Working with output objects
R For SAS Users
Melinda Higgins, PhD
Research Professor/Senior Biostatistician Emory University
Output from summary
# Save summary output, view davissmry
davissmry <- daviskeep %>%
select(weight, height, bmi) %>%
summary()
# Display summary output object
davissmry
weight height bmi
Min. : 39.0 Min. :148.0 Min. :15.82
1st Qu.: 55.0 1st Qu.:164.0 1st Qu.:20.22
Median : 63.0 Median :170.0 Median :21.80
Mean : 65.3 Mean :170.6 Mean :22.26
3rd Qu.: 73.5 3rd Qu.:177.5 3rd Qu.:23.94
Max. :119.0 Max. :197.0 Max. :36.73
Output from summary
# Class of davissmry
class(davissmry)
# Check davissmry is also a matrix
is.matrix(davissmry)
# Display dimensions of davissmry
dim(davissmry)
[1] "table"
[1] TRUE
[1] 6 3
Select elements from summary object
# Display columns 1 to 2 from output
davissmry[,1:2]
weight height
Min. : 39.0 Min. :148.0
1st Qu.: 55.0 1st Qu.:164.0
Median : 63.0 Median :170.0
Mean : 65.3 Mean :170.6
3rd Qu.: 73.5 3rd Qu.:177.5
Max. :119.0 Max. :197.0
# Display rows 4 to 6 from output
davissmry[4:6,]
weight height bmi
Mean : 65.3 Mean :170.6 Mean :22.26
3rd Qu.: 73.5 3rd Qu.:177.5 3rd Qu.:23.94
Max. :119.0 Max. :197.0 Max. :36.73
Output from dplyr summarise
# Save output from summarise
davissmall <- daviskeep %>%
select(weight, height) %>%
summarise(across(everything(),
list(mean = ~mean(.x),
sd = ~sd(.x))))
# Display davissmall output object
davissmall
weight_mean weight_sd height_mean height_sd
1 65.29648 13.34346 170.5879 8.948848
# Show structure of davissmall object
str(davissmall)
'data.frame': 1 obs. of 4 variables:
$ weight_mean: num 65.3
$ weight_sd : num 13.3
$ height_mean: num 171
$ height_sd : num 8.95
Display elements from summarise output
# Display column 3 for mean height
davissmall[, 3]
[1] 170.5879
# Display element name height_mean
davissmall$height_mean
[1] 170.5879
Output from dplyr group_by
# Use group_by get stats for bmi by sex
davisbmisex <- daviskeep %>%
group_by(sex) %>%
select(bmi, sex) %>%
summarise(across(everything(),
list(mean = ~mean(.x),
sd = ~sd(.x))))
# Display output object
davisbmisex
# A tibble: 2 × 3
sex bmi_mean bmi_sd
<fct> <dbl> <dbl>
1 F 21.0 2.18
2 M 23.9 3.12
# Get structure of davisbmisex
str(davisbmisex)
tibble [2 × 3] (S3: tbl_df/tbl/data.frame)
$ sex : Factor w/ 2 levels "F","M": 1 2
$ bmi_mean: num [1:2] 21 23.9
$ bmi_sd : num [1:2] 2.18 3.12
1 The sex variable was automatically coded as a Factor class type.
Display elements from group_by output
# Display column 2 of davisbmisex
davisbmisex[, 2]
# A tibble: 2 × 1
bmi_mean
<dbl>
1 21.0
2 23.9
# Display row 1 of davisbmisex
davisbmisex[1,]
# A tibble: 1 × 3
sex bmi_mean bmi_sd
<fct> <dbl> <dbl>
1 F 21.0 2.18
Display elements from group_by output
# Display sd element from davisbmisex
davisbmisex$bmi_sd
[1] 2.176094 3.120285
# Display row for males
davisbmisex %>%
filter(sex == "M")
# A tibble: 1 × 3
sex bmi_mean bmi_sd
<fct> <dbl> <dbl>
1 M 23.9 3.12
Output from psych describe
# Save psych::describe() output as davispsych
davispsych <- daviskeep %>%
select(weight, height, bmi) %>%
psych::describe()
# Display davispsych output object
davispsych
vars n mean sd median trimmed mad min max range skew kurtosis se
weight 1 199 65.30 13.34 63.0 64.12 11.86 39.00 119.00 80.00 0.91 0.84 0.95
height 2 199 170.59 8.95 170.0 170.40 10.38 148.00 197.00 49.00 0.21 -0.38 0.63
bmi 3 199 22.26 3.01 21.8 22.08 2.55 15.82 36.73 20.91 0.91 1.91 0.21
Class and structure of psych describe output
str(davispsych)
Classes ‘psych’, ‘describe’ and 'data.frame':
3 obs. of 13 variables:
$ vars : int 1 2 3
$ n : num 199 199 199
$ mean : num 65.3 170.6 22.3
$ sd : num 13.34 8.95 3.01
$ median : num 63 170 21.8
$ trimmed : num 64.1 170.4 22.1
$ mad : num 11.86 10.38 2.55
$ min : num 39 148 15.8
$ max : num 119 197 36.7
$ range : num 80 49 20.9
$ skew : num 0.905 0.21 0.913
$ kurtosis: num 0.843 -0.379 1.914
$ se : num 0.946 0.634 0.213
Display psych describe output elements
# Display trimmed means
davispsych$trimmed
[1] 64.12422 170.40373 22.08452
# Display row 2 for height
davispsych %>%
slice(2)
vars n mean sd median trimmed mad min max range skew kurtosis se
1 2 199 170.59 8.95 170 170.4 10.38 148 197 49 0.21 -0.38 0.63
Display psych describe output elements
# Display sample size, median, min and max elements
davispsych %>%
select(n, median, min, max)
n median min max
weight 199 63.0 39.00 119.00
height 199 170.0 148.00 197.00
bmi 199 21.8 15.82 36.73
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