Nothing
R/create_example_tables.R
In vigicaen: 'VigiBase' Pharmacovigilance Database Toolbox
Defines functions
f_sets_meddra
f_sets_who
f_sets_sub
f_sets_main_pq
f_sets_main
create_ex_main_pq
create_ex_meddra_asc
create_ex_who_txt
create_ex_sub_txt
create_ex_main_txt
Documented in
create_ex_main_pq
create_ex_main_txt
create_ex_meddra_asc
create_ex_sub_txt
create_ex_who_txt
#' Example source tables for VigiBase and MedDRA
#'
#' @description `r lifecycle::badge('experimental')` Write some example
#' tables as source text/ascii/parquet files.
#'
#' @details VigiBase tables and MedDRA tables are provided respectively
#' as text files and ascii files. The `tb_*` family turns them
#' into parquet files. These `create_example_*` functions are only used to produce
#' example source files to illustrate the `tb_*` family, and parquet files for the
#' same purpose.
#'
#' @param path Character string. A folder on your computer where the tables should
#' be written.
#' @importFrom utils write.table
#'
#' @returns A set of text/ascii files,
#' as received by the Uppsala Monitoring Centre or MedDRA
#' \itemize{
#' \item For [create_ex_main_txt()],
#' DEMO.txt, DRUG.txt, LINK.txt, FOLLOWUP.txt,
#' ADR.txt, OUT.txt, SRCE.txt, and IND.txt
#' \item For [create_ex_sub_txt()],
#' AgeGroup_Lx.txt, Dechallenge_Lx.txt, Dechallenge2_Lx.txt,
#' Frequency_Lx.txt, Gender_Lx.txt, Notifier_Lx.txt, Outcome_Lx.txt,
#' Rechallenge_Lx.txt, Rechallenge2_Lx.txt, Region_Lx.txt, RepBasis_Lx.txt,
#' ReportType_Lx.txt, RouteOfAdm_Lx.txt, Seriousness_Lx.txt,
#' and SizeUnit_Lx.txt
#' \item For [create_ex_who_txt()],
#' ATC.txt, CCODE.txt, ING.txt, MP.txt, ORG.txt,
#' PF.txt, PP.txt, PRT.txt, PRG.txt, SRCE.txt, STR.txt,
#' SUN.txt, ThG.txt, and Unit-X.txt
#' \item For [create_ex_meddra_asc()],
#' llt.asc, mdhier.asc, smq_content.asc, smq_list.asc
#' \item For [create_ex_main_pq()],
#' demo.parquet, adr.parquet, drug.parquet, link.parquet,
#' srce.parquet, ind.parquet, out.parquet, followup.parquet, suspdup.parquet
#' }
#' @seealso [tb_vigibase()], [tb_who()], [tb_meddra()]
#' @export
#'
#' @name create_example_tables
#'
#' @examples
#'
#' path <- paste0(tempdir(), "/crex/")
#'
#' dir.create(path)
#'
#' # You may want to use different paths for each type of tables
#' create_ex_main_txt(path)
#'
#' create_ex_sub_txt(path)
#'
#' create_ex_who_txt(path)
#'
#' create_ex_meddra_asc(path)
#'
#' create_ex_main_pq(path)
#'
#' # Remove temporary folders when you're done
#' unlink(path, recursive = TRUE)
create_ex_main_txt <-
function(
path
){
purrr::iwalk(f_sets_main(), function(d_, name_)
write.table(d_, file = paste0(path, name_),
row.names = FALSE, quote = FALSE, col.names = FALSE)
)
}
#' @describeIn create_example_tables sub txt tables
#' @export
create_ex_sub_txt <-
function(
path
){
purrr::iwalk(f_sets_sub(), function(d_, name_)
write.table(d_, file = paste0(path, name_),
row.names = FALSE, quote = FALSE, col.names = FALSE)
)
}
#' @describeIn create_example_tables WHO txt tables
#' @export
create_ex_who_txt <-
function(
path
){
purrr::iwalk(f_sets_who(), function(d_, name_)
write.table(d_, file = paste0(path, name_),
row.names = FALSE, quote = FALSE, col.names = FALSE)
)
}
#' @describeIn create_example_tables MedDRA txt tables
#' @export
create_ex_meddra_asc <-
function(
path
){
