Tag Archives: Reproducible Research

Statistical Software and Data Workshops, Spring 2018

New Brunswick Libraries Data Workshop Series

Spring 2018

This Spring, Ryan Womack, Data Librarian, will repeat the series of workshops on statistical software and data visualization as part of New Brunswick Libraries Data Management Services.   A detailed calendar and descriptions of each workshop are below.  The workshop on reproducible research is moving online to YouTube – stay tuned for an upcoming blog post and announcement on its availability.

This semester each workshop topic will be repeated twice, once at the Library of Science and Medicine on Busch Campus, and once at Alexander Library on College Ave.  These sessions will be identical except for location. Sessions will run approximately 3 hours.  Workshops in parts will divide the time in thirds.  For example, the first SPSS, Stata, and SAS workshop (running from 12-3 pm) would start with SPSS at 12 pm, Stata at 1 pm, and SAS at 2 pm.  You are free to come only to those segments that interest you.  There is no need to register, just come!

Logistics

Location: The Library of Science and Medicine (LSM on Busch) workshops will be held in the Conference Room on the 1st floor of LSM on Mondays from 12 to 3 pm.  The Alexander Library (College Ave) workshops will be held in room 413 of the Scholarly Communication Center (4th floor of Alexander Library) from on Tuesdays from 1:10 to 4:10 pm.

For both locations, you are encouraged to bring your own laptop to work in your native environment.  Alternatively, at Alexander Library, you can use a library desktop computer instead of your own laptop.  At LSM, we will have laptops available to borrow for the session if you don’t bring your own.  Room capacity is 25 in both locations, first come, first served.

If you can’t make the workshops, or would like a preview or refresher, screencast versions of many of the presentations are already available at http://libguides.rutgers.edu/data and https://youtube.com/librarianwomack. Additional screencasts are continually being added to this series.  Note that the “special topics” [Time Series, Survival Analysis, and Big Data] are no longer offered in person, but are available via screencast.

Calendar of workshops

Monday (LSM)

12 noon – 3 pm

  Tuesday (Alexander)

1:10 pm -4:10 pm 

January 29 Introduction to SPSS, Stata, and SAS January 30
February 5 Introduction to R February 6
February 12 Data Visualization in R February 13

Description of Workshops:

§ Introduction to SPSS, Stata, and SAS (January 29 or January 30) provides overviews of these three popular commercial statistical software programs, covering the basics of navigation, loading data, graphics, and elementary descriptive statistics and regression using a sample dataset.  If you are already using these packages with some degree of success, you may find these sessions too basic for you.

  • SPSS is widely used statistical software with strengths in survey analysis and other social science disciplines.  Copies of the workshop materials, a screencast, and additional SPSS resources can be found here: http://libguides.rutgers.edu/content.php?pid=115296&sid=1208425. SPSS is made available by OIRT at a discounted academic rate, currently $100/academic year.  Find it at software.rutgers.edu.  SPSS is also available in campus computer labs and via the Apps server (see below).
  • Stata is flexible and allows relatively easy access to programming features.  It is popular in economics among other areas.  Copies of the workshop materials, a screencast, and additional Stata resources can be found here: http://libguides.rutgers.edu/content.php?pid=115296&sid=1208427. Stata is made available by OIRT via campus license with no additional charge to install for Rutgers users.  Find it at software.rutgers.edu.
  • SAS is a powerful and long-standing system that handles large data sets well, and is popular in the pharmaceutical industry and health sciences, among other applications. Copies of the workshop materials, a screencast, and additional SAS resources can be found here: http://libguides.rutgers.edu/content.php?pid=115296&sid=1208423. SAS is made available by OIRT at a discounted academic rate, currently $100/academic year.  Find it at software.rutgers.edu.  SAS is also available in campus computer labs, online via the SAS University Edition cloud service, and via the Apps server (see below).

Note: Accessing software via apps.rutgers.edu

SPSS, SAS, Stata, and R are available for remote access on apps.rutgers.eduapps.rutgers.edu does not require any software installation, but you must activate the service first at netid.rutgers.edu.

§ Introduction to R (February 5 or February 6) – This session provides a three-part orientation to the R programming environment.  R is freely available, open source statistical software that has been widely adopted in the research community.  Due to its open nature, thousands of additional packages have been created by contributors to implement the latest statistical techniques, making R a very powerful tool.  No prior knowledge is assumed. The three parts cover:

  • Statistical Techniques: getting around in R, descriptive statistics, regression, significance tests, working with packages
  • Graphics:  comparison of graphing techniques in base R, lattice, and ggplot2 packages
  • Data Manipulation:  data import and transformation, additional methods for working with large data sets, also dplyr and other packages from the tidyverse useful for manipulation.

