A first example - file connections | Protect against non-exportable objects | Packages with non-exportable objects

Introduction | Installation & Dependencies | The General Transit Feed Specification | Read a GTFS Feed | Feed Validation Results | Finding More GTFS Feeds | Feed registries | Using MobilityData

Filtering by agency_id, route_id, service_id, shape_id, stop_id, trip_id or route_type: | Filtering by day of the week or time of the day: | Filtering using a spatial extent

Mapping the transit network | Mapping routes by speed | Mapping stops by frequency

Setting route frequencies | Setting trip speeds | Converting stop times to frequencies | Interpolating stop times

Trips per day | Overlap periods

GTFS feeds | Basic usage | Read feeds | Analyse feeds | Manipulate feeds | Write feeds

Frequencies and timetables | Trip lengths, durations and speeds | Summarising a feed

Introduction | Installation | Basic Usage | Downloading a single state and year | Multiple states and years | Aggregation levels | Attaching spatial geometries | Geographic crosswalk | Analytical Functions | Commute flow statistics | Longitudinal change | Earnings tier shares | Mapping LODES Data | Caching | Citation

1. Introduction | 2. Build routable transport network with build_network() | Increase Java memory and load libraries | 3. Accessibility: quick and easy approach | 4. Accessibility: flexible approach | 5. Map Accessibility | 5.1 Choropleth maps | 5.2 Spatial interpolation | Cleaning up after usage | References

1. Introduction | 1.1 Details | 2. Reprex: the public transport system of Porto Alegre | 3. Setting up the fare structure | 3.1 Global Properties | max_discounted_transfers | transfer_time_allowance | fare_cap | 3.2 Configure fares by transport mode | 3.3 Configure fares by transfers | 3.4 Routes configuration | 4. Calculating travel time and accessibility accounting for monetary costs | 4.1 Travel time with monetary cost | 4.2 Calculating accessibility with monetary cost | Cleaning up after usage

1. Why do some trips from/to the same ID have travel times larger than zero? | 2. Is it possible to run r5r with custom modifications to street network data? | 3. Why are the output results of travel_time_matrix() and detailed_itineraries() different? | 4. What does the ERROR "Geographic extent of street layer exceeds limit" mean? and what to do about it? | 5. Is it possible to use custom car speed data with r5r? | 6. Why do I get identical results by public transport and walking?

1. Introduction | 2. Installation | 3. Usage | 3.1 Data requirements: | 4. Demonstration on sample data | Data | 4.1 Building routable transport network with build_network() | 4.2 Accessibility analysis | 4.3 Routing analysis | Fast many to many travel time matrix | Expanded travel time matrix with minute-by-minute estimates | Detailed itineraries | Visualize results | Cleaning up after usage

1. Introduction | 2. Build routable transport network with build_network() | Increase Java memory and load libraries | 3. Calculating and visualizing isochrones | 3.1 Polygon-based isochrones | 3.2 Line-based isochrones | Cleaning up after usage

1. Introduction | 2. What the pareto_frontier means. | 3. Demonstration of pareto_frontier(). | 3.1 Build routable transport network with build_network() | 3.2 Set up the fare structure | 3.3 Calculating a pareto_frontier(). | Cleaning up after usage | References

1. Introduction | 2. Build routable transport network with build_network() | 3. The travel_time_matrix() function | 4. The expanded_travel_time_matrix() function | 5. The arrival_travel_time_matrix() function | Cleaning up after usage | References

1. Introduction | 2. Build routable transport network with build_network() | 3. Detailed info by trip segment for multiple trip alternatives | 3.1 Visualize results | 4. Other options | 5. Hack for frequency-based GTFS feeds | Cleaning up after usage

1. Introduction | 2. Changing car speeds | 2.1 Changing car speeds by OSM edge | 2.1.1 Setting different congestion levels by road hierarchy | 2.1.2 Setting the same speed limit for the selected road types | Extra tip: | 2.2 Changing car speeds with a spatial polygon | 3. Changing cycling LTS values | 3.1 Changing LTS by OSM edge | 3.2. Changing LTS with spatial lines | Cleaning up after usage

1. Introduction | The problem | The solution | 2. How the time_window works and how to interpret the results. | 3. Demonstration of time_window. | 3.1 Build routable transport network with build_network() | 3.2 Accessibility with time_window. | 3.3 Travel time matrix with time_window. | 3.4 Expanded travel time matrix with time_window. | 3.5 Detailed itineraries with time_window. | Cleaning up after usage | References

Publication | Presentation | Statistical backend of | Suggestions

Summary | Statement of Need | Benefits | Future Scope | Learn More | Licensing and Availability | Acknowledgements | References