purrr::iwalk(f_sets_meddra(), function(d_, name_)
write.table(d_, file = paste0(path, name_),
row.names = FALSE, quote = FALSE, col.names = FALSE)
)
}
#' @describeIn create_example_tables main parquet tables
#' @export
create_ex_main_pq <-
function(
path
){
purrr::iwalk(
f_sets_main_pq(),
function(dataset, name)
arrow::write_parquet(
dataset |>
arrow::as_arrow_table(),
sink = paste0(path, "/", name, ".parquet")
)
)
}
# Helpers ------
# File sets for each type of table
f_sets_main <-
function() {
list(
DEMO.txt = data.frame(f0 = c("96548661 32194501051119460820")),
DRUG.txt = data.frame(f0 =
c(
"70548965 8 4901354 064392080055011 31- 806"
)),
LINK.txt = data.frame(f0 = c(
"2 654654 51---0.78991 0.98745 ", "2 456456 51---6.98789 - "
)),
FOLLOWUP.txt = data.frame(f0 = c("0548978 0254687 ", "7568798 4565321 ")),
ADR.txt = data.frame(f0 = c(
"96570161 14 100474561", "70578465 17 145078144"
)),
OUT.txt = data.frame(f0 = c("70547815 - N", "96575661 - Y")),
SRCE.txt = data.frame(f0 = c("4898765 1 ", "9804562 1 ")),
IND.txt = data.frame(
# 266 length
f0 = paste0(
"780954 Cutaneous diseases due to other mycobacteria",
rep(" ", 211)
)
)
)
}
f_sets_main_pq <-
function() {
rlang::list2(
demo =
data.table(
UMCReportId = c(1, 2, 3, 4),
AgeGroup = c(1, 2, 7, 9)
),
drug =
data.table(
UMCReportId = c(1, 2, 3, 4),
Drug_Id = c("d1", "d2", "d3", "d4"),
DrecNo = c(133138448, 133138448, 111841511, 111841511),
MedicinalProd_Id = c(25027716, 97354576, 104264760, 37484408)
),
adr =
data.table(
UMCReportId = c(1, 2, 3, 4),
Adr_Id = c("a1", "a2", "a3", "a4"),
MedDRA_Id = c(110049083, 146319904, 146319904, 72535511)
),
link =
data.table(
Drug_Id = c("d1", "d2", "d3", "d4"),
Adr_Id = c("a1", "a2", "a3", "a4")
),
srce =
data.table(UMCReportId = c(1, 2, 3, 4)),
ind =
data.table(Drug_Id = c("d1", "d2", "d3", "d4")),
out =
data.table(UMCReportId = c(1, 2, 3, 4)),
followup =
data.table(UMCReportId = c(1, 2, 3, 4)),
suspdup =
data.table(
UMCReportId = c(3),
SuspectedduplicateReportId = c(4)
)
)
}
f_sets_sub <-
function() {
list(
SUSPECTEDDUPLICATES.txt = data.frame(f0 = c("789054 789542 ", "780546 654352 ")),
AgeGroup_Lx.txt = data.frame(f0 = c("1An age range ")),
Dechallenge_Lx.txt = data.frame(f0 = paste0("1Some drug action", rep(" ", 237))),
Dechallenge2_Lx.txt = data.frame(f0 = paste0("1Some outcome occurring", rep(" ", 231))),
Frequency_Lx.txt =
data.frame(f0 =
paste0(
"123Some frequency of administration", rep(" ", 221)
)),
Gender_Lx.txt = data.frame(f0 = paste0("1Some gender", rep(" ", 242))),
Notifier_Lx.txt = data.frame(f0 = paste0("1 Some notifier", rep(" ", 240))),
Outcome_Lx.txt = data.frame(f0 = paste0("1Some outcome", rep(" ", 241))),
Rechallenge_Lx.txt = data.frame(f0 = paste0("1A rechallenge action", rep(" ", 60))),
Rechallenge2_Lx.txt =
data.frame(f0 = paste0(
"1A reaction recurrence status", rep(" ", 36)
)),
Region_Lx.txt = data.frame(f0 = paste0("1A world region", rep(" ", 36))),
RepBasis_Lx.txt = data.frame(f0 = paste0("1A reputation basis", rep(" ", 32))),
ReportType_Lx.txt = data.frame(f0 = paste0("1A type of report", rep(" ", 237))),
RouteOfAdm_Lx.txt = data.frame(f0 = paste0("1 A route of admnistration", rep(" ", 56))),
Seriousness_Lx.txt = data.frame(f0 = paste0(
"1 Some seriousness criteria", rep(" ", 224)
)),
SizeUnit_Lx.txt = data.frame(f0 = paste0("1 A dosing unit", rep(" ", 66)))
)