Additional R resources, including handouts, scripts, and screencast versions of the workshops, can be found here: http://libguides.rutgers.edu/data_R

R is freely downloadable from http://r-project.org

§ Data Visualization in R  (February 12 or February 13) discusses principles for effective data visualization, and demonstrates techniques for implementing these using R.  Some prior familiarity with R is assumed (packages, structure, syntax), but the presentation can be followed without this background.  The three parts are:

  • Principles & Use in lattice and ggplot2: discusses classic principles of data visualization (Tufte, Cleveland) and illustrates them with the use of the lattice and ggplot2 packages.  Some of the material here overlaps with Intro to R, pt 2, but at a higher level.
  • Miscellany of Methods: illustrates a wide range of specific graphics for different contexts
  • 3-D, Interactive, and Big Data: presentation of 3-D data, interactive exploration data, and techniques for large datasets. Relevant packages such as shiny and tessera are explored.

Additional R resources can be found here: http://libguides.rutgers.edu/data_R

R is freely downloadable from http://r-project.org

pyramid

 § Special Topics

Note that the following special topics are no longer covered by in-person workshops, but are available via screencast.

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Statistical Software and Data Workshops, Fall 2017

New Brunswick Libraries Data Workshop Series

Fall 2017

This Fall, Ryan Womack, Data Librarian, will offer a series of workshops on statistical software, data visualization, and reproducible research as part of New Brunswick Libraries Data Management Services.   A detailed calendar and descriptions of each workshop are below.  This semester each workshop topic will be repeated twice, once at the Library of Science and Medicine on Busch Campus, and once at Alexander Library on College Ave.  These sessions will be identical except for location. Sessions will run approximately 3 hours.  Workshops in parts will divide the time in thirds.  For example, the first SPSS, Stata, and SAS workshop (running from 12-3 pm) would start with SPSS at 12 pm, Stata at 1 pm, and SAS at 2 pm.  You are free to come only to those segments that interest you.  There is no need to register, just come!

Logistics

Location: The Library of Science and Medicine (LSM on Busch) workshops will be held in the Conference Room on the 1st floor of LSM on Wednesdays from 12 to 3 pm.  The Alexander Library (College Ave) workshops will be held in room 413 of the Scholarly Communication Center (4th floor of Alexander Library) from on Tuesdays from 1:10 to 4:10 pm.

For both locations, you are encouraged to bring your own laptop to work in your native environment.  Alternatively, at Alexander Library, you can use a library desktop computer instead of your own laptop.  At LSM, we will have laptops available to borrow for the session if you don’t bring your own.  Room capacity is 25 in both locations, first come, first served.

If you can’t make the workshops, or would like a preview or refresher, screencast versions of many of the presentations are already available at http://libguides.rutgers.edu/data and https://youtube.com/librarianwomack. Additional screencasts are continually being added to this series.  Note that the “special topics” [Time Series, Survival Analysis, and Big Data] are no longer offered in person, but are available via screencast.

Calendar of workshops

Tuesday (Alexander)

1:10 pm -4:10 pm

   Wednesday (LSM)

12 noon – 3 pm

September 12 Introduction to SPSS, Stata, and SAS September 13
September 19 Introduction to R September 20
September 26 Data Visualization in R September 27
October 3 Reproducible Research October 18

Description of Workshops:

§ Introduction to SPSS, Stata, and SAS (September 12 or September 13) provides overviews of these three popular commercial statistical software programs, covering the basics of navigation, loading data, graphics, and elementary descriptive statistics and regression using a sample dataset.  If you are already using these packages with some degree of success, you may find these sessions too basic for you.

  • SPSS is widely used statistical software with strengths in survey analysis and other social science disciplines.  Copies of the workshop materials, a screencast, and additional SPSS resources can be found here: http://libguides.rutgers.edu/content.php?pid=115296&sid=1208425. SPSS is made available by OIRT at a discounted academic rate, currently $100/academic year.  Find it at software.rutgers.edu.  SPSS is also available in campus computer labs and via the Apps server (see below).
  • Stata is flexible and allows relatively easy access to programming features.  It is popular in economics among other areas.  Copies of the workshop materials, a screencast, and additional Stata resources can be found here: http://libguides.rutgers.edu/content.php?pid=115296&sid=1208427. Stata is made available by OIRT via campus license with no additional charge to install for Rutgers users.  Find it at software.rutgers.edu.
  • SAS is a powerful and long-standing system that handles large data sets well, and is popular in the pharmaceutical industry and health sciences, among other applications. Copies of the workshop materials, a screencast, and additional SAS resources can be found here: http://libguides.rutgers.edu/content.php?pid=115296&sid=1208423. SAS is made available by OIRT at a discounted academic rate, currently $100/academic year.  Find it at software.rutgers.edu.  SAS is also available in campus computer labs, online via the SAS University Edition cloud service, and via the Apps server (see below).

