several variables simultaneously
- dataset
- splitting / Splitting a dataset
- data tables
- used, for combining data / Slicing, dicing, and combining data with data tables, How to do it..., How it works...
- used, for slicing data / Slicing, dicing, and combining data with data tables, How to do it..., How it works...
- used, for dicing data / Slicing, dicing, and combining data with data tables, How to do it..., How it works...
- multiple aggregated columns, adding / Adding multiple aggregated columns
- column, deleting / Deleting a column
- joining / Joining data tables
- symbols, using / Using symbols
- date objects
- creating / Creating and examining date objects, How to do it..., How it works...
- examining / Creating and examining date objects, How to do it..., How it works...
- format specifier / How it works...
- operating / Operating on date objects, How to do it..., How it works...
- decompose function / How to do it...
- density() function / Overlay a density plot on a histogram
- diff function / How it works...
- downloaded Google map
- data, overlaying / Overlaying data on the downloaded Google map, How to do it..., How it works...
- dsn (data source name) / How it works...
- dummies
- creating, for categorical variables / Creating dummies for categorical variables, How it works...
- duplicate cases
- removing / Removing duplicate cases
- duplicates, identifying / Identifying duplicates (without deleting them)
E
- echo option / There's more...
- edge lists
- error/classification-confusion matrices
- generating / Generating error/classification-confusion matrices, How it works...
- visualizing / Visualizing the error/classification confusion matrix
- models performance, comparing / Comparing the model's performance for different classes
- error option / There's more...
- ESRI shape files
- importing, into R / Importing ESRI shape files into R, How to do it..., How it works...
- eval option / There's more...
- Excel
- connecting, with xlsx package / Using the xlsx package to connect to Excel, How to do it..., How it works...
F
- F-statistic / How it works...
- filter function / Filtering time series data
- fit$betweenss command / How it works...
- fit$centers command / How it works...
- fit$cluster command / How it works...
- fit$ifault command / How it works...
- fit$iter command / How it works...
- fit$size command / How it works...
- fit$tot.withinss command / How it works...
- fit$totss command / How it works...
- fit$withinss command / How it works...
- fixed width formatted files
- data, reading / Reading data from fixed-width formatted files, Files with headers
- files, with headers / Files with headers
- columns, excluding from data / Excluding columns from data
- format function / How it works...
- fromJSON function / How it works...
- functions
- applying, to subsets of vector / Getting ready, There's more...
- applying, on groups from data frame / Applying a function on groups from a data frame
G
- geographic data
- plotting, with sp package / Using the sp package to plot geographic data, How to do it..., How it works...
- geoms / Creating plots with the ggplot2 package
- geom_smooth function / How it works...
- GetMap function / How it works...
- ggplot2 package
- used, for creating plots / Creating plots with the ggplot2 package, How it works..., There's more...
- Google map
- of specific area, downloading / Downloading and plotting a Google map of an area, How it works..., There's more...
- of specific area, plotting / Downloading and plotting a Google map of an area, How it works..., There's more...
- downloaded map, saving as image file / Saving the downloaded map as an image file
- satellite image, obtaining / Getting a satellite image
- graphics device
- selecting / Selecting a graphics device
- grid
- multiple plots, generating / Generating multiple plots on a grid, How it works...
- graphics parameters / Graphics parameters
H
- hierarchical clustering
- used, for performing cluster analysis / Performing cluster analysis using hierarchical clustering, How to do it..., How it works...
- histograms
- about / Histograms
- working / Histograms
- density plot, overlaying / Overlay a density plot on a histogram
- Holt-Winters method
- used, for smoothing / Smoothing and forecasting using the Holt-Winters method, How to do it..., How it works...
- used, for forecasting / Getting ready, How to do it..., How it works...
I
- interactive web applications
- creating, with shiny / Creating interactive web applications with shiny, Getting ready, How to do it..., How it works...
- images, adding / Adding images
- HTML, adding / Adding HTML
- tab sets, adding / Adding tab sets
- dynamic UI, adding / Adding a dynamic UI
- single file web application, creating / Creating single file web application
J
- JAR files
- URL / Getting ready, Getting ready
- Java
- R functions, calling with Rserve / Using Rserve to call R functions from Java , Getting ready, How it works..., There's more...
- R scripts, executing from / Executing R scripts from Java , How it works...
- Java Native Interface (JNI) / Introduction
- Java objects
- using, in R / Getting ready, How to do it..., How it works...
- JVM properties, checking / Checking JVM properties
- available methods, displaying / Displaying available methods
- Java Virtual Machine (JVM) / How it works...
