Group by 和 运行 R 中的多个 t 检验
Group by and run multiple t tests in R
我有以下数据集（dput here）：
# A tibble: 3,713 x 17
ID Age Group RHR HRV Sleep.Onset Wake.Onset Hours.in.Bed Hours.of.Sleep Sleep.Disturbances Latency.min Cycles REM.Sleep.hours Deep.Sleep.hours
<int> <chr> <chr> <int> <int> <dbl> <dbl> <dbl> <dbl> <int> <dbl> <int> <dbl> <dbl>
1 5027 Young Increase 58 73 0.180 0.458 6.66 5.33 9 8.98 6 1.4 0.32
2 5027 Young Increase 83 27 0.162 0.542 9.1 6.84 15 3.48 9 1.19 1.54
3 5027 Young Increase 57 85 0.113 0.318 4.92 4.43 5 1.98 4 1.32 0.44
4 5027 Young Increase 60 70 0.0975 0.319 5.32 3.75 3 26.5 4 1.02 0.14
5 5027 Young Increase 63 72 0.105 0.329 5.38 4.74 5 2.48 5 1.32 0.07
6 5027 Young Increase 62 61 0.983 0.472 11.8 9.44 9 4.48 8 2.07 0.84
7 5027 Young Increase 66 68 0.142 0.426 6.83 5.48 15 2.98 6 1.48 0.35
8 5027 Young Increase 81 28 0.0908 0.177 2.06 1.93 2 2.48 1 0.22 0.22
9 5027 Young Increase 69 57 0.158 0.443 6.85 6.58 13 0.48 6 2.43 0
10 5027 Young Increase 63 60 0.0859 0.318 5.58 5.47 4 0.48 5 1.34 0.13
# ... with 3,703 more rows, and 3 more variables: Light.Sleep.hours <dbl>, Awake.hours <dbl>, Session <chr>
我正在尝试计算每个变量的 t 检验，按 Age 和 Group 在 Session（pre 或 post）之间分组。
df %>%
select(-ID) %>%
group_by(Age, Group) %>%
summarize_at(
vars(-group_cols(), -Session),
list(p.value = ~ t.test(. ~ Session)$p.value))
我的 p 值很成功：
# A tibble: 4 x 15
# Groups: Age [2]
Age Group RHR_p.value HRV_p.value Sleep.Onset_p.value Wake.Onset_p.value Hours.in.Bed_p.value Hours.of.Sleep_p~ Sleep.Disturban~ Latency.min_p.v~
<chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 Old Decrease 0.0594 0.865 0.495 0.885 0.316 0.307 0.148 0.00237
2 Old Increase 0.00920 0.634 0.0979 0.0514 0.00774 0.00762 0.247 0.933
3 Young Decrease 0.0975 0.259 0.779 0.760 0.959 0.975 0.256 0.181
4 Young Increase 0.115 0.604 0.846 0.164 0.140 0.242 0.692 0.412
# ... with 5 more variables: Cycles_p.value <dbl>, REM.Sleep.hours_p.value <dbl>, Deep.Sleep.hours_p.value <dbl>, Light.Sleep.hours_p.value <dbl>,
# Awake.hours_p.value <dbl>
但是，我正在努力计算这些之间的其他 t 统计量（mean、sd、t、df、95%CI） pre-post 以及正确的 p 值组。我正在努力做到这一点，因此感谢您的帮助。
我想我可能需要转换长数据并使用类似这样的东西？
df %>%
group_by(Age, Group) %>%
t_test(mean ~ ., by = "Session") %>%
adjust_pvalue(method = "bonferroni") %>%
add_significance()
Dn 数据框只能有某些对象 类 作为列类型。一种
htest 不是其中之一。
但是，我们可以将列表存储为 list-columns。
如果我们调整当前代码以输出列表 htests 作为结果，我们可以稍后单独提取测试的元素。
library(dplyr)
output <- df %>%
select(-ID) %>%
group_by(Age, Group) %>%
summarize_at(
vars(-group_cols(), -Session),
list(t.test = ~ list(t.test(. ~ Session))))
output
# A tibble: 4 × 15
# Groups: Age [2]
Age Group RHR_t.test HRV_t.test Sleep.Onset_t.test Wake.Onset_t.test Hours.in.Bed_t.test Hours.of.Sleep_t.test Sleep.Disturbance… Latency.min_t.t… Cycles_t.test REM.Sleep.hours…