Note: Accessing software via apps.rutgers.edu

SPSS, SAS, Stata, and R are available for remote access on apps.rutgers.eduapps.rutgers.edu does not require any software installation, but you must activate the service first at netid.rutgers.edu.

 

§ Introduction to R (September 19 or September 20) – This session provides a three-part orientation to the R programming environment.  R is freely available, open source statistical software that has been widely adopted in the research community.  Due to its open nature, thousands of additional packages have been created by contributors to implement the latest statistical techniques, making R a very powerful tool.  No prior knowledge is assumed. The three parts cover:

  • Statistical Techniques: getting around in R, descriptive statistics, regression, significance tests, working with packages
  • Graphics:  comparison of graphing techniques in base R, lattice, and ggplot2 packages
  • Data Manipulation:  data import and transformation, additional methods for working with large data sets, also dplyr and other packages from the tidyverse useful for manipulation.

Additional R resources, including handouts, scripts, and screencast versions of the workshops, can be found here: http://libguides.rutgers.edu/data_R

R is freely downloadable from http://r-project.org

 

§ Data Visualization in R  (September 26 or September 27) discusses principles for effective data visualization, and demonstrates techniques for implementing these using R.  Some prior familiarity with R is assumed (packages, structure, syntax), but the presentation can be followed without this background.  The three parts are:

  • Principles & Use in lattice and ggplot2: discusses classic principles of data visualization (Tufte, Cleveland) and illustrates them with the use of the lattice and ggplot2 packages.  Some of the material here overlaps with Intro to R, pt 2, but at a higher level.
  • Miscellany of Methods: illustrates a wide range of specific graphics for different contexts
  • 3-D, Interactive, and Big Data: presentation of 3-D data, interactive exploration data, and techniques for large datasets. Relevant packages such as shiny and tessera are explored.

Additional R resources can be found here: http://libguides.rutgers.edu/data_R

R is freely downloadable from http://r-project.org

pyramid

 

§ Reproducible Research (October 3 or October 18) covers

  • Reproducible research describes the growing movement to make the products of research accessible and usable by others in order to verify, replicate, and extend research findings.  This session reviews how to plan research, to create publications, code, and data in open, reusable formats, and maximize the impact of shared research findings.  Examples in LaTeX and Rmarkdown are discussed, along with platforms for reusability such as the Open Science Foundation.

Additional resources on reproducible research and data management, including presentation slides, can be found here: http://libguides.rutgers.edu/datamanagement

 

§ Special Topics

Note that the following special topics are no longer covered by in-person workshops, but are available via screencast.

Spring 2016 Data Management Workshops

This semester, the Libraries will offer a workshop covering:

  • Best Practices for Managing Your Data
  • Data Management Plans, Data Sharing and Archiving
  • Reproducible Research

The workshop will repeat in two locations on:

  • Monday, March 7, 12-1:30 pm in the Library of Science and Medicine Conference Room (1st Floor)
  • Tuesday, March 8, 1:10 to 2:40 pm in Alexander Library Teleconference Lecture Hall (4th floor)

The two sessions are identical – no need to come to both.

The first part of the session will focus on Best Practices for Managing Your Data. 

  • We discuss methods to organize, describe, backup, and archive your research data in order to ensure its future usability and accessibility.  Developing good habits for handling your data from the start will save time and frustration later, and increase the ultimate impact of your research.

The second part covers Data Management Plans, Data Sharing and Archiving.

  • This portion is targeted to researchers who need to write data management plans (DMPs) and share their data as part of their grant application, research and publication process.  It reviews DMP guidelines, checklist, and general advice, along with options for sharing and permanently archiving research data.

The third part discusses Reproducible Research.

  • We cover the growing movement to make the products of research accessible and usable by others in order to verify, replicate, and extend research findings.  We review how to plan research, to create publications, code, and data in open, reusable formats, and maximize the impact of shared research findings.

No need to register, just come for what you are interested in.

