library(readxl)
collecte_tb_covid_survey<- read_excel("~/Dropbox (Compte personnel)/TB_COVID_G_N/collecte_tb_covid_Final_Netoyer.xlsx")
View(collecte_tb_covid_survey) ## Warning in system2("/usr/bin/otool", c("-L", shQuote(DSO)), stdout = TRUE):
## running command ''/usr/bin/otool' -L '/Library/Frameworks/R.framework/Resources/
## modules/R_de.so'' had status 1#names(collecte_tb_covid_survey)
#recodage des données
pays=as.factor(collecte_tb_covid_survey$`selectionner un pays` )
testes_covid19=collecte_tb_covid_survey$`Nombre de cas présumés/contact testés pour la Covid-19`
positifs_covid19=collecte_tb_covid_survey$`Nombre de cas positifs à la Covid-19`
negatifs_covid19=collecte_tb_covid_survey$`Nombre négatifs à la Covid-19`
gueris_covid_19=collecte_tb_covid_survey$`Nombre cas guéris de covid-19`
nomb_test_TB=collecte_tb_covid_survey$`Nombre de patients présumés, positifs ou guérie Covid-19 testé pour la TB`
#creation d'un dataframe
data1=data.frame(pays,testes_covid19,positifs_covid19,negatifs_covid19,gueris_covid_19,nomb_test_TB)
# define function for lower and upper bounds of the mean CI
ll <- function(x) t.test(x)$conf.int[1]
ul <- function(x) t.test(x)$conf.int[2]
#Description des donneées]
library("gtsummary", lib.loc="/Library/Frameworks/R.framework/Versions/4.0/Resources/library")
t1 <-
data1%>%
#select(testes_covid19,positifs_covid19,negatifs_covid19,gueris_covid_19,nomb_test_TB)
tbl_summary(by = pays,statistic = all_continuous() ~ "{sum}")%>%
add_overall()
# modify_header(stat_0 ~ "**Mean (SD)**")
t1| Characteristic | Overall, N = 2191 | Gui, N = 1591 | Nig, N = 601 |
|---|---|---|---|
| testes_covid19 | 2,646 | 2,520 | 126 |
| positifs_covid19 | 153.00 | 59.00 | 94.00 |
| Unknown | 1 | 1 | 0 |
| negatifs_covid19 | 2,438 | 2,438 | NA |
| Unknown | 60 | 0 | 60 |
| gueris_covid_19 | 175.00 | 117.00 | 58.00 |
| nomb_test_TB | 846.0 | 758.0 | 88.0 |
|
1
Statistics presented: sum
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#plot t2
t2 <-
data1%>%
#select(testes_covid19,positifs_covid19,negatifs_covid19,gueris_covid_19,nomb_test_TB)
tbl_summary(statistic = all_continuous() ~ "{ll}, {ul}",by = pays)
#modify_header(stat_0 ~ "**95% CI for Mean**")
t2| Characteristic | Gui, N = 1591 | Nig, N = 601 |
|---|---|---|
| testes_covid19 | 13, 18 | 2, 3 |
| positifs_covid19 | 0.21, 0.53 | 0.96, 2.17 |
| Unknown | 1 | 0 |
| negatifs_covid19 | 13, 18 | NA, NA |
| Unknown | 0 | 60 |
| gueris_covid_19 | 0.47, 1.00 | 0.48, 1.46 |
| nomb_test_TB | 4.0, 5.5 | 1.1, 1.9 |
|
1
Statistics presented: ll, ul
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tbl_merge(list(t1, t2)) %>%
#modify_footnote(everything() ~ NA_character_)
modify_spanning_header(everything() ~ NA_character_)| Characteristic | Overall, N = 2191 | Gui, N = 1591 | Nig, N = 601 | Gui, N = 1592 | Nig, N = 602 |
|---|---|---|---|---|---|
| testes_covid19 | 2,646 | 2,520 | 126 | 13, 18 | 2, 3 |
| positifs_covid19 | 153.00 | 59.00 | 94.00 | 0.21, 0.53 | 0.96, 2.17 |
| Unknown | 1 | 1 | 0 | 1 | 0 |
| negatifs_covid19 | 2,438 | 2,438 | NA | 13, 18 | NA, NA |
| Unknown | 60 | 0 | 60 | 0 | 60 |
| gueris_covid_19 | 175.00 | 117.00 | 58.00 | 0.47, 1.00 | 0.48, 1.46 |
| nomb_test_TB | 846.0 | 758.0 | 88.0 | 4.0, 5.5 | 1.1, 1.9 |
|
1
Statistics presented: sum
2
Statistics presented: ll, ul
