---
title: Side-by-side by Design Pharma Data Handling with Merge, Join, Match, and Hash in R
tags: 
author: [森岡裕[SASユーザー総会世話人]](https://image.docswell.com/user/6484025)
site: [Docswell](https://www.docswell.com/)
thumbnail: https://bcdn.docswell.com/page/G75182L5E4.jpg?width=480
description: Side-by-side by Design Pharma Data Handling with Merge, Join, Match, and Hash in R by 森岡裕[SASユーザー総会世話人]
published: November 04, 25
canonical: https://image.docswell.com/s/6484025/5VM3PQ-2025-11-04-143449
---
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2025-11-04
ver1.1
Side-by-side by Design: Pharma
Data Handling with Merge, Join,
Match, and Hash in R
Yutaka Morioka
Yuki Nakagawa
EPS corporation
morioka.yutaka038@eps.co.jp


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Yutaka Morioka
Title: SAS Guru
Organization: EPS Corporation
A SAS programmer based in Japan and clinical data scientist. I actively
disseminate SAS programming techniques from introductory to advanced
levels and have presented at international and regional conferences
including SAS Global Forum, CDISC Interchange Japan, Phuse Japan
SDE, and PharmaSUG SDE. As an organizer of the SAS User’s Group in
Japan, I also focus on fostering collaboration between SAS and R
programmers, aiming to create synergy across both communities.
Yuki Nakagawa
Title: SAS Programmer / Biostatistician
Organization: EPS Corporation
Since joining the Statistical Analysis Department of EPS Corporation in
2019, Yuki Nakagawa has been engaged in clinical trials service from
SDTM to statistical analyses as the SAS Programmer and biostatistician.
Copyright©EPS All rights reserved.
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Disclaimer and Disclosures
• The opinions expressed are those of the authors and do not necessarily reflect
the official views or positions of their organizations.
• This presentation introduces various approaches to data joining,
but it does not intend to determine or recommend a single “best” method.
• The authors declare no conflicts of interest related to any of the methods,
packages, or tools mentioned in this presentation.
• In this presentation, I will limit the discussion to merging two tables due to time
constraints.
The picture can change when merging three or more tables, but that will be for
another occasion.
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Instruction
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Instruction
In clinical trial data handling, data merging is arguably the most frequently used operation.
Especially in the derivation of SDTM and ADaM datasets, programmers often perform left joins using
uniquely identifying keys such as USUBJID, SUBJID, VISIT, or TESTCD.However, few
programmers take the time to re-examine what “joining” really means.
There are multiple ways to perform a join, each based on a different conceptual foundation.
Moreover, the behavior of merge in SAS differs significantly from that in R, which often leads to
confusion for programmers swiching from SAS to R.
Since misunderstanding how joins work can easily lead to unintended data errors, this presentation
aims to take a deep and careful look at data joins from both a conceptual and practical perspective.
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Base.R merge function
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TEST data - Base.R merge
# DataFrame 11
df11 &lt;- data.frame(
id = c(1, 2, 3),
value_A = c(&quot;A1&quot;, &quot;A2&quot;, &quot;A3&quot;))
# DataFrame 12
df12 &lt;- data.frame(
id = c(2, 3, 4),
value_B = c(&quot;B2&quot;, &quot;B3&quot;, &quot;B4&quot;))
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TEST data(SAS dataset) -- Base.R merge
data wk11;
do id = 1 , 2, 3;
value_A = choosec(id,&quot;A1&quot;,&quot;A2&quot;,&quot;A3&quot;);
output;
end;
run;
data wk12;
do id = 2, 3, 4;
value_B = choosec(id-1,&quot;B2&quot;,&quot;B3&quot;,&quot;B4&quot;);
output;
end;
run;
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Inner Join - Base.R merge
inner_joined &lt;- merge(df11, df12, by = &quot;id&quot;)
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Full Outer Join - Base.R merge
full_outer_joined &lt;- merge(df11, df12, by = &quot;id&quot;, all = TRUE)
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Left Outer Join - Base.R merge
left_joined &lt;- merge(df11, df12, by = &quot;id&quot;, all.x = TRUE)
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Cross Join - Base.R merge
cross_joined &lt;- merge(df11, df12, by = character())
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Base.R merge
merge(x, y,
by = intersect(names(x), names(y)),
by.x = by, by.y = by,
all = FALSE,
all.x = all, all.y = all,
sort = TRUE,
suffixes = c(&quot;.x&quot;, &quot;.y&quot;),
incomparables = NULL,
...)
