library(BSDA)#> Loading required package: lattice#>#> Attaching package: 'BSDA'#> The following object is masked from 'package:datasets':#>#>     Orangelibrary(parameters)library(broom)library(assertthat)library(waldo)## Examples taken from tsum.test help text## One-sample testhtest1<- tsum.test(mean.x=5.6,s.x=2.1,n.x=16,mu=4.9,alternative="greater")#> Warning in tsum.test(mean.x = 5.6, s.x = 2.1, n.x = 16, mu = 4.9, alternative =#> "greater"): argument 'var.equal' ignored for one-sample test.## Do an equivalent test with t.testtt1<- t.test(scale(rnorm(16))*2.1+5.6,mu=4.9,alternative="greater")## Examine differencescompare(tt1,htest1,x_arg="t.test",y_arg="tsum.test",tolerance=1e-10)#> `t.test` is length 10#> `tsum.test` is length 9#>#>      names(t.test) | names(tsum.test)#>  [1] "statistic"   | "statistic"      [1]#>  [2] "parameter"   - "parameters"     [2]#>  [3] "p.value"     | "p.value"        [3]#>  [4] "conf.int"    | "conf.int"       [4]#>  [5] "estimate"    | "estimate"       [5]#>  [6] "null.value"  | "null.value"     [6]#>  [7] "stderr"      -#>  [8] "alternative" | "alternative"    [7]#>  [9] "method"      | "method"         [8]#> [10] "data.name"   | "data.name"      [9]#>#> `t.test$parameter` is a double vector (15)#> `tsum.test$parameter` is absent#>#>    `t.test$conf.int`: 4.7 Inf#> `tsum.test$conf.int`: 4.7  NA#>#> `t.test$stderr` is a double vector (0.525)#> `tsum.test$stderr` is absent#>#> `t.test$method`:    "One Sample t-test"#> `tsum.test$method`: "One-sample t-Test"#>#> `t.test$data.name`:    "scale(rnorm(16)) * 2.1 + 5.6"#> `tsum.test$data.name`: "Summarized x"#>#> `t.test$parameters` is absent#> `tsum.test$parameters` is a double vector (15)## Gives correct infotidy(htest1)#> # A tibble: 1 × 7#>   estimate statistic p.value conf.low conf.high method            alternative#>      <dbl>     <dbl>   <dbl>    <dbl>     <dbl> <chr>             <chr>#> 1      5.6      1.33   0.101     4.68        NA One-sample t-Test greater## Thinks it's a different kind of testparameters(htest1)#> One-sample t-Test#>#> Parameter1   |  tau |    z | df |     p#> ---------------------------------------#> Summarized x | 5.60 | 1.33 | 15 | 0.101#>#> Alternative hypothesis: true mean is greater than 4.9## No t statisticassert_that("t"%in% names(parameters(htest1)))#> Error: `%in%`(x = "t", table = names(parameters(htest1))) is not TRUE## Looks like the problem is a slightly different value for "method".## We can "fix" it by copying the method from t.testhtest1_fixed<-htest1htest1_fixed$method<-tt1$methodparameters(htest1_fixed)#> One Sample t-test#>#> Parameter    | Mean |   mu | Difference |    95% CI | t(15) |     p#> -------------------------------------------------------------------#> Summarized x | 5.60 | 4.90 |       0.70 | [4.68,  ] |  1.33 | 0.101#>#> Alternative hypothesis: true mean is greater than 4.9assert_that("t"%in% names(parameters(htest1_fixed)))#> [1] TRUE## Two-sample testx<- c(7.8,6.6,6.5,7.4,7.3,7.0,6.4,7.1,6.7,7.6,6.8)y<- c(4.5,5.4,6.1,6.1,5.4,5.0,4.1,5.5)htest2<- tsum.test(  mean(x),s.x=sd(x),n.x=length(x),  mean(y),s.y=sd(y),n.y=length(y),mu=2)## Gives correct infotidy(htest2)#> # A tibble: 1 × 8#>   estimate1 estimate2 statistic p.value conf.low conf.high method    alternative#>       <dbl>     <dbl>     <dbl>   <dbl>    <dbl>     <dbl> <chr>     <chr>#> 1      7.02      