# Codify all patients from `ex_people` with their ICD-10 codes from `ex_icd10`
x <- codify(ex_people, ex_icd10, id = "name", code = "icd10")
x
#>
#> The printed data is of class: codified, data.table, data.frame.
#> It has 700 row(s).
#> It is here previewed as a tibble
#> Use `print(x, n = NULL)` to print as is (or use `n` to specify the number of rows to preview)!
#>
#> # A tibble: 10 × 6
#> name admission icd10 hdia in_period surgery
#> <chr> <date> <chr> <lgl> <lgl> <date>
#> 1 Archer, Leon Hunter 2025-02-17 B469 FALSE TRUE 2024-12-15
#> 2 Archer, Leon Hunter 2024-06-27 E012 FALSE TRUE 2024-12-15
#> 3 Archer, Leon Hunter 2025-03-06 R900 FALSE TRUE 2024-12-15
#> 4 Archer, Leon Hunter 2024-09-02 V7413 FALSE TRUE 2024-12-15
#> 5 Archer, Leon Hunter 2024-07-19 V8698 FALSE TRUE 2024-12-15
#> 6 Archer, Leon Hunter 2024-08-09 X3403 FALSE TRUE 2024-12-15
#> 7 Archer, Leon Hunter 2024-08-08 X4128 FALSE TRUE 2024-12-15
#> 8 Archer, Leon Hunter 2024-08-25 Z752 FALSE TRUE 2024-12-15
#> 9 Awtrey, Antonio 2025-04-17 N608 FALSE TRUE 2025-04-12
#> 10 Awtrey, Antonio 2025-02-17 W0341 FALSE TRUE 2025-04-12
# Only consider codes if recorded at hospital admissions within one year prior
# to surgery
codify(
ex_people,
ex_icd10,
id = "name",
code = "icd10",
date = "surgery",
code_date = "admission",
days = c(-365, 0) # admission during one year before surgery
)
#>
#> The printed data is of class: codified, data.table, data.frame.
#> It has 378 row(s).
#> It is here previewed as a tibble
#> Use `print(x, n = NULL)` to print as is (or use `n` to specify the number of rows to preview)!
#>
#> # A tibble: 10 × 6
#> name surgery admission icd10 hdia in_period
#> <chr> <date> <date> <chr> <lgl> <lgl>
#> 1 Archer, Leon Hunter 2024-12-15 2024-06-27 E012 FALSE TRUE
#> 2 Archer, Leon Hunter 2024-12-15 2024-07-19 V8698 FALSE TRUE
#> 3 Archer, Leon Hunter 2024-12-15 2024-08-08 X4128 FALSE TRUE
#> 4 Archer, Leon Hunter 2024-12-15 2024-08-09 X3403 FALSE TRUE
#> 5 Archer, Leon Hunter 2024-12-15 2024-08-25 Z752 FALSE TRUE
#> 6 Archer, Leon Hunter 2024-12-15 2024-09-02 V7413 FALSE TRUE
#> 7 Awtrey, Antonio 2025-04-12 2024-08-05 X3322 FALSE TRUE
#> 8 Awtrey, Antonio 2025-04-12 2024-10-26 Y1614 FALSE TRUE
#> 9 Awtrey, Antonio 2025-04-12 2024-10-29 X7564 FALSE TRUE
#> 10 Awtrey, Antonio 2025-04-12 2024-12-16 X6542 FALSE TRUE
# Only consider codes if recorded after surgery
codify(
ex_people,
ex_icd10,
id = "name",
code = "icd10",
date = "surgery",
code_date = "admission",
days = c(1, Inf) # admission any time after surgery
)
#>
#> The printed data is of class: codified, data.table, data.frame.
#> It has 355 row(s).
#> It is here previewed as a tibble
#> Use `print(x, n = NULL)` to print as is (or use `n` to specify the number of rows to preview)!
