knitr::opts_chunk$set(echo = TRUE)
library(readxl)
library(dplyr)
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
library(janitor)
##
## Attaching package: 'janitor'
## The following objects are masked from 'package:stats':
##
## chisq.test, fisher.test
library(skimr)
library(xlsx)
ca_pulmon <- read_excel("BASE DE DATOS CA PULMONAR 14 DIC 2020.xlsx",
sheet = "tb_modulo_pulmon_iniciales")
pulmon2 <- ca_pulmon %>%
filter(tipo_histologico == 1 | 2 | 3)
pulmon2$estadio_dx[pulmon2$estadio_dx == 98] <- "NA"
pulmon2$estadio_dx[is.na(pulmon2$estadio_dx)] <- "NA"
pulmon2$quimioterapia_celula_no_peque[pulmon2$quimioterapia_celula_no_peque == 98] <- "NA"
pulmon2$quimioterapia_celula_no_peque[is.na(pulmon2$quimioterapia_celula_no_peque)] <- "NA"
#### Quimio
pulmon2 %>%
tabyl(estadio_dx, quimioterapia_celula_no_peque) %>%
adorn_totals(c("row")) %>%
adorn_percentages(denominator = "row") %>%
adorn_pct_formatting() %>%
adorn_ns(position = "front") %>%
adorn_title()
## quimioterapia_celula_no_peque
## estadio_dx 1 3 4 5
## 1 0 (0.0%) 0 (0.0%) 1 (5.6%) 0 (0.0%)
## 2 1 (11.1%) 1 (11.1%) 0 (0.0%) 0 (0.0%)
## 3 0 (0.0%) 1 (16.7%) 0 (0.0%) 1 (16.7%)
## 4 3 (17.6%) 1 (5.9%) 0 (0.0%) 0 (0.0%)
## 5 4 (26.7%) 0 (0.0%) 0 (0.0%) 0 (0.0%)
## 6 2 (11.1%) 0 (0.0%) 4 (22.2%) 0 (0.0%)
## 7 0 (0.0%) 1 (8.3%) 1 (8.3%) 0 (0.0%)
## 8 12 (11.3%) 10 (9.4%) 20 (18.9%) 0 (0.0%)
## 9 16 (9.2%) 12 (6.9%) 26 (15.0%) 0 (0.0%)
## NA 4 (11.4%) 1 (2.9%) 0 (0.0%) 0 (0.0%)
## Total 42 (10.3%) 27 (6.6%) 52 (12.7%) 1 (0.2%)
##
## 6 7 8 9 NA NULL
## 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 16 (88.9%) 1 (5.6%)
## 0 (0.0%) 0 (0.0%) 0 (0.0%) 1 (11.1%) 6 (66.7%) 0 (0.0%)
## 1 (16.7%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 3 (50.0%) 0 (0.0%)
## 0 (0.0%) 1 (5.9%) 1 (5.9%) 0 (0.0%) 10 (58.8%) 1 (5.9%)
## 0 (0.0%) 1 (6.7%) 0 (0.0%) 2 (13.3%) 8 (53.3%) 0 (0.0%)
## 3 (16.7%) 0 (0.0%) 1 (5.6%) 0 (0.0%) 8 (44.4%) 0 (0.0%)
## 2 (16.7%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 8 (66.7%) 0 (0.0%)
## 1 (0.9%) 2 (1.9%) 0 (0.0%) 3 (2.8%) 58 (54.7%) 0 (0.0%)
## 9 (5.2%) 0 (0.0%) 0 (0.0%) 7 (4.0%) 99 (57.2%) 4 (2.3%)
## 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 29 (82.9%) 1 (2.9%)
## 16 (3.9%) 4 (1.0%) 2 (0.5%) 13 (3.2%) 245 (59.9%) 7 (1.7%)
### Radio
pulmon2 %>%
tabyl(estadio_dx, radioterapia_profilactica) %>%