- JRI
- about / Introduction
- used, for calling R functions from Java / Using JRI to call R functions from Java, How it works..., There's more...
- JSON data
- reading / Reading JSON data, How it works...
K
- k-fold cross-validation
- performing / Performing k-fold cross-validation, How to do it..., How it works...
- K-means clustering
- used, for performing cluster analysis / Performing cluster analysis using K-means clustering, Getting ready, How to do it..., How it works...
- K value, selecting with convenience function / Use a convenience function to choose a value for K
- kmeans function / How it works...
- knitr
- about / Generating reports of your data analysis with R Markdown and knitr
- used, for generating data analysis reports / Generating reports of your data analysis with R Markdown and knitr, How to do it..., How it works..., There's more...
- render function, using / Using the render function
- output options, adding / Adding output options
- KNN
- running, with cross-validation / Running KNN with cross-validation in place of validation partition
- running, with convenience function / Using a convenience function to run KNN
- running, with convenience function for multiple k values / Using a convenience function to run KNN for multiple k values , See also...
- KNN approach
- used, for classification / Classifying using the KNN approach, How it works...
- running process, automating / Automating the process of running KNN for many k values
- used, for computing raw probabilities / Using KNN to compute raw probabilities instead of classifications
- KNN models, for regression
L
- lapply function
- used, for applying function to collection elements / Applying a function to all elements of a collection with lapply and sapply, How to do it..., How it works...
- lattice package
- used, for creating plots / Creating plots with the lattice package, How it works..., There's more...
- legend function / How it works...
- linear discriminant function analysis
- used, for classification / Classifying using linear discriminant function analysis, How it works...
- formula interface, using / Using the formula interface for lda
- linear regression
- performing / Performing linear regression, How to do it..., How it works...
- relevel function, using / Forcing lm to use a specific factor level as the reference
- options, using in formula expression / Using other options in the formula expression for linear models
- variable selection, performing / Performing variable selection in linear regression, How to do it..., How it works...
- lines() function / Overlay a density plot on a histogram
- logistic regression
- used, for classification / Classifying using logistic regression, How to do it..., How it works...
- LOOCV
- performing, for overfitting limitation / Performing leave-one-out-cross-validation to limit overfitting, How it works...
M
- map2SpatialPolygons function / How it works...
- MapBackground function / How it works...
- maps
- obtaining, from maps package / Getting maps from the maps package, How it works...
- maps package
- maps, obtaining / Getting maps from the maps package, How it works...
- mean() function / Finding the mean and standard deviation
- Meetup
- URL / How to do it...
- message option / There's more...
- missing values
- replacing, with mean / Replacing missing values with the mean, There's more...
- random values sampled, imputing from nonmissing values / Imputing random values sampled from nonmissing values
- MongoDB
- JSON, validating / Validating your JSON
- multiple plots
- creating, on grid / Generating multiple plots on a grid, How it works...
- multivariate plots
- creating / Creating multivariate plots, How to do it..., How it works...
- MySQL
- data, reading from / Reading data from relational databases – MySQL, Getting ready
N
- naiveBayes() function / How it works...
- Naive Bayes approach
- used, for classification / Classifying using the Naïve Bayes approach, How it works...
- network metrics
- computing / Getting ready, How to do it..., How it works..., There's more...
- degree / How it works...
- centrality / How it works...
- betweenness / How it works...
- closeness / How it works...
- edge sequences, obtaining / Getting edge sequences
- neighbors, obtaining / Getting immediate and distant neighbors
- vertices or nodes, adding / Adding vertices or nodes
- edges, adding / Adding edges
- isolates, deleting from graph / Deleting isolates from a graph
- subgraphs, creating / Creating subgraphs
- neural networks
- used, for classification / Using neural networks for classification, Getting ready, How it works...
- greater control over net, exercising / Exercising greater control over nnet
- raw probabilities, generating / Generating raw probabilities
- ROC curve, plotting / Generating raw probabilities
- for generation, using / Using neural networks for regression, How to do it..., How it works..., See also...
- NoSQL database
- data, reading from / Reading data from NoSQL databases – MongoDB, How it works...
- numerical data
- binning / Binning numerical data, How to do it..., There's more...
- specified number of intervals, creating / Creating a specified number of intervals automatically
O
- ODBC (Open Database Connectivity) / Reading data from relational databases – MySQL
- out of bag (OOB) predictions / How to do it...
P
- PDF presentations
- creating, with R Presentation / Creating PDF presentations of your analysis with R Presentation, How to do it..., How it works..., There's more...
- plot function / How it works..., How it works...