#>
#> # A tibble: 10 × 6
#> name surgery admission icd10 hdia in_period
#> <chr> <date> <date> <chr> <lgl> <lgl>
#> 1 Archer, Leon Hunter 2024-12-15 2025-02-17 B469 FALSE TRUE
#> 2 Archer, Leon Hunter 2024-12-15 2025-03-06 R900 FALSE TRUE
#> 3 Awtrey, Antonio 2025-04-12 2025-04-17 N608 FALSE TRUE
#> 4 Bammesberger, Jozi 2024-10-15 2024-11-18 V4931 FALSE TRUE
#> 5 Bammesberger, Jozi 2024-10-15 2024-12-02 V4960 FALSE TRUE
#> 6 Bammesberger, Jozi 2024-10-15 2025-01-22 X6414 FALSE TRUE
#> 7 Bammesberger, Jozi 2024-10-15 2025-02-10 Y1513 FALSE TRUE
#> 8 Bammesberger, Jozi 2024-10-15 2025-05-01 P293A FALSE TRUE
#> 9 Banks, Silbret 2025-01-08 2025-01-26 D229D FALSE TRUE
#> 10 Banks, Silbret 2025-01-08 2025-02-15 V7452 TRUE TRUE
# Dirty code data ---------------------------------------------------------
# Assume that codes contain unwanted "dirty" characters
# Those could for example be a dot used by ICD-10 (i.e. X12.3 instead of X123)
dirt <- c(strsplit(c("!#%&/()=?`,.-_"), split = ""), recursive = TRUE)
rdirt <- function(x) sample(x, nrow(ex_icd10), replace = TRUE)
sub <- function(i) substr(ex_icd10$icd10, i, i)
ex_icd10$icd10 <-
paste0(
rdirt(dirt), sub(1),
rdirt(dirt), sub(2),
rdirt(dirt), sub(3),
rdirt(dirt), sub(4),
rdirt(dirt), sub(5)
)
head(ex_icd10)
#> # A tibble: 6 × 4
#> name admission icd10 hdia
#> <chr> <date> <chr> <lgl>
#> 1 Tran, Kenneth 2024-11-02 -S_1.3(4,A FALSE
#> 2 Tran, Kenneth 2025-04-18 #W%3#3.1,9 FALSE
#> 3 Tran, Kenneth 2025-03-28 _Y/0?2%6`2 TRUE
#> 4 Tran, Kenneth 2025-02-18 )X!0=4_8/8 FALSE
#> 5 Sommerville, Dominic 2025-04-09 ,V%8(1)0_4 FALSE
#> 6 Sommerville, Dominic 2024-11-18 _B(8_5(3( FALSE
# Use `alnum = TRUE` to ignore non alphanumeric characters
codify(ex_people, ex_icd10, id = "name", code = "icd10", alnum = TRUE)
#>
#> The printed data is of class: codified, data.table, data.frame.
#> It has 700 row(s).
#> It is here previewed as a tibble
#> Use `print(x, n = NULL)` to print as is (or use `n` to specify the number of rows to preview)!
#>
#> # A tibble: 10 × 6
#> name admission icd10 hdia in_period surgery
#> <chr> <date> <chr> <lgl> <lgl> <date>
#> 1 Archer, Leon Hunter 2024-08-08 X4128 FALSE TRUE 2024-12-15
#> 2 Archer, Leon Hunter 2025-02-17 B469 FALSE TRUE 2024-12-15
#> 3 Archer, Leon Hunter 2024-07-19 V8698 FALSE TRUE 2024-12-15
#> 4 Archer, Leon Hunter 2024-08-09 X3403 FALSE TRUE 2024-12-15
#> 5 Archer, Leon Hunter 2024-08-25 Z752 FALSE TRUE 2024-12-15
#> 6 Archer, Leon Hunter 2024-06-27 E012 FALSE TRUE 2024-12-15
#> 7 Archer, Leon Hunter 2024-09-02 V7413 FALSE TRUE 2024-12-15
#> 8 Archer, Leon Hunter 2025-03-06 R900 FALSE TRUE 2024-12-15
#> 9 Awtrey, Antonio 2025-02-17 W0341 FALSE TRUE 2025-04-12
#> 10 Awtrey, Antonio 2024-08-05 X3322 FALSE TRUE 2025-04-12
# Big data ----------------------------------------------------------------
# If `data` or `codedata` are large compared to available
# Random Access Memory (RAM) it might not be possible to make internal copies
# of those objects. Setting `.copy = FALSE` might help to overcome such problems
# If no copies are made internally, however, the input objects (if data tables)
# would change in the global environment
x2 <- data.table::as.data.table(ex_icd10)
head(x2) # Look at the "icd10" column (with dirty data)
#> name admission icd10 hdia
#> <char> <Date> <char> <lgcl>
#> 1: Tran, Kenneth 2024-11-02 -S_1.3(4,A FALSE
#> 2: Tran, Kenneth 2025-04-18 #W%3#3.1,9 FALSE
#> 3: Tran, Kenneth 2025-03-28 _Y/0?2%6`2 TRUE
#> 4: Tran, Kenneth 2025-02-18 )X!0=4_8/8 FALSE
#> 5: Sommerville, Dominic 2025-04-09 ,V%8(1)0_4 FALSE
#> 6: Sommerville, Dominic 2024-11-18 _B(8_5(3( FALSE
# Use `alnum = TRUE` combined with `.copy = FALSE`
codify(ex_people, x2, id = "name", code = "icd10", alnum = TRUE, .copy = FALSE)
#>
#> The printed data is of class: codified, data.table, data.frame.
