library(tidyverse)
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library(finalfit)
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library(rmarkdown)
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library(knitr)
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library(markdown)
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standard IOT/mortalité J28

dependent_1="IOT_mortalite_J28"
explanatory_standard=c("Age","sexe","IMC","Vaccination","ATCD_Diabète ","ATCD_HTA","ATCD_ID","ATCD_Path_respi","ATCD_Cardiopathie","ATCD_IR_Dialyse")
res_glm_uni_std <- Oxy_cov%>%
    glmuni(dependent_1, explanatory_standard) %>% 
    fit2df(estimate_suffix=" (univarié)")
kable(res_glm_uni_std,row.names=FALSE, align=c("l", "l", "r", "r", "r", "r"))
explanatory OR (univarié)
Age 1.02 (1.00-1.06, p=0.115)
sexeM 0.78 (0.36-1.73, p=0.529)
IMCIMC>30 2.17 (1.01-4.73, p=0.049)
VaccinationOui 0.90 (0.13-3.81, p=0.899)
ATCD_DiabèteOui 1.41 (0.59-3.23, p=0.421)
ATCD_HTAOui 1.61 (0.76-3.44, p=0.218)
ATCD_IDOui 3.15 (0.74-12.59, p=0.101)
ATCD_Path_respiOui 2.42 (0.97-5.82, p=0.051)
ATCD_CardiopathieOui 1.18 (0.40-3.07, p=0.752)
ATCD_IR_DialyseOui 1.22 (0.06-9.84, p=0.868) 
res_glm_uni_multi_std <- Oxy_cov%>%
    finalfit(dependent_1, explanatory_standard)
 

kable(res_glm_uni_multi_std,row.names=FALSE, align=c("l", "l", "r", "r", "r", "r"))
Dependent: IOT_mortalite_J28 unit value Coefficient (univariable) Coefficient (multivariable)
Age [24.0,89.0] Mean (sd) 0.2 (0.4) 0.00 (-0.00 to 0.01, p=0.113) 0.00 (-0.00 to 0.01, p=0.111)
sexe F Mean (sd) 0.2 (0.4) - -
M Mean (sd) 0.2 (0.4) -0.04 (-0.18 to 0.09, p=0.531) 0.00 (-0.14 to 0.14, p=0.983)
IMC IMC<30 Mean (sd) 0.2 (0.4) - -
IMC>30 Mean (sd) 0.3 (0.5) 0.14 (0.00 to 0.27, p=0.046) 0.19 (0.04 to 0.34, p=0.014)
Vaccination Non Mean (sd) 0.2 (0.4) - -
Oui Mean (sd) 0.2 (0.4) -0.02 (-0.28 to 0.25, p=0.899) -0.13 (-0.42 to 0.15, p=0.357)
ATCD_Diabète Non Mean (sd) 0.2 (0.4) - -
Oui Mean (sd) 0.3 (0.4) 0.06 (-0.09 to 0.21, p=0.423) 0.03 (-0.13 to 0.20, p=0.712)
ATCD_HTA Non Mean (sd) 0.2 (0.4) - -
Oui Mean (sd) 0.3 (0.4) 0.08 (-0.05 to 0.21, p=0.218) -0.04 (-0.20 to 0.12, p=0.625)
ATCD_ID Non Mean (sd) 0.2 (0.4) - -
Oui Mean (sd) 0.4 (0.5) 0.24 (-0.04 to 0.52, p=0.088) 0.28 (-0.02 to 0.58, p=0.066)
ATCD_Path_respi Non Mean (sd) 0.2 (0.4) - -
Oui Mean (sd) 0.4 (0.5) 0.17 (0.00 to 0.34, p=0.046) 0.16 (-0.02 to 0.33, p=0.089)
ATCD_Cardiopathie Non Mean (sd) 0.2 (0.4) - -
Oui Mean (sd) 0.2 (0.4) 0.03 (-0.15 to 0.21, p=0.754) -0.03 (-0.24 to 0.17, p=0.742)
ATCD_IR_Dialyse Non Mean (sd) 0.2 (0.4) - -
Oui Mean (sd) 0.2 (0.5) 0.03 (-0.38 to 0.45, p=0.868) 0.01 (-0.42 to 0.44, p=0.958)

facteurs hospit IOT/mortalité J28

dependent_1="IOT_mortalite_J28"
explanatory_hospitalisation=c("J_symptome_USIR","J_symptome_hospit","Duree_Hospit","J_symptome_hospit ")
res_glm_uni_hospit <- Oxy_cov%>%
    finalfit(dependent_1, explanatory_hospitalisation)
 

