METHOD GUIDE
Independent Samples t-Test in R
Why R Runs Welch and How to Report It
Called with no extra arguments, t.test() does not assume equal variances, and it prints an interval for the mean difference with every call. Reading that interval with the right sign, and naming the version of the test in the methods, is where most write-ups of this comparison need care.
IN SHORT
What the Comparison Estimates and How R Reports It
An independent samples t-test estimates how far the mean of a continuous outcome differs between two unrelated groups, and how precisely the data pin that difference down. To run an independent samples t-test in R, call t.test() with the outcome and a two-level grouping factor, leave var.equal at its default of FALSE to obtain the Welch version, and report the mean difference with its confidence interval. Because the Welch version stays valid when variances and group sizes differ, no preliminary variance test is needed to choose it. OnlineSPSS, a specialist statistical consultancy for academic, clinical and professional research, carries out and reviews this analysis through an in-house PhD-level statistician.
ANALYSIS SUPPORT
Analysis Support for This Method
Whether the mean difference, a rank-based comparison or a model with covariates answers the question is a design matter, and R will run whichever call it is given.
Independent Samples t-Test
The comparison of two independent groups on a continuous outcome, carried out in R or another program, with the interval, the effect size and the reporting agreed for your design.
Mann-Whitney U Test
A rank-based comparison of two independent groups, for an ordinal outcome or when the distributional assumptions behind a comparison of means are not tenable.
BEFORE YOU RUN IT
What to Settle Before Calling t.test()
Whether the interval can be reported as it stands is decided by how participants were sampled and how the groups are coded, and both can be checked against the data frame before the first call.
Participants Counted Once Each participant appears once, in one group. Repeated visits or matched pairs call for a paired analysis, and participants clustered in classes or clinics need a model that allows for the clustering.
A Factor With Set Levels Make the grouping variable a factor with exactly two levels. Text labels are ordered alphabetically unless you set the order, and that order decides the sign of the difference and the interval.
Welch Without a Pre-Test The Welch t-test in R is the default, so no variance test has to come first. Pooled variances, set with var.equal = TRUE, are justified mainly by a reason stated before the data were seen.
Outcome Scale and Shape The outcome should be continuous or close to it. Judge the shape inside each group by plot and by sample size, since skew and outliers matter most in small groups, and settle the response before looking at p.
IN R
How to Run the Independent Samples t-Test in R
The t.test function in R belongs to the stats package that loads with every session of R. The standardized effect size comes from an add-on package, which is named in the methods together with its version.
- Confirm the design: one continuous outcome, two independent groups, one row per participant.
- Convert the grouping variable with factor() and set the order of its levels.
- Plot the outcome by group, for example with boxplot(outcome ~ group, data = d), and compare spread, skew and outliers.
- Run t.test(outcome ~ group, data = d); the default is the Welch version, and var.equal = TRUE switches to pooled variances.
- Read the group means, the difference, the 95 percent interval, t, df and the p-value together.
- Get Hedges’ g with its interval, for example with hedges_g() in the effectsize package, and save the script.
READING THE OUTPUT
Reading the Welch Output of t.test() Line by Line
R prints a short block of text, not a set of tables, so the lines worth matching to your write-up are the header, the statistic line, the interval and the two group means.
| Output element | What it tells you | What to check |
|---|---|---|
| Header line | Welch Two Sample t-test, or Two Sample t-test when pooled variances were requested | That the test named in the methods is the test that ran |
| data line | The outcome and grouping variable the call used | That the variable names are the intended ones |
| t, df and p-value | The statistic, the Welch-adjusted degrees of freedom and the two-sided p | That df is quoted as printed; a non-integer is expected |
| Alternative hypothesis | The direction tested, in wording that differs by R version | That a two-sided test was kept unless a direction was stated in advance |
| 95 percent confidence interval | The interval for the difference between the group means | That its sign is read from the level order and described in words |
| Sample estimates | The mean of each group, labeled by the levels of the factor | That the two means are the ones in the reported descriptives |
| Effect size output | A standardized difference with its interval, from an add-on package | That the standardizer used, pooled or not, is named in the text |
REPORTING
Reporting the Welch Result With an Effect Size
Welch's degrees of freedom and the sign of the difference are the two details most often copied wrongly from the console into this sentence.