adorn_totals(c("row")) %>%
adorn_percentages(denominator = "row") %>%
adorn_pct_formatting() %>%
adorn_ns(position = "front") %>%
adorn_title()
## radioterapia_profilactica
## estadio_dx 0 1 98 NULL
## 1 0 (0.0%) 0 (0.0%) 17 (94.4%) 1 (5.6%)
## 2 1 (11.1%) 0 (0.0%) 8 (88.9%) 0 (0.0%)
## 3 0 (0.0%) 0 (0.0%) 6 (100.0%) 0 (0.0%)
## 4 2 (11.8%) 0 (0.0%) 14 (82.4%) 1 (5.9%)
## 5 3 (20.0%) 0 (0.0%) 12 (80.0%) 0 (0.0%)
## 6 4 (22.2%) 0 (0.0%) 14 (77.8%) 0 (0.0%)
## 7 2 (16.7%) 0 (0.0%) 10 (83.3%) 0 (0.0%)
## 8 13 (12.3%) 1 (0.9%) 92 (86.8%) 0 (0.0%)
## 9 35 (20.2%) 9 (5.2%) 125 (72.3%) 4 (2.3%)
## NA 0 (0.0%) 0 (0.0%) 34 (97.1%) 1 (2.9%)
## Total 60 (14.7%) 10 (2.4%) 332 (81.2%) 7 (1.7%)
# Radio Torax
pulmon2 %>%
tabyl(estadio_dx, radioterapia_toracica) %>%
adorn_totals(c("row")) %>%
adorn_percentages(denominator = "row") %>%
adorn_pct_formatting() %>%
adorn_ns(position = "front") %>%
adorn_title()
## radioterapia_toracica
## estadio_dx 0 1 98 99 NULL
## 1 0 (0.0%) 0 (0.0%) 17 (94.4%) 0 (0.0%) 1 (5.6%)
## 2 0 (0.0%) 1 (11.1%) 8 (88.9%) 0 (0.0%) 0 (0.0%)
## 3 0 (0.0%) 0 (0.0%) 6 (100.0%) 0 (0.0%) 0 (0.0%)
## 4 0 (0.0%) 2 (11.8%) 14 (82.4%) 0 (0.0%) 1 (5.9%)
## 5 1 (6.7%) 1 (6.7%) 11 (73.3%) 1 (6.7%) 0 (0.0%)
## 6 0 (0.0%) 4 (22.2%) 14 (77.8%) 0 (0.0%) 0 (0.0%)
## 7 0 (0.0%) 2 (16.7%) 10 (83.3%) 0 (0.0%) 0 (0.0%)
## 8 12 (11.3%) 3 (2.8%) 89 (84.0%) 1 (0.9%) 0 (0.0%)
## 9 39 (22.5%) 8 (4.6%) 119 (68.8%) 1 (0.6%) 4 (2.3%)
## NA 0 (0.0%) 0 (0.0%) 34 (97.1%) 0 (0.0%) 1 (2.9%)
## Total 52 (12.7%) 21 (5.1%) 322 (78.7%) 3 (0.7%) 7 (1.7%)
##
## NA_
## 0 (0.0%)
## 0 (0.0%)
## 0 (0.0%)
## 0 (0.0%)
## 1 (6.7%)
## 0 (0.0%)
## 0 (0.0%)
## 1 (0.9%)
## 2 (1.2%)
## 0 (0.0%)
## 4 (1.0%)
# Cirugia
pulmon2 %>%
tabyl(estadio_dx, cirugia) %>%
adorn_totals(c("row")) %>%
adorn_percentages(denominator = "row") %>%
adorn_pct_formatting() %>%
adorn_ns(position = "front") %>%
adorn_title()
## cirugia
## estadio_dx 0 1 98 NA NA_
## 1 0 (0.0%) 17 (94.4%) 1 (5.6%) 0 (0.0%) 0 (0.0%)
## 2 1 (11.1%) 8 (88.9%) 0 (0.0%) 0 (0.0%) 0 (0.0%)
## 3 0 (0.0%) 5 (83.3%) 1 (16.7%) 0 (0.0%) 0 (0.0%)
## 4 4 (23.5%) 10 (58.8%) 3 (17.6%) 0 (0.0%) 0 (0.0%)
## 5 3 (20.0%) 7 (46.7%) 5 (33.3%) 0 (0.0%) 0 (0.0%)
## 6 9 (50.0%) 5 (27.8%) 3 (16.7%) 0 (0.0%) 1 (5.6%)
## 7 7 (58.3%) 4 (33.3%) 1 (8.3%) 0 (0.0%) 0 (0.0%)
## 8 55 (51.9%) 29 (27.4%) 20 (18.9%) 0 (0.0%) 2 (1.9%)
## 9 133 (76.9%) 23 (13.3%) 16 (9.2%) 0 (0.0%) 1 (0.6%)
## NA 14 (40.0%) 2 (5.7%) 18 (51.4%) 1 (2.9%) 0 (0.0%)
## Total 226 (55.3%) 110 (26.9%) 68 (16.6%) 1 (0.2%) 4 (1.0%)
# Inhibitors TK
pulmon2 %>%