kable(res_glm_uni_hospit,row.names=FALSE, align=c("l", "l", "r", "r", "r", "r"))
Dependent: IOT_mortalite_J28 unit value Coefficient (univariable) Coefficient (multivariable)
J_symptome_USIR [2.0,51.0] Mean (sd) 0.2 (0.4) -0.00 (-0.01 to 0.01, p=0.422) -0.00 (-0.02 to 0.01, p=0.398)
J_symptome_hospit [1.0,51.0] Mean (sd) 0.2 (0.4) -0.01 (-0.02 to 0.01, p=0.424) 0.00 (-0.01 to 0.02, p=0.813)
J_symptome_hospit [1.0,51.0] Mean (sd) 0.2 (0.4) -0.01 (-0.02 to 0.01, p=0.424) 0.00 (-0.01 to 0.02, p=0.813)
Duree_Hospit [4.0,143.0] Mean (sd) 0.2 (0.4) 0.01 (0.01 to 0.01, p<0.001) 0.01 (0.01 to 0.01, p<0.001) 
res_glm_uni_multi_hospit <- Oxy_cov%>%
     finalfit(dependent_1, explanatory_hospitalisation)
  

 kable(res_glm_uni_multi_hospit,row.names=FALSE, align=c("l", "l", "r", "r", "r", "r"))
Dependent: IOT_mortalite_J28 unit value Coefficient (univariable) Coefficient (multivariable)
J_symptome_USIR [2.0,51.0] Mean (sd) 0.2 (0.4) -0.00 (-0.01 to 0.01, p=0.422) -0.00 (-0.02 to 0.01, p=0.398)
J_symptome_hospit [1.0,51.0] Mean (sd) 0.2 (0.4) -0.01 (-0.02 to 0.01, p=0.424) 0.00 (-0.01 to 0.02, p=0.813)
J_symptome_hospit [1.0,51.0] Mean (sd) 0.2 (0.4) -0.01 (-0.02 to 0.01, p=0.424) 0.00 (-0.01 to 0.02, p=0.813)
Duree_Hospit [4.0,143.0] Mean (sd) 0.2 (0.4) 0.01 (0.01 to 0.01, p<0.001) 0.01 (0.01 to 0.01, p<0.001)

IOT mortalité J28 Rox

dependent_1="IOT_mortalite_J28"
explanatory_Rox=c("Rox_H1","Rox_H24","Rox_H48","Rox_H72")
res_glm_uni_Rox <- Oxy_cov%>%
    finalfit(dependent_1, explanatory_Rox)
 

kable(res_glm_uni_Rox,row.names=FALSE, align=c("l", "l", "r", "r", "r", "r"))
Dependent: IOT_mortalite_J28 unit value Coefficient (univariable) Coefficient (multivariable)
Rox_H1 [2.0,71.0] Mean (sd) 0.2 (0.4) 0.00 (-0.00 to 0.00, p=0.335) 0.00 (-0.00 to 0.00, p=0.295)
Rox_H24 [2.0,77.0] Mean (sd) 0.2 (0.4) -0.00 (-0.00 to 0.00, p=0.421) -0.00 (-0.00 to 0.00, p=0.262)
Rox_H48 [2.0,65.0] Mean (sd) 0.2 (0.4) 0.00 (-0.00 to 0.01, p=0.318) 0.00 (-0.00 to 0.01, p=0.298)
Rox_H72 [2.0,54.0] Mean (sd) 0.2 (0.4) 0.00 (-0.00 to 0.01, p=0.422) 0.00 (-0.00 to 0.01, p=0.608) 
res_glm_uni_multi_Rox <- Oxy_cov%>%
     finalfit(dependent_1, explanatory_Rox)
  

 kable(res_glm_uni_multi_Rox,row.names=FALSE, align=c("l", "l", "r", "r", "r", "r"))
Dependent: IOT_mortalite_J28 unit value Coefficient (univariable) Coefficient (multivariable)
Rox_H1 [2.0,71.0] Mean (sd) 0.2 (0.4) 0.00 (-0.00 to 0.00, p=0.335) 0.00 (-0.00 to 0.00, p=0.295)
Rox_H24 [2.0,77.0] Mean (sd) 0.2 (0.4) -0.00 (-0.00 to 0.00, p=0.421) -0.00 (-0.00 to 0.00, p=0.262)
Rox_H48 [2.0,65.0] Mean (sd) 0.2 (0.4) 0.00 (-0.00 to 0.01, p=0.318) 0.00 (-0.00 to 0.01, p=0.298)
Rox_H72 [2.0,54.0] Mean (sd) 0.2 (0.4) 0.00 (-0.00 to 0.01, p=0.422) 0.00 (-0.00 to 0.01, p=0.608)