Additional data management resources, including presentation slides, can be found here: http://libguides.rutgers.edu/datamanagement

Fall 2015 Data Management Workshops

This semester, the Libraries will offer a workshop covering:

  • Best Practices for Managing Your Data
  • Data Management Plans, Data Sharing and Archiving
  • Reproducible Research

The workshop will repeat in two locations on:

  • Monday, October 19, 12-3 pm in the Library of Science and Medicine Conference Room (1st Floor)
  • Thursday, October 22, 1:10 to 4:10 pm in Alexander Library Room 415

The two sessions are identical – no need to come to both.

The first hour of the session will focus on Best Practices for Managing Your Data. 

  • We discuss methods to organize, describe, backup, and archive your research data in order to ensure its future usability and accessibility.  Developing good habits for handling your data from the start will save time and frustration later, and increase the ultimate impact of your research.

The second hour covers Data Management Plans, Data Sharing and Archiving.

  • This portion is targeted to researchers who need to write data management plans (DMPs) and share their data as part of their grant application, research and publication process.  It reviews DMP guidelines, checklist, and general advice, along with options for sharing and permanently archiving research data.

The third hour discusses Reproducible Research.

  • We cover the growing movement to make the products of research accessible and usable by others in order to verify, replicate, and extend research findings.  We review how to plan research, to create publications, code, and data in open, reusable formats, and maximize the impact of shared research findings.

No need to register, just come for portions you are interested in.

Additional data management resources, including presentation slides, can be found here: http://libguides.rutgers.edu/datamanagement

Reproducibility Events from Center for Open Science on Monday, Feb 9

Courtney Soderberg of the Center for Open Science will be visiting Rutgers on Monday, February 9th to present two workshops on techniques to enhance reproducibility and transparency in research.  See below details and registration.

Practical Steps for increasing openness and reproducibility in scientific research

Want to be ahead of the curve of changing incentives and mandates from funders and journals about transparent and open research? Join us for a workshop on reproducible research, hosted by the Center for Open Science (http://centerforopenscience.org). Learn about factors that contribute to low levels of reproducibility, and easy, practical steps researchers can take to increase the reproducibility of their work. Using hands-on examples, attendees will actively participate in creating a reproducible project from start to finish, using open source tools like the Center for Open Science’s Open Science Framework (https://osf.io/), and learn about ways to implement these new skills in their own projects.

Date: Monday, February 9th

Time: 9:30am – 11:30am

Location: Alexander Library, Room 413, 169 College Ave, New Brunswick

Please RVSP as space is limited, using the link below
https://docs.google.com/a/cos.io/forms/d/1wXC494Sj8nvvPtIAaHHgK2YYm44LoqK2Xfp0dB-Bk3k/edit

Using R to create reproducible code

Recently, there has been a growing call from journals and funders for scientists to make their research findings more reproducible. An important part of this is creating reproducible analysis scripts and papers. Join us for a workshop on reproducible coding, hosted by the Center for Open Science (http://centerforopenscience.org). This workshop will discuss how R can be used to meet these goals. The workshop will go over good coding practices as well teach the basics of tools like R Markdown and KnitR that can be used to create reproducible documents. Some background in R is suggested.

Date: Monday, February 9th

Time: 2pm – 3:30am

Location: Alexander Library, Room 413, 169 College Ave, New Brunswick

Please RVSP as space is limited, using the link below
https://docs.google.com/forms/d/15LmwNDx0_r1FImSx4WVPg_-ziuoMqybXPx5cT5lWk1U/viewform?usp=send_form

Statistical Software and Data Workshops – Spring 2015

Rutgers University Libraries Data Services Workshop Series (New Brunswick)

January 2015

This Spring, Ryan Womack, Data Librarian, will give a series of workshops on statistical software, data visualization, and data management, as part of the Rutgers University Libraries Data Services.  To go directly to the registration page, click here.  A detailed calendar and descriptions of each workshop are below.

Logistics

All workshops for Spring 2015 will be held in the Conference Room on the 1st floor of the Library of Science and Medicine (Busch Campus).  Workshops are held on Wednesday afternoons from 3:20 to 4:40 pm or Thursday afternoons from 1:40 to 3:00 pm.  The Wednesday series covers many aspects of the R open source statistical software environment.  The early Thursday sessions are introductions to commerical statisical software  (SPSS, Stata, SAS).  Later in the semester, the Thursday sessions will cover several aspects of research data management.

You are encouraged to bring your own laptop for these sessions.  Laptops are also available for borrowing during the workshops.  Room capacity is approximately 25.  SPSS, Stata, and SAS sessions will use the apps.rutgers.edu remote system.

