TABLA 1

library(readxl)
BASE <- read_excel("BASE_PIERNAS.xlsx")
library(dplyr)
cat(names(BASE), sep = ", ")
## ID, Genero, Edad, Talla, Peso, Regurgitacion, Pirosis, Dolor toracico, Tipo de Union, Hernia Hiatal, Tamaño cm, P basal LES, IRP, DCI, Dx MAR, Delta Esofagico, D gastrico, TEA, Deemester, IBMN, SAP, No. Episodios de reflujo, DIAGNOSTICO
library(stringr)
BASE$DIAGNOSTICO <- str_to_title(tolower(BASE$DIAGNOSTICO))
BASE$DIAGNOSTICO <- case_when(
  BASE$DIAGNOSTICO%in% c("pirsis", "pirosis", "Pirsis") ~ "Pirosis",
  BASE$DIAGNOSTICO %in% c("nerd") ~ "NERD",
  TRUE ~ BASE$DIAGNOSTICO
)

BASE$Regurgitacion <- trimws(tolower(BASE$Regurgitacion))
BASE$Pirosis <- trimws(tolower(BASE$Pirosis))
BASE$`Hernia Hiatal` <- trimws(tolower(BASE$`Hernia Hiatal`))
BASE$`Dx MAR` <- trimws(tolower(BASE$`Dx MAR`))
BASE$`D gastrico` <- trimws(tolower(BASE$`D gastrico`))

BASE$`Dolor toracico` <- case_when(
  BASE$`Dolor toracico`%in% c("so", "si") ~ "si",
  BASE$`Dolor toracico` %in% c("no") ~ "no",
  TRUE ~ BASE$`Dolor toracico`
)

library(gtsummary)

#cat(names(BASE), sep = ",")
tabla1 <- BASE %>%
   dplyr::select(Genero, Edad, Talla, Peso, Regurgitacion, Pirosis, `Dolor toracico`, `Tipo de Union`, `Hernia Hiatal`, `P basal LES`, IRP, DCI, `Dx MAR`, `Delta Esofagico`, `D gastrico`, TEA, Deemester,`No. Episodios de reflujo`, DIAGNOSTICO) %>%
  tbl_summary(
    by = DIAGNOSTICO,
    type = list(
      all_continuous()                    ~ "continuous2",
      c( Regurgitacion, Pirosis, `Dolor toracico`, `Tipo de Union`, `Hernia Hiatal`, `Dx MAR`, `D gastrico`)            ~ "categorical"
    ),
    label = list(
      Genero ~ "Sexo", 
      Edad ~ "Edad", 
      Talla ~ "Altura", 
      Peso ~ "Peso", 
      Regurgitacion ~ "Regurgitación", 
      Pirosis ~ "Pirosis", 
      `Dolor toracico` ~ "Dolor toracico", 
      `Tipo de Union` ~ "Tipo de unión", 
      `Hernia Hiatal` ~ "Hernia Hiatal", 
      `P basal LES` ~ "P basal LES",
       IRP ~ "IRP", 
      DCI ~ "DCI", 
      `Dx MAR` ~ "dx Mar", 
      `Delta Esofagico` ~ "Delta esofágico", 
      `D gastrico` ~ "D. gástrico", 
      TEA ~ "Timpo exposición ácida", 
      Deemester ~"Deemester", 
      `No. Episodios de reflujo` ~ "`Episodios de reflujo`"
    ),
    statistic = list(
      all_continuous2()  ~ c(
        "{mean} ({sd})",
        "{median} ({p25}, {p75})",
        "{min} - {max}"
      ),
      all_categorical() ~ "{n} ({p}%)"
    ),
    digits = list(
      all_continuous()  ~ 2,
      all_categorical() ~ 1
    ),
    missing = "ifany",
    missing_text = "Sin dato"
  ) %>%
  add_p(
    test = list(
      all_continuous2()  ~ "kruskal.test",  
      all_categorical() ~ "chisq.test"
    ),
    pvalue_fun = ~ style_pvalue(.x, digits = 3)
  ) %>%
  add_overall() %>%
  modify_header(label ~ "**Variable**") %>%
  bold_labels() %>%
  bold_p(t = 0.05) %>%
  modify_caption("**Tabla 1**")


tabla1
Tabla 1
Variable Overall
N = 691		 Nerd
N = 281		 Pirosis
N = 411		 p-value2
Sexo


0.888
    F 56.0 (81.2%) 22.0 (78.6%) 34.0 (82.9%)
    M 13.0 (18.8%) 6.0 (21.4%) 7.0 (17.1%)
Edad


0.087
    Mean (SD) 51.91 (13.02) 55.57 (13.82) 49.41 (11.97)
    Median (Q1, Q3) 51.00 (42.00, 62.00) 61.00 (42.00, 65.00) 48.00 (42.00, 57.00)
    Min - Max 22.00 - 78.00 30.00 - 78.00 22.00 - 72.00
Altura


0.599
    Mean (SD) 159.36 (8.21) 160.18 (9.37) 158.80 (7.39)
    Median (Q1, Q3) 158.00 (154.00, 165.00) 159.00 (153.00, 166.00) 158.00 (154.00, 161.00)
    Min - Max 143.00 - 180.00 143.00 - 180.00 145.00 - 174.00
Peso