}
f_sets_who <-
function() {
# just in case you want to remember how you made this list
# run each reading from an example dataset, without processing it.
#df_expr <- list(atc , ccode , ing ,
# mp , org , pf ,
# pp , prt , srce,
# str , sun , thg ,
# unitx) |>
# rlang::set_names(
# "atc", "ccode", "ing",
# "mp", "org", "pf",
# "pp", "prt", "srce",
# "str", "sun", "thg",
# "unitx"
# ) |>
# rlang::set_names(~ paste0(stringr::str_to_upper(.x), ".txt")) |>
# purrr::map(
# function(d_){
#
# string <- d_ |> head(1) |> collect() |> pull()
# rlang::expr(data.frame(f0 = !!string))
# }
# )
#rlang::call2(expr(list2), !!!df_expr)
list(
ATC.txt = data.frame(f0 = "A 1ALIMENTARY TRACT AND METABOLISM "),
CCODE.txt = data.frame(f0 = "ABW Aruba "),
ING.txt = data.frame(f0 = "1 198512312301 38 1 1 "),
MP.txt = data.frame(f0 = "1 0000010100100000000010000000001YMethyldopa N/A 0 001 N/A 001 0 1985123120170907"),
ORG.txt = data.frame(f0 = "0 None UNS "),
PF.txt = data.frame(f0 = "001 Unspecified "),
PP.txt = data.frame(f0 = "1 001 1 0119851231"),
PRT.txt = data.frame(f0 = "001 Medicinal product "),
PRG.txt = data.frame(f0 = "0 None 20020701"),
SRCE.txt = data.frame(f0 = "001 INN - International Nonproprietary Names - WHO N/A "),
STR.txt = data.frame(f0 = "000001 Unspecified "),
SUN.txt = data.frame(f0 = "1 0000050000EN Formaldehyde solution 180 "),
ThG.txt = data.frame(f0 = "100007 N06BA 19890630Y40683 "),
`Unit-X.txt` = data.frame(f0 = "01 kg ")
)
}
f_sets_meddra <-
function() {
list(
llt.asc = data.frame(
f0 = c(
'486813518$A first LLT name$6548988$$$$$$$N$$',
'568798788$A second LLT name$47984764$$$$$$$Y$$'
)
),
mdhier.asc = data.frame(
f0 = c(
"6548988$84068465$98765468$8746878$A PT name$An HLT class$An HLGT class$A SOC class$A SOC class abrev$$12365489$Y$",
"47984764$7852085$6852245$2358467$A 2nd PT name$HLT class$HLGT class$SOC class$SOC abrev$$10005329$Y$"
)
),
smq_content.asc = data.frame(
f0 = c(
"20486512$6548641$5$1$A$0$A$7.1$7.1$",
"20904441$98143546$5$1$A$0$A$7.1$7.1$"
)
),
smq_list.asc = data.frame(
f0 = c(
"20486512$The SMQ name (SMQ)$1$Long text describing this SMQ to provide context to the user$References$$26.1$A$N$",
"20904441$Another name (SMQ)$1$Another long text$References$$26.1$A$N$"
)
)
)
}
Try the vigicaen package in your browser
Any scripts or data that you put into this service are public.
