psi.fct: Compute the PSI (pneumonia severity index).

In maciejrosolowski/progressdatenbankderivate: Extract and Process Data from the Database of the PROGESS Study

Compute the PSI (pneumonia severity index).

Description

Compute the PSI (pneumonia severity index).

Usage

psi.fct(
  DID_PROBAND,
  FRM_BAS,
  FRM_BEF,
  FRM_B24,
  FRM_RR,
  FRM_O2A,
  FRM_DIL_LABORWERTE,
  FRM_VIS,
  zp_fabian = "d0",
  event2zeitpunkt_df = progressdatenbankderivate::event2zeitpunkt_table
)

Arguments

DID_PROBAND	data.table containing the table with the same name from the database of the PROGRESS study
FRM_BAS	data.table containing the table with the same name from the database of the PROGRESS study
FRM_BEF	data.table containing the table with the same name from the database of the PROGRESS study
FRM_B24	data.table containing the table with the same name from the database of the PROGRESS study
FRM_RR	data.table containing the table with the same name from the database of the PROGRESS study
FRM_O2A	data.table containing the table with the same name from the database of the PROGRESS study
FRM_DIL_LABORWERTE	data.table containing the table with the same name from the database of the PROGRESS study
FRM_VIS	data.table containing the table with the same name from the database of the PROGRESS study
zp_fabian	vector of characters. They must be present in event2zeitpunkt_table$zp_fabianref.
event2zeitpunkt_df	data.table event2zeitpunkt_table (available with the package).

Value

a named list with components: input, input2 and out. out is a data.table with one row corresponding to a combination of PATSTUID (patient) and "EVENT" (time point). Column "psi" contains the PSI values computed by imputing non-critical values, if some components of the score were missing. The column "psi_filt" contains NAs, if any of the components needed for computing the PSI score were missing. The column vollstaendig.von.20 contains information about the number of components having values available out of the overall 20 components of the PSI score.

Examples

## Not run: 
excel_fn <- paste0("/net/ifs1/san_projekte/projekte/",
"PROGRESS/Datenmanagement/Data_freezes/",
"20190320/PROGRESS-freeze_201903_01.xlsx")
DID_PROBAND <- readxl::read_excel(excel_fn, 'DID_PROBAND')
FRM_BAS <- readxl::read_excel(excel_fn, 'FRM_BAS')
FRM_BEF <- readxl::read_excel(excel_fn, 'FRM_BEF')
FRM_B24 <- readxl::read_excel(excel_fn, 'FRM_B24')
FRM_RR <- readxl::read_excel(excel_fn, 'FRM_RR')
FRM_O2A <- readxl::read_excel(excel_fn, 'FRM_O2A')
FRM_DIL_LABORWERTE <- readxl::read_excel(excel_fn, "FRM_DIL_LABORWERTE")
FRM_VIS <- readxl::read_excel(excel_fn, 'FRM_VIS')
data.table::setDT(DID_PROBAND)
data.table::setDT(FRM_BAS)
data.table::setDT(FRM_BEF)
data.table::setDT(FRM_B24)
data.table::setDT(FRM_RR)
data.table::setDT(FRM_O2A)
data.table::setDT(FRM_DIL_LABORWERTE)
data.table::setDT(FRM_VIS)
erg_d0 <- psi.fct(DID_PROBAND, FRM_BAS, FRM_BEF, FRM_B24, FRM_RR, FRM_O2A,
FRM_DIL_LABORWERTE,FRM_VIS, zp_fabian = "d0")
erg_d0
erg_d1 <- psi.fct(DID_PROBAND, FRM_BAS, FRM_BEF, FRM_B24, FRM_RR, FRM_O2A,
FRM_DIL_LABORWERTE,FRM_VIS, zp_fabian = "d1")
erg_d1

## End(Not run)

maciejrosolowski/progressdatenbankderivate documentation built on Nov. 29, 2024, 3:39 a.m.