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Minor fixes to fake data #87

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merged 4 commits into from
May 16, 2024
Merged

Minor fixes to fake data #87

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34cdb30
fixed NPU code length to "NPU" + 5 digits
May 13, 2024
c81984b
Edited to_wwyy() to account for years with week 53 (was previously fo…
May 13, 2024
e170967
Edited LPR3's diagnosetype to match the output of LPR2's c_diagtype (…
May 13, 2024
9364062
Merge branch 'main' into minor-fixes-to-fake-data
lwjohnst86 May 16, 2024
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4 changes: 2 additions & 2 deletions data-raw/simulate-data.R
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Original file line number Diff line number Diff line change
Expand Up @@ -83,7 +83,7 @@ create_padded_integer <- function(n, length) {
create_fake_npu <- function(n) {
stringr::str_c(
"NPU",
create_padded_integer(n, 8)
create_padded_integer(n, 5)
)
}

Expand All @@ -105,7 +105,7 @@ create_fake_drug_name <- function(atc) {
}

to_wwyy <- function(x) {
format(lubridate::as_date(x), format = "%W%y")
paste0(lubridate::isoweek(lubridate::as_date(x)), stringr::str_sub(lubridate::isoyear(lubridate::as_date(x)), -2))
}

to_yyyymmdd <- function(x) {
Expand Down
78 changes: 39 additions & 39 deletions data-raw/simulation-definitions.csv
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Original file line number Diff line number Diff line change
@@ -1,39 +1,39 @@
register_abbrev,variable_name,data_type,format,generator,explanation_of_values,comments
bef,koen,integer,binary,"draw_binary(0.5, N = N) + 1","2 is woman, 1 is man",
bef,pnr,string,12 digits zero-padded,"create_padded_integer(N, 12)",,
bef,foed_dato,date,YYYYMMDD,"to_yyyymmdd(create_fake_date(N, from = ""1900-01-01""))",,
lmdb,volume,double,standard,"runif(N, 1, 10)",,
lmdb,pnr,string,12 digits zero-padded,"create_padded_integer(N, 12)",,
lmdb,eksd,date,YYYYMMDD,"to_yyyymmdd(create_fake_date(N, from = ""1995-01-01""))",,
lmdb,atc,string,7 digits,create_fake_atc(N),"""^A10"" is glucose-lowering medications",
lmdb,apk,integer,standard,"runif(N, 1, 10)",,
lmdb,indo,string,blank or 7 digits zero-padded,"create_padded_integer(N, 7)",refer to the KAT classification,"the only used values are ""0000092"", ""0000276"", ""0000781"""
lmdb,name,string,natural language,,,"Need to run create_fake_drug_name() afterwards, since it depends on atc"
lmdb,vnr,string,6 digits zero-padded,"create_padded_integer(N, 6)",,
lpr_adm,c_spec,string,2 digits zero-padded,"create_padded_integer(N, 2)",,c_blok is derived from c_spec
lpr_adm,pnr,string,12 digits zero-padded,"create_padded_integer(N, 12)",,
lpr_adm,recnum,string,18 digits zero-padded,"create_padded_integer(N, 18)",,
lpr_adm,d_inddto,date,YYYYMMDD,to_yyyymmdd(create_fake_date(N)),,
lpr_diag,c_diagtype,string,"1 digit (A, B, H, +)","draw_categorical(N = N, prob = c(0.3, 0.7), category_labels = c('A', 'B'))",,
lpr_diag,recnum,string,18 digits zero-padded,"create_padded_integer(N, 18)",,
lpr_diag,c_diag,string,icd8 or icd10,create_fake_icd(N),"""^249|^250|^DE1[0-4]"" are diabetes codes",
kontakter,cpr,string,12 digits zero-padded,"create_padded_integer(N, 12)",,lpr3 equivalent to pnr
kontakter,dw_ek_kontakt,string,18 digits zero-padded,"create_padded_integer(N, 18)",,lpr3 equivalent to recnum
kontakter,dato_start,date,YYYYMMDD,to_yyyymmdd(create_fake_date(N)),,lpr3 equivalent to inddto
kontakter,hovedspeciale_ans,string,natural language,create_fake_hovedspeciale_ans(N),Is the LPR3 equivalent to c_spec but with different format,need to copy lpr2-lpr3 conversion table from dst
diagnoser,dw_ek_kontakt,string,18 digits zero-padded,"create_padded_integer(N, 18)",,lpr3 equivalent to recnum
diagnoser,diagnosekode,string,icd10,create_fake_icd10(N),"""^DE1[0-4]"" are diabetes codes",
diagnoser,diagnosetype,string,"1 digit (A, B, H, +)","draw_binary(0.3, N = N)","0/A is a primary diagnosis, 1/B is a secondary diagnosis",
diagnoser,senere_afkraeftet,string,Binary natural language,"draw_categorical(N = N, prob = c(0.2, 0.8), category_labels = c('Ja', 'Nej'))",,
sysi,pnr,string,12 digits zero-padded,"create_padded_integer(N, 12)",,
sysi,barnmak,integer,binary,"draw_binary(0.1, N = N)",0 is no,
sysi,speciale,string,5 digits,"create_padded_integer(N, 5)","""^54"" is diabetes-specific podiatrist service",
sysi,honuge,string,"4 digits: WWyy (2 digits week number, 2 digits year)","to_wwyy(create_fake_date(N, from = ""1990-01-01""))",,
sssy,pnr,string,12 digits zero-padded,"create_padded_integer(N, 12)",,
