library(readxl)
## Warning: package 'readxl' was built under R version 4.5.3
library(janitor)
## Warning: package 'janitor' was built under R version 4.5.3
##
## Attaching package: 'janitor'
## The following objects are masked from 'package:stats':
##
## chisq.test, fisher.test
library(dplyr)
## Warning: package 'dplyr' was built under R version 4.5.3
##
## 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
ckd <- read_excel(file.choose(), sheet = "Sheet1") %>%
clean_names() %>%
mutate(across(where(is.character), as.factor))
# Cek nama kolom
names(ckd)
## [1] "age_of_the_patient"
## [2] "blood_pressure_mm_hg"
## [3] "red_blood_cells_in_urine"
## [4] "bacteria_in_urine"
## [5] "blood_urea_mg_dl"
## [6] "serum_creatinine_mg_dl"
## [7] "hemoglobin_level_gms"
## [8] "hypertension_yes_no"
## [9] "diabetes_mellitus_yes_no"
## [10] "coronary_artery_disease_yes_no"
## [11] "anemia_yes_no"
## [12] "urine_protein_to_creatinine_ratio"
## [13] "urine_output_ml_day"
## [14] "cholesterol_level"
## [15] "family_history_of_chronic_kidney_disease"
## [16] "smoking_status"
## [17] "body_mass_index_bmi"
## [18] "physical_activity_level"
## [19] "ckd_status"
library(tidyr)
library(ggplot2)
## Warning: package 'ggplot2' was built under R version 4.5.3
num_vars <- c("age_of_the_patient", "blood_pressure_mm_hg",
"blood_urea_mg_dl", "serum_creatinine_mg_dl",
"hemoglobin_level_gms", "urine_protein_to_creatinine_ratio",
"urine_output_ml_day", "cholesterol_level",
"body_mass_index_bmi")
ckd %>%
select(all_of(num_vars)) %>%
pivot_longer(everything(), names_to = "variabel", values_to = "nilai") %>%
ggplot(aes(x = nilai, fill = variabel)) +
geom_histogram(bins = 12, color = "white", alpha = 0.85) +
facet_wrap(~ variabel, scales = "free", ncol = 3) +
labs(title = "Distribusi Semua Variabel Numerik CKD",
x = NULL, y = "Frekuensi") +
theme_minimal(base_size = 10) +
theme(legend.position = "none",
strip.text = element_text(face = "bold", size = 10))
ckd %>%
select(all_of(num_vars)) %>%
pivot_longer(everything(), names_to = "variabel", values_to = "nilai") %>%
ggplot(aes(x = variabel, y = nilai, fill = variabel)) +
geom_boxplot(alpha = 0.85) +
facet_wrap(~ variabel, scales = "free", ncol = 3) +
labs(title = "Boxplot Semua Variabel Numerik CKD",
x = NULL, y = NULL) +
theme_minimal(base_size = 10) +
theme(legend.position = "none",
strip.text = element_text(face = "bold", size = 9),
axis.text.x = element_text(angle = 45, hjust = 1, size = 7))
GGally::ggpairs(
ckd %>% select(age_of_the_patient,
blood_pressure_mm_hg,
serum_creatinine_mg_dl,
hemoglobin_level_gms,
body_mass_index_bmi,
ckd_status),
aes(color = ckd_status, alpha = 0.6),
lower = list(continuous = GGally::wrap("smooth", alpha = 0.3, size = 0.8)),
upper = list(continuous = GGally::wrap("cor", size = 3)),
diag = list(continuous = GGally::wrap("densityDiag", alpha = 0.4))
) +
scale_color_manual(values = c("No" = "#4CAF50", "Yes" = "#E53935")) +
scale_fill_manual(values = c("No" = "#4CAF50", "Yes" = "#E53935")) +
theme_minimal(base_size = 10)
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's fill values.
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's fill values.
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's fill values.
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's fill values.
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's fill values.
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's fill values.
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's fill values.
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's fill values.
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's fill values.
## No shared levels found between `names(values)` of the manual scale and the
## data's fill values.
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's fill values.
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's fill values.
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's fill values.
