Duration 21:38
16+
Play
Video

Publication Ready Summary Tables with the {gtsummary} Package (Daniel Sjoberg, Karissa Whiting)

Daniel Sjoberg
Research Biostatistician at Memorial Sloan Kettering Cancer Center
+ 1 speaker
  • Video
  • Table of contents
  • Video
R/Medicine 2020
August 28, 2020, Online, USA
R/Medicine 2020
Request Q&A
Video
Publication Ready Summary Tables with the {gtsummary} Package (Daniel Sjoberg, Karissa Whiting)
Available
In cart
Free
Free
Free
Free
Free
Free
Free
Free
Add to favorites
2.28 K
I like 0
I dislike 0
Available
In cart
Free
Free
Free
Free
Free
Free
Free
Free
  • Description
  • Transcript
  • Discussion

About speakers

Daniel Sjoberg
Research Biostatistician at Memorial Sloan Kettering Cancer Center
Karissa Whiting
Research Biostatistician at Memorial Sloan Kettering Cancer Center

About the talk

This video is part of the R/Medicine 2020 Virtual Conference.

Share

And I'm very, very happy to introduce Samuel. Spielberg been through it. So I think we're going to be talking to us about the awesome GT summary package, taken away, guys. Oh, you never never mind. This is going to be up for you before you talk to me. You're going to be in the background listening at your questions. And I wasn't talking about this over the last few decades, and then being able to integrate like code. Along with the report has been incredibly valuable that

nobody wants to Bridge and that is A summary was 212 to make the output look exactly when it's ready for publication and three most frequent table. One is a description of your cohorts, to summarize. Regression models, trait cost, hydrations and summarize survival, they do make these resulting tables. Very easy to work with. It's not infrequent that. I need to regression model side-by-side so it's easy to convert any to Yuki Sandra table. What other Gatherings that bridge when the package is that, once you created your beautiful table,

when you're writing a report, if you're talking about the odds ratios that you have estimated the pocket of the flexibility, we also need to do some things. Now things are coming up and you can around once and it will change the default for all of your summary tables. You can send a theme that says, oh I'm going to be publishing, let me use the jemicy. And now all of your results will follow the JAMA recording guide. Life summary is our primary function that summarizes Deus Ex So, this is the day that we're going

to be using that as an example is called trial, but I'm making a small version of it. So that's SM trial. It only has four columns. And each of these columns has been labeled a package. Get started with the most basic summary. We are taking our data set, SM trial and we're passing it to the TV show summary function and were using it. So what is it takes every column in your date? Is that So when you pass a dataframe to tvl summary, is going to do a lot of inspection of your data to find out what the best people should be

right here. That's definitely a continuous variable and it's going to be presenting the median in the IQR for you. It's been an ex looking great day, okay, three unique levels, definitely, that is a categorical variable, let me forget that that way and then lastly or false? Yes or no. And it's going to automatically assume that an economist life and we're only going to present the yes or true or one or both of us is true or false. The nursing portion of tumors that responded on a single line at her age. We are showing the

results to the nearest integer when TV on Summer. Is a continuous variable searching based off of data in this example. So I'm going to record the mean and standard deviation in parentheses. So what I'm doing here is using the statistic argument and I'm selecting all continuous variables and I'm telling you, I want the meaning of Santa TV addition. So, this string that I'm passing right here as mean, and curly brackets, that has a set of parentheses sitting in the curly brackets

is going to be evaluated just like it would be in a glue Simplex type, where is taking within the curly brackets and it's it's going to have In this case, it's doing to fix. It's looking for the mean function and saying, oh, I'm going to take that injector of age when I can factor of continuous variable. And I'm going to execute the new phone, also the SD function later. And I'm going to put the results in the format indicated that the strip. So, this is a very concise way to record. So, here's a quick schematic that shows what parts of the tables. Each of those

arguments are modified. So here in Orange, change the age from the digits argument change from the default 0, decimal places for a grade, the legal arguments in Chains. Throughout the GT summary package, we use a special formula notation for selecting variables and telling it what we want those variables. So here's a quick example of how you can you can use the bear named age. You can put the names in a vector see you can use to diesel starts with and do a couple of internal functions Within

Start the top. This is the simplest form, you can just stay here. I'm saying and I'm saying here to display it to the nearest integer or tequila and for this I can change the right side. Earlier as well. So, it's quite flexible or summaries for anything that you might need each of those arguments. So, there's an ad Family, add add an additional. So I P value. Pellet review, an example, using VIP and a few of these other phone. Here's a schematic showing how to add a

header over the treatment, A, and B conversation at the bottom in ink. Modify news to update the standard footnote that is show. Orange, Justice purple, the labels for a blueberry and there's a Code example. Like you give a x out to clipping their talk to us about models with the TV. Show me what you can do on your knees. I already have a package package and we're interested in. So we're probably interested in. I'm here at the basic cable and the very basic cable.