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SAS Merge
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SAS merge – Inner Join
proc sort data=wk11;
by id;
run;
proc sort data=wk12;
by id;
run;
data inner_join;
merge wk11(in=in11)
wk12(in=in22);
by id;
if in11 and in22;
run;
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SAS merge – Full Outer Join
proc sort data=wk11;
by id;
run;
proc sort data=wk12;
by id;
run;
data outer_join;
merge wk11
wk12;
by id;
run;
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SAS merge – Left Outer Join
proc sort data=wk11;
by id;
run;
proc sort data=wk12;
by id;
run;
data left_outer_join;
merge wk11(in=in11)
wk12(in=in22);
by id;
if in11;
run;
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SAS – Cross Join
data cross_join;
set wk11;
do i=1 to wk12obs;
set wk12 nobs=wk12obs point=i;
output;
end;
run;
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R.Base merge VS SAS merge
df21 &lt;- data.frame(
id = c(1, 2, 3),
score = c(90, 80, 70)
)
df22 &lt;- data.frame(
id = c(2, 3, 4),
score = c(85, 75, 65)
)
merged &lt;- merge(df21, df22, by = &quot;id&quot;)
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data wk21;
do id = 1 , 2, 3;
score= choosen(id,90,80,70);
output;
end;
run;
data wk22;
do id = 2, 3, 4;
score = choosen(id-1,85,75,65);
output;
end;
run;
proc sort data=wk21;
by id;
run;
proc sort data=wk22;
by id;
run;
data sas_merged;
merge wk21(in=in11)
wk22(in=in22);
by id;
if in11 and in22;
run;
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Concepts of Internal Processing in SAS and R
R.merge Function
SQL Join
SAS
“Sequential processing” refers to the concept of implicitly looping
through all records by reading one record, processing it, and then
outputting one record — repeating this sequence for every record.
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dplyr
https://dplyr.tidyverse.org/
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Test data – dplyr
library(dplyr)
df31 &lt;- tibble(
id = c(1, 2, 3),
value_A = c(&quot;A1&quot;, &quot;A2&quot;, &quot;A3&quot;)
)
df32 &lt;- tibble(
id = c(2, 3, 4),
value_B = c(&quot;B2&quot;, &quot;B3&quot;, &quot;B4&quot;)
)
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Join – dplyr
inner_join &lt;- inner_join(df31, df32, by = &quot;id&quot;)
full_join &lt;- full_join(df31, df32, by = &quot;id&quot;)
left_join &lt;- left_join(df31, df32, by = &quot;id&quot;)
cross_join &lt;- cross_join(df31, df32)
#Cross Join (Before dplyr v1.1.0)
cross_join2 &lt;- df31 %&gt;%
mutate(dummy = 1) %&gt;%
inner_join(df32 %&gt;% mutate(dummy = 1), by =
&quot;dummy&quot;) %&gt;%
select(-dummy)
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dplyr:full_join ≠ SAS merge
library(dplyr)
wk1 &lt;- tibble(id = 1:3, val = c(&quot;A&quot;, &quot;B&quot;, &quot;C&quot;))
wk2 &lt;- tibble(id = 2:4, val = c(&quot;D&quot;, &quot;E&quot;, &quot;F&quot;))
out1 &lt;- full_join(wk1, wk2, by = &quot;id&quot;)
data sas_out1 ;
merge wk1 wk2;
by id;
run;
dplyr:full_join ≠
out2 &lt;- rows_upsert(wk1, wk2, by = &quot;id&quot;)
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SAS merge
In this case, `rows_upsert`
behaves similarly to a SAS
merge rather than a full join.
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sassy
https://sassy.r-sassy.org/index.html
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sassy – merge
wk1 &lt;- tibble(id = 1:3, val = c(&quot;A&quot;, &quot;B&quot;, &quot;C&quot;))
wk3 &lt;- tibble(id = 2:4, val = c(&quot;D&quot;, &quot;E&quot;, &quot;F&quot;),val2 = c(&quot;D&quot;, &quot;E&quot;, &quot;F&quot;) )
out3 &lt;- rows_upsert(wk1, wk3, by = &quot;id&quot;)
library(sassy)
out4 &lt;- datastep(
merge(wk1, wk3, by = &quot;id&quot;, type = &quot;full&quot;),
{}
)
Even when using the sassy package to replicate SAS behavior in R, it does not
fully replicate the merge statement.
