This package is designed for identifying disease cases from admin data for epidemiological studies. The implementation focused on code readability and re-usability. Three types of functions are included:
Interactive functions (e.g.,
identify_row(), exclude(),
fetch_var()) based on filter and joins from dplyr with
tweaks that fix SQL translation or add features that are not natively
support by SQL. They also work for local data.frame, and some use
‘data.table’ package
(vignette("datatable-intro", package = "data.table")) to
speed up processing time for large data. These functions are not as
flexible as dplyr::filter(), but they are general enough to
be useful even outside health research.
Call-building functions (e.g., build_def(),
execute_def()) that facilitate batch execution and re-use
of case definitions. In essence, build_def creates codes of
definitions (which is chain of the interactive functions, e.g.,
define_case()) that are not immediately ran.
execute_def runs built definitions with different input
data.
Miscellaneous functions such as computing age
compute_duration(), collapsing records within a time range
into one episode collapse_episode(), and more (on-going
effort). Most of these functions have built-in checks signalling when
things might go wrong, e.g., missing values in calculated ages.
In health research and surveillance, identifying diseases or events from administrative databases is often the initial step. However, crafting case-finding algorithms is a complex task. Existing algorithms, often written in SAS by experienced analysts, can be complex and difficult to decipher for the growing number of analysts trained primarily in R.
These algorithms may also affect performance if they depend on Data Step in SAS, due to a lack of translation between Data Step and SQL. This can result in SAS downloading data from a remote database to a local machine, leading to poor performance when handling large, population-based databases.
The ‘healthdb’ R package was created to address these challenges. It
minimizes the need to download data and offers an easy-to-use interface
for working with healthcare databases. It also includes capabilities not
supported by ‘SQL’, such as matching strings by ‘stringr’ style regular
expressions, and can compute comorbidity scores
(compute_comorbidity()) directly on a database server. This
vignette will present an example of common use cases.
Simply run:
We will need the following packages for this demo.
Consider the case definition of substance use disorder (SUD) from British Columbia Centre for Disease Control’s Chronic Disease Dashboard,
One or more hospitalization with a substance use disorder diagnostic code, OR Two or more physician visits with a substance use disorder diagnostic code within one year.
We are going to implement this definition. First, let’s make a demo data sets for the two sources:
Physician claims with multiple columns of ICD-9 diagnostic codes
# make_test_dat() makes either a toy data.frame or database table in memory with known number of rows that satisfy the query we will show later
claim_db <- make_test_dat(vals_kept = c("303", "304", "305", "291", "292", glue("30{30:59}"), glue("29{10:29}"), noise_val = c("999", "111")), type = "database")
# this is a database table
# note that in-memory SQLite database stores dates as numbers
claim_db %>% head()
#> # Source: SQL [?? x 6]
#> # Database: sqlite 3.51.0 [:memory:]
#> uid clnt_id dates diagx diagx_1 diagx_2
#> <int> <int> <dbl> <chr> <chr> <chr>
#> 1 17 1 16684 999 3031 <NA>
#> 2 54 1 17280 999 999 <NA>
#> 3 51 1 17650 999 999 <NA>
#> 4 55 1 18353 999 <NA> <NA>
#> 5 83 2 16611 999 <NA> <NA>
#> 6 95 2 16822 999 <NA> <NA>Hospitalization with ICD-10 codes
hosp_df <- make_test_dat(vals_kept = c(glue("F{10:19}"), glue("F{100:199}"), noise_val = "999"), type = "data.frame")
# this is a local data.frame/tibble
hosp_df %>% head()
#> uid clnt_id dates diagx diagx_1 diagx_2
#> 1 74 1 2017-07-13 999 999 999
#> 2 84 2 2016-10-25 999 <NA> 999
#> 3 6 2 2018-06-04 F166 F192 999
#> 4 78 2 2019-05-05 999 999 <NA>
#> 5 9 3 2015-03-10 F166 F143 999
#> 6 14 3 2015-10-17 F15 999 999
# convert Date to numeric to be consistent with claim_db
hosp_df <- hosp_df %>%
mutate(dates = julian(dates))Let’s focus on the physician claims. Extracting clients with at least two records within a year is not difficult, and involves only a few steps. The codes could look like the following using dplyr, however, it does not work because: 1. SQL does not support multiple patterns in one LIKE operation, 2. dbply currently have issue with translating n_distinct.