#> It has 700 row(s).
#> It is here previewed as a tibble
#> Use `print(x, n = NULL)` to print as is (or use `n` to specify the number of rows to preview)!
#>
#> # A tibble: 10 × 6
#> name admission icd10 hdia in_period surgery
#> <chr> <date> <chr> <lgl> <lgl> <date>
#> 1 Archer, Leon Hunter 2025-03-06 R900 FALSE TRUE 2024-12-15
#> 2 Archer, Leon Hunter 2024-08-09 X3403 FALSE TRUE 2024-12-15
#> 3 Archer, Leon Hunter 2024-08-08 X4128 FALSE TRUE 2024-12-15
#> 4 Archer, Leon Hunter 2024-08-25 Z752 FALSE TRUE 2024-12-15
#> 5 Archer, Leon Hunter 2024-06-27 E012 FALSE TRUE 2024-12-15
#> 6 Archer, Leon Hunter 2024-09-02 V7413 FALSE TRUE 2024-12-15
#> 7 Archer, Leon Hunter 2024-07-19 V8698 FALSE TRUE 2024-12-15
#> 8 Archer, Leon Hunter 2025-02-17 B469 FALSE TRUE 2024-12-15
#> 9 Awtrey, Antonio 2024-12-16 X6542 FALSE TRUE 2025-04-12
#> 10 Awtrey, Antonio 2025-03-20 X4078 FALSE TRUE 2025-04-12
# Even though no explicit assignment was specified
# (neither for the output of codify(), nor to explicitly alter `x2`,
# the `x2` object has changed (look at the "icd10" column!):
head(x2)
#> name admission icd10 hdia
#> <char> <Date> <char> <lgcl>
#> 1: Tran, Kenneth 2024-11-02 S134A FALSE
#> 2: Tran, Kenneth 2025-04-18 W3319 FALSE
#> 3: Tran, Kenneth 2025-03-28 Y0262 TRUE
#> 4: Tran, Kenneth 2025-02-18 X0488 FALSE
#> 5: Sommerville, Dominic 2025-04-09 V8104 FALSE
#> 6: Sommerville, Dominic 2024-11-18 B853 FALSE
# Hence, the `.copy` argument should only be used if necessary
# and if so, with caution!
# print.codify() ----------------------------------------------------------
x # Preview first 10 rows as a tibble
#>
#> The printed data is of class: codified, data.table, data.frame.
#> It has 700 row(s).
#> It is here previewed as a tibble
#> Use `print(x, n = NULL)` to print as is (or use `n` to specify the number of rows to preview)!
#>
#> # A tibble: 10 × 6
#> name admission icd10 hdia in_period surgery
#> <chr> <date> <chr> <lgl> <lgl> <date>
#> 1 Archer, Leon Hunter 2025-02-17 B469 FALSE TRUE 2024-12-15
#> 2 Archer, Leon Hunter 2024-06-27 E012 FALSE TRUE 2024-12-15
#> 3 Archer, Leon Hunter 2025-03-06 R900 FALSE TRUE 2024-12-15
#> 4 Archer, Leon Hunter 2024-09-02 V7413 FALSE TRUE 2024-12-15
#> 5 Archer, Leon Hunter 2024-07-19 V8698 FALSE TRUE 2024-12-15
#> 6 Archer, Leon Hunter 2024-08-09 X3403 FALSE TRUE 2024-12-15
#> 7 Archer, Leon Hunter 2024-08-08 X4128 FALSE TRUE 2024-12-15
#> 8 Archer, Leon Hunter 2024-08-25 Z752 FALSE TRUE 2024-12-15
#> 9 Awtrey, Antonio 2025-04-17 N608 FALSE TRUE 2025-04-12
#> 10 Awtrey, Antonio 2025-02-17 W0341 FALSE TRUE 2025-04-12
print(x, n = 20) # Preview first 20 rows as a tibble
#>
#> The printed data is of class: codified, data.table, data.frame.