Beginner FAQs | Why do DT[ , 5] and DT[2, 5] return a 1-column data.table rather than vectors like data.frame? | Why does DT[,"region"] return a 1-column data.table rather than a vector? | Why does DT[, region] return a vector for the "region" column? I'd like a 1-column data.table. | Why does DT[ , x, y, z] not work? I wanted the 3 columns x,y and z. | I assigned a variable mycol="x" but then DT[, mycol] returns an error. How do I get it to look up the column name contained in the mycol variable? | What are the benefits of being able to use column names as if they are variables inside DT[...]? | OK, I'm starting to see what data.table is about, but why didn't you just enhance data.frame in R? Why does it have to be a new package? | Why are the defaults the way they are? Why does it work the way it does? | Isn't this already done by with() and subset() in base? | Why does X[Y] return all the columns from Y too? Shouldn't it return a subset of X? | What is the difference between X[Y] and merge(X, Y)? | Anything else about X[Y, sum(foo*bar)]? | That's nice. How did you manage to change it given that users depended on the old behaviour? | General Syntax | How can I avoid writing a really long j expression? You've said that I should use the column names, but I've got a lot of columns. | Why is the default for mult now "all"? | I'm using c() in j and getting strange results. | I have built up a complex table with many columns. I want to use it as a template for a new table; i.e., create a new table with no rows, but with the column names and types copied from my table. Can I do that easily? | Is a null data.table the same as DT[0]? | Why has the DT() alias been removed? | But my code uses j = DT(...) and it works. The previous FAQ says that DT() has been removed. | What are the scoping rules for j expressions? | Can I trace the j expression as it runs through the groups? | Inside each group, why are the group variables length-1? | Only the first 10 rows are printed, how do I print more? | With an X[Y] join, what if X contains a column called "Y"? | X[Z[Y]] is failing because X contains a column "Y". I'd like it to use the table Y in calling scope. | Can you explain further why data.table is inspired by A[B] syntax in base? | Can base be changed to do this then, rather than a new package? | I've heard that data.table syntax is analogous to SQL. | What are the smaller syntax differences between data.frame and data.table | I'm using j for its side effect only, but I'm still getting data returned. How do I stop that? | Why does [.data.table now have a drop argument from v1.5? | Rolling joins are cool and very fast! Was that hard to program? | Why does DT[i, col := value] return the whole of DT? I expected either no visible value (consistent with <-), or a message or return value containing how many rows were updated. It isn't obvious that the data has indeed been updated by reference. | OK, thanks. What was so difficult about the result of DT[i, col := value] being returned invisibly? | Why do I have to type DT sometimes twice after using := to print the result to console? | I've noticed that base::cbind.data.frame (and base::rbind.data.frame) appear to be changed by data.table. How is this possible? Why? | I've read about method dispatch (e.g. merge may or may not dispatch to merge.data.table) but how does R know how to dispatch? Are dots significant or special? How on earth does R know which function to dispatch and when? | Why do T and F behave differently from TRUE and FALSE in some data.table queries? | Questions relating to compute time | I have 20 columns and a large number of rows. Why is an expression of one column so quick? | I don't have a key on a large table, but grouping is still really quick. Why is that? | Why is grouping by columns in the key faster than an ad hoc by? | What are primary and secondary indexes in data.table? | Error messages | "Could not find function DT" | "unused argument(s) (MySum = sum(v))" | "translateCharUTF8 must be called on a CHARSXP" | cbind(DT, DF) returns a strange format, e.g. Integer,5 | "cannot change value of locked binding for .SD" | "cannot change value of locked binding for .N" | Warning messages | "The following object(s) are masked from package:base: cbind, rbind" | "Coerced numeric RHS to integer to match the column's type" | Reading data.table from RDS or RData file | General questions about the package | v1.3 appears to be missing from the CRAN archive? | Is data.table compatible with S-plus? | Is it available for Linux, Mac and Windows? | I think it's great. What can I do? | I think it's not great. How do I warn others about my experience? | I have a question. I know the r-help posting guide tells me to contact the maintainer (not r-help), but is there a larger group of people I can ask? | Where are the datatable-help archives? | I'd prefer not to post on the Issues page, can I mail just one or two people privately? | I have created a package that uses data.table. How do I ensure my package is data.table-aware so that inheritance from data.frame works?

Posit Professional Drivers | Drivers | Databases | PostgreSQL | MySQL | SQL Server test setup | SQLite | Oracle | On MacOS | On Linux | Snowflake | Amazon Redshift | RODBC

Introduction | To duckplyr | From files | From DuckDB | Materialization | To files | Memory usage | The big picture

Introduction | Eager and lazy computation | Example | Comparison | Prudence | Concept | Enforcing DuckDB operation | From stingy to lavish | Thrift | File ingestion and custom limits | Conclusion

Introduction | DuckDB mode | Relation objects | Help from dplyr | Enforce DuckDB operation | Configure fallbacks | Conclusion

Data types | Verbs | Functions within verbs | Parentheses | Comparison operators | Basic arithmetics | Math functions | Logical operators | Branching and conversion | String manipulation | Date manipulation | Aggregation | Shifting | Ranking | Special cases | Contributing | Known incompatibilities | Output order stability | sum() | Empty vectors in aggregate functions | min() and max() for logical input | n_distinct() and multiple arguments | is.na() and NaN values | Row names | Other differences

Introduction | From duckplyr to dbplyr | Call arbitrary functions in duckplyr | Conclusion

Introduction | External data with explicit qualification | Restoring dplyr methods | Own data | In other packages

LISTEN / NOTIFY | SKIP LOCKED | Implementing our worker

Creating a new database | Loading data | Queries | Batched queries | Multiple parameterised queries | Statements

Version | Introduction | DBI Classes and Methods | Class DBIObject | Class DBIDriver | Class DBIConnection | Class DBIResult | Data Type Mappings | Utilities | Open Issues and Limitations | Resources

Computing with Distributed Data | A Common Interface | Interface Classes | Class dbManager | Class dbConnection | Class dbResult | Class dbResultSet | Data Type Mappings | Open Issues | Limitations | Other Approaches | Open Database Connectivity (ODBC) | Java Database Connectivity (JDBC) | CORBA and a 3-tier Architecture | Resources | Acknowledgements | The S Version 4 Definitions

Who this tutorial is for | How to run more complex queries using DBI | How to read part of a table from a database | How to use parameters (safely) in SQL queries | Quoting | Parameterized queries | SQL data manipulation - UPDATE, DELETE and friends | SQL transactions with DBI | Conclusion

Getting started | Testing | Driver | Connection | Results | SQL methods | Metadata methods | Full DBI compliance

Who this tutorial is for | How to connect to a database using DBI | Secure password storage | How to retrieve column names for a table | Read a table into a data frame | Read only selected rows and columns into a data frame | How to end a DBMS session | Conclusion | Further Reading

Who this tutorial is for | Rationale | New classes and generics | Prepare | Read all rows from a table | Run queries | Prepared queries | Manual flow | Writing data | Appending data | Conclusion

What is Polars? | Documentation and tutorials | Series and DataFrames | Methods and pipelines | Subset | Aggregate and modify | Reshape | Join | Lazy execution | Data import | Execute R functions within a Polars query | Data types

Introduction | Main Features | Symbology | Map Layout | Themes | Export | Examples of thematic maps | Base map | Proportional Symbols | Choropleth Map | Typology Map | Proportional Symbols using Choropleth Coloration | Proportional Symbols using Typology Coloration | Label Map | Links Map