5.26    -0.853   0.411     1.13      2.38 Welch Mo… two.sided## Throws errorparameters(htest2)#> Error in `$<-.data.frame`(`*tmp*`, "tau", value = c(`mean of x` = 7.01818181818182, : replacement has 2 rows, data has 1## Regular t-test on same data works correctlytt2<- t.test(x,y,mu=2)parameters(tt2)#> Welch Two Sample t-test#>#> Parameter1 | Parameter2 | Mean_Parameter1 | Mean_Parameter2 | Difference#> ------------------------------------------------------------------------#> x          |          y |            7.02 |            5.26 |       1.76#>#> Parameter1 |       95% CI | t(11.30) |     p#> --------------------------------------------#> x          | [1.13, 2.38] |    -0.85 | 0.411#>#> Alternative hypothesis: true difference in means is not equal to 2## Structural differences,compare(tt2,htest2,tolerance=1e-10,x_arg="t.test",y_arg="tsum.test")#> `t.test` is length 10#> `tsum.test` is length 9#>#>      names(t.test) | names(tsum.test)#>  [1] "statistic"   | "statistic"      [1]#>  [2] "parameter"   - "parameters"     [2]#>  [3] "p.value"     | "p.value"        [3]#>  [4] "conf.int"    | "conf.int"       [4]#>  [5] "estimate"    | "estimate"       [5]#>  [6] "null.value"  | "null.value"     [6]#>  [7] "stderr"      -#>  [8] "alternative" | "alternative"    [7]#>  [9] "method"      | "method"         [8]#> [10] "data.name"   | "data.name"      [9]#>#> `t.test$parameter` is a double vector (11.3029200067925)#> `tsum.test$parameter` is absent#>#> `t.test$stderr` is a double vector (0.286497791189657)#> `tsum.test$stderr` is absent#>#> `t.test$method`:    "Welch Two Sample t-test"#> `tsum.test$method`: "Welch Modified Two-Sample t-Test"#>#> `t.test$data.name`:    "x and y"#> `tsum.test$data.name`: "Summarized x and y"#>#> `t.test$parameters` is absent#> `tsum.test$parameters` is a double vector (11.3029200067925)## Again, we can fix it by sett2ing the correct method value from t.testhtest2_fixed<-htest2htest2_fixed$method<-tt2$methodhtest2_fixed$data.name<-tt2$data.namecompare(tt2,htest2_fixed,tolerance=1e-10,x_arg="t.test",y_arg="tsum.test")#> `t.test` is length 10#> `tsum.test` is length 9#>#>      names(t.test) | names(tsum.test)#>  [1] "statistic"   | "statistic"      [1]#>  [2] "parameter"   - "parameters"     [2]#>  [3] "p.value"     | "p.value"        [3]#>  [4] "conf.int"    | "conf.int"       [4]#>  [5] "estimate"    | "estimate"       [5]#>  [6] "null.value"  | "null.value"     [6]#>  [7] "stderr"      -#>  [8] "alternative" | "alternative"    [7]#>  [9] "method"      | "method"         [8]#> [10] "data.name"   | "data.name"      [9]#>#> `t.test$parameter` is a double vector (11.3029200067925)#> `tsum.test$parameter` is absent#>#> `t.test$stderr` is a double vector (0.286497791189657)#> `tsum.test$stderr` is absent#>#> `t.test$parameters` is absent#> `tsum.test$parameters` is a double vector (11.3029200067925)parameters(htest2_fixed)#> Welch Two Sample t-test#>#> Parameter1 | Parameter2 | Mean_Parameter1 | Mean_Parameter2 | Difference#> ------------------------------------------------------------------------#> x          |          y |            7.02 |            5.26 |       1.76#>#> Parameter1 |       95% CI | t(11.30) |     p#> --------------------------------------------#> x          | [1.13, 2.38] |    -0.85 | 0.411#>#> Alternative hypothesis: true difference in means is not equal to 2