## not run
claim_db %>%
# identify the target codes
filter(if_any(starts_with("diagx"), ~ str_like(., c("291%", "292%", "303%", "304%", "305%")))) %>%
# each clnt has at least 2 records on different dates
group_by(clnt_id) %>%
# the n_distinct step is mainly for reducing computation in the next step
filter(n_distinct(dates) >= 2) %>%
# any two dates within one year?
filter((max(dates) - min(dates)) <= 365)
## endHere’s how you could use healthdb to achieve these
steps:
Identify rows contains the target codes. Use
?identify_row to see a list of supported matching
types.
result1 <- claim_db %>%
identify_row(
vars = starts_with("diagx"),
match = "start",
vals = c(291:292, 303:305)
)
#> ℹ Identify records with condition(s):
#> • where at least one of the diagx, diagx_1, diagx_2 column(s) in each record
#> • contains a value satisfied SQL LIKE pattern: 291% OR 292% OR 303% OR 304% OR 305%
#> ℹ To see the final query generated by 'dbplyr', use dplyr::show_query() on the output.
#> To extract the SQL string, use dbplyr::remote_query().Bonus: remove clients with exclusion codes
This step is not in the substance use disorder definition, but other disease definitions often require exclusion of some ICDs that contradicts the ones of interest. Let’s say we want to remove clients with code “111” here.
We first identify “111” from the source, then exclude clients in the
output from the previous step’s result. exclude() take
either a data set (via the excl argument) or expression (condition
argument) as input. For the former, it performs an anti join matching on
the by argument (see dplyr::join_by()). For the latter, it
is the opposite of filter, i.e.,
filter(!(some_expression)).
result2 <- result1 %>%
exclude(
excl = identify_row(claim_db, starts_with("diagx"), "in", "111"),
by = "clnt_id"
)
#> ℹ Identify records with condition(s):
#> • where at least one of the diagx, diagx_1, diagx_2 column(s) in each record
#> • contains a value exactly matched values in set: "111"
#> ℹ Exclude records in `data` through anti_join with `excl` matching on (by argument): "clnt_id"Restrict the number of records per client
result3 <- result2 %>% restrict_n(
clnt_id = clnt_id,
n_per_clnt = 2,
count_by = dates,
# here we use filter mode to remove records that failed the restriction
mode = "filter"
)
#> ℹ Apply restriction that each client must have at least 2 records with distinct
#> dates. Clients/groups which did not met the condition were excluded.Restrict the temporal pattern of diagnoses
restrict_date() supports more complicated patterns like
having n diagnoses at least i days apart within j years. Note that when
SQL interpret order of dates, the result could be not deterministic if
there were duplicate dates within client. Therefore, a unique row id
(uid) has to be supplied to get consistent result.
result4 <- result3 %>% restrict_date(
clnt_id = clnt_id,
date_var = dates,
n = 2,
within = 365,
uid = uid,
# here we use flag mode to flag records that met the restriction instead of removing those
mode = "flag"
)
#> ℹ Apply restriction that each client must have 2 records that were within 365
#> days. Records that met the condition were flagged.Fetch variables from other tables by matching common keys
Up to this point, the result is only a query and have not been downloaded. Hopefully, the data has been shrunken to a manageable size for collection.
# Class of result4
class(result4)
#> [1] "tbl_SQLiteConnection" "tbl_dbi" "tbl_sql"
#> [4] "tbl_lazy" "tbl"
# execute query and download the result
result_df <- result4 %>% collect()
# Number of rows in source
nrow(claim_db %>% collect())
#> [1] 100
# Number of rows in the current result
nrow(result_df)
#> [1] 28Our data now only contains diagnoses which are probably not enough
for further analyses. Let’s say we want to gather client demographics
such as age and sex from other sources. This certainly can be done with
multiple dplyr::left_join() calls. Here we provide the
fetch_var() function to make the codes more concise. Note
that the input must be a named object and not from a pipe (i.e., don’t
do this data %>% some_action %>% fetch_var()).