Built-In Structured Documentation | DeepWiki | JSS Article | Cheatsheet | Vignettes | Blog | Presentations and Slides

Basic Examples | write.xlsx | write list of data.frames to xlsx-file | write.xlsx also accepts styling parameters | The simplest way is to set default options and set column class | Workbook styles | define a style for column headers | When writing a list, the stylings will apply to all list elements | write.xlsx returns the workbook object for further editing | Workbook creation walk-through | create workbook and set default border Colour and style | Add Sheets | write data to sheet 1 | write data to sheet 2 | add write group means | add write group variances | add style mean & variance table headers | save workbook | Gallery | Further Examples | Stock Price | Image Compression using PCA

Request interfaces | Getting in memory | Downloading to disk | Streaming data | Non blocking connections | Async requests | Exception handling | Error automatically | Check manually | Customizing requests | Setting handle options | ENUM (long) options | Disabling HTTP/2 | Performing the request | Reading cookies | On reusing handles | Posting forms | Using pipes

Introduction | Structure of a {gtsummary} object | table_body | table_styling | Constructing a {gtsummary} object | Printing a {gtsummary} object | The .$cards object

Data | Introduction | 1. Reference semantics | a) Background | shallow vs deep copy | b) The := operator | 2. Add/update/delete columns by reference | a) Add columns by reference | -- How can we add columns speed and total delay of each flight to flights data.table? | Note that | b) Update some rows of columns by reference - sub-assign by reference | -- Replace those rows where hour == 24 with the value 0 | Exercise: | c) Delete column by reference | -- Remove delay column | d) := along with grouping using by | -- How can we add a new column which contains for each orig,dest pair the maximum speed? | Note on zero-length RHS and by | e) Multiple columns and := | -- How can we add two more columns computing max() of dep_delay and arr_delay for each month, using .SD? | -- How can we update multiple existing columns in place using .SD? | 3. := and copy() | a) := for its side effect | b) The copy() function | c) Selecting columns: $ / [[...]] vs [, col] | d) Side effects and testing | Summary | The := operator

1. fread() | 1.1 Using command line tools directly | 1.1.1 Reading directly from a text string | 1.1.2 Reading from URLs | 1.1.3 Automatic decompression of compressed files | 1.2 Automatic separator and skip detection | 1.3 High-Quality Automatic Column Type Detection | 1.4 Early Error Detection at End-of-File | 1.5 integer64 Support | 1.6 Drop or Select Columns by Name or Position | 1.7 Automatic Quote Escape Detection (Including No-Escape) | 2. fwrite() | 2.1 Intelligent and Minimalist Quoting (quote="auto") | 2.2 Fine-Grained Date/Time Serialization (dateTimeAs argument) | 2.3 Handling of bit64::integer64 | 2.4 Column Order and Subset Control | 3. A Note on Performance

Plot methods for sf and sfc objects | Geometry only: sfc | Geometry with attributes: sf | Color key place and size | Class intervals | How does sf project geographic coordinates? | Graticules | Plotting sf objects with other packages | grid: st_as_grob | ggplot2 | mapview | tmap

First steps | Handling workbooks | Importing as workbook | Exporting data | Exporting data frames or vectors | Exporting a wbWorkbook | dims/ wb_dims() | A note on speed and memory usage

Data analysis using data.table | Data | Introduction | 1. Basics | a) What is data.table? | Note that: | b) General form - in what way is a data.table enhanced? | The way to read it (out loud) is: | c) Subset rows in i | -- Get all the flights with "JFK" as the origin airport in the month of June. | -- Get the first two rows from flights. | -- Sort flights first by column origin in ascending order, and then by dest in descending order: | order() is internally optimised | d) Select column(s) in j | -- Select arr_delay column, but return it as a vector. | -- Select arr_delay column, but return as a data.table instead. | Tip: | -- Select both arr_delay and dep_delay columns. | -- Select both arr_delay and dep_delay columns and rename them to delay_arr and delay_dep. | e) Compute or do in j | -- How many trips have had total delay < 0? | What's happening here? | f) Subset in i and do in j | -- Calculate the average arrival and departure delay for all flights with "JFK" as the origin airport in the month of June. | -- How many trips have been made in 2014 from "JFK" airport in the month of June? | g) Handle non-existing elements in i | -- What happens when querying for non-existing elements? | Special symbol .N: | h) Great! But how can I refer to columns by names in j (like in a data.frame)? | -- Select both arr_delay and dep_delay columns the data.frame way. | -- Select columns named in a variable using the .. prefix | -- Select columns named in a variable using with = FALSE | 2. Aggregations | a) Grouping using by | -- How can we get the number of trips corresponding to each origin airport? | -- How can we calculate the number of trips for each origin airport for carrier code "AA"? | -- How can we get the total number of trips for each origin, dest pair for carrier code "AA"? | -- How can we get the average arrival and departure delay for each orig,dest pair for each month for carrier code "AA"? | b) Sorted by: keyby | -- So how can we directly order by all the grouping variables? | c) Chaining | -- How can we order ans using the columns origin in ascending order, and dest in descending order? | d) Expressions in by | -- Can by accept expressions as well or does it just take columns? | e) Multiple columns in j - .SD | -- Do we have to compute mean() for each column individually? | Special symbol .SD: | -- How can we specify just the columns we would like to compute the mean() on? | .SDcols | f) Subset .SD for each group: | -- How can we return the first two rows for each month? | g) Why keep j so flexible? | -- How can we concatenate columns a and b for each group in ID? | -- What if we would like to have all the values of column a and b concatenated, but returned as a list column? | Summary | Using i: | Using j: | Using by: | And remember the tip:

Why to import data.table | Importing data.table is easy | DESCRIPTION file | NAMESPACE file | Usage | Testing | Testing using testthat | Dealing with "undefined global functions or variables" | Care needed when providing and using options | Troubleshooting | License | Optionally import data.table: Suggests | data.table in Imports but nothing imported | Further information on dependencies | Importing data.table C routines | How to convert your Depends dependency on data.table to Imports | Step 0. Ensure your package is passing R CMD check initially | Step 1. Update the DESCRIPTION file to put data.table in Imports, not Depends | Step 2.1: Run R CMD check | Step 2.2: Modify the NAMESPACE file | Blanket import | Step 3: Update Your R code files outside the package's R/ directory | Benefits of using Imports