<chr> <chr> <list> <list> <list> <list> <list> <list> <list> <list> <list> <list>
1 Old Decrease <htest> <htest> <htest> <htest> <htest> <htest> <htest> <htest> <htest> <htest>
2 Old Increase <htest> <htest> <htest> <htest> <htest> <htest> <htest> <htest> <htest> <htest>
3 Young Decrease <htest> <htest> <htest> <htest> <htest> <htest> <htest> <htest> <htest> <htest>
4 Young Increase <htest> <htest> <htest> <htest> <htest> <htest> <htest> <htest> <htest> <htest>
有了这个 output data.frame，我们可以根据需要从中提取单个测试和值：
output$RHR_t.test
[[1]]
Welch Two Sample t-test
data: . by Session
t = -1.8965, df = 188.22, p-value = 0.05942
alternative hypothesis: true difference in means between group Post and group Pre is not equal to 0
95 percent confidence interval:
-3.09118590 0.06082897
sample estimates:
mean in group Post mean in group Pre
62.28902 63.80420
[[2]]
Welch Two Sample t-test
data: . by Session
t = -2.6271, df = 226.21, p-value = 0.009199
alternative hypothesis: true difference in means between group Post and group Pre is not equal to 0
95 percent confidence interval:
-3.3949577 -0.4848655
sample estimates:
mean in group Post mean in group Pre
57.95946 59.89937
[[3]]
Welch Two Sample t-test
data: . by Session
t = 1.6633, df = 251.75, p-value = 0.0975
alternative hypothesis: true difference in means between group Post and group Pre is not equal to 0
95 percent confidence interval:
-0.2074028 2.4611194
sample estimates:
mean in group Post mean in group Pre
60.58255 59.45570
[[4]]
Welch Two Sample t-test
data: . by Session
t = 1.5849, df = 208.4, p-value = 0.1145
alternative hypothesis: true difference in means between group Post and group Pre is not equal to 0
95 percent confidence interval:
-0.244287 2.247775
sample estimates:
mean in group Post mean in group Pre
60.23462 59.23288
output$RHR_t.test %>%
map_dbl('p.value')
[1] 0.059424354 0.009199459 0.097497620 0.114502332
我们还可以使用 broom::tidy
将这些列表转换为 user-friendly tibbles
output %>%
mutate(across(ends_with('t.test'), map, broom::tidy))
# A tibble: 4 × 15
# Groups: Age [2]
Age Group RHR_t.test HRV_t.test Sleep.Onset_t.te… Wake.Onset_t.test Hours.in.Bed_t.t… Hours.of.Sleep_… Sleep.Disturbanc… Latency.min_t.t… Cycles_t.test REM.Sleep.hours…
<chr> <chr> <list> <list> <list> <list> <list> <list> <list> <list> <list> <list>
1 Old Decrease <tibble [1 × 10]> <tibble [1 … <tibble [1 × 10]> <tibble [1 × 10]> <tibble [1 × 10]> <tibble [1 × 10… <tibble [1 × 10]> <tibble [1 × 10… <tibble [1 ×… <tibble [1 × 10…