0.096
    Mean (SD) 67.22 (12.95) 69.04 (10.31) 65.95 (14.52)
    Median (Q1, Q3) 65.00 (58.00, 73.00) 67.00 (60.50, 75.00) 64.00 (56.50, 69.50)
    Min - Max 43.00 - 120.00 55.00 - 93.00 43.00 - 120.00
    Sin dato 1 0 1
Regurgitación


0.912
    no 14.0 (20.3%) 5.0 (17.9%) 9.0 (22.0%)
    si 55.0 (79.7%) 23.0 (82.1%) 32.0 (78.0%)
Pirosis


0.453
    no 22.0 (31.9%) 7.0 (25.0%) 15.0 (36.6%)
    si 47.0 (68.1%) 21.0 (75.0%) 26.0 (63.4%)
Dolor toracico


0.198
    no 49.0 (71.0%) 17.0 (60.7%) 32.0 (78.0%)
    si 20.0 (29.0%) 11.0 (39.3%) 9.0 (22.0%)
Tipo de unión


0.202
    I 33.0 (47.8%) 15.0 (53.6%) 18.0 (43.9%)
    II 7.0 (10.1%) 1.0 (3.6%) 6.0 (14.6%)
    IIIa 17.0 (24.6%) 9.0 (32.1%) 8.0 (19.5%)
    IIIb 12.0 (17.4%) 3.0 (10.7%) 9.0 (22.0%)
Hernia Hiatal


>0.999
    no 40.0 (58.0%) 16.0 (57.1%) 24.0 (58.5%)
    si 29.0 (42.0%) 12.0 (42.9%) 17.0 (41.5%)
P basal LES


0.083
    Mean (SD) 25.34 (12.99) 21.92 (10.50) 27.68 (14.10)
    Median (Q1, Q3) 22.10 (15.20, 32.60) 19.15 (13.85, 28.95) 23.90 (17.20, 35.20)
    Min - Max 3.30 - 67.00 3.30 - 48.00 5.30 - 67.00
IRP


0.409
    Mean (SD) 8.25 (3.56) 8.66 (3.55) 7.97 (3.59)
    Median (Q1, Q3) 8.10 (4.90, 11.10) 9.20 (5.65, 11.80) 7.70 (4.20, 11.00)
    Min - Max 1.10 - 14.00 2.20 - 14.00 1.10 - 13.80
DCI


0.286
    Mean (SD) 341.54 (655.90) 242.04 (522.05) 409.49 (731.94)
    Median (Q1, Q3) 90.00 (50.00, 100.00) 90.00 (25.00, 100.00) 90.00 (60.00, 653.00)
    Min - Max 0.00 - 3,451.00 0.00 - 2,461.00 0.00 - 3,451.00
dx Mar


0.130
    ca 1.0 (1.4%) 0.0 (0.0%) 1.0 (2.4%)
    mei 23.0 (33.3%) 13.0 (46.4%) 10.0 (24.4%)
    normal 45.0 (65.2%) 15.0 (53.6%) 30.0 (73.2%)
Delta esofágico


0.482
    Mean (SD) 22.46 (24.77) 28.78 (28.22) 18.14 (21.41)
    Median (Q1, Q3) 10.60 (2.90, 39.80) 25.45 (2.55, 45.40) 7.80 (3.10, 25.70)
    Min - Max 0.10 - 89.20 0.10 - 89.20 0.40 - 83.70
D. gástrico


0.044
    negativo 36.0 (52.2%) 10.0 (35.7%) 26.0 (63.4%)
    positivo 33.0 (47.8%) 18.0 (64.3%) 15.0 (36.6%)
Timpo exposición ácida


<0.001
    Mean (SD) 5.48 (5.54) 10.58 (5.35) 2.00 (1.45)
    Median (Q1, Q3) 3.50 (1.70, 7.80) 8.40 (6.60, 14.45) 1.80 (0.50, 2.90)
    Min - Max 0.10 - 24.90 4.10 - 24.90 0.10 - 5.70
Deemester


<0.001
    Mean (SD) 39.36 (65.54) 63.44 (69.24) 22.92 (58.17)
    Median (Q1, Q3) 17.60 (8.10, 35.90) 38.70 (24.10, 60.05) 9.00 (4.20, 15.10)
    Min - Max 0.30 - 288.00 12.90 - 267.00 0.30 - 288.00
`Episodios de reflujo`


0.002
    Mean (SD) 53.59 (40.76) 66.93 (43.74) 44.49 (36.37)
    Median (Q1, Q3) 44.00 (29.00, 58.00) 55.50 (43.00, 87.00) 36.00 (25.00, 49.00)
    Min - Max 1.00 - 217.00 8.00 - 217.00 1.00 - 189.00
1 n (%)
2 Pearson’s Chi-squared test; Kruskal-Wallis rank sum test 
library(flextable)
tabla1 %>%
  as_flex_table() %>%
  save_as_docx(path = "tabla1.docx")