vigicaen documentation built on April 3, 2025, 8:55 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions f_sets_meddra f_sets_who f_sets_sub f_sets_main_pq f_sets_main create_ex_main_pq create_ex_meddra_asc create_ex_who_txt create_ex_sub_txt create_ex_main_txt
Documented in create_ex_main_pq create_ex_main_txt create_ex_meddra_asc create_ex_sub_txt create_ex_who_txt
#' Example source tables for VigiBase and MedDRA
#'
#' @description `r lifecycle::badge('experimental')` Write some example
#' tables as source text/ascii/parquet files.
#'
#' @details VigiBase tables and MedDRA tables are provided respectively
#' as text files and ascii files. The `tb_*` family turns them
#' into parquet files. These `create_example_*` functions are only used to produce
#' example source files to illustrate the `tb_*` family, and parquet files for the
#' same purpose.
#'
#' @param path Character string. A folder on your computer where the tables should
#' be written.
#' @importFrom utils write.table
#'
#' @returns A set of text/ascii files,
#' as received by the Uppsala Monitoring Centre or MedDRA
#' \itemize{
#' \item For [create_ex_main_txt()],
#' DEMO.txt, DRUG.txt, LINK.txt, FOLLOWUP.txt,
#' ADR.txt, OUT.txt, SRCE.txt, and IND.txt
#' \item For [create_ex_sub_txt()],
#' AgeGroup_Lx.txt, Dechallenge_Lx.txt, Dechallenge2_Lx.txt,
#' Frequency_Lx.txt, Gender_Lx.txt, Notifier_Lx.txt, Outcome_Lx.txt,
#' Rechallenge_Lx.txt, Rechallenge2_Lx.txt, Region_Lx.txt, RepBasis_Lx.txt,
#' ReportType_Lx.txt, RouteOfAdm_Lx.txt, Seriousness_Lx.txt,
#' and SizeUnit_Lx.txt
#' \item For [create_ex_who_txt()],
#' ATC.txt, CCODE.txt, ING.txt, MP.txt, ORG.txt,
#' PF.txt, PP.txt, PRT.txt, PRG.txt, SRCE.txt, STR.txt,
#' SUN.txt, ThG.txt, and Unit-X.txt
#' \item For [create_ex_meddra_asc()],
#' llt.asc, mdhier.asc, smq_content.asc, smq_list.asc
#' \item For [create_ex_main_pq()],
#' demo.parquet, adr.parquet, drug.parquet, link.parquet,
#' srce.parquet, ind.parquet, out.parquet, followup.parquet, suspdup.parquet
#' }
#' @seealso [tb_vigibase()], [tb_who()], [tb_meddra()]
#' @export
#'
#' @name create_example_tables
#'
#' @examples
#'
#' path <- paste0(tempdir(), "/crex/")
#'
#' dir.create(path)
#'
#' # You may want to use different paths for each type of tables
#' create_ex_main_txt(path)
#'
#' create_ex_sub_txt(path)
#'
#' create_ex_who_txt(path)
#'
#' create_ex_meddra_asc(path)
#'
#' create_ex_main_pq(path)
#'
#' # Remove temporary folders when you're done
#' unlink(path, recursive = TRUE)
create_ex_main_txt <-
function(
path
){
purrr::iwalk(f_sets_main(), function(d_, name_)
write.table(d_, file = paste0(path, name_),
row.names = FALSE, quote = FALSE, col.names = FALSE)
)
}
#' @describeIn create_example_tables sub txt tables
#' @export
create_ex_sub_txt <-
function(
path
){
purrr::iwalk(f_sets_sub(), function(d_, name_)
write.table(d_, file = paste0(path, name_),
row.names = FALSE, quote = FALSE, col.names = FALSE)
)
}
#' @describeIn create_example_tables WHO txt tables
#' @export
create_ex_who_txt <-
function(
path
){
purrr::iwalk(f_sets_who(), function(d_, name_)
write.table(d_, file = paste0(path, name_),
row.names = FALSE, quote = FALSE, col.names = FALSE)
)
}
#' @describeIn create_example_tables MedDRA txt tables
#' @export
create_ex_meddra_asc <-
function(
path
){