2 Old Increase <tibble [1 × 10]> <tibble [1 … <tibble [1 × 10]> <tibble [1 × 10]> <tibble [1 × 10]> <tibble [1 × 10… <tibble [1 × 10]> <tibble [1 × 10… <tibble [1 ×… <tibble [1 × 10…
3 Young Decrease <tibble [1 × 10]> <tibble [1 … <tibble [1 × 10]> <tibble [1 × 10]> <tibble [1 × 10]> <tibble [1 × 10… <tibble [1 × 10]> <tibble [1 × 10… <tibble [1 ×… <tibble [1 × 10…
4 Young Increase <tibble [1 × 10]> <tibble [1 … <tibble [1 × 10]> <tibble [1 × 10]> <tibble [1 × 10]> <tibble [1 × 10… <tibble [1 × 10]> <tibble [1 × 10… <tibble [1 ×… <tibble [1 × 10…
# … with 3 more variables: Deep.Sleep.hours_t.test <list>, Light.Sleep.hours_t.test <list>, Awake.hours_t.test <list>
要让所有测试都“统计”，我们可以这样做：
tidy_output %>%
mutate(across(ends_with('t.test'), sapply, pull, 'statistic'))
# A tibble: 4 × 15
# Groups: Age [2]
Age Group RHR_t.test HRV_t.test Sleep.Onset_t.test Wake.Onset_t.test Hours.in.Bed_t.test Hours.of.Sleep_t.test Sleep.Disturbance… Latency.min_t.t… Cycles_t.test REM.Sleep.hours…
<chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 Old Decrease -1.90 0.171 0.684 -0.145 -1.01 -1.02 -1.45 3.05 -0.928 -0.906
2 Old Increase -2.63 0.477 -1.66 -1.96 -2.69 -2.69 -1.16 0.0848 -1.76 -1.87
3 Young Decrease 1.66 1.13 0.281 -0.305 0.0509 -0.0320 1.14 -1.34 -0.675 0.672
4 Young Increase 1.58 0.519 0.195 -1.40 -1.48 -1.17 0.397 -0.821 -1.73 0.886
# … with 3 more variables: Deep.Sleep.hours_t.test <dbl>, Light.Sleep.hours_t.test <dbl>, Awake.hours_t.test <dbl>
我有以下数据集（dput here）：
# A tibble: 3,713 x 17
ID Age Group RHR HRV Sleep.Onset Wake.Onset Hours.in.Bed Hours.of.Sleep Sleep.Disturbances Latency.min Cycles REM.Sleep.hours Deep.Sleep.hours
<int> <chr> <chr> <int> <int> <dbl> <dbl> <dbl> <dbl> <int> <dbl> <int> <dbl> <dbl>
1 5027 Young Increase 58 73 0.180 0.458 6.66 5.33 9 8.98 6 1.4 0.32
2 5027 Young Increase 83 27 0.162 0.542 9.1 6.84 15 3.48 9 1.19 1.54
3 5027 Young Increase 57 85 0.113 0.318 4.92 4.43 5 1.98 4 1.32 0.44
4 5027 Young Increase 60 70 0.0975 0.319 5.32 3.75 3 26.5 4 1.02 0.14
5 5027 Young Increase 63 72 0.105 0.329 5.38 4.74 5 2.48 5 1.32 0.07
6 5027 Young Increase 62 61 0.983 0.472 11.8 9.44 9 4.48 8 2.07 0.84
7 5027 Young Increase 66 68 0.142 0.426 6.83 5.48 15 2.98 6 1.48 0.35
8 5027 Young Increase 81 28 0.0908 0.177 2.06 1.93 2 2.48 1 0.22 0.22
9 5027 Young Increase 69 57 0.158 0.443 6.85 6.58 13 0.48 6 2.43 0
10 5027 Young Increase 63 60 0.0859 0.318 5.58 5.47 4 0.48 5 1.34 0.13
# ... with 3,703 more rows, and 3 more variables: Light.Sleep.hours <dbl>, Awake.hours <dbl>, Session <chr>
我正在尝试计算每个变量的 t 检验，按 Age 和 Group 在 Session（pre 或 post）之间分组。
df %>%
select(-ID) %>%
group_by(Age, Group) %>%
summarize_at(
vars(-group_cols(), -Session),
list(p.value = ~ t.test(. ~ Session)$p.value))
我的 p 值很成功：
