README.md

In roistats: Convenience Functions for Applying Basic Stats to Sub-Groups

roistats

The goal of this package is to apply t-tests and basic data description across several sub-groups, with the output being a nice arranged data.frame instead of detailed listed information. Multiple comparison and significance symbols are wrapped in as options.

This kind of analyses are commonly seen in ROI (Region-of-interest) analyses for brain imaging data and this is why the package is called roistats.

Installation

You can install the released version of roistats from CRAN with:

install.packages("roistats")

And the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("Irisfee/roistats")

Usage

See Get Started page for detailed usage

Get some basic description about the data by brain region

library(roistats)
library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
color_index %>% 
  group_by(roi_id) %>%   
  df_sem(color_index) 
#> # A tibble: 8 x 5
#>   roi_id  mean_color_index         sd     n          se
#>   <chr>              <dbl>      <dbl> <int>       <dbl>
#> 1 AnG          0.005370652 0.05071557    29 0.009417644
#> 2 dLatIPS      0.01588446  0.05096974    29 0.009464843
#> 3 LO           0.01806413  0.04284959    29 0.007956968
#> 4 pIPS         0.01019600  0.02971026    29 0.005517056
#> 5 V1           0.009550089 0.04211448    29 0.007820463
#> 6 vIPS         0.01623826  0.03271157    29 0.006074385
#> 7 vLatIPS      0.01617011  0.05141337    29 0.009547223
#> 8 VTC          0.004683526 0.02181639    29 0.004051201

One-sample t-tests for all sub-groups

color_index %>% 
  group_by(roi_id) %>% 
  t_test_one_sample(color_index)
#> # A tibble: 8 x 5
#> # Groups:   roi_id [8]
#>   roi_id     tvalue    df          p p_bonferroni
#>   <chr>       <dbl> <dbl>      <dbl>        <dbl>
#> 1 AnG     0.5702755    28 0.5730390    1         
#> 2 dLatIPS 1.678259     28 0.1044252    0.8354017 
#> 3 LO      2.270227     28 0.03108491   0.2486792 
#> 4 pIPS    1.848088     28 0.07517831   0.6014264 
#> 5 V1      1.221167     28 0.2322062    1         
#> 6 vIPS    2.673234     28 0.01238958   0.09911667
#> 7 vLatIPS 1.693697     28 0.1014206    0.8113652 
#> 8 VTC     1.156083     28 0.2574165    1

With significance symbol as output

color_index_one_sample_t_with_sig <- color_index %>% 
  group_by(roi_id) %>% 
  t_test_one_sample(color_index, p_adjust = c("bonferroni","fdr")) %>% 
  mutate(sig_origin_p = p_range(p))

knitr::kable(color_index_one_sample_t_with_sig, digits = 3)

| roi_id | tvalue | df | p | p_bonferroni | p_fdr | sig_origin_p | | :------ | -----: | -: | ----: | ------------: | -----: | :------------- | | AnG | 0.570 | 28 | 0.573 | 1.000 | 0.573 | | | dLatIPS | 1.678 | 28 | 0.104 | 0.835 | 0.167 | | | LO | 2.270 | 28 | 0.031 | 0.249 | 0.124 | * | | pIPS | 1.848 | 28 | 0.075 | 0.601 | 0.167 | | | V1 | 1.221 | 28 | 0.232 | 1.000 | 0.294 | | | vIPS | 2.673 | 28 | 0.012 | 0.099 | 0.099 | * | | vLatIPS | 1.694 | 28 | 0.101 | 0.811 | 0.167 | | | VTC | 1.156 | 28 | 0.257 | 1.000 | 0.294 | |

Two-sample t-tests for all sub-groups

color_index_two_sample %>% 
  group_by(roi_id) %>% 
  t_test_two_sample(x = color_effect, y = group, paired = TRUE)
#> # A tibble: 8 x 5
#> # Groups:   roi_id [8]
#>   roi_id     tvalue    df          p p_bonferroni
#>   <chr>       <dbl> <dbl>      <dbl>        <dbl>
#> 1 AnG     0.5702755    28 0.5730390    1         
#> 2 dLatIPS 1.678259     28 0.1044252    0.8354017 
#> 3 LO      2.270227     28 0.03108491   0.2486792 
#> 4 pIPS    1.848088     28 0.07517831   0.6014264 
#> 5 V1      1.221167     28 0.2322062    1         
#> 6 vIPS    2.673234     28 0.01238958   0.09911667
#> 7 vLatIPS 1.693697     28 0.1014206    0.8113652 
#> 8 VTC     1.156083     28 0.2574165    1

roistats documentation built on March 11, 2021, 1:07 a.m.