purrr::iwalk(f_sets_meddra(), function(d_, name_)
write.table(d_, file = paste0(path, name_),
row.names = FALSE, quote = FALSE, col.names = FALSE)
)
}
#' @describeIn create_example_tables main parquet tables
#' @export
create_ex_main_pq <-
function(
path
){
purrr::iwalk(
f_sets_main_pq(),
function(dataset, name)
arrow::write_parquet(
dataset |>
arrow::as_arrow_table(),
sink = paste0(path, "/", name, ".parquet")
)
)
}
# Helpers ------
# File sets for each type of table
f_sets_main <-
function() {
list(
DEMO.txt = data.frame(f0 = c("96548661 32194501051119460820")),
DRUG.txt = data.frame(f0 =
c(
"70548965 8 4901354 064392080055011 31- 806"
)),
LINK.txt = data.frame(f0 = c(
"2 654654 51---0.78991 0.98745 ", "2 456456 51---6.98789 - "
)),
FOLLOWUP.txt = data.frame(f0 = c("0548978 0254687 ", "7568798 4565321 ")),
ADR.txt = data.frame(f0 = c(
"96570161 14 100474561", "70578465 17 145078144"
)),
OUT.txt = data.frame(f0 = c("70547815 - N", "96575661 - Y")),
SRCE.txt = data.frame(f0 = c("4898765 1 ", "9804562 1 ")),
IND.txt = data.frame(
# 266 length
f0 = paste0(
"780954 Cutaneous diseases due to other mycobacteria",
rep(" ", 211)
)
)
)
}
f_sets_main_pq <-
function() {
rlang::list2(
demo =
data.table(
UMCReportId = c(1, 2, 3, 4),
AgeGroup = c(1, 2, 7, 9)
),
drug =
data.table(
UMCReportId = c(1, 2, 3, 4),
Drug_Id = c("d1", "d2", "d3", "d4"),
DrecNo = c(133138448, 133138448, 111841511, 111841511),
MedicinalProd_Id = c(25027716, 97354576, 104264760, 37484408)
),
adr =
data.table(
UMCReportId = c(1, 2, 3, 4),
Adr_Id = c("a1", "a2", "a3", "a4"),
MedDRA_Id = c(110049083, 146319904, 146319904, 72535511)
),
link =
data.table(
Drug_Id = c("d1", "d2", "d3", "d4"),
Adr_Id = c("a1", "a2", "a3", "a4")
),
srce =
data.table(UMCReportId = c(1, 2, 3, 4)),
ind =
data.table(Drug_Id = c("d1", "d2", "d3", "d4")),
out =
data.table(UMCReportId = c(1, 2, 3, 4)),
followup =
data.table(UMCReportId = c(1, 2, 3, 4)),
suspdup =
data.table(
UMCReportId = c(3),
SuspectedduplicateReportId = c(4)
)
)
}
f_sets_sub <-
function() {
list(
SUSPECTEDDUPLICATES.txt = data.frame(f0 = c("789054 789542 ", "780546 654352 ")),
AgeGroup_Lx.txt = data.frame(f0 = c("1An age range ")),
Dechallenge_Lx.txt = data.frame(f0 = paste0("1Some drug action", rep(" ", 237))),
Dechallenge2_Lx.txt = data.frame(f0 = paste0("1Some outcome occurring", rep(" ", 231))),
Frequency_Lx.txt =
data.frame(f0 =
paste0(
"123Some frequency of administration", rep(" ", 221)
)),
Gender_Lx.txt = data.frame(f0 = paste0("1Some gender", rep(" ", 242))),
Notifier_Lx.txt = data.frame(f0 = paste0("1 Some notifier", rep(" ", 240))),
Outcome_Lx.txt = data.frame(f0 = paste0("1Some outcome", rep(" ", 241))),
Rechallenge_Lx.txt = data.frame(f0 = paste0("1A rechallenge action", rep(" ", 60))),
Rechallenge2_Lx.txt =
data.frame(f0 = paste0(
"1A reaction recurrence status", rep(" ", 36)
)),
Region_Lx.txt = data.frame(f0 = paste0("1A world region", rep(" ", 36))),
RepBasis_Lx.txt = data.frame(f0 = paste0("1A reputation basis", rep(" ", 32))),
ReportType_Lx.txt = data.frame(f0 = paste0("1A type of report", rep(" ", 237))),
RouteOfAdm_Lx.txt = data.frame(f0 = paste0("1 A route of admnistration", rep(" ", 56))),
Seriousness_Lx.txt = data.frame(f0 = paste0(
"1 Some seriousness criteria", rep(" ", 224)
)),
SizeUnit_Lx.txt = data.frame(f0 = paste0("1 A dosing unit", rep(" ", 66)))
)