Add plot to workbook | Add {ggplot2} plot to workbook | Add plot via | Adding {encharter} plots | Add and fill a chartsheet | Add {mschart} plots

Installation | Basic usage | Reading feeds | Writing feeds | Checking GTFS objects

Introduction | A Quick Example | The Usage | Loading Fonts | Working with R Markdown | CJK Fonts | How showtext Works | Compatibility with RStudio

Writing functions using polars expressions | Using purrr | Conclusion

Introduction | Implicit or Explicit Futures | Controlling How Futures are Resolved | Failed Futures | Globals | Constraints when using Implicit Futures | Demos

The future smell test | Avoid changing the future backend | Avoid changing the future options | Writing examples | Writing vignettes | Testing a package that relies on futures | Making sure to stop parallel workers

Issues with globals and packages | ‘…’ used in an incorrect context | Non-exportable objects | Trying to pass an unresolved future to another future | Miscellaneous

Example: High-Throughput Sequencing | Example: A Remote Compute Cluster | Example: Adjust the Number of Workers for Each Cluster Node

Future frontends | Capturing output | Suppressing messages | Known limitations

Setup | Option 1: Trade money for convenience | Option 2: Reduce extract size | Remove unused data | Select cases | Use a sampled subset of the data | Option 3: Process the data in pieces | Reading chunked data | Chunked tabulation | Chunked regression | Reading yielded data | Yielded tabulation | Yielded GLM regression | Option 4: Use a database | Importing data into the database | Connecting to a database with dbplyr | Learning more

How to install | From R-multiverse (recommended) | From GitHub | Details of installation | Pre-built Rust library binaries | Rust build time options | Features | Profile | Minimum Supported Rust Version (MSRV) | Builds for WASM/Emscripten

The Remotes field | GitHub | Other sources | CRAN submission

Reading and writing through GDAL | Using st_read | Using st_write | Guessing a driver for output | Dataset and layer reading or creation options | Reading and writing directly to and from spatial databases | Conversion to other formats: WKT, WKB, sp | Conversion to and from well-known text | Conversion to and from well-known binary | Conversion to and from sp

Type transformations | For single geometries | For collections of geometry (sfc) and simple feature collections (sf) | Affine transformations | Coordinate reference systems conversion and transformation | Getting and setting coordinate reference systems of sf objects | Coordinate reference system transformations | Geometrical operations | Unary operations | Binary operations: distance and relate | Binary logical operations: | Operations returning a geometry

Subsetting feature sets | Aggregating or summarizing feature sets | Joining two feature sets based on attributes | Joining two feature sets based on geometries

Installing magick | Build from source | Image IO | Read and write | Converting formats | Preview | Transformations | Cut and edit | Filters and effects | Kernel convolution | Text annotation | Combining with pipes | Image Vectors | Layers | Combining | Pages | Animation | Drawing and Graphics | Graphics device | Drawing device | Animated Graphics | Raster Images | Base R rasters | The grid package | OCR text extraction

What is a feature? | Dimensions | Simple feature geometry types | Coordinate reference system | How simple features in R are organized | sf: objects with simple features | sfc: simple feature geometry list-column | Mixed geometry types | sfg: simple feature geometry | Well-known text, well-known binary, precision | WKT and WKB | Precision | Reading and writing | Driver-specific options | Create, read, update and delete | Connection to spatial databases | Coordinate reference systems and transformations | Conversion, including to and from sp | Geometrical operations | Non-simple and non-valid geometries | Units | How attributes relate to geometries

API availability | Set up your API key | Define an extract request | Extract request objects | Submit an extract request | Wait for an extract request to complete | Download an extract | Get info on past extracts | Share an extract definition | Revise a previous extract request | Putting it all together

Obtaining IPUMS data | Obtaining data via an IPUMS project website | Downloading from microdata projects | Downloading from aggregate data projects | Obtaining data via the IPUMS API | Extract support | Metadata support | Workflow | Reading IPUMS data | Microdata files | NHGIS files | Spatial boundary files | Ancillary files | Exploring file metadata | Labelled values

Supported microdata collections | Basic IPUMS microdata concepts | IPUMS microdata metadata | Defining an IPUMS microdata extract request | Detailed variable specifications | Syntax | Case selections | Attached characteristics | Data quality flags | Monetary value adjustment | Time use variables | Data structure | Data file format | Next steps

Styling showcase | Colors, text rotation and number formats | the quick way: using high-level functions | the long way: using bare-metal functions | Working with number formats | numfmts | numfmts2 | Modifying the column widths | wb_set_col_widths | Adding borders | add borders | styled table | the long way: creating everything from the bone | Use workbook colors and modify them | Copy cell styles | Style strings | Create custom table styles

Importing data | Basic import | col_names - first row as column name | detect_dates - convert cells to R dates | show_formula - show formulas instead of results | dims - read specific dimension | cols - read selected columns | rows - read selected rows | convert - convert input to guessed type | skip_empty_rows - remove empty rows | skip_empty_cols - remove empty columns | row_names - keep rownames from input | types - convert column to specific type | start_row - where to begin | na - define missing values

1. Defining example data | 2. data.table joining syntax | 3. Equi joins | 3.1. Right join | 3.1.1. Joining by a list argument | 3.1.2. Alternatives to define the on argument | 3.1.3. Operations after joining | Managing shared column Names with the j argument | Summarizing with on in data.table | 3.1.4. Joining based on several columns | 3.2. Inner join | 3.3. Anti-join | 3.4. Semi join | 3.5. Left join | 3.5.1. Joining after chain operations | 3.6. Many to many join | 3.6.1. Selecting one match | 3.6.2. Cross join | 3.7. Full join | 4. Non-equi join | 4.1 Output column names in non-equi joins | 5. Rolling join | 6. Taking advantage of joining speed | 6.1. Subsets as joins | 6.2. Updating by reference | Reference