# A tibble: 4 x 15
# Groups: Age [2]
Age Group RHR_p.value HRV_p.value Sleep.Onset_p.value Wake.Onset_p.value Hours.in.Bed_p.value Hours.of.Sleep_p~ Sleep.Disturban~ Latency.min_p.v~
<chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 Old Decrease 0.0594 0.865 0.495 0.885 0.316 0.307 0.148 0.00237
2 Old Increase 0.00920 0.634 0.0979 0.0514 0.00774 0.00762 0.247 0.933
3 Young Decrease 0.0975 0.259 0.779 0.760 0.959 0.975 0.256 0.181
4 Young Increase 0.115 0.604 0.846 0.164 0.140 0.242 0.692 0.412
# ... with 5 more variables: Cycles_p.value <dbl>, REM.Sleep.hours_p.value <dbl>, Deep.Sleep.hours_p.value <dbl>, Light.Sleep.hours_p.value <dbl>,
# Awake.hours_p.value <dbl>
但是，我正在努力计算这些之间的其他 t 统计量（mean、sd、t、df、95%CI） pre-post 以及正确的 p 值组。我正在努力做到这一点，因此感谢您的帮助。
我想我可能需要转换长数据并使用类似这样的东西？
df %>%
group_by(Age, Group) %>%
t_test(mean ~ ., by = "Session") %>%
adjust_pvalue(method = "bonferroni") %>%
add_significance()
Dn 数据框只能有某些对象 类 作为列类型。一种
htest 不是其中之一。
但是，我们可以将列表存储为 list-columns。
如果我们调整当前代码以输出列表 htests 作为结果，我们可以稍后单独提取测试的元素。
library(dplyr)
output <- df %>%
select(-ID) %>%
group_by(Age, Group) %>%
summarize_at(
vars(-group_cols(), -Session),
list(t.test = ~ list(t.test(. ~ Session))))
output
# A tibble: 4 × 15
# Groups: Age [2]
Age Group RHR_t.test HRV_t.test Sleep.Onset_t.test Wake.Onset_t.test Hours.in.Bed_t.test Hours.of.Sleep_t.test Sleep.Disturbance… Latency.min_t.t… Cycles_t.test REM.Sleep.hours…
<chr> <chr> <list> <list> <list> <list> <list> <list> <list> <list> <list> <list>
1 Old Decrease <htest> <htest> <htest> <htest> <htest> <htest> <htest> <htest> <htest> <htest>
2 Old Increase <htest> <htest> <htest> <htest> <htest> <htest> <htest> <htest> <htest> <htest>
3 Young Decrease <htest> <htest> <htest> <htest> <htest> <htest> <htest> <htest> <htest> <htest>
4 Young Increase <htest> <htest> <htest> <htest> <htest> <htest> <htest> <htest> <htest> <htest>
有了这个 output data.frame，我们可以根据需要从中提取单个测试和值：
output$RHR_t.test
[[1]]
Welch Two Sample t-test
data: . by Session
t = -1.8965, df = 188.22, p-value = 0.05942
alternative hypothesis: true difference in means between group Post and group Pre is not equal to 0
95 percent confidence interval:
-3.09118590 0.06082897
sample estimates:
mean in group Post mean in group Pre
62.28902 63.80420
[[2]]
Welch Two Sample t-test
data: . by Session
t = -2.6271, df = 226.21, p-value = 0.009199
alternative hypothesis: true difference in means between group Post and group Pre is not equal to 0
95 percent confidence interval:
-3.3949577 -0.4848655
sample estimates:
mean in group Post mean in group Pre
57.95946 59.89937
[[3]]
Welch Two Sample t-test
data: . by Session
t = 1.6633, df = 251.75, p-value = 0.0975