- PlotOnStaticMap function / How it works..., How it works...
- plots
- creating, with lattice package / Creating plots with the lattice package, How it works...
- graphs, customizing / Adding flair to your graphs
- creating, with ggplot2 package / Creating plots with the ggplot2 package, How it works..., There's more...
- conditioning, on continuous numeric variables / Condition plots on continuous numeric variables
- plyr function
- split-apply-combine strategy, using with / Using the split-apply-combine strategy with plyr, Getting ready, How it works...
- new column, adding with transform / Adding a new column using transform
- summarize, using / Using summarize along with the plyr function
- list of data frames, concatenating into big data frame / Concatenating the list of data frames into a big data frame
- principal component analysis
- used, for reducing dimensionality / Getting ready, How to do it..., How it works...
- principal component analysis (PCA) / Introduction
- public APIs
- used, for downloading / How it works...
R
- R
- professional presentation, tasks / Introduction
- ESRI shape files, importing into / Importing ESRI shape files into R, How to do it..., How it works...
- Java objects, using / Using Java objects in R, Getting ready, How to do it..., How it works...
- array, retrieving / Retrieving an array from R
- random data partitions
- creating / Creating random data partitions
- numerical target variable and two partitions / Case 1 – numerical target variable and two partitions
- numerical target variable and three partitions / Case 2 – numerical target variable and three partitions
- categorical target variable and two partitions / Case 3 – categorical target variable and two partitions
- categorical target variable and three partition / Case 4 – categorical target variable and three partitions
- working / How it works...
- convenience function, using / Using a convenience function for partitioning
- sampling, from set of values / Sampling from a set of values
- randomForest function / How it works...
- random forest models
- for regression, building / Getting ready, How to do it..., How it works...
- forest generation, controlling / Controlling forest generation, See also...
- Random Forest models
- using, for classification / Using random forest models for classification, How to do it..., How it works...
- raw probabilities, computing / Computing raw probabilities
- ROC chart, generating / Generating the ROC chart
- cutoffs, specifying for classification / Specifying cutoffs for classification
- R data file
- attaching/detaching, to environment / Attaching/detaching R data files to an environment
- read.csv() function / How it works...
- readOGR function / How it works...
- regression
- random forest models, building for / Getting ready, How to do it..., How it works...
- neural networks, using for / Using neural networks for regression, How to do it..., How it works...
- regression trees
- building / Building regression trees, How to do it..., How it works..., There's more…
- generating, for categorical predictors data / Generating regression trees for data with categorical predictors, See also...
- relational databases
- data, reading from / Reading data from relational databases – MySQL, Getting ready
- RODBC, using / Using RODBC, Using RODBC
- RMySQL, using / Using RMySQL, Using RMySQL
- RJDBC, using / Using RJDBC, Using RJDBC
- rows, fetching / Fetching all rows
- SQL query / When the SQL query is long
- render function / Using the render function
- Residual standard error / How it works...
- results option / There's more...
- R files
- data, reading from / Reading data from R files and R libraries, How to do it...
- R functions
- calling, from Java with JRI / Using JRI to call R functions from Java, How it works..., There's more...
- calling, from Java with Rserve / Using Rserve to call R functions from Java , Getting ready, How it works...
- R libraries
- data, reading from / Reading data from R files and R libraries, How it works...
- R Markdown
- about / Generating reports of your data analysis with R Markdown and knitr
- used, for generating data analysis reports / Generating reports of your data analysis with R Markdown and knitr, How to do it..., How it works..., There's more...
- URL / There's more...
- render function, using / Using the render function
- output options, adding / Adding output options
- RMS error
- computing / Computing the root mean squared error, Getting ready, How it works...
- computing, with convenience function / Using a convenience function to compute the RMS error
- R objects
- saving, in session / To save all objects in a session
- selectively saving, in session / To selectively save objects in a session
- ROC charts
- generating / Generating ROC charts, How to do it..., How it works...
- arbitrary class labels, using / Using arbitrary class labels
- R Presentation
- used, for creating PDF analysis presentations / Creating PDF presentations of your analysis with R Presentation, How to do it..., How it works...
- hyperlinks, using / Using hyperlinks
- display, controlling / Controlling the display
- appearance, enhancing / Enhancing the look of the presentation
- R scripts
- executing, from Java / Executing R scripts from Java , How it works...
- Rserve
- about / Introduction
- used, for calling R functions from Java / Using Rserve to call R functions from Java , Getting ready, How it works..., There's more...
S
- sapply function
- used, for applying function to collection elements / Applying a function to all elements of a collection with lapply and sapply, How to do it..., How it works...