1. Installation | 2. Reformat R code | 3. The Graphical User Interface | 4. Evaluate the code and mask output in comments | 5. Showcase | Substitute = with <- | Discard blank lines | Reindent code (2 spaces instead of 4) | Start function arguments on a new line | The pipe operators %>% and |> | Move left braces { to new lines | Do not wrap comments | Discard comments | 6. Further notes | Inline comments after an incomplete expression or ; | Inappropriate blank lines | ? with comments | 7. How does tidy_source() actually work? | 8. Global options

R options | Environment variables | Command-line options

Future API Backend Specification | Introduction | Feedback | Overview of the Future API | Requirements for the backend Future API

Introduction | Projected and geographic coordinates | Fundamental differences | Polygons on $S^2$ divide the sphere in two parts | Semi-open polygon boundaries | Bounding cap, bounding rectangle | Switching between S2 and GEOS | Measures | Area | Length | Distances | Predicates | Transformations | Buffers | st_buffer or st_is_within_distance? | References

Introduction | The skim() function | Skimming data frames | Skimming vectors | Skimming matrices | Skimming without modification | Reshaping the results from skim() | Rendering the results of skim() | Customizing print options | Modifying skim() | Extending skimr | Solutions to common rendering problems

Data | Introduction | 1. Keys | a) What is a key? | Keys and their properties | b) Set, get and use keys on a data.table | -- How can we set the column origin as key in the data.table flights? | set* and :=: | -- Use the key column origin to subset all rows where the origin airport matches "JFK" | -- How can we get the column(s) a data.table is keyed by? | c) Keys and multiple columns | -- How can I set keys on both origin and dest columns? | -- Subset all rows using key columns where first key column origin matches "JFK" and second key column dest matches "MIA" | How does the subset work here? | -- Subset all rows where just the first key column origin matches "JFK" | -- Subset all rows where just the second key column dest matches "MIA" | What's happening here? | 2. Combining keys with j and by | a) Select in j | -- Return arr_delay column as a data.table corresponding to origin = "LGA" and dest = "TPA". | b) Chaining | -- On the result obtained above, use chaining to order the column in decreasing order. | c) Compute or do in j | -- Find the maximum arrival delay corresponding to origin = "LGA" and dest = "TPA". | d) sub-assign by reference using := in j | e) Aggregation using by | -- Get the maximum departure delay for each month corresponding to origin = "JFK". Order the result by month | 3. Additional arguments - mult and nomatch | a) The mult argument | -- Subset only the first matching row from all rows where origin matches "JFK" and dest matches "MIA" | -- Subset only the last matching row of all the rows where origin matches "LGA", "JFK", "EWR" and dest matches "XNA" | b) The nomatch argument | -- From the previous example, Subset all rows only if there's a match | 4. binary search vs vector scans | a) Performance of binary search approach | b) Why does keying a data.table result in blazing fast subsets? | Vector scan approach | Binary search approach | Summary

Introduction | Problem description | Example | Approaches to the problem | Avoid lazy evaluation | Use of parse / eval | Computing on the language | Use third party packages | Substituting variables and names | Substitute functions | Substitute variables and character values | Substituting lists of arbitrary length | Substitution of a complex query | Common mistakes | Use env argument from inside another function | Retired interfaces | get | mget | eval

Data | Introduction | 1. Secondary indices | a) What are secondary indices? | Keyed vs. Indexed Subsetting | b) Set and get secondary indices | -- How can we set the column origin as a secondary index in the data.table flights? | -- How can we get all the secondary indices set so far in flights? | c) Why do we need secondary indices? | -- Reordering a data.table can be expensive and not always ideal | setkey() requires: | -- There can be only one key at the most | -- Secondary indices can be reused | -- The new on argument allows for cleaner syntax and automatic creation and reuse of secondary indices | on argument | 2. Fast subsetting using on argument and secondary indices | a) Fast subsets in i | -- Subset all rows where the origin airport matches "JFK" using on | -- How can I subset based on origin and dest columns? | b) Select in j | -- Return arr_delay column alone as a data.table corresponding to origin = "LGA" and dest = "TPA" | c) Chaining | -- On the result obtained above, use chaining to order the column in decreasing order. | d) Compute or do in j | -- Find the maximum arrival delay corresponding to origin = "LGA" and dest = "TPA". | e) sub-assign by reference using := in j | f) Aggregation using by | -- Get the maximum departure delay for each month corresponding to origin = "JFK". Order the result by month | g) The mult argument | -- Subset only the first matching row where dest matches "BOS" and "DAY" | -- Subset only the last matching row where origin matches "LGA", "JFK", "EWR" and dest matches "XNA" | h) The nomatch argument | -- From the previous example, subset all rows only if there's a match | 3. Auto indexing

fread: clear caches | subset: threshold for index optimization on compound queries | subset: index aware benchmarking | by reference operations | try to benchmark atomic processes | avoid class coercion | avoid microbenchmark(..., times=100) | multithreaded processing | inside a loop prefer set instead of := | inside a loop prefer setDT instead of data.table()

Data | Introduction | 1. Default functionality | a) melting data.tables (wide to long) | - Convert DT to long form where each dob is a separate observation. | - Name the variable and value columns to child and dob respectively | b) dcasting data.tables (long to wide) | - How can we get back to the original data table DT from DT.m1? | - Starting from DT.m1, how can we get the number of children in each family? | 2. Limitations in previous melt/dcast approaches | Issues | 3. Enhanced (new) functionality | a) Enhanced melt | - melt multiple columns simultaneously | - Using patterns() | - Using measure() to specify measure.vars via separator or pattern | b) Enhanced dcast | - Casting multiple value.vars simultaneously | Multiple functions to fun.aggregate:

What is .SD? | Loading and Previewing Lahman Data | .SD on Ungrouped Data | Column Subsetting: .SDcols | Column Type Conversion | Controlling a Model's Right-Hand Side | Conditional Joins | Grouped .SD operations | Group Subsetting | Group Optima | Grouped Regression