If you can’t make the workshops, or would like a preview or refresher, screencast versions of many of the presentations are already available at http://libguides.rutgers.edu/data.  Additional screencasts are continually being added to this series.

Calendar of workshops

Wednesday   Thursday
Jan 28 Intro to R, part I, Statistical Functions Intro to SPSS Jan 29
Feb 4 Intro to R, part II, Graphics Intro to Stata Feb 5
Feb 11 Intro to R, part III, Data Manipulation Intro to SAS Feb 12
Feb 18 Data Visualization, part I, Principles & Use in lattice and ggplot2
Feb 25 Data Visualization, part II, Miscellany of Methods Best Practices for Managing your Research Data Feb 26
March 4 Data Visualization, part III, 3-D, Interactive and Big Data Data Management Plans, Data Sharing and Archiving March 5
March 11 Survival Analysis in R Reproducible Research  March 12
March 25 Time Series in R

 Register for the workshops here

Description of Workshops:

§ Introduction to R (Jan 28, Feb 4, and Feb 11) – This 3-part series provides an orientation to the R programming environment.  R is freely available, open source statistical software that has been widely adopted in the research community.  Due to its open nature, thousands of additional packages have been created by contributors to implement the latest statistical techniques, making R a very powerful tool.  No prior knowledge is assumed. The three parts cover:

(Jan 28) Part I – Statistical Techniques: getting around in R, descriptive statistics, regression, significance tests, working with packages

(Feb 4) Part II – Graphics:  comparison of graphing techniques in base R, lattice, and ggplot2 packages

(Feb 11) Part III – Data Manipulation:  data import and transformation, additional methods for working with large data sets

Additional R resources, including handouts, scripts, and screencast versions of the workshops, can be found here: http://libguides.rutgers.edu/data_R

R is freely downloadable from http://r-project.org

§ Introduction to SPSS (Jan 29) provides a single session overview of navigating the basics of SPSS.  SPSS is widely used statistical software with strengths in survey analysis and other social science disciplines.  If you are already using SPSS with some degree of success, this session may be too basic for you.

Copies of the workshop materials, a screencast, and additional SPSS resources can be found here: http://libguides.rutgers.edu/content.php?pid=115296&sid=1208425

SPSS is made available by OIRT at a discounted academic rate, currently $100/academic year.  Find it at software.rutgers.edu.  SPSS is also available in campus computer labs and via the Apps server (see below).

§ Introduction to Stata (Feb 5) provides a single session overview of navigating the basics of Stata.  Stata is flexible and allows relatively easy access to programming features.  It is popular in economics among other areas. If you are already using Stata with some degree of success, this session may be too basic for you.

Copies of the workshop materials, a screencast, and additional Stata resources can be found here: http://libguides.rutgers.edu/content.php?pid=115296&sid=1208427

Stata is made available by OIRT via campus license with no additional charge to install for Rutgers users.  Find it at software.rutgers.edu.

§ Introduction to SAS (Feb 12) provides a single session overview of navigating the basics of SAS.  SAS is a powerful and long-standing system that handles large data sets well, and is popular in the pharmaceutical industry, among other applications. If you are already using SAS with some degree of success, this session may be too basic for you.

Copies of the workshop materials, a screencast, and additional SAS resources can be found here: http://libguides.rutgers.edu/content.php?pid=115296&sid=1208423

SAS is made available by OIRT at a discounted academic rate, currently $100/academic year.  Find it at software.rutgers.edu.  SAS is also available in campus computer labs, online via the SAS University Edition cloud service, and via the Apps server (see below).
 

Note: Accessing software via apps.rutgers.edu

SPSS, SAS, Stata, and R are available for remote access on apps.rutgers.eduapps.rutgers.edu does not require any software installation, but you must activate the service first at netid.rutgers.edu.

On Wednesdays, the R series will continue, including:

§ Data Visualization in R  in 3 parts (basics, more methods, interactive & big data)

§ Time Series in R 

§ Survival Analysis in R 

On Thursdays, other topics in Data Management will be addressed, including:

§ Data Management Best Practices 

§ Data Management Plans, Data Sharing and Archiving

§ Reproducible Research

Additional data management resources can be found here: http://libguides.rutgers.edu/datamanagement

Logistics, again

To repeat, All workshops for Spring 2015 will be held in the Conference Room on the 1st floor of the Library of Science and Medicine (Busch Campus) on Wednesday afternoons (starting at 3:20) and Thursday afternoons (starting at 1:40).  Bring your own laptop if you can, although there will be laptops available to borrow.

 Register for the workshops here