sssy,barnmak,integer,binary,"draw_binary(0.1, N = N)",0 is no,
sssy,speciale,string,5 digits,"create_padded_integer(N, 5)","""^54"" is diabetes-specific podiatrist service",
sssy,honuge,string,"4 digits: WWyy (2 digits week number, 2 digits year)","to_wwyy(create_fake_date(N, from = ""1990-01-01""))",,
lab_forsker,patient_cpr,string,12 digits zero-padded,"create_padded_integer(N, 12)",,
lab_forsker,samplingdate,date,YYYYMMDD,"to_yyyymmdd(create_fake_date(N, from = ""2011-01-01""))",,
lab_forsker,analysiscode,string,8 digit NPU code,create_fake_npu(N),NPU27300 is HbA1c in modern units (IFCC),NPU03835 is HbA1c in old units
lab_forsker,value,double,standard,"runif(N, 1, 180)",,
register_abbrev;variable_name;data_type;format;generator;explanation_of_values;comments
bef;koen;integer;binary;draw_binary(0.5, N = N) + 1;2 is woman, 1 is man;NA
bef;pnr;string;12 digits zero-padded;create_padded_integer(N, 12);NA;NA
bef;foed_dato;date;YYYYMMDD;"to_yyyymmdd(create_fake_date(N, from = ""1900-01-01""))";NA;NA
lmdb;volume;double;standard;runif(N, 1, 10);NA;NA
lmdb;pnr;string;12 digits zero-padded;create_padded_integer(N, 12);NA;NA
lmdb;eksd;date;YYYYMMDD;"to_yyyymmdd(create_fake_date(N, from = ""1995-01-01""))";NA;NA
lmdb;atc;string;7 digits;create_fake_atc(N);"""^A10"" is glucose-lowering medications";NA
lmdb;apk;integer;standard;runif(N, 1, 10);NA;NA
lmdb;indo;string;blank or 7 digits zero-padded;create_padded_integer(N, 7);refer to the KAT classification;"the only used values are ""0000092"", ""0000276"", ""0000781"""
lmdb;name;string;natural language;NA;NA;Need to run create_fake_drug_name() afterwards, since it depends on atc
lmdb;vnr;string;6 digits zero-padded;create_padded_integer(N, 6);NA;NA
lpr_adm;c_spec;string;2 digits zero-padded;create_padded_integer(N, 2);NA;c_blok is derived from c_spec
lpr_adm;pnr;string;12 digits zero-padded;create_padded_integer(N, 12);NA;NA
lpr_adm;recnum;string;18 digits zero-padded;create_padded_integer(N, 18);NA;NA
lpr_adm;d_inddto;date;YYYYMMDD;to_yyyymmdd(create_fake_date(N));NA;NA
lpr_diag;c_diagtype;string;1 digit (A, B, H, +);draw_categorical(N = N, prob = c(0.3, 0.7), category_labels = c('A', 'B'));NA;NA
lpr_diag;recnum;string;18 digits zero-padded;create_padded_integer(N, 18);NA;NA
lpr_diag;c_diag;string;icd8 or icd10;create_fake_icd(N);"""^249|^250|^DE1[0-4]"" are diabetes codes";NA
kontakter;cpr;string;12 digits zero-padded;create_padded_integer(N, 12);NA;lpr3 equivalent to pnr
kontakter;dw_ek_kontakt;string;18 digits zero-padded;create_padded_integer(N, 18);NA;lpr3 equivalent to recnum
kontakter;dato_start;date;YYYYMMDD;to_yyyymmdd(create_fake_date(N));NA;lpr3 equivalent to inddto
kontakter;hovedspeciale_ans;string;natural language;create_fake_hovedspeciale_ans(N);Is the LPR3 equivalent to c_spec but with different format;need to copy lpr2-lpr3 conversion table from dst
diagnoser;dw_ek_kontakt;string;18 digits zero-padded;create_padded_integer(N, 18);NA;lpr3 equivalent to recnum
diagnoser;diagnosekode;string;icd10;create_fake_icd10(N);"""^DE1[0-4]"" are diabetes codes";NA
diagnoser;diagnosetype;string;1 digit (A, B, H, +);draw_categorical(N = N, prob = c(0.3, 0.7), category_labels = c('A', 'B'));0/A is a primary diagnosis, 1/B is a secondary diagnosis;NA
diagnoser;senere_afkraeftet;string;Binary natural language;draw_categorical(N = N, prob = c(0.2, 0.8), category_labels = c('Ja', 'Nej'));NA;NA
sysi;pnr;string;12 digits zero-padded;create_padded_integer(N, 12);NA;NA
sysi;barnmak;integer;binary;draw_binary(0.1, N = N);0 is no;NA
sysi;speciale;string;5 digits;create_padded_integer(N, 5);"""^54"" is diabetes-specific podiatrist service";NA
sysi;honuge;string;4 digits: WWyy (2 digits week number, 2 digits year);"to_wwyy(create_fake_date(N, from = ""1990-01-01""))";NA;NA
sssy;pnr;string;12 digits zero-padded;create_padded_integer(N, 12);NA;NA
sssy;barnmak;integer;binary;draw_binary(0.1, N = N);0 is no;NA
sssy;speciale;string;5 digits;create_padded_integer(N, 5);"""^54"" is diabetes-specific podiatrist service";NA
sssy;honuge;string;4 digits: WWyy (2 digits week number, 2 digits year);"to_wwyy(create_fake_date(N, from = ""1990-01-01""))";NA;NA
lab_forsker;patient_cpr;string;12 digits zero-padded;create_padded_integer(N, 12);NA;NA
lab_forsker;samplingdate;date;YYYYMMDD;"to_yyyymmdd(create_fake_date(N, from = ""2011-01-01""))";NA;NA
lab_forsker;analysiscode;string;8 digit NPU code;create_fake_npu(N);NPU27300 is HbA1c in modern units (IFCC);NPU03835 is HbA1c in old units
lab_forsker;value;double;standard;runif(N, 1, 180);NA;NA
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