tabyl(estadio_dx, tipo_inhibidor) %>%
adorn_totals(c("row")) %>%
adorn_percentages(denominator = "row") %>%
adorn_pct_formatting() %>%
adorn_ns(position = "front") %>%
adorn_title()
## tipo_inhibidor
## estadio_dx 1 2 3 5 98 NA
## 1 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 17 (94.4%) 1 (5.6%)
## 2 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 9 (100.0%) 0 (0.0%)
## 3 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 6 (100.0%) 0 (0.0%)
## 4 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 16 (94.1%) 1 (5.9%)
## 5 1 (6.7%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 14 (93.3%) 0 (0.0%)
## 6 1 (5.6%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 17 (94.4%) 0 (0.0%)
## 7 0 (0.0%) 0 (0.0%) 1 (8.3%) 0 (0.0%) 11 (91.7%) 0 (0.0%)
## 8 4 (3.8%) 0 (0.0%) 0 (0.0%) 2 (1.9%) 100 (94.3%) 0 (0.0%)
## 9 16 (9.2%) 2 (1.2%) 0 (0.0%) 5 (2.9%) 150 (86.7%) 0 (0.0%)
## NA 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 34 (97.1%) 1 (2.9%)
## Total 22 (5.4%) 2 (0.5%) 1 (0.2%) 7 (1.7%) 374 (91.4%) 3 (0.7%)
# Tto Antiangiogenico
pulmon2 %>%
tabyl(estadio_dx, tratamiento_antiangionenico) %>%
adorn_totals(c("row")) %>%
adorn_percentages(denominator = "row") %>%
adorn_pct_formatting() %>%
adorn_ns(position = "front") %>%
adorn_title()
## tratamiento_antiangionenico
## estadio_dx 0 1 98 NULL
## 1 16 (88.9%) 0 (0.0%) 1 (5.6%) 1 (5.6%)
## 2 9 (100.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%)
## 3 5 (83.3%) 0 (0.0%) 1 (16.7%) 0 (0.0%)
## 4 11 (64.7%) 0 (0.0%) 3 (17.6%) 1 (5.9%)
## 5 9 (60.0%) 0 (0.0%) 5 (33.3%) 0 (0.0%)
## 6 13 (72.2%) 1 (5.6%) 3 (16.7%) 0 (0.0%)
## 7 10 (83.3%) 1 (8.3%) 1 (8.3%) 0 (0.0%)
## 8 72 (67.9%) 8 (7.5%) 20 (18.9%) 0 (0.0%)
## 9 135 (78.0%) 5 (2.9%) 16 (9.2%) 4 (2.3%)
## NA 16 (45.7%) 0 (0.0%) 18 (51.4%) 1 (2.9%)
## Total 296 (72.4%) 15 (3.7%) 68 (16.6%) 7 (1.7%)
##
## NA_
## 0 (0.0%)
## 0 (0.0%)
## 0 (0.0%)
## 2 (11.8%)
## 1 (6.7%)
## 1 (5.6%)
## 0 (0.0%)
## 6 (5.7%)
## 13 (7.5%)
## 0 (0.0%)
## 23 (5.6%)
# Innmunoterapia
pulmon2 %>%
tabyl(estadio_dx, inmunoterapia) %>%
adorn_totals(c("row")) %>%
adorn_percentages(denominator = "row") %>%