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#Importation de countrepeat
datarepeat <- read_excel("~/Dropbox (Compte personnel)/TB_COVID_G_N/collecte_tb_covid_Final_Netoyer.xlsx", sheet = "patient_repeat")
#names(datarepeat)
t3 <-
datarepeat%>%
select(Age,Sexe,Pays,`Antécédent de traitement TB`,`Avez vous tousse au delà de 2 semaines ?`,`Avez-vous de la fièvre activement ?`,`Avez-vous cohabite avec un tousseur ?`,`Avez-vous de la fièvre activement ?`,`Avez-vous perdu du poids ces derniers temps ?`,`Resultats du test Covod-19 (PCR)`,`Quel examen a été realisé pour la recherche de la TB`,`Resultats de la microscopie`,`Résistance à la rifampicine`,`Tuberculose confirmée`)%>%
tbl_summary(by = Pays,statistic = all_continuous() ~ "{mean} ({sd})")
t4 <-
datarepeat%>%
select(Age,Sexe,Pays,`Antécédent de traitement TB`,`Avez vous tousse au delà de 2 semaines ?`,`Avez-vous de la fièvre activement ?`,`Avez-vous cohabite avec un tousseur ?`,`Avez-vous de la fièvre activement ?`,`Avez-vous perdu du poids ces derniers temps ?`,`Resultats du test Covod-19 (PCR)`,`Quel examen a été realisé pour la recherche de la TB`,`Resultats de la microscopie`,`Résistance à la rifampicine`,`Tuberculose confirmée`)%>%
tbl_summary(statistic = all_continuous() ~ "{ll}, {ul}",by = Pays)%>%
add_overall()
tbl_merge(list(t3, t4)) %>%
#modify_footnote(everything() ~ NA_character_)
modify_spanning_header(everything() ~ NA_character_)| Characteristic | Guinee, N = 7581 | Niger, N = 1051 | Overall, N = 8632 | Guinee, N = 7582 | Niger, N = 1052 |
|---|---|---|---|---|---|
| Age | 36 (14) | 50 (20) | 36, 38 | 35, 37 | 46, 54 |
| Sexe | |||||
| f | 314 (41%) | 28 (27%) | 342 (40%) | 314 (41%) | 28 (27%) |
| m | 444 (59%) | 77 (73%) | 521 (60%) | 444 (59%) | 77 (73%) |
| Antécédent de traitement TB | 38 (5.1%) | 2 (1.9%) | 40 (4.7%) | 38 (5.1%) | 2 (1.9%) |
| Unknown | 6 | 1 | 7 | 6 | 1 |
| Avez vous tousse au delà de 2 semaines ? | 369 (49%) | 58 (55%) | 427 (49%) | 369 (49%) | 58 (55%) |
| Avez-vous de la fièvre activement ? | 335 (44%) | 49 (47%) | 384 (45%) | 335 (44%) | 49 (47%) |
| Unknown | 4 | 1 | 5 | 4 | 1 |
| Avez-vous cohabite avec un tousseur ? | 133 (18%) | 7 (6.7%) | 140 (16%) | 133 (18%) | 7 (6.7%) |
| Unknown | 4 | 1 | 5 | 4 | 1 |
| Avez-vous perdu du poids ces derniers temps ? | 211 (28%) | 50 (48%) | 261 (30%) | 211 (28%) | 50 (48%) |
| Unknown | 2 | 1 | 3 | 2 | 1 |
| Resultats du test Covod-19 (PCR) | |||||
| neg | 744 (98%) | 57 (54%) | 801 (93%) | 744 (98%) | 57 (54%) |
| pos | 13 (1.7%) | 48 (46%) | 61 (7.1%) | 13 (1.7%) | 48 (46%) |
| Unknown | 1 | 0 | 1 | 1 | 0 |
| Quel examen a été realisé pour la recherche de la TB | |||||
| GeneXp | 32 (4.2%) | 29 (28%) | 61 (7.1%) | 32 (4.2%) | 29 (28%) |
| Mic_Xpert | 1 (0.1%) | 14 (13%) | 15 (1.7%) | 1 (0.1%) | 14 (13%) |
| Microscop | 722 (95%) | 62 (59%) | 784 (91%) | 722 (95%) | 62 (59%) |
| rad | 3 (0.4%) | 0 (0%) | 3 (0.3%) | 3 (0.4%) | 0 (0%) |
| Resultats de la microscopie | |||||
| neg | 726 (97%) | 98 (96%) | 824 (97%) | 726 (97%) | 98 (96%) |
| other | 1 (0.1%) | 0 (0%) | 1 (0.1%) | 1 (0.1%) | 0 (0%) |
| plus_plus | 4 (0.5%) | 3 (2.9%) | 7 (0.8%) | 4 (0.5%) | 3 (2.9%) |
| rare | 3 (0.4%) | 1 (1.0%) | 4 (0.5%) | 3 (0.4%) | 1 (1.0%) |
| une_croix | 13 (1.7%) | 0 (0%) | 13 (1.5%) | 13 (1.7%) | 0 (0%) |
