data-raw/create_DENOM.R

In INESSSQC/variation: Analyse Coefficient Variation Systématique

library(usethis)
library(data.table)
library(variation)

data("equivalenceRLS")
equivalenceRLS <- equivalenceRLS[, lapply(.SD, as.numeric)]
names(equivalenceRLS) <- c("RLS15", "RLS14")

MED_desc <- readRDS("V:/GI-Data/_MedPersAg/VARIATION/Requete Houssem_Ancienne_Extraction/Requete Houssem/BD Rstudio/MED_desc.rds")

#### antibiotiques ####
# 2006
antibio06 <- fread("V:/GI-Data/_MedPersAg/VARIATION/Requete Houssem_Ancienne_Extraction/Requete Houssem/BD/BC02_Antibio2006_65ansPlus.txt")
# 332355 obs

antibio06 <- antibio06[
  , .(ANNEE = 2006,
      ID = T1_nib,
      RLS = as.numeric(T1_RLS),
      AGE = T1_age,
      SEXE = T1_sexe,
      DENOM = T1_gr_denom)
][
  !is.na(RLS)
]  # 331750 obs

# Convertir les RLS
antibio06 <- merge(antibio06, equivalenceRLS,
                   by.x = "RLS", by.y = "RLS14", all.x = T)
antibio06[is.na(RLS15), RLS15 := RLS]
antibio06[, `:=` (RLS = RLS15,
                  RLS15 = NULL)]


# 2011
antibio11 <- fread("V:/GI-Data/_MedPersAg/VARIATION/Requete Houssem_Ancienne_Extraction/Requete Houssem/BD/BC02_Antibio2011_65ansPlus.txt")
# 431581 obs

antibio11 <- antibio11[
  , .(ANNEE = 2011,
      ID = T1_nib,
      RLS = as.numeric(T1_RLS),
      AGE = T1_age,
      SEXE = T1_sexe,
      DENOM = T1_gr_denom)
][
  !is.na(RLS)
]  # 430870 obs

# Convertir les RLS
antibio11 <- merge(antibio11, equivalenceRLS,
                   by.x = "RLS", by.y = "RLS14", all.x = T)
antibio11[is.na(RLS15), RLS15 := RLS]
antibio11[, `:=` (RLS = RLS15,
                  RLS15 = NULL)]


# 2016
antibio16 <- fread("V:/GI-Data/_MedPersAg/VARIATION/Requete Houssem_Ancienne_Extraction/Requete Houssem/BD/BC02_Antibio2016_65ansPlus.txt")
# 525871 obs

antibio16 <- antibio16[
  , .(ANNEE = 2016,
      ID = T1_nib,
      RLS = as.numeric(T1_RLS),
      AGE = T1_age,
      SEXE = T1_sexe,
      DENOM = T1_gr_denom)
][
  !is.na(RLS)
]  # 524980 obs

# Convertir les RLS
antibio16 <- merge(antibio16, equivalenceRLS,
                   by.x = "RLS", by.y = "RLS14", all.x = T)
antibio16[is.na(RLS15), RLS15 := RLS]
antibio16[, `:=` (RLS = RLS15,
                  RLS15 = NULL)]



#### DENOM  E01 + E02 ####
E.06 <- fread("V:/GI-Data/_MedPersAg/VARIATION/Requete Houssem_Ancienne_Extraction/Requete Houssem/BD/SourceE01E02_2006-2007.txt")
# 207277 obs
E.06 <- E.06[
  , .(ANNEE = 2006,
      ID = T1_nib,
      RLS = as.numeric(T1_RLS),
      AGE = T1_age,
      SEXE = T1_sexe,
      DENOM = T1_gr_denom)
  ][
    !is.na(RLS)
    ]  # 206924 obs

# Convertir les RLS
E.06 <- merge(E.06, equivalenceRLS,
              by.x = "RLS", by.y = "RLS14", all.x = T)
E.06[is.na(RLS15), RLS15 := RLS]
E.06[, `:=` (RLS = RLS15,
             RLS15 = NULL)]


E.11 <- fread("V:/GI-Data/_MedPersAg/VARIATION/Requete Houssem_Ancienne_Extraction/Requete Houssem/BD/SourceE01E02_2011-2012.txt")
# 260829 obs
E.11 <- E.11[
  , .(ANNEE = 2011,
      ID = T1_nib,
      RLS = as.numeric(T1_RLS),
      AGE = T1_age,
      SEXE = T1_sexe,
      DENOM = T1_gr_denom)
  ][
    !is.na(RLS)
    ]  # 260440 obs

