{"id":11655,"date":"2019-12-25T12:58:37","date_gmt":"2019-12-25T10:58:37","guid":{"rendered":"https:\/\/www.datanovia.com\/en\/?post_type=dt_lessons&#038;p=11655"},"modified":"2019-12-25T12:58:37","modified_gmt":"2019-12-25T10:58:37","slug":"pairwise-t-test","status":"publish","type":"dt_lessons","link":"https:\/\/www.datanovia.com\/en\/lessons\/pairwise-t-test\/","title":{"rendered":"Pairwise T-Test"},"content":{"rendered":"<div id=\"rdoc\">\n<p>This article describes how to compute <strong>pairwise T-test<\/strong> in R between groups with corrections for multiple testing. The pairwise t-test consists of calculating <strong>multiple t-test<\/strong> between all possible combinations of groups.<\/p>\n<p>You will learn how to:<\/p>\n<ul>\n<li>Calculate pairwise t-test for unpaired and paired groups<\/li>\n<li>Display the p-values on a boxplot.<\/li>\n<\/ul>\n<p>Contents:<\/p>\n<div id=\"TOC\">\n<ul>\n<li><a href=\"#prerequisites\">Prerequisites<\/a><\/li>\n<li><a href=\"#pairwise-t-test-for-independent-groups\">Pairwise t-test for independent groups<\/a><\/li>\n<li><a href=\"#pairwise-t-test-for-paired-groups\">Pairwise t-test for paired groups<\/a><\/li>\n<li><a href=\"#related-articles\">Related articles<\/a><\/li>\n<\/ul>\n<\/div>\n<div class='dt-sc-hr-invisible-medium  '><\/div>\n<div class='dt-sc-ico-content type1'><div class='custom-icon' ><a href='https:\/\/www.datanovia.com\/en\/product\/practical-statistics-in-r-for-comparing-groups-numerical-variables\/' target='_blank'><span class='fa fa-book'><\/span><\/a><\/div><h4><a href='https:\/\/www.datanovia.com\/en\/product\/practical-statistics-in-r-for-comparing-groups-numerical-variables\/' target='_blank'> Related Book <\/a><\/h4>Practical Statistics in R II - Comparing Groups: Numerical Variables<\/div>\n<div class='dt-sc-hr-invisible-medium  '><\/div>\n<div id=\"prerequisites\" class=\"section level2\">\n<h2>Prerequisites<\/h2>\n<p>Make sure you have the following R packages:<\/p>\n<ul>\n<li><code>tidyverse<\/code> for data manipulation and visualization<\/li>\n<li><code>ggpubr<\/code> for creating easily publication ready plots<\/li>\n<li><code>rstatix<\/code> provides pipe-friendly R functions for easy statistical analyses<\/li>\n<li><code>datarium<\/code>: contains required data sets for this chapter<\/li>\n<\/ul>\n<p>Load required R packages:<\/p>\n<pre class=\"r\"><code>library(tidyverse)\r\nlibrary(ggpubr)\r\nlibrary(rstatix)<\/code><\/pre>\n<\/div>\n<div id=\"pairwise-t-test-for-independent-groups\" class=\"section level2\">\n<h2>Pairwise t-test for independent groups<\/h2>\n<p>This section shows how to perform multiple independent t-tests between groups.<\/p>\n<pre class=\"r\"><code># Load and inspect the demo data\r\ndata(\"PlantGrowth\")\r\nset.seed(1234)\r\nPlantGrowth %&gt;% sample_n_by(group, size = 2)<\/code><\/pre>\n<pre><code>## # A tibble: 6 x 2\r\n##   weight group\r\n##    &lt;dbl&gt; &lt;fct&gt;\r\n## 1   5.58 ctrl \r\n## 2   4.61 ctrl \r\n## 3   6.03 trt1 \r\n## 4   3.83 trt1 \r\n## 5   5.8  trt2 \r\n## 6   5.29 trt2<\/code><\/pre>\n<pre class=\"r\"><code># Pairwise comparisons\r\npwc &lt;- PlantGrowth %&gt;% \r\n  pairwise_t_test(\r\n    weight ~ group, pool.sd = FALSE,\r\n    p.adjust.method = \"bonferroni\"\r\n    )\r\npwc<\/code><\/pre>\n<pre><code>## # A tibble: 3 x 10\r\n##   .y.    group1 group2    n1    n2 statistic    df     p p.adj p.adj.signif\r\n## * &lt;chr&gt;  &lt;chr&gt;  &lt;chr&gt;  &lt;int&gt; &lt;int&gt;     &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;chr&gt;       \r\n## 1 weight ctrl   trt1      10    10      1.19  16.5 0.25  0.75  ns          \r\n## 2 weight ctrl   trt2      10    10     -2.13  16.8 0.048 0.144 ns          \r\n## 3 weight trt1   trt2      10    10     -3.01  14.1 0.009 0.028 *<\/code><\/pre>\n<pre class=\"r\"><code># Visualization: box plots with p-values\r\npwc &lt;- pwc %&gt;% add_xy_position(x = \"group\", step.increase = 1)\r\nggboxplot(PlantGrowth, x = \"group\", y = \"weight\") +\r\n  stat_pvalue_manual(pwc, hide.ns = TRUE) <\/code><\/pre>\n<p><img decoding=\"async\" src=\"https:\/\/www.datanovia.com\/en\/wp-content\/uploads\/dn-tutorials\/r-statistics-2-comparing-groups-means\/figures\/073-pairwise-t-test-independent-groups-1.png\" width=\"480\" \/><\/p>\n<\/div>\n<div id=\"pairwise-t-test-for-paired-groups\" class=\"section level2\">\n<h2>Pairwise t-test for paired groups<\/h2>\n<p>This section shows how to perform multiple paired t-tests between groups. We\u2019ll use the self-esteem score dataset measured over three time points. The data is available in the datarium package.