#> It has 700 row(s).
#> It is here previewed as a tibble
#> Use `print(x, n = NULL)` to print as is (or use `n` to specify the number of rows to preview)!
#>
#> # A tibble: 20 × 6
#> name admission icd10 hdia in_period surgery
#> <chr> <date> <chr> <lgl> <lgl> <date>
#> 1 Archer, Leon Hunter 2025-02-17 B469 FALSE TRUE 2024-12-15
#> 2 Archer, Leon Hunter 2024-06-27 E012 FALSE TRUE 2024-12-15
#> 3 Archer, Leon Hunter 2025-03-06 R900 FALSE TRUE 2024-12-15
#> 4 Archer, Leon Hunter 2024-09-02 V7413 FALSE TRUE 2024-12-15
#> 5 Archer, Leon Hunter 2024-07-19 V8698 FALSE TRUE 2024-12-15
#> 6 Archer, Leon Hunter 2024-08-09 X3403 FALSE TRUE 2024-12-15
#> 7 Archer, Leon Hunter 2024-08-08 X4128 FALSE TRUE 2024-12-15
#> 8 Archer, Leon Hunter 2024-08-25 Z752 FALSE TRUE 2024-12-15
#> 9 Awtrey, Antonio 2025-04-17 N608 FALSE TRUE 2025-04-12
#> 10 Awtrey, Antonio 2025-02-17 W0341 FALSE TRUE 2025-04-12
#> 11 Awtrey, Antonio 2024-08-05 X3322 FALSE TRUE 2025-04-12
#> 12 Awtrey, Antonio 2025-03-20 X4078 FALSE TRUE 2025-04-12
#> 13 Awtrey, Antonio 2024-12-16 X6542 FALSE TRUE 2025-04-12
#> 14 Awtrey, Antonio 2024-10-29 X7564 FALSE TRUE 2025-04-12
#> 15 Awtrey, Antonio 2025-02-11 Y0492 FALSE TRUE 2025-04-12
#> 16 Awtrey, Antonio 2024-10-26 Y1614 FALSE TRUE 2025-04-12
#> 17 Bammesberger, Jozi 2025-05-01 P293A FALSE TRUE 2024-10-15
#> 18 Bammesberger, Jozi 2024-06-12 V1051 FALSE TRUE 2024-10-15
#> 19 Bammesberger, Jozi 2024-08-19 V1392 FALSE TRUE 2024-10-15
#> 20 Bammesberger, Jozi 2024-11-18 V4931 FALSE TRUE 2024-10-15
print(x, n = NULL) # Print as data.table (ignoring the 'classified' class)
#>
#> The printed data is of class: codified, data.table, data.frame.
#> It has 700 row(s).
#> It is here previewed as a tibble
#> Use `print(x, n = NULL)` to print as is (or use `n` to specify the number of rows to preview)!
#>
#> # A tibble: 10 × 6
#> name admission icd10 hdia in_period surgery
#> <chr> <date> <chr> <lgl> <lgl> <date>
#> 1 Archer, Leon Hunter 2025-02-17 B469 FALSE TRUE 2024-12-15
#> 2 Archer, Leon Hunter 2024-06-27 E012 FALSE TRUE 2024-12-15
#> 3 Archer, Leon Hunter 2025-03-06 R900 FALSE TRUE 2024-12-15
#> 4 Archer, Leon Hunter 2024-09-02 V7413 FALSE TRUE 2024-12-15
#> 5 Archer, Leon Hunter 2024-07-19 V8698 FALSE TRUE 2024-12-15
#> 6 Archer, Leon Hunter 2024-08-09 X3403 FALSE TRUE 2024-12-15
#> 7 Archer, Leon Hunter 2024-08-08 X4128 FALSE TRUE 2024-12-15
#> 8 Archer, Leon Hunter 2024-08-25 Z752 FALSE TRUE 2024-12-15
#> 9 Awtrey, Antonio 2025-04-17 N608 FALSE TRUE 2025-04-12
#> 10 Awtrey, Antonio 2025-02-17 W0341 FALSE TRUE 2025-04-12
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