adorn_pct_formatting() %>%
adorn_ns(position = "front") %>%
adorn_title()
## inmunoterapia
## estadio_dx 0 1 98 NA NA_
## 1 17 (94.4%) 0 (0.0%) 1 (5.6%) 0 (0.0%) 0 (0.0%)
## 2 9 (100.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%)
## 3 5 (83.3%) 0 (0.0%) 1 (16.7%) 0 (0.0%) 0 (0.0%)
## 4 13 (76.5%) 1 (5.9%) 3 (17.6%) 0 (0.0%) 0 (0.0%)
## 5 9 (60.0%) 1 (6.7%) 5 (33.3%) 0 (0.0%) 0 (0.0%)
## 6 15 (83.3%) 0 (0.0%) 3 (16.7%) 0 (0.0%) 0 (0.0%)
## 7 11 (91.7%) 0 (0.0%) 1 (8.3%) 0 (0.0%) 0 (0.0%)
## 8 71 (67.0%) 14 (13.2%) 20 (18.9%) 0 (0.0%) 1 (0.9%)
## 9 148 (85.5%) 8 (4.6%) 16 (9.2%) 0 (0.0%) 1 (0.6%)
## NA 16 (45.7%) 0 (0.0%) 18 (51.4%) 1 (2.9%) 0 (0.0%)
## Total 314 (76.8%) 24 (5.9%) 68 (16.6%) 1 (0.2%) 2 (0.5%)
# Paliativo
pulmon2 %>%
tabyl(estadio_dx, paliativo) %>%
adorn_totals(c("row")) %>%
adorn_percentages(denominator = "row") %>%
adorn_pct_formatting() %>%
adorn_ns(position = "front") %>%
adorn_title()
## paliativo
## estadio_dx 0 1 98 NA
## 1 16 (88.9%) 1 (5.6%) 1 (5.6%) 0 (0.0%)
## 2 9 (100.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%)
## 3 5 (83.3%) 0 (0.0%) 1 (16.7%) 0 (0.0%)
## 4 12 (70.6%) 2 (11.8%) 3 (17.6%) 0 (0.0%)
## 5 10 (66.7%) 0 (0.0%) 5 (33.3%) 0 (0.0%)
## 6 13 (72.2%) 2 (11.1%) 3 (16.7%) 0 (0.0%)
## 7 5 (41.7%) 6 (50.0%) 1 (8.3%) 0 (0.0%)
## 8 49 (46.2%) 37 (34.9%) 20 (18.9%) 0 (0.0%)
## 9 101 (58.4%) 56 (32.4%) 16 (9.2%) 0 (0.0%)
## NA 10 (28.6%) 6 (17.1%) 18 (51.4%) 1 (2.9%)
## Total 230 (56.2%) 110 (26.9%) 68 (16.6%) 1 (0.2%)
#### Mortalidad
pulmon2 <- pulmon2 %>%
mutate(mortalidad = ifelse(fecha_muerte == "NULL",0,1)) #### Variable transformada
pulmon2 %>%
tabyl(mortalidad)
## mortalidad n percent
## 0 296 0.7237164
## 1 113 0.2762836
pulmon2 %>%
tabyl(estadio_dx, mortalidad) %>%
adorn_totals(c("row")) %>%
adorn_percentages(denominator = "row") %>%
adorn_pct_formatting() %>%
adorn_ns(position = "front") %>%
adorn_title()
## mortalidad
## estadio_dx 0 1
## 1 17 (94.4%) 1 (5.6%)
## 2 7 (77.8%) 2 (22.2%)
## 3 6 (100.0%) 0 (0.0%)
## 4 16 (94.1%) 1 (5.9%)
## 5 12 (80.0%) 3 (20.0%)
## 6 11 (61.1%) 7 (38.9%)
## 7 5 (41.7%) 7 (58.3%)
## 8 71 (67.0%) 35 (33.0%)
## 9 127 (73.4%) 46 (26.6%)
## NA 24 (68.6%) 11 (31.4%)
## Total 296 (72.4%) 113 (27.6%)
####################################
#### CX y Radio
###################################
pulmon2 <- pulmon2 %>%