<\/p>\n<pre class=\"r\"><code># Data preparation: Wide format\r\ndata(\"selfesteem\", package = \"datarium\")\r\nhead(selfesteem, 3)<\/code><\/pre>\n<pre><code>## # A tibble: 3 x 4\r\n##      id    t1    t2    t3\r\n##   &lt;int&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt;\r\n## 1     1  4.01  5.18  7.11\r\n## 2     2  2.56  6.91  6.31\r\n## 3     3  3.24  4.44  9.78<\/code><\/pre>\n<pre class=\"r\"><code># Gather columns t1, t2 and t3 into long format\r\n# Convert id and time into factor variables\r\nselfesteem &lt;- selfesteem %&gt;%\r\n  gather(key = \"time\", value = \"score\", t1, t2, t3) %&gt;%\r\n  convert_as_factor(id, time)\r\nhead(selfesteem, 3)<\/code><\/pre>\n<pre><code>## # A tibble: 3 x 3\r\n##   id    time  score\r\n##   &lt;fct&gt; &lt;fct&gt; &lt;dbl&gt;\r\n## 1 1     t1     4.01\r\n## 2 2     t1     2.56\r\n## 3 3     t1     3.24<\/code><\/pre>\n<pre class=\"r\"><code># Pairwise comparisons\r\npwc &lt;- selfesteem %&gt;%\r\n  pairwise_t_test(\r\n    score ~ time, paired = TRUE,\r\n    p.adjust.method = \"bonferroni\"\r\n    )\r\npwc<\/code><\/pre>\n<pre><code>## # A tibble: 3 x 10\r\n##   .y.   group1 group2    n1    n2 statistic    df           p    p.adj p.adj.signif\r\n## * &lt;chr&gt; &lt;chr&gt;  &lt;chr&gt;  &lt;int&gt; &lt;int&gt;     &lt;dbl&gt; &lt;dbl&gt;       &lt;dbl&gt;    &lt;dbl&gt; &lt;chr&gt;       \r\n## 1 score t1     t2        10    10     -4.97     9 0.000772    0.002    **          \r\n## 2 score t1     t3        10    10    -13.2      9 0.000000334 0.000001 ****        \r\n## 3 score t2     t3        10    10     -4.87     9 0.000886    0.003    **<\/code><\/pre>\n<pre class=\"r\"><code># Visualization: box plots with p-values\r\npwc &lt;- pwc %&gt;% add_xy_position(x = \"time\")\r\nggboxplot(selfesteem, x = \"time\", y = \"score\", add = \"point\") +\r\n  stat_pvalue_manual(pwc)<\/code><\/pre>\n<p><img decoding=\"async\" src=\"https:\/\/www.datanovia.com\/en\/wp-content\/uploads\/dn-tutorials\/r-statistics-2-comparing-groups-means\/figures\/073-pairwise-t-test-paired-groups-1.png\" width=\"480\" \/><\/p>\n<\/div>\n<div id=\"related-articles\" class=\"section level2\">\n<h2>Related articles<\/h2>\n<ul>\n<li><a href=\"\/?p=10872\">ANOVA in R<\/a><\/li>\n<li><a href=\"\/?p=10873\">Repeated Measures ANOVA in R<\/a><\/li>\n<\/ul>\n<\/div>\n<\/div>\n<p><!--end rdoc--><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Describes how to compute the pairwise T-test in R between groups with corrections for multiple testing. The pairwise t-test consists of calculating multiple t-test between all possible combinations of groups. You will learn how to:  1) Calculate pairwise t-test for unpaired and paired groups; 2) Display the p-values on a boxplot.<\/p>\n","protected":false},"author":1,"featured_media":9088,"parent":0,"menu_order":73,"comment_status":"open","ping_status":"closed","template":"","class_list":["post-11655","dt_lessons","type-dt_lessons","status-publish","has-post-thumbnail","hentry"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v25.2 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Pairwise T-Test : Excellent Reference You Will Love - Datanovia<\/title>\n<meta name=\"description\" content=\"Describes how to compute the pairwise T-test in R between groups with corrections for multiple testing. The pairwise t-test consists of calculating multiple t-test between all possible combinations of groups. 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