Summarising sf Data Frames | Selecting Columns and Subsetting | Aggregation and Grouping | Indexing | Unique Values, Ordering, Splitting, Binding | Transformations | Conversion to and from sf | Support for units | Conclusion

Namespace and Global Options | Using the Fast Statistical Functions | Writing Efficient Code | Using Internal Grouping | Conclusion

Overview | General Principles | Specific Functions and Classes | Object Conversions | Selecting Columns by Data Type | Parsing of Time-IDs | xts/zoo Time Series | Support for sf and units | Support for data.table | Class-Agnostic Grouped and Indexed Data Frames | Conclusion

Introduction | Point 1: Be Minimalistic in Computations | Point 2: Think About Memory and Optimize | Point 3: Internally Favor Primitive R Objects and Functions | Some Notes on Global Options | Conclusion

Rule applies to all each cell in range | Highlight row dependent on first cell in row | Highlight column dependent on first cell in column | Highlight cell dependent on | Highlight entire range cols X rows dependent only on cell A1 | Highlight cells in column 1 based on value in column 2 | Highlight duplicates using default style | Cells containing text | Cells not containing text | Cells begins with text | Cells ends with text | Colorscale colors cells based on cell value | Databars | Between | Top N | Bottom N | Logical Operators

Basic read and write functions | Read xlsx or xlsm files | Write xlsx files | Basic workbook functions | Loading a workbook | Styles | Conditional formatting | Data validation | Saving | Why openxlsx2? | Invitation to contribute

Best practice | URL validity

Create a request | Perform a request and fetch the response | Control the request process

Function Overview | Description of Parameters | Formatting, Printing and Plotting | Dimension Reduction and Clustering | Plotting Functions

Preface | Supported data structures | Data: nycflights13 | Data diagnosis | General diagnosis of all variables with diagnose() | Diagnosis of numeric variables with diagnose_numeric() | Diagnosis of categorical variables with diagnose_category() | Diagnosing outliers with diagnose_outlier() | Visualization of outliers using plot_outlier() | Visualization for missing values | visualize pareto chart using plot_na_pareto() | visualize combination chart using plot_na_hclust() | visualize combination chart using plot_na_intersect() | Automated report | Create a diagnostic report using diagnose_web_report() | Contents of dynamic web report | Some arguments for dynamic web report | Screenshot of dynamic report | Create a diagnostic report using diagnose_paged_report() | Contents of static paged report | Some arguments for static paged report | Screenshot of static report | Diagnosing tables in DBMS | Preparing table data | Diagnose data quality of variables in the DBMS | Diagnose data quality of categorical variables in the DBMS | Diagnose data quality of numerical variables in the DBMS | Diagnose outlier of numerical variables in the DBMS | Plot outlier information of numerical data diagnosis in the DBMS | Reporting the information of data diagnosis for table of thr DBMS

Preface | datasets | Imputation of missing values | imputes the missing value with imputate_na() | Collaboration with dplyr | Impute outliers | imputes the outliers with imputate_outlier() | Standardization and Resolving Skewness | Introduction to the use of transform() | Standardization with transform() | Resolving Skewness data with transform() | Binning | Binning of individual variables using binning() | Optimal Binning with binning_by() | Automated report | Create a dynamic report using transformation_web_report() | Contents of dynamic web report | Some arguments for dynamic web report | Screenshot of dynamic report | Create a static report using transformation_paged_report() | Contents of static paged report | Some arguments for static paged report | Screenshot of static report

Preface | Supported data structures | datasets | Univariate data EDA | Calculating descriptive statistics using describe() | Test of normality on numeric variables using normality() | Visualization of normality of numerical variables using plot_normality() | EDA of bivariate data | Calculation of correlation coefficient using correlate() | Visualization of the correlation matrix using plot.correlate() | EDA based on target variable | Definition of target variable | EDA when target variable is categorical variable | Cases where predictors are numeric variable | Cases where predictors are categorical variable | EDA when target variable is numerical variable | Automated report | Create a dynamic report using eda_web_report() | Contents of dynamic web report | Some arguments for dynamic web report | Screenshot of dynamic report | Create a EDA report using eda_paged_report() | Contents of static paged report | Some arguments for static paged report | Screenshot of static report | Exploratory data analysis for tables in DBMS | Preparing table data | Calculating descriptive statistics of numerical column of table in the DBMS | Test of normality on numeric columns using in the DBMS | Normalization visualization of numerical column in the DBMS | Compute the correlation coefficient between two columns of the table in DBMS | Visualize correlation plot of numerical columns in the DBMS | Reporting the information of EDA for table of the DBMS

Overview | Prepare data | Analyse Data | Exploration Plot | Names for service patterns | Visualise services | Plot calendar for each service pattern | Plot number of trips per day as calendar

Read GTFS data | trip_origin and trip_headsign | Create A Departure Time Table | Trips departing from stop | add route info (route_short_name) | Extract a single day | Simple plot

Introduction | Setup | Outline | 1) Import Transit Data (GTFS) | 2) Identify Weekday Schedules of Service | 3) Calculate Headways | 4) Map Headways By Route | 5) Map Departures by Stop and Route

Introduction | Skimming objects that are not coercible to data frames | Defining sfl's for a package | Adding new methods | Conclusion

Lazy vs eager execution | Order of operations | How does polars help? | Use the streaming engine | Use polars functions

Package functions | A note on the tidyverse and other metapackages | Usage in RStudio | Annotate package calls in active file | Annotate package repository sources in active file | Annotate titles and repository sources in active file | Annotate each package's function calls | Annotate each package's datasets | Expand metapackages

Barplots in grey-scaled colors | Lineplots in b/w with different linetypes

Tweaking plot appearance | Using the Color Brewer palettes | Plot with flipped coordinates | Adding plot margins | Theme options | Pre-defined themes | Pre-defined scales | Set up own themes based on existing themes | Further customization options | Plot legend

Performing an item analysis of a scale or index | Index score with one component | Index score with more than one component | Adding further statistics