mutate(cxradio = ifelse(cirugia == "1"| radioterapia_profilactica == "1" | radioterapia_toracica == "1",1,0))
### Cirugia and Radiotherapy
pulmon2 %>%
tabyl(cxradio)
## cxradio n percent valid_percent
## 0 266 0.6503667 0.6633416
## 1 135 0.3300733 0.3366584
## NA 8 0.0195599 NA
###### TTO SISTEMICO
#quimio
pulmon2$quimioterapia_celula_no_peque[pulmon2$quimioterapia_celula_no_peque == "NULL"] <- NA
pulmon2 %>%
tabyl(quimioterapia_celula_no_peque)
## quimioterapia_celula_no_peque n percent valid_percent
## 1 42 0.102689487 0.104477612
## 3 27 0.066014670 0.067164179
## 4 52 0.127139364 0.129353234
## 5 1 0.002444988 0.002487562
## 6 16 0.039119804 0.039800995
## 7 4 0.009779951 0.009950249
## 8 2 0.004889976 0.004975124
## 9 13 0.031784841 0.032338308
## NA 245 0.599022005 0.609452736
## <NA> 7 0.017114914 NA
#inhibidores TKS
pulmon2 %>%
tabyl(inhibidores_tirosinkinasa) ### 1
## inhibidores_tirosinkinasa n percent
## 0 306 0.748166259
## 1 33 0.080684597
## 98 69 0.168704156
## NA 1 0.002444988
pulmon2 %>%
tabyl(tratamiento_antiangionenico) ### 1
## tratamiento_antiangionenico n percent valid_percent
## 0 296 0.72371638 0.76683938
## 1 15 0.03667482 0.03886010
## 98 68 0.16625917 0.17616580
## NULL 7 0.01711491 0.01813472
## <NA> 23 0.05623472 NA
pulmon2 %>%
tabyl(inmunoterapia) ### 1
## inmunoterapia n percent valid_percent
## 0 314 0.767726161 0.771498771
## 1 24 0.058679707 0.058968059
## 98 68 0.166259169 0.167076167
## NA 1 0.002444988 0.002457002
## <NA> 2 0.004889976 NA
############################
pulmon2 <- pulmon2 %>%
mutate(ttosistemico = ifelse(quimioterapia_celula_no_peque != "NA" |
inhibidores_tirosinkinasa == "1" |
tratamiento_antiangionenico == "1" |
inmunoterapia == "1",1,0))
pulmon2 %>%
tabyl(ttosistemico)
## ttosistemico n percent valid_percent
## 0 197 0.48166259 0.4974747
## 1 199 0.48655257 0.5025253
## NA 13 0.03178484 NA
pulmon2$ttosistemico[is.na(pulmon2$ttosistemico)] <- 0
################################################
##### Cx-Radio
pulmon2$cxradio <- as.factor(pulmon2$cxradio)
levels(pulmon2$cxradio) <- c("No", "Yes")
pulmon2 %>%
tabyl(estadio_dx, cxradio) %>%
adorn_totals(c("row")) %>%
adorn_percentages(denominator = "row") %>%
adorn_pct_formatting() %>%
adorn_ns(position = "front") %>%
adorn_title()