}
f_sets_who <-
function() {
# just in case you want to remember how you made this list
# run each reading from an example dataset, without processing it.
#df_expr <- list(atc , ccode , ing ,
# mp , org , pf ,
# pp , prt , srce,
# str , sun , thg ,
# unitx) |>
# rlang::set_names(
# "atc", "ccode", "ing",
# "mp", "org", "pf",
# "pp", "prt", "srce",
# "str", "sun", "thg",
# "unitx"
# ) |>
# rlang::set_names(~ paste0(stringr::str_to_upper(.x), ".txt")) |>
# purrr::map(
# function(d_){
#
# string <- d_ |> head(1) |> collect() |> pull()
# rlang::expr(data.frame(f0 = !!string))
# }
# )
#rlang::call2(expr(list2), !!!df_expr)
list(
ATC.txt = data.frame(f0 = "A 1ALIMENTARY TRACT AND METABOLISM "),
CCODE.txt = data.frame(f0 = "ABW Aruba "),
ING.txt = data.frame(f0 = "1 198512312301 38 1 1 "),
MP.txt = data.frame(f0 = "1 0000010100100000000010000000001YMethyldopa N/A 0 001 N/A 001 0 1985123120170907"),
ORG.txt = data.frame(f0 = "0 None UNS "),
PF.txt = data.frame(f0 = "001 Unspecified "),
PP.txt = data.frame(f0 = "1 001 1 0119851231"),
PRT.txt = data.frame(f0 = "001 Medicinal product "),
PRG.txt = data.frame(f0 = "0 None 20020701"),
SRCE.txt = data.frame(f0 = "001 INN - International Nonproprietary Names - WHO N/A "),
STR.txt = data.frame(f0 = "000001 Unspecified "),
SUN.txt = data.frame(f0 = "1 0000050000EN Formaldehyde solution 180 "),
ThG.txt = data.frame(f0 = "100007 N06BA 19890630Y40683 "),
`Unit-X.txt` = data.frame(f0 = "01 kg ")
)
}
f_sets_meddra <-
function() {
list(
llt.asc = data.frame(
f0 = c(
'486813518$A first LLT name$6548988$$$$$$$N$$',
'568798788$A second LLT name$47984764$$$$$$$Y$$'
)
),
mdhier.asc = data.frame(
f0 = c(
"6548988$84068465$98765468$8746878$A PT name$An HLT class$An HLGT class$A SOC class$A SOC class abrev$$12365489$Y$",
"47984764$7852085$6852245$2358467$A 2nd PT name$HLT class$HLGT class$SOC class$SOC abrev$$10005329$Y$"
)
),
smq_content.asc = data.frame(
f0 = c(
"20486512$6548641$5$1$A$0$A$7.1$7.1$",
"20904441$98143546$5$1$A$0$A$7.1$7.1$"
)
),
smq_list.asc = data.frame(
f0 = c(
"20486512$The SMQ name (SMQ)$1$Long text describing this SMQ to provide context to the user$References$$26.1$A$N$",
"20904441$Another name (SMQ)$1$Another long text$References$$26.1$A$N$"
)
)
)
}
Try the vigicaen package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.