Fitting a logistic regression model | Plotting estimates of generalized linear models | Sorting estimates | Estimates on the untransformed scale | Showing value labels | Labelling the plot | Pick or remove specific terms from plot | Standardized estimates | Bayesian models (fitted with Stan) | Tweaking plot appearance | References

Marginal effects | Marginal effects for different groups | Marginal effects at specific values or levels | Polynomial terms and splines | Different constant values for factors | Interaction terms

Basic IPUMS aggregate data concepts | Metadata for aggregate data projects | Summary metadata | Detailed metadata | Defining an IPUMS aggregate data extract request | Basic extract definitions | Dataset specifications | Time series table specifications | Shapefile specifications | Invalid specifications | More complicated extract definitions | Data layout and file format | Next steps

IPUMS extract structure | Reading IPUMS microdata extracts | Hierarchical extracts | Reading IPUMS aggregate data extracts | Variable metadata | Handling multiple files | Reading spatial data | Harmonized vs. non-harmonized data

Introduction | Three steps of data documentation | Function templates | Writing a summaryFunction | Writing a visualFunction | Writing a checkFunction | A worked example | summaryFunction examples: countZeros() and meanSummary() | countZeros --- a simple summaryFunction | meanSummary --- an S3 generic summary function | visualFunction examples: mosaicVisual() and prettierHist() | mosaicVisual --- a new visualFunction for categorical data | prettierHist() --- a customized ggplot2 histogram | checkFunction examples: isID() and identifyColons() | isID --- a new checkFunction without problem values | identifyColons --- a new checkFunction with problem values | Calling the new summarize/visualize/check functions from makeDataReport() | A dataMaid report with user-defined functions: Documenting artData

Simple formulas | Array formulas | Array formulas creating multiple fields | cells metadata (cm) formulas | dataTable formulas^[this example was originally provided by @zykezero for openxlsx.] | dataTable formula differences

Before we start | Selections as dots or as named arguments | Do you need tidyselect? | The selection evaluators | Defusing and resuming evaluation of R code | Resuming defused R code with tidyselect rules | Simple selections with dots | Simple selections with named arguments | Renaming selections | Creating selection helpers | Handling duplicate variables

Sets of variables | Bare names | The : operator | Boolean operators | Dots and c() | Renaming variables | Name combination and propagation | Set combination with named variables | Predicate functions | Selection helpers | Supported data types | Evaluation | Data-expressions and env-expressions | Arithmetic operators | Selecting versus renaming | All renaming inputs must be named | Renaming to an existing variable name | Duplicate columns in data frames | Acknowledgements

Multiple SSL Backends | Using a Proxy Server | Discovering Your Proxy Server

Summary | Tidyverse package | Components | Design principles | Acknowledgments | References

Reuse existing data structures | Compose simple functions with the pipe | Embrace functional programming | Design for humans

Get started | Disclaimer | Installation | Setting up API key | Directions | Isochrones | Matrix | Geocoding | POIs | Elevation | Optimization

Formatting with writeData and writeDataTable | Use of pre-defined table styles | Date Formatting | DateTime Formatting | Conditional Formatting | Numeric Formatting

IPUMS variable metadata | Value labels | labelled vs. factor | Cautions regarding labelled variables | Prepping data with value labels | Convert labelled values to other data types | Create missing values based on value labels | Syntax for value label functions | Relabel values | Relabeling caveats | Remove unused value labels | Add new labels | Other resources

How styler works | Implementation details | Showcasing the development of a styling rule | Cache invalidation

Reference implementations | Design patterns

Note | Introduction | Package structure and functionality | Core functions and classes | Accessing and processing transport data | Creating geographic desire lines | Allocating flows to the transport network | Modelling travel catchment areas | Modelling and visualisation | Modelling mode choice | Models of travel behaviour | Visualisation | Future directions of travel | References

Shapefiles | Helper package | Caveat about longitude-latitude coordinates | How to read shapefiles into spatstat

Target network preprocessing

Installation | Windows | MacOS | Linux - Debian / Ubuntu | Driver configuration | Data source configuration | Debugging driver and data source configurations | Setting ODBCSYSINI

What is this EPSG code all about? | Why should we use OGC:CRS84 instead of EPSG:4326? | How does sf deal with secondary geometry columns? | Does st_simplify preserve topology? | Why do my dplyr verbs not work for sf objects?

Entry-points | Passing arguments to the style guide | Invasiveness | scope: What to style? | How strict do you want styler to be? | Ignoring certain lines | Caching | Dry mode | More configuration options | Roxygen code example styling | Custom math token spacing | Custom indention | Custom style guides

Preface | Supported data structures | List of supported tasks of data analytics | Diagnose Data | Overall Diagnose Data | Visualize Missing Values | Reporting | EDA | Univariate EDA | Bivariate EDA | Normality Test | Relationship between target variable and predictors | Transform Data | Find Variables | Imputation | Binning | Diagnose Binned Variable | Transformation | Miscellaneous | Statistics | Programming

Setup | Writing | Reading

Package remotes | GitHub | Other sources | CRAN submission

1 Background: GTFS and other R packages | 2. Routing | 2.1 GTFS Timetables | 2.2. Routing by mode of transport | 2.3. Routing for earliest arrivals or earliest departures | 3. Convenience Functions: go_home() and go_to_work()

Basic Usage | Extending transfer tables | Modifying transfer tables | Transfer distances | Transfer distances and travel times | A more realistic example

Maximum Traveltimes | Fastest Routes versus Minimal-Transfer Routes | The Traveltimes Algorithm

Introduction: what is OD data? | The importance of OD data | An example OD dataset | Origin-destination pairs (long form) | Origin destination matrices | Inter and intra-zonal flows | Oneway lines | Desire lines | Non-matching IDs | A larger example: commuter trips in London | Plotting origin-destination data | Summaries by origin and destination | Further reading | Summary | References

Introduction | Installing stplanr | OD data to desire lines and routes | Converting OD data to desire lines with R | Motivations | Further resources | Contributing | References

Introduction | Creating route networks from overlapping routes | Identifying route network groups | Routing on route networks | Adding new nodes | Other approaches

Motivation: why tabyl? | How it works | Examples | One-way tabyl | Two-way tabyl | Three-way tabyl | Other features of tabyls | The adorn_* functions | The adorn functions are: | BYOt (Bring Your Own tabyl) | Questions? Comments?

