Forestplot in r

Posted on 21.11.2020 Comments

Optional user-specified x-axis tick marks. Specify NULL to use the defaults, numeric 0 to omit the x-axis. This function is more flexible than metaplot and the plot methods for meta-analysis objects, but requires more work by the user. In particular, it allows for a table of text, and clips confidence intervals to arrows when they exceed specified limits.

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Man pages R Description Draw a forest plot together with a table of text. Related to forestplot in rmeta R Package Documentation rdrr. We want your feedback! Note that we can't provide technical support on individual packages. You should contact the package authors for that. Tweet to rdrrHQ. GitHub issue tracker. Personal blog. What can we improve?

The page or its content looks wrong. I can't find what I'm looking for. I have a suggestion. Extra info optional. Embedding an R snippet on your website. Add the following code to your website. Vector giving alignment lrc for columns of table.You can report issue about the content on this page here Want to share your content on R-bloggers? Displaying large regression models without overwhelming the reader can be challenging.

I believe that forestplots are amazingly well suited for this. The plot gives a quick understanding of the estimates position in comparison to other estimates, while also showcasing the uncertainty.

This project started with some minor tweaks to prof. Thomas Lumleys forestplot and ended up in a complete remake of the function. We were interested in comparing if there was a difference between common explanatory variables in Denmark and Sweden, i. The Swedish data set was vast while the Danish was a tiny sample resulting in very different confidence intervals.

You can find the main graph below. Lets start with the basic code to generate a simple forestplot. The xticks parameter is not necessary but in this particular example the 0. Note: you need to download my package, you can find the Gmisc-package herefor this tutorial to work.

One of the first things that got me tweaking the original forestplot function was that I wanted to have a simple expression in the header. Getting a matrix into the original function was rather simple, as you can see below:. The number of elements in the list have to be m x n as in any matrix, below is the example plot that I was originally aiming for:. After this set-back I was at least familiar with the forestplot function allowing further tweaking.

Early on I realized that it can be convenient to display the same risk factors multiple times. The idea was that in situations where there are different outcomes, for instance hip replacement re-operation due to infection, dislocation or fracture it can be useful to see the estimates adjacent to each-other. I also used it for comparing Cox proportional hazards models with competing risk regressions and Poisson regression.

It turned out to be rather useful. The code is fairly straight forward, you now need to have to provide the function with a m x n matrix for the mean, lower and upper parameters. The n should be the number of comparison groups, in the Sweden vs Denmark paper the groups are two:. Originally I was using the legend function but it turned out to be rather complicated. Want to share your content on R-bloggers? Never miss an update!By using our site, you acknowledge that you have read and understand our Cookie PolicyPrivacy Policyand our Terms of Service.

Stack Overflow for Teams is a private, secure spot for you and your coworkers to find and share information. I am creating a forestplot in R.

I would like to superscript the very last label for Heterogeniety. R does not allow you to create a matrix of expression. Also mentioned in the documentation for forestplot.

forestplot in r

Luckily, the documentation for forestplot also mentioned that it can take in a list for labeltext. The list should be wrapped in m x n number to resemble a matrix: list list "rowname 1 col 1", "rowname 2 col 1"list "r1c2", expression beta. Learn more. Forestplot in R superscript in tabletext matrix Ask Question.

Asked 3 years, 3 months ago. Active 3 years, 3 months ago. Viewed times. Active Oldest Votes. Also mentioned in the documentation for forestplotYou can also provide a matrix although this cannot have expressions by design Luckily, the documentation for forestplot also mentioned that it can take in a list for labeltext. That works well, but now I have a new problem. I cannot position the graph between in between the case numbers and the ORs anymore using graph. You have provided the value '4'.

Is there a way of changing the position of the plot? Sign up or log in Sign up using Google. Sign up using Facebook. Sign up using Email and Password. Post as a guest Name. Email Required, but never shown. The Overflow Blog. The Overflow Checkboxland. Tales from documentation: Write for your dumbest user. Upcoming Events. Featured on Meta.

Feedback post: New moderator reinstatement and appeal process revisions. The new moderator agreement is now live for moderators to accept across the…. Allow bountied questions to be closed by regular users. Hot Network Questions. Question feed. Stack Overflow works best with JavaScript enabled.To build a Forest Plot often the forestplot package is used in R.

However, I find the ggplot2 to have more advantages in making Forest Plots, such as enable inclusion of several variables with many categories in a lattice form. You can also use any scale of your choice such as log scale etc. In this post, I will introduce how to plot Risk Ratios and their Confidence Intervals of several conditions. The current data is in long format; if your data is not in this format, check out the melt function, in the reshape package, it provides a really easy way to reshape data into long format.

For the sake of easy demonstrations and simplicity, we truncate the upper limits to 2 as maximum and lower limits to 0. Gives this plot:. Note that, position can be used to change where you want the axis to appear in this case I chose top but default is bottom. I have explored how to make lattice-like forest plots in R using gplot2. Note that you can tweak the graphs by playing with the arguments in the functions. Share: Twitter Facebook. Faisal Atakora.

Share it. Facebook Twitter Reddit Linkedin Email this. Related Posts. Online Courses. Connect with Us.A logical indicating whether study labels should be printed in the graph. A logical indicating whether overall summaries should be plotted.