# Convertir les RLS
E.11 <- merge(E.11, equivalenceRLS,
              by.x = "RLS", by.y = "RLS14", all.x = T)
E.11[is.na(RLS15), RLS15 := RLS]
E.11[, `:=` (RLS = RLS15,
             RLS15 = NULL)]


E.16 <- fread("V:/GI-Data/_MedPersAg/VARIATION/Requete Houssem_Ancienne_Extraction/Requete Houssem/BD/SourceE01E02_2016-2017.txt")
# 293591 obs
E.16 <- E.16[
  , .(ANNEE = 2016,
      ID = T1_nib,
      RLS = as.numeric(T1_RLS),
      AGE = T1_age,
      SEXE = T1_sexe,
      DENOM = T1_gr_denom)
  ][
    !is.na(RLS)
    ]  # 293191 obs

# Convertir les RLS
E.16 <- merge(E.16, equivalenceRLS,
              by.x = "RLS", by.y = "RLS14", all.x = T)
E.16[is.na(RLS15), RLS15 := RLS]
E.16[, `:=` (RLS = RLS15,
             RLS15 = NULL)]



#### DENOM ####
Source06 <- fread("V:/GI-Data/_MedPersAg/VARIATION/Requete Houssem_Ancienne_Extraction/Requete Houssem/BD/SourceHxx_2006-2007.txt")
# 4474646 obs
Source06 <- Source06[
  , .(ANNEE = 2006,
      ID = T1_nib,
      RLS = as.numeric(T1_RLS),
      AGE = T1_age,
      SEXE = T1_sexe,
      DENOM = T1_gr_denom)
][
  !is.na(RLS)
]  # 4466654 obs

# Convertir les RLS
Source06 <- merge(Source06, equivalenceRLS,
                  by.x = "RLS", by.y = "RLS14", all.x = T)
Source06[is.na(RLS15), RLS15 := RLS]
Source06[, `:=` (RLS = RLS15,
                 RLS15 = NULL)]


Source11 <- fread("V:/GI-Data/_MedPersAg/VARIATION/Requete Houssem_Ancienne_Extraction/Requete Houssem/BD/SourceHxx_2011-2012.txt")
# 5824602 obs
Source11 <- Source11[
  , .(ANNEE = 2011,
      ID = T1_nib,
      RLS = as.numeric(T1_RLS),
      AGE = T1_age,
      SEXE = T1_sexe,
      DENOM = T1_gr_denom)
][
  !is.na(RLS)
]  # 5815347 obs

# Convertir les RLS
Source11 <- merge(Source11, equivalenceRLS,
                  by.x = "RLS", by.y = "RLS14", all.x = T)
Source11[is.na(RLS15), RLS15 := RLS]
Source11[, `:=` (RLS = RLS15,
                 RLS15 = NULL)]


Source16 <- fread("V:/GI-Data/_MedPersAg/VARIATION/Requete Houssem_Ancienne_Extraction/Requete Houssem/BD/SourceHxx_2016-2017.txt")
# 7190344 obs
Source16 <- Source16[
  , .(ANNEE = 2016,
      ID = T1_nib,
      RLS = as.numeric(T1_RLS),
      AGE = T1_age,
      SEXE = T1_sexe,
      DENOM = T1_gr_denom)
  ][
    !is.na(RLS)
    ]  # 7178751 obs

# Convertir les RLS
Source16 <- merge(Source16, equivalenceRLS,
                  by.x = "RLS", by.y = "RLS14", all.x = T)
Source16[is.na(RLS15), RLS15 := RLS]
Source16[, `:=` (RLS = RLS15,
                 RLS15 = NULL)]



#### Save ####
DENOM <- rbind(antibio06, antibio11, antibio16,
               # E.06, E.11, E.16,
               Source06, Source11, Source16)
setorder(DENOM, ANNEE, ID)

DENOM <- merge(DENOM, MED_desc,
               by.x = "DENOM", by.y = "Code", all.x = T)
setnames(DENOM, "Descriptif", "DESCRIPTIF")
DENOM[DENOM == "H42", DESCRIPTIF := "Laxatifs"]
# Supprimer RLS = 801 qui n'existe pas
DENOM <- DENOM[RLS != 801]

saveRDS(DENOM, "V:/GI-Data/_MedPersAg/VARIATION/Requete Houssem_Ancienne_Extraction/Requete Houssem/BD Rstudio/DENOM.rds")