## No shared levels found between `names(values)` of the manual scale and the
## data's fill values.
## No shared levels found between `names(values)` of the manual scale and the
## data's fill values.
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's fill values.
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's fill values.
## No shared levels found between `names(values)` of the manual scale and the
## data's fill values.
## No shared levels found between `names(values)` of the manual scale and the
## data's fill values.
## No shared levels found between `names(values)` of the manual scale and the
## data's fill values.
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## `stat_bin()` using `bins = 30`. Pick better value `binwidth`.
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## `stat_bin()` using `bins = 30`. Pick better value `binwidth`.
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## `stat_bin()` using `bins = 30`. Pick better value `binwidth`.
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## `stat_bin()` using `bins = 30`. Pick better value `binwidth`.
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## `stat_bin()` using `bins = 30`. Pick better value `binwidth`.
## Warning: No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
## No shared levels found between `names(values)` of the manual scale and the
## data's colour values.
# Buat data_num — hanya kolom numerik
data_num <- ckd %>% select(where(is.numeric))
# Cek
dim(data_num) # 50 9
## [1] 50 9
names(data_num)
## [1] "age_of_the_patient" "blood_pressure_mm_hg"
## [3] "blood_urea_mg_dl" "serum_creatinine_mg_dl"
## [5] "hemoglobin_level_gms" "urine_protein_to_creatinine_ratio"
## [7] "urine_output_ml_day" "cholesterol_level"
## [9] "body_mass_index_bmi"
# Statistik deskriptif
hasil <- data.frame(
Mean = sapply(data_num, mean, na.rm = TRUE),
Median = sapply(data_num, median, na.rm = TRUE),
SD = sapply(data_num, sd, na.rm = TRUE),
Min = sapply(data_num, min, na.rm = TRUE),
Max = sapply(data_num, max, na.rm = TRUE)
)
print(round(hasil, 2))
## Mean Median SD Min Max
## age_of_the_patient 56.90 54.50 20.08 25.00 90.00
## blood_pressure_mm_hg 131.90 127.50 29.45 80.00 179.00
## blood_urea_mg_dl 101.27 97.62 58.01 8.69 198.73
## serum_creatinine_mg_dl 7.61 8.17 3.88 0.76 14.58
## hemoglobin_level_gms 12.09 11.85 3.37 6.00 17.50
## urine_protein_to_creatinine_ratio 2.30 2.38 1.23 0.24 4.49
## urine_output_ml_day 1739.52 1740.50 802.09 308.00 2933.00
## cholesterol_level 199.52 214.00 66.92 100.00 298.00
## body_mass_index_bmi 26.33 25.10 7.64 15.20 39.00
# ============================================================
# HEATMAP KORELASI — TANPA reshape2
# ============================================================
library(readxl); library(janitor); library(dplyr)
library(tidyr); library(ggplot2)
# Import
ckd <- read_excel(file.choose(), sheet = "Sheet1") %>%
clean_names() %>%
mutate(across(where(is.character), as.factor))
# Data numerik
data_num <- ckd %>% select(where(is.numeric))
# Matriks korelasi (Spearman)
cor_mat <- cor(data_num, use = "complete.obs", method = "spearman")
# Long format dengan pivot_longer
cor_long <- cor_mat %>%
as.data.frame() %>%
tibble::rownames_to_column("Var1") %>%
pivot_longer(-Var1, names_to = "Var2", values_to = "value")
# Heatmap
ggplot(cor_long, aes(x = Var1, y = Var2, fill = value)) +
geom_tile(color = "white") +
geom_text(aes(label = round(value, 2)), size = 3.5, color = "black") +
scale_fill_gradient2(
low = "#E63946",
mid = "white",
high = "#2E86AB",
midpoint = 0,
limits = c(-1, 1),
name = "r"
) +
labs(
title = "Heatmap Korelasi Antar Variabel Numerik Pasien CKD",
x = "", y = ""
) +
theme_minimal(base_size = 12) +
theme(
plot.title = element_text(hjust = 0.5, face = "bold"),
axis.text.x = element_text(angle = 45, hjust = 1, face = "bold"),
axis.text.y = element_text(face = "bold"),
panel.grid = element_blank()
)