Interested in customizing music. Example of the old Fashions, like, fold labels, bulky play calculate level specific. Schematics. Addition to the table and I'm passing knows this stuff by which of those is there outside. I just want to talk with me about this really helpful function in my text. So this with any sort of objects So for example, if I want to report to our and then when I did it and this is really nice. I'm just very briefly going to talk about these two functions table emergency. And these are just bumped. His little light, Vine results from any of

the other cops will you be regressing people. If I use the stable marriage function, I can go ahead and say Similarly tables. Just stopped. You showed how to customize individual elements is stable and then you can easily see the prosti reporteri their functions. Do for example, dancing inside that with the additional options and we already have a couple of things. I'm ready to use but it's also very easy. I just to go over a couple of the currently available.

Seems we have a couple cereal seems, and these are great because they already have a lot of settings on built-ins. Give you the exact specifics for medical needs. Additionally, we have supper. And then we have already seen still the same contact Just Energy mentioned before. It's really easy grader. Crazy thing where I read my rainbow back to Dan, who's going to talk a little bit more about how we'd like to finish my talking a little bit before Max and printed and see that are available within GT summary. Obviously, the package is optimized to use the GT package

as your primary printer with HTML output, has a fantastic engine or under construction. You may find yourself needing something else. For example, I often use a Plex table, when I need word out to use any of these print engines, you simply take any GT summary object and you type it. Read into Sgt more as flexible, for example, and what will happen, is it a series of 4matic functions? Within each of those packages will be applied to your GT summary of. The result is it will no longer

allows you to have a lump of stone. If you already know a family of four main functions and know it, well, it's easy to just stick with that and what you already know. Leslie, just thank you all for taking the time to listen to us. Talk about our package, and the many people Sloan-Kettering who have tested. The package of the last year has been our pleasure to be here with you. Thank you. Thank you all very much for the presentation. That was that was fantastic and there's I see

there's a quite a few quite a few questions. The first one that has the most responses. It's not a question just want to say thank you for this awesome package. Next runner-up is how difficult it is to change. The format of the output presentation. For example, I mean put mean median and IQ are in a different Row for a continuous variable. So, if you put them on separate actual rose in the table, the moment, a text in open, pull request, there are a little bit of work around. If using the flex table output, you can use

that escaped and to do a line break, within a cell to get it on separate roses. Well, Okay, great. I think I can sneak you in another question. In terms of adding statistics with GT summary, is it possible to do post-hoc analysis. So there is a very general function call, Dad staff, that you can add literally any statistic that you want to see bill summary object. So in that sense, yes, you can add almost anything you want, and we try to create Consciousness to do the most common stock. Okay, great. Looks like we're out of time. And should probably move to the

next session. Thank you guys very much for your talk. I think that was fantastic. Thank you. Timing.

Cackle comments for the website

Buy this talk

Access to the talk “Publication Ready Summary Tables with the {gtsummary} Package (Daniel Sjoberg, Karissa Whiting)”
Available
In cart
Free
Free
Free
Free
Free
Free
Free
Free

Ticket

Get access to all videos “R/Medicine 2020”
Available
In cart
Free
Free
Free
Free
Free
Free
Free
Free
Ticket

Interested in topic “Medicine, Health and MedTech”?

You might be interested in videos from this event

August 18 - 20, 2020
Online
6
35
bud, compliance, covid-19, hospital pharmacies, pharmaceutical compounding, preparation, science, stability testing

Similar talks

Michael Kane
Machine Learning and Biomedicine at Presagia Inc
Available
In cart
Free
Free
Free
Free
Free
Free
Free
Free
Trang Le
Postdoctoral fellow at University of Pennsylvania
+ 1 speaker
Jason Moore
Director at Penn Institute for Biomedical Informatics
+ 1 speaker
Available
In cart
Free
Free
Free
Free
Free
Free
Free
Free
Maya Gans
R and JavaScript developer at Atorus
+ 1 speaker
Marly Gotti
Senior Data Scientist at Biogen
+ 1 speaker
Available
In cart
Free
Free
Free
Free
Free
Free
Free
Free

Buy this video

Video

Access to the talk “Publication Ready Summary Tables with the {gtsummary} Package (Daniel Sjoberg, Karissa Whiting)”
Available
In cart
Free
Free
Free
Free
Free
Free
Free
Free

Conference Cast

With ConferenceCast.tv, you get access to our library of the world's best conference talks.

Conference Cast
735 conferences
30224 speakers
11293 hours of content
Daniel Sjoberg
Karissa Whiting