Major functions | Cleaning | Clean data.frame names with clean_names() | Do those data.frames actually contain the same columns? | Check with compare_df_cols() | Exploring | tabyl() - a better version of table() | Explore records with duplicated values for specific combinations of variables with get_dupes() | Explore relationships between columns with get_one_to_one() | Minor functions | Manipulate vectors of names with make_clean_names() | Validate that a column has a single_value() per group | remove_empty() rows and columns | remove_constant() columns | Directionally-consistent rounding behavior with round_half_up() | Round decimals to precise fractions of a given denominator with round_to_fraction() | Fix dates stored as serial numbers with excel_numeric_to_date() | Convert a mix of date and datetime formats to date | Elevate column names stored in a data.frame row | Find the header row buried within a messy data.frame | Count factor levels in groups of high, medium, and low with top_levels()

Overview | Examples | Details | Function calls | Comments | Assignment

Theory | Practice | Some other rules and their transformers

Bayesian models summaries as HTML table | Multivariate response models | Show two Credible Interval-column | Mixing multivariate and univariate response models

Two-Way-Interactions | Three-Way-Interactions | References

Example plots | Basic use | Controlling layout | Stacking and packing plots | Annotating the composition | Want more?

Validating Data | Format Issues | External Spatial Data | sp Data | Data From tidycensus and tigris | Tabular Data | Coordinate Systems | Variable Conflicts | Subsetting

Motivation | Getting Started | Installation | Functions | Data | Preparing Data | Areal Weighted Interpolation | Getting Help | Suggesting Features or Changes

Classical Regression Models | Robust Covariance Matrix Estimation from Model Parameters | Cluster-Robust Covariance Matrix Estimation (sandwich) | Cluster-Robust Covariance Matrix Estimation (clubSandwich) | Robust Covariance Matrix Estimation on Standardized Model Parameters | Mixed Models | Robust Covariance Matrix Estimation for Mixed Models | Robust Covariance Matrix Estimation on Standardized Mixed Model Parameters

Introduction | Why Should I Use stargazer? | Citing stargazer in Research Publications

A bidirectional mapping | Paging with jsonlite | Automatically combining many pages

Github | CitiBike NYC | Ergast | ProPublica | New York Times | Twitter

Use esquisse as a Shiny module | Module for saving a ggplot object | Module to render a plot and add export options | Input widgets | dragulaInput | dropInput | colorPicker | palettePicker

Launch the addin | Import data into | Create a plot | Controls | Labels & titles | Plot options | Appearance | Filter | Code | Export | Addin options | Internationalization

Introduction | Three steps of data documentation | Function templates | Writing a summaryFunction | Writing a visualFunction | Writing a checkFunction | A worked example | summaryFunction examples: countZeros() and meanSummary() | countZeros --- a simple summaryFunction | meanSummary --- an S3 generic summary function | visualFunction examples: mosaicVisual() and prettierHist() | mosaicVisual --- a new visualFunction for categorical data | prettierHist() --- a customized ggplot2 histogram | checkFunction examples: isID() and identifyColons() | isID --- a new checkFunction without problem values | identifyColons --- a new checkFunction with problem values | Calling the new summarize/visualize/check functions from makeDataReport() | A dataReporter report with user-defined functions: Documenting artData

Introduction | OSRM

A simple HTML table from regression results | Automatic labelling | Turn off automatic labelling | More than one model | Generalized linear models | Untransformed estimates on the linear scale | More complex models | Show or hide further columns | Adding columns | Removing columns | Removing and sorting columns | Collapsing columns | Defining own labels | Including reference level of categorical predictors | Style of p-values | Automatic matching for named vectors | Keep or remove coefficients from the table

Copying table output to office or word processors | Export table as HTML file to open in word processors | Drag and drop from browser or RStudio viewer pane | Customizing table output with the CSS parameter | Retrieving customizable styles | Pre-defined Table-Layouts

With old route_cyclestreets function | With new route function | With new route function in parallel | In parallel with quietness plan | Tests

Mixed models summaries as HTML table | Generalized linear mixed models | More complex models | References

Typical Usage with Rstudio | Pasting a table as a formatted tibble definition with tribble_paste() | Pasting a list as a horizontal vector with vector_paste() | Pasting a list as a vertical vector with vector_paste_vertical() | Outputting data from your R environment | Output to R with dpasta() | Avoiding fiddly data formatting | Fiddle Selections until they're better | Toggle Quotes | Output to clipboard with dmdclip() | Usage without RStudio | Custom Behaviour for Your Unique Snowflake Setup | Configurable Options | Upping the row guard | Dealing with "," decimal marks

Fallback 1: Text selection | Fallback 2: Pop-up text editor | Configuration

Introduction | The base skimmers | Default skimmers

Introduction

Introduction to Areal Weighted Interpolation | Step 1: Intersection | Step 2: Areal Weights | Step 3: Estimate Population | Step 4: Summarize Data | Extensive and Intensive Interpolations | Extensive Interpolations | Calculating Weights for Extensive Interpolations | Weights Example 1: Non-Overlap Due to Data Quality | Weights Example 2: Non-Overlap Due to Differing Boundaries | Intensive Interpolations | Mixed Interpolations | Output Options | Other Features of aw_interpolate | Manual Workflow | Intersect Data | Calculate Total Area | Calculate Areal Weight | Calculate Estimated Population | Aggregate Estimated Population by Target ID

Constructing a gtable | Components of a gtable | Modifying a gtable | Examples to alter ggplot2 plots with gtable

Basic usage | Spacing | Aesthetic formatting | Text justification | Further gtable processing and integration | Borders and separators | Accessing existing grobs in the table | Faster tables: an alternative grid function

Simplification | Atomic Vectors | Data Frames | Matrices and Arrays

Basic usage | Rotated and stretched polygons | Ellipses

Basic usage | Title and/or annotations | Complex layouts | Nested layouts with arrangeGrob | Multiple pages output