## cxradio
## estadio_dx No Yes NA_
## 1 1 (5.6%) 17 (94.4%) 0 (0.0%)
## 2 1 (11.1%) 8 (88.9%) 0 (0.0%)
## 3 1 (16.7%) 5 (83.3%) 0 (0.0%)
## 4 6 (35.3%) 11 (64.7%) 0 (0.0%)
## 5 7 (46.7%) 7 (46.7%) 1 (6.7%)
## 6 9 (50.0%) 8 (44.4%) 1 (5.6%)
## 7 6 (50.0%) 6 (50.0%) 0 (0.0%)
## 8 71 (67.0%) 32 (30.2%) 3 (2.8%)
## 9 131 (75.7%) 39 (22.5%) 3 (1.7%)
## NA 33 (94.3%) 2 (5.7%) 0 (0.0%)
## Total 266 (65.0%) 135 (33.0%) 8 (2.0%)
pulmon2 %>%
tabyl(estadio_dx, ttosistemico) %>%
adorn_totals(c("row")) %>%
adorn_percentages(denominator = "row") %>%
adorn_pct_formatting() %>%
adorn_ns(position = "front") %>%
adorn_title()
## ttosistemico
## estadio_dx 0 1
## 1 17 (94.4%) 1 (5.6%)
## 2 6 (66.7%) 3 (33.3%)
## 3 3 (50.0%) 3 (50.0%)
## 4 10 (58.8%) 7 (41.2%)
## 5 6 (40.0%) 9 (60.0%)
## 6 7 (38.9%) 11 (61.1%)
## 7 7 (58.3%) 5 (41.7%)
## 8 48 (45.3%) 58 (54.7%)
## 9 76 (43.9%) 97 (56.1%)
## NA 30 (85.7%) 5 (14.3%)
## Total 210 (51.3%) 199 (48.7%)
#### TTO GLOBAL
pulmon2 <- pulmon2 %>%
mutate(ttoglobal = ifelse(cxradio == 1 & (quimioterapia_celula_no_peque != "NA" |
inhibidores_tirosinkinasa == "1" |
tratamiento_antiangionenico == "1" |
inmunoterapia == "1"),1,0))
pulmon2 %>%
tabyl(cxradio, ttosistemico) %>%
adorn_totals(c("row")) %>%
adorn_percentages(denominator = "row") %>%
adorn_pct_formatting() %>%
adorn_ns(position = "front") %>%
adorn_title()
## ttosistemico
## cxradio 0 1
## No 135 (50.8%) 131 (49.2%)
## Yes 73 (54.1%) 62 (45.9%)
## <NA> 2 (25.0%) 6 (75.0%)
## Total 210 (51.3%) 199 (48.7%)
class(pulmon2$cxradio)
## [1] "factor"
class(pulmon2$ttosistemico)
## [1] "numeric"
pulmon2 <- pulmon2 %>%
mutate(all_tto = ifelse(cxradio == "Yes" & ttosistemico == 1,1,0))
### All TTO
pulmon2$all_tto <- as.factor(pulmon2$all_tto)
levels(pulmon2$all_tto) <- c("No", "Yes")
pulmon2 %>%
tabyl(estadio_dx, all_tto) %>%
adorn_totals(c("row")) %>%
adorn_percentages(denominator = "row") %>%
adorn_pct_formatting() %>%
adorn_ns(position = "front") %>%
adorn_title()
## all_tto
## estadio_dx No Yes NA_
## 1 17 (94.4%) 1 (5.6%) 0 (0.0%)
## 2 6 (66.7%) 3 (33.3%) 0 (0.0%)
## 3 3 (50.0%) 3 (50.0%) 0 (0.0%)
## 4 14 (82.4%) 3 (17.6%) 0 (0.0%)
## 5 10 (66.7%) 4 (26.7%) 1 (6.7%)
## 6 12 (66.7%) 5 (27.8%) 1 (5.6%)
## 7 9 (75.0%) 3 (25.0%) 0 (0.0%)
## 8 83 (78.3%) 20 (18.9%) 3 (2.8%)
## 9 152 (87.9%) 20 (11.6%) 1 (0.6%)
## NA 35 (100.0%) 0 (0.0%) 0 (0.0%)
## Total 341 (83.4%) 62 (15.2%) 6 (1.5%)