- dynamic output / Dynamic output
- caution / One caution
- saveRDS() function / How it works...
- scatterplot
- creating / Scatterplots
- matrices / Scatterplot matrices
- regression line, overlaying / Overlay a regression line on a scatterplot
- color-specific points / Color specific points on a scatterplot
- sd() function / Finding the mean and standard deviation
- selectInput function / How it works...
- shiny
- used, for creating interactive web applications / Creating interactive web applications with shiny, How to do it..., How it works...
- URL / There's more...
- shinyServer function / How it works...
- shinyUI function / How it works...
- social network data
- downloading, with public APIs / Downloading social network data using public APIs, Getting ready, How to do it..., How it works...
- plotting / Plotting social network data, How to do it..., How it works...
- plotting preferences, specifying / Specifying plotting preferences
- directed graphs, plotting / Plotting directed graphs
- graph object, creating with weights / Creating a graph object with weights
- network as adjacency matrix, extracting / Extracting the network as an adjacency matrix from the graph object
- adjacency matrix with weights, extracting / Extracting an adjacency matrix with weights
- edge list, extracting from graph objects / Extracting edge list from graph object
- bipartite network graph, creating / Creating bipartite network graph
- bipartite network projections, generating / Generating projections of a bipartite network
- spatial data frames
- creating, from regular data frames / Creating spatial data frames from regular data frames containing spatial and other data, How to do it..., How it works...
- creating, by combining regular data frame with spatial objects / Creating spatial data frames by combining regular data frames with spatial objects, Getting ready, How to do it..., How it works...
- creating, by combining regular data frame with spatial objects / How it works...
- SpatialPolygonsDataFrame function / How it works...
- split(auto, auto$cylinders) function / How it works...
- split-apply-combine strategy
- using, with plyr function / Using the split-apply-combine strategy with plyr, Getting ready, How it works...
- sp package
- used, for plotting geographic data / Using the sp package to plot geographic data, Getting ready, How to do it..., How it works...
- spplot function / How it works...
- standard data summaries
- creating / Getting ready, How it works...
- str() function, using / Using the str() function for an overview of a data frame
- single variable summary, computing / Computing the summary for a single variable
- mean, finding / Finding the mean and standard deviation
- standard deviation, finding / Finding the mean and standard deviation
- standard plots
- generating / Generating standard plots such as histograms, boxplots, and scatterplots, How to do it...
- histograms / Histograms
- boxplot / Boxplots
- scatterplot / Scatterplots
- scatterplot matrices / Scatterplot matrices, How it works...
- stl function / How to do it...
- str() function / Using the str() function for an overview of a data frame
- strsplit function / How it works...
- subset function / How it works...
- subset of dataset
- extracting / Extracting a subset of a dataset, How it works..., There's more...
- columns, excluding / Excluding columns
- multiple value based selections / Selecting based on multiple values
- logical vector, used for selections / Selecting using logical vector
- subsets of vector
- functions, applying to / Applying functions to subsets of a vector, There's more...
- summary() function / How it works...
- SVM
- used, for classification / Getting ready, How to do it..., How it works...
- variable scaling, controlling / Controlling scaling of variables
- model type, determining / Determining the type of SVM model
- weights, assigning to classes / Assigning weights to the classes
T
- table() function / How it works...
- tabPanel() function / Adding tab sets
- tapply function / Applying functions to subsets of a vector
- time series
- decomposing / Decomposing time series, How to do it..., How it works...
- time series data
- preliminary analyses, performing / Performing preliminary analyses on time series data, How to do it..., How it works...
- filtering / Filtering time series data, How it works..., See also...
- time series objects
- using / Getting ready, How to do it..., How it works...
- ts function / How it works...
V
- variables
- rescaling / Rescaling a variable to [0,1], There's more...
- multiple variables, rescaling / Rescaling many variables at once
- adding, to existing spatial data frame / Adding variables to an existing spatial data frame, How it works...
- variable selection, linear regression
- performing / Getting ready, How to do it..., How it works...
- vectorized operations
- exploiting / Exploiting vectorized operations, How it works...
W
- Ward's method / How it works...
- warning option / There's more...
- World Geodetic System 1984 (WGS84) / How it works...
X
- xlsx package
- used, for connecting to Excel / Using the xlsx package to connect to Excel, How to do it..., How it works...
- XML data
- reading / Reading XML data, How to do it..., How it works...
- HTML table data, extracting from web page / Extracting HTML table data from a web page
- single HTML table, extracting from web page / Extracting a single HTML table from a web page