# make two look up tables
age_tab <- data.frame(
clnt_id = 1:50,
age = sample(1:90, 50),
sex = sample(c("F", "M"), 50, replace = TRUE)
)
address_tab <- data.frame(
clnt_id = rep(1:50, 5), year = rep(2016:2020, each = 50),
area_code = sample(0:200, 50, replace = TRUE)
)
# get year from dates for matching
result_df <- result_df %>% mutate(year = lubridate::year(as.Date(dates, origin = "1970-01-01")))
# note that keys must be present in all tables
fetch_var(result_df,
keys = c(clnt_id, year),
linkage = list(
# the formula means from_table ~ get_variable
# |clnt_id means matching on clnt_id only
age_tab ~ c(age, sex) | clnt_id,
address_tab ~ area_code
)
) %>%
select(uid, clnt_id, dates, age, sex, area_code) %>%
head()
#> # A tibble: 6 × 6
#> uid clnt_id dates age sex area_code
#> <int> <int> <dbl> <int> <chr> <int>
#> 1 22 4 17472 19 F 119
#> 2 39 4 18445 19 F 119
#> 3 40 11 16843 72 F 58
#> 4 20 11 16943 72 F 58
#> 5 8 11 17645 72 F 58
#> 6 21 11 18608 72 F 58To complete the definition, we need to repeat the process shown above
with hospitalization data. Some studies may use more than a handful of
data sources to define their sample. We packed steps 1-4 in one function
define_case(), and provide tools to perform batch execution
with different data and parameters to meet those needs.
# build the full definition of SUD
sud_def <- build_def(
# name of definition
def_lab = "SUD",
# place holder names for sources
src_labs = c("claim", "hosp"),
def_fn = define_case, # you could alter it and supply your own function
# below are argumets of define_case
fn_args = list(
# if length = 1, the single element will be use for every source
vars = list(starts_with("diagx")),
match = "start", # match ICD starts with vals
vals = list(c(291:292, 303:305), glue("F{10:19}")),
clnt_id = clnt_id,
n_per_clnt = c(2, 1),
date_var = dates,
within = c(365, NULL),
uid = uid,
mode = "flag"
)
)
sud_def
#> # A tibble: 2 × 5
#> def_lab src_labs def_fn fn_args fn_call
#> <chr> <chr> <chr> <list> <list>
#> 1 SUD claim define_case <named list [9]> <language>
#> 2 SUD hosp define_case <named list [9]> <language>Let’s look inside the fn_call list column. Two calls of
define_case() have been made with different parameters. The
data arguments are left empty on purpose for re-usability. For example,
you may want to repeat the analysis with data from different regions or
study periods.
sud_def$fn_call
#> [[1]]
#> define_case(data = , vars = starts_with("diagx"), match = "start",
#> vals = c(291:292, 303:305), clnt_id = clnt_id, n_per_clnt = 2,
#> date_var = dates, within = 365, uid = uid, mode = "flag")
#>
#> [[2]]
#> define_case(data = , vars = starts_with("diagx"), match = "start",
#> vals = glue("F{10:19}"), clnt_id = clnt_id, n_per_clnt = 1,
#> date_var = dates, within = NULL, uid = uid, mode = "flag")Executing the definition is simply a call of
execute_def(). If verbose option is not turned off by
options(healthdb.verbose = FALSE), the output message will
explain what has been done. You could append multiple
build_def() outputs together and execute them all at once.
Definition and source labels will be added to the result to identify
outputs from different calls.
# execute the definition
result_list <- sud_def %>%
execute_def(with_data = list(
claim = claim_db,
hosp = hosp_df
))
#>
#> Actions for definition SUD using source claim_db:
#> → --------------Inclusion step--------------
#> ℹ Identify records with condition(s):
#> • where at least one of the diagx, diagx_1, diagx_2 column(s) in each record
#> • contains a value satisfied SQL LIKE pattern: 291% OR 292% OR 303% OR 304% OR 305%
#> → --------------No. rows restriction--------------
#>
#> ℹ Apply restriction that each client must have at least 2 records with distinct dates. Records that met the condition were flagged.
#> → --------------Time span restriction--------------
#>
#> ℹ Apply restriction that each client must have 2 records that were within 365 days. Records that met the condition were flagged.
#> → -------------- Output all records--------------
#>
#>
#> Actions for definition SUD using source hosp_df:
#>
#> → --------------Inclusion step--------------
#>
#> ℹ Identify records with condition(s):
#> • where at least one of the diagx, diagx_1, diagx_2 column(s) in each record
#> • contains a value satisfied regular expression: ^F10|^F11|^F12|^F13|^F14|^F15|^F16|^F17|^F18|^F19
#>
#> All unique value(s) and frequency in the result (as the conditions require just one of the columns containing target values; irrelevant values may come from other vars columns):
#> 999 F10 F100 F101 F104 F106 F108 F109 F112 F113 F116 F119 F12 F120 F121 F122
#> 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
#> F126 F127 F128 F129 F130 F131 F132 F133 F134 F135 F136 F138 F139 F14 F141 F142
#> 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
#> F143 F145 F147 F15 F150 F155 F156 F158 F16 F160 F163 F166 F168 F169 F17 F171
#> 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
#> F172 F173 F175 F177 F180 F181 F182 F183 F184 F185 F186 F188 F189 F19 F192 F195
#> 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
#> F196 F197 F198 F199 NA's
#> 1 1 1 1 1
#> → -------------- Output all records--------------Let’s check the results!