alternative hypothesis: true difference in means between group Post and group Pre is not equal to 0
95 percent confidence interval:
-0.2074028 2.4611194
sample estimates:
mean in group Post mean in group Pre
60.58255 59.45570
[[4]]
Welch Two Sample t-test
data: . by Session
t = 1.5849, df = 208.4, p-value = 0.1145
alternative hypothesis: true difference in means between group Post and group Pre is not equal to 0
95 percent confidence interval:
-0.244287 2.247775
sample estimates:
mean in group Post mean in group Pre
60.23462 59.23288
output$RHR_t.test %>%
map_dbl('p.value')
[1] 0.059424354 0.009199459 0.097497620 0.114502332
我们还可以使用 broom::tidy
output %>%
mutate(across(ends_with('t.test'), map, broom::tidy))
# A tibble: 4 × 15
# Groups: Age [2]
Age Group RHR_t.test HRV_t.test Sleep.Onset_t.te… Wake.Onset_t.test Hours.in.Bed_t.t… Hours.of.Sleep_… Sleep.Disturbanc… Latency.min_t.t… Cycles_t.test REM.Sleep.hours…
<chr> <chr> <list> <list> <list> <list> <list> <list> <list> <list> <list> <list>
1 Old Decrease <tibble [1 × 10]> <tibble [1 … <tibble [1 × 10]> <tibble [1 × 10]> <tibble [1 × 10]> <tibble [1 × 10… <tibble [1 × 10]> <tibble [1 × 10… <tibble [1 ×… <tibble [1 × 10…
2 Old Increase <tibble [1 × 10]> <tibble [1 … <tibble [1 × 10]> <tibble [1 × 10]> <tibble [1 × 10]> <tibble [1 × 10… <tibble [1 × 10]> <tibble [1 × 10… <tibble [1 ×… <tibble [1 × 10…
3 Young Decrease <tibble [1 × 10]> <tibble [1 … <tibble [1 × 10]> <tibble [1 × 10]> <tibble [1 × 10]> <tibble [1 × 10… <tibble [1 × 10]> <tibble [1 × 10… <tibble [1 ×… <tibble [1 × 10…
4 Young Increase <tibble [1 × 10]> <tibble [1 … <tibble [1 × 10]> <tibble [1 × 10]> <tibble [1 × 10]> <tibble [1 × 10… <tibble [1 × 10]> <tibble [1 × 10… <tibble [1 ×… <tibble [1 × 10…
# … with 3 more variables: Deep.Sleep.hours_t.test <list>, Light.Sleep.hours_t.test <list>, Awake.hours_t.test <list>
要让所有测试都“统计”，我们可以这样做：
tidy_output %>%
mutate(across(ends_with('t.test'), sapply, pull, 'statistic'))
# A tibble: 4 × 15
# Groups: Age [2]
Age Group RHR_t.test HRV_t.test Sleep.Onset_t.test Wake.Onset_t.test Hours.in.Bed_t.test Hours.of.Sleep_t.test Sleep.Disturbance… Latency.min_t.t… Cycles_t.test REM.Sleep.hours…
<chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 Old Decrease -1.90 0.171 0.684 -0.145 -1.01 -1.02 -1.45 3.05 -0.928 -0.906
2 Old Increase -2.63 0.477 -1.66 -1.96 -2.69 -2.69 -1.16 0.0848 -1.76 -1.87
3 Young Decrease 1.66 1.13 0.281 -0.305 0.0509 -0.0320 1.14 -1.34 -0.675 0.672
4 Young Increase 1.58 0.519 0.195 -1.40 -1.48 -1.17 0.397 -0.821 -1.73 0.886
# … with 3 more variables: Deep.Sleep.hours_t.test <dbl>, Light.Sleep.hours_t.test <dbl>, Awake.hours_t.test <dbl>