| Unknown | 11 | 3 | 14 | 11 | 3 |
| Résistance à la rifampicine | |||||
| det | 1 (7.7%) | 0 (0%) | 1 (5.9%) | 1 (7.7%) | 0 (0%) |
| nondet | 12 (92%) | 4 (100%) | 16 (94%) | 12 (92%) | 4 (100%) |
| Unknown | 745 | 101 | 846 | 745 | 101 |
| Tuberculose confirmée | |||||
| TB_No | 723 (95%) | 97 (92%) | 820 (95%) | 723 (95%) | 97 (92%) |
| TB_Yes | 35 (4.6%) | 8 (7.6%) | 43 (5.0%) | 35 (4.6%) | 8 (7.6%) |
|
1
Statistics presented: Mean (SD); n (%)
2
Statistics presented: ll, ul; n (%)
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t5 <-
datarepeat%>%
select(Age,Sexe,Pays,`Antécédent de traitement TB`,`Avez vous tousse au delà de 2 semaines ?`,`Avez-vous de la fièvre activement ?`,`Avez-vous cohabite avec un tousseur ?`,`Avez-vous de la fièvre activement ?`,`Avez-vous perdu du poids ces derniers temps ?`,`Resultats du test Covod-19 (PCR)`,`Quel examen a été realisé pour la recherche de la TB`,`Resultats de la microscopie`,`Résistance à la rifampicine`,`Tuberculose confirmée`)%>%
tbl_summary(by =`Tuberculose confirmée` ,statistic = all_continuous() ~ "{mean} ({sd})") %>%
add_overall()%>%
add_p()## There was an error in 'add_p()' for variable 'Résistance à la rifampicine', p-value omitted:
## Error in stats::fisher.test(data[[variable]], as.factor(data[[by]])): 'x' and 'y' must have at least 2 levelst5| Characteristic | Overall, N = 8631 | TB_No, N = 8201 | TB_Yes, N = 431 | p-value2 |
|---|---|---|---|---|
| Age | 37 (16) | 37 (16) | 38 (17) | >0.9 |
| Sexe | 0.036 | |||
| f | 342 (40%) | 332 (40%) | 10 (23%) | |
| m | 521 (60%) | 488 (60%) | 33 (77%) | |
| Pays | 0.3 | |||
| Guinee | 758 (88%) | 723 (88%) | 35 (81%) | |
| Niger | 105 (12%) | 97 (12%) | 8 (19%) | |
| Antécédent de traitement TB | 40 (4.7%) | 38 (4.7%) | 2 (4.9%) | >0.9 |
| Unknown | 7 | 5 | 2 | |
| Avez vous tousse au delà de 2 semaines ? | 427 (49%) | 392 (48%) | 35 (81%) | <0.001 |
| Avez-vous de la fièvre activement ? | 384 (45%) | 344 (42%) | 40 (93%) | <0.001 |
| Unknown | 5 | 5 | 0 | |
| Avez-vous cohabite avec un tousseur ? | 140 (16%) | 133 (16%) | 7 (16%) | >0.9 |
| Unknown | 5 | 5 | 0 | |
| Avez-vous perdu du poids ces derniers temps ? | 261 (30%) | 222 (27%) | 39 (91%) | <0.001 |
| Unknown | 3 | 3 | 0 | |
| Resultats du test Covod-19 (PCR) | 0.2 | |||
| neg | 801 (93%) | 763 (93%) | 38 (88%) | |
| pos | 61 (7.1%) | 56 (6.8%) | 5 (12%) | |
| Unknown | 1 | 1 | 0 | |
| Quel examen a été realisé pour la recherche de la TB | <0.001 | |||
| GeneXp | 61 (7.1%) | 46 (5.6%) | 15 (35%) | |
| Mic_Xpert | 15 (1.7%) | 13 (1.6%) | 2 (4.7%) | |
| Microscop | 784 (91%) | 759 (93%) | 25 (58%) | |
| rad | 3 (0.3%) | 2 (0.2%) | 1 (2.3%) | |
| Resultats de la microscopie | <0.001 | |||
| neg | 824 (97%) | 819 (100%) | 5 (17%) | |
| other | 1 (0.1%) | 0 (0%) | 1 (3.4%) | |
| plus_plus | 7 (0.8%) | 1 (0.1%) | 6 (21%) | |
| rare | 4 (0.5%) | 0 (0%) | 4 (14%) | |
| une_croix | 13 (1.5%) | 0 (0%) | 13 (45%) | |
| Unknown | 14 | 0 | 14 | |
| Résistance à la rifampicine | ||||
| det | 1 (5.9%) | 0 (NA%) | 1 (5.9%) | |
| nondet | 16 (94%) | 0 (NA%) | 16 (94%) | |
| Unknown | 846 | 820 | 26 | |
|
1
Statistics presented: Mean (SD); n (%)
2
Statistical tests performed: Wilcoxon rank-sum test; chi-square test of independence; Fisher's exact test
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