Write t(df) = ___, p = ___ for the Welch test, with df exactly as printed, then the mean difference in the original units with its 95% CI [___, ___], and the mean and standard deviation of each group. Say in words which group scored higher, because the sign follows the order of the factor levels. Add Hedges’ g = ___ with its 95% CI [___, ___] and name the standardizer. Base R’s t.test prints no standardized effect size and no standard deviations, so these come from sd() and an add-on package. State the n per group and how missing values were handled, since the formula method drops incomplete rows. Call the test Welch’s unequal variances t-test, and name the pooled-variance version only if var.equal = TRUE was set.
COMMON MISTAKES
Welch Reports: Slips That Draw Reviewer Queries
Each slip below can be traced to one line of the console output, so the reported sentence is compared with the printed block before submission.
Pooled Test Named, Welch Run The methods describe a pooled-variance t-test while t.test() ran the Welch version by default. The test named in the text must be the test that produced the numbers, with df as printed.
Outliers Removed After the Result Dropping an extreme value because it moved the p-value changes the analysis after the data were seen. A rule for outliers is set in advance, and when it removes cases, the result is shown with and without them.
Direction Reversed The sign of the difference follows the order of the factor levels. A text saying the second group scored higher while R printed first minus second reverses the finding.
Interval Left Out A p-value alone hides the size of the difference. The console prints the interval, and the text should carry it in the original units next to a standardized effect.
Pooled df With Welch t Quoting N minus 2 degrees of freedom beside a Welch statistic mixes two tests. The adjusted value printed by R belongs in the sentence, to one or two decimals.
Log Scale Read as a Raw Difference After a log transformation, the back-transformed difference between the groups is a ratio of geometric means, not a difference in arithmetic means, and the text should describe it as a ratio.
Unsure your sentence matches the console? Independent Statistical Review checks the code, the printed output and the reported sentence against each other before you submit.
FREQUENTLY ASKED QUESTIONS
Questions About the t.test() Output
Each answer starts from something the console printed or refused to print, beginning with the message R gives when the grouping variable has the wrong number of levels.
Why does t.test() stop with a message about exactly 2 levels?
The grouping variable has one level or more than two among the rows used, so R cannot define two groups. A typing variant of a label or a third category is the usual cause. Check the counts with table(), correct the coding, and if three groups really exist, a comparison across several groups is needed, not a t-test.
Why does my p-value differ from another program's?
R reports the Welch test unless var.equal = TRUE is set, while some programs print both versions or default to pooled variances. The two agree closely when variances and group sizes are similar and diverge when they are not. Report the version that matches the design, and name it in the methods.
What does t.test() do with missing values, and what do I report?
With the formula method, rows with a missing outcome or group are dropped before the test. Report the n per group that entered the comparison and the number excluded, and say whether missingness could differ between the groups, since the test cannot correct for that and the comparison then describes the complete cases.
Would OnlineSPSS compare my t.test() code with the sentence I wrote?
Yes. An in-house PhD-level statistician can match the factor coding, the printed interval and Hedges’ g against your reported sentence, or run the comparison on your data. Where the result is final and only the write-up needs attention, the relevant service is Results Reporting & Interpretation. What the difference means for your field is your judgment.
How do you protect my research data and confidentiality?
Your data and project details are handled confidentially, and project information is not published. Researcher names and institutions are not used publicly without permission. An NDA is available where required and can be arranged before sensitive materials are shared. Read more about confidentiality and data security.
What happens when I request an assessment, and how long does it take?
You share your research question, design and relevant materials, such as the dataset or the output you have, and a statistically trained Research Coordinator reviews the request and responds the same day. The analysis, deliverables, timeline and one fixed project fee are then confirmed before any work begins, so the timeline follows from the agreed scope.
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