# view the results
purrr::walk(result_list, ~ head(.) %>% print())
#> # Source: SQL [?? x 10]
#> # Database: sqlite 3.51.0 [:memory:]
#> def src uid clnt_id dates diagx diagx_1 diagx_2 flag_restrict_n
#> <chr> <chr> <int> <int> <dbl> <chr> <chr> <chr> <int>
#> 1 SUD claim 17 1 16684 999 3031 <NA> 0
#> 2 SUD claim 6 2 18290 304 2920 999 0
#> 3 SUD claim 22 4 17472 2910 2929 <NA> 1
#> 4 SUD claim 39 4 18445 3052 3047 <NA> 1
#> 5 SUD claim 11 5 16807 3042 3045 999 1
#> 6 SUD claim 28 5 16842 2914 111 999 1
#> # ℹ 1 more variable: flag_restrict_date <int>
#> def src uid clnt_id dates diagx diagx_1 diagx_2
#> 1 SUD hosp 6 2 17686 F166 F192 999
#> 2 SUD hosp 9 3 16504 F166 F143 999
#> 3 SUD hosp 14 3 16725 F15 999 999
#> 4 SUD hosp 47 3 18495 F195 F171 F12
#> 5 SUD hosp 42 6 16598 F126 F171 F138
#> 6 SUD hosp 20 6 17841 F121 F14 <NA>At this point, the result from the claim database
(result[[1]]) has not been collected locally. You could
collect it manually, do further filtering, and then combine with the
result from hospitalization data in any way you want. If you just need a
simple row bind, we have bind_source() with convenient
naming feature.
bind_source(result_list,
# output_name = c(names in the list elements)
src = "src",
uid = "uid",
clnt_id = "clnt_id",
flag = c("flag_restrict_date", NA),
# force_proceed is needed to collect remote tables to local memory
force_proceed = TRUE
)
#> # A tibble: 100 × 5
#> src_No src uid clnt_id flag
#> <int> <chr> <int> <int> <int>
#> 1 1 claim 17 1 0
#> 2 1 claim 6 2 0
#> 3 1 claim 22 4 0
#> 4 1 claim 39 4 0
#> 5 1 claim 11 5 1
#> 6 1 claim 28 5 0
#> 7 1 claim 43 6 0
#> 8 1 claim 25 7 0
#> 9 1 claim 23 10 0
#> 10 1 claim 40 11 1
#> # ℹ 90 more rowspool_case() goes a few steps further than row bind. It
also filters records with valid flags and can summarize by client/group.
Since we had to decide which variables to be summarized in advance, the
output may not be flexible enough to meet your needs.
pool_case(result_list,
def = sud_def,
# your could skip summary with output_lvl = "raw"
output_lvl = "clnt",
# include records only from sources having valid records, see function documentation for more detail and other options
include_src = "has_valid",
force_proceed = TRUE
)
#> # A tibble: 34 × 10
#> def clnt_id first_valid_date first_valid_src last_entry_date last_entry_src
#> <chr> <int> <dbl> <chr> <dbl> <chr>
#> 1 SUD 2 17686 hosp 17686 hosp
#> 2 SUD 3 16504 hosp 18495 hosp
#> 3 SUD 5 16807 claim 16842 claim
#> 4 SUD 6 16598 hosp 18362 hosp
#> 5 SUD 7 16803 hosp 16803 hosp
#> 6 SUD 9 17367 hosp 17367 hosp
#> 7 SUD 10 16704 hosp 17465 hosp
#> 8 SUD 11 16843 claim 18608 hosp
#> 9 SUD 14 17430 hosp 17430 hosp
#> 10 SUD 16 17083 hosp 17083 hosp
#> # ℹ 24 more rows
#> # ℹ 4 more variables: raw_in_claim <dbl>, raw_in_hosp <dbl>,
#> # valid_in_claim <int>, valid_in_hosp <int>