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This argument is useful in a meta-analysis with subgroups if summaries should only be plotted on group level. A logical indicating whether subgroup results should be shown in forest plot. This argument is useful in a meta-analysis with subgroups if summaries should not be plotted on group level. A logical indicating whether the name of the grouping variable should be printed in front of the group labels. A character string to label the pooled fixed effect estimate within subgroups, or a character vector of same length as number of subgroups with corresponging labels.

A character string to label the pooled random effect estimate within subgroups, or a character vector of same length as number of subgroups with corresponging labels. A logical indicating whether results for individual studies should be shown in the figure useful to only plot subgroup results. A character string indicating weighting used to determine size of squares or diamonds argument type. One of missing, "same""fixed"or "random"can be abbreviated.

Plot symbols have the same size for all studies or represent study weights from fixed effect or random effects model. One of missing, "same"or "weight"can be abbreviated. Plot symbols have the same size for all subgroup results or represent subgroup weights from fixed effect or random effects model. A numeric giving scaling factor for printing of single event probabilities or risk differences, i.

A numeric defining a scaling factor for printing of single incidence rates or incidence rate differences, i.

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A numerical giving the reference value to be plotted as a line in the forest plot. No reference line is plotted if argument ref is equal to NA. A numerical giving the lower limit of equivalence to be plotted as a line in the forest plot.

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No line is plotted if argument lower. A numerical giving the upper limit of equivalence to be plotted as a line in the forest plot.

No line is plotted if argument upper.

forestplot in r

A character vector specifying additional columns to be plotted on the left side of the forest plot or a logical value see Details. A character vector specifying additional columns to be plotted on the right side of the forest plot or a logical value see Details.

A character vector specifying labels for additional columns on left side of the forest plot see Details. A character vector specifying labels for additional columns on right side of the forest plot see Details.

forest.meta

A character specifying the column name where label lab. A logical indicating whether labels on right and left side should be printed at bottom or top of forest plot. A character string to label missing values in individual treatment estimates and confidence intervals.

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The line width, see par. A logical value indicating whether to draw the labels on the tick marks, or an expression or character vector which specify the labels to use. See grid. A character string or vector specifying how to plot treatment effects and confidence intervals for individual studies see Details.You can report issue about the content on this page here Want to share your content on R-bloggers?

I had a post on this subject and one of the suggestions I got from the comments was the ability to change the default box marker to something else. This idea had been in my mind for a while and I therefore put it into practice. They are an excellent tool to display lots of estimates and confidence intervals. If the list is one-leveled or you have a vector in a multi-line situation it will try to identify if the length matches row or column.

The function tries to rewrite to match your the dimension of your multi-line plot, hence you can write:. If you use the same number of lines as the lines the legend will automatically use your custom markers although you can always just use the legendMarkerFn argument:. Now for the pch -argument in the fpDrawPointCI you can use any of the predefined integers:. If you are still not satisfied you have always the option of writing your own function. I suggest you start with copying the fpDrawNormalCI and see what you want to change:.

Note that all the regression functions in the Gmisc-package have moved to the Greg -package, soon to be available on CRAN… but until I have added some more unit tests you need to use the GitHub version.

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Subscribe to R-bloggers to receive e-mails with the latest R posts. You will not see this message again.Forest plots date back to s and are most frequently seen in meta-analysisbut are in no way restricted to these. The forestplot package is all about providing these in R.

Note: An important difference from the original forestplot is that the current function interprets xlog as the x-axis being in log-format, i. Below is a basic example from the original forestplot function that shows how to use a table of text:.

We can also choose what lines we want by provifing a list where the name is the line number affected, in the example below 3rd line and 11th counting the first line to be above the first row not that there is an empty row before summary :.

In forestplot you simply specify the vertices argument:. You can also choose to have the graph positioned within the text table by specifying the graph. If we present a regression output it is sometimes convenient to have non-ascii letters. We will use my study comparing health related quality of life 1 year after total hip arthroplasties between Sweden and Denmark for this section:. Clipping the interval is convenient for uncertain estimates in order to retain the resolution for those of more interest.

The clipping simply adds an arrow to the confidence interval, see the bottom estimate below:. This efficiently increases the data-ink ratio while making the comparison between the two bands trivial. Here the clipping also becomes obvious as the Danish sample was much smaller, resulting in wider confidence intervals. You can choose between a number of different estimate indicators.

Using the example above we can set the Danish results to circles. You can furthermore choose between all available line types through the lty. Sometimes you have a very tall graph and you want to add helper lines in order to make it easier to see the tick marks.

This can be useful in non-inferiority or equivalence studies. You can do this through the grid argument:. You can easily customize both what grid lines to use and what type they should be by adding the gpar object to a vector:.

forestplot in r

If you are unfamiliar with the structure call it is equivalent to generating a vector and then setting an attribute, eg:. Text Table of text Summary lines Adding vertices to the whiskers Positioning the graph element Using expressions Altering fonts Confidence intervals Multiple confidence bands Estimate indicator Choosing line type Legends Ticks and grids.

Text A forest plot is closely connected to text and the ability to customize the text is central. Positioning the graph element You can also choose to have the graph positioned within the text table by specifying the graph. Using expressions If we present a regression output it is sometimes convenient to have non-ascii letters. Confidence intervals Clipping the interval is convenient for uncertain estimates in order to retain the resolution for those of more interest.

Estimate indicator You can choose between a number of different estimate indicators.