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“Perfect replication” is difficult because the SAS merge ...
by ...; relies on a unique execution model :
• PDV (Program Data Vector): values from the other dataset are retained and carried
forward.
• Sequential matching within BY groups: duplicates are matched in order, not as a
SQL-style Cartesian join.
• Overwriting of same-named variables: variables from later datasets overwrite
earlier ones, while at the same time special flags like IN=, FIRST., and LAST. are
available.
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SQL
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SQL – Join
/*Inner join*/
select coalesce(wk11.id, wk12.id) as id
,value_A
, value_B
from wk11 inner join wk12 on wk11.id = wk12.id;
/*full outer join*/
select coalesce(wk11.id, wk12.id) as id
,value_A
, value_B
from wk11 full outer join wk12 on wk11.id = wk12.id;
/*left outer join*/
select coalesce(wk11.id, wk12.id) as id
,value_A
, value_B
from wk11 left outer join wk12 on wk11.id = wk12.id;
/*cross join*/
select coalesce(wk11.id, wk12.id) as id
,value_A
, value_B
from wk11 cross join wk12 ;
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Various Ways to Implement SQL in R
library(sqldf)
sqldf &lt;- sqldf(&quot;SELECT a.id, a.value_A, b.value_B
FROM df11 a
INNER JOIN df12 b
ON a.id = b.id&quot;)
1. sqldf packageThe most well-known
methodAllows direct handling of dataframes
with SQLUses SQLite internally for processing
library(DBI)
library(RSQLite)
con &lt;- dbConnect(RSQLite::SQLite(), &quot;:memory:&quot;)
dbWriteTable(con, &quot;df11&quot;, df11)
dbWriteTable(con, &quot;df12&quot;, df12)
dbi1 &lt;- dbGetQuery(con, &quot;SELECT a.id, a.value_A, b.value_B
FROM df11 a
INNER JOIN df12 b
ON a.id = b.id&quot;)
2. DBI + dplyr/dbplyrCombining R&#039;s
database connection API (DBI) with
dbplyr—an extension of dplyr—enables
you to convert dplyr code into SQL for
execution on databases.Furthermore,
using DBI::dbGetQuery() allows you to
write raw SQL directly.
library(duckdb)
con &lt;- dbConnect(duckdb())
dbWriteTable(con, &quot;df11&quot;, df11)
dbWriteTable(con, &quot;df12&quot;, df12)
duckdb &lt;- dbGetQuery(con, &quot;SELECT a.id, a.value_A, b.value_B
FROM df11 a
INNER JOIN df12 b
ON a.id = b.id&quot;)
3. duckdb PackageUse DuckDB, an
ultra-fast embedded DB engine, in
RRun SQL queries directly on
dataframesIt&#039;s becoming a staple for
large-scale data processing
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Base.R match
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Base.R match
The match function compares vectors and returns an index .
x &lt;- c(&quot;B&quot;, &quot;C&quot;, &quot;A&quot;, &quot;D&quot;)
table &lt;- c(&quot;A&quot;, &quot;B&quot;, &quot;C&quot;)
match(x, table)
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Base.R match
df41 &lt;- data.frame(
ID = c(101, 102, 103, 104),
Name = c(&quot;Alice&quot;, &quot;Bob&quot;, &quot;Carol&quot;, &quot;Dave&quot;)
)
df42 &lt;- data.frame(
ID = c(103, 101, 105),
Score = c(88, 85, 90)
)
match &lt;- df41
match$Score &lt;- df42$Score[ match(df41$ID, df42$ID) ]
In short, match() is a “position-return” type join method a
simplified version of SQL JOIN (limited to many-to-one, left
joins)useful for fetching values in a lookup-like manner.
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hash
https://cran.r-project.org/web/packages/hash/index.html
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hash
library(hash)
# Creating a Hash
h &lt;- hash(keys = c(&quot;a&quot;, &quot;b&quot;, &quot;c&quot;), values = c(1, 2, 3))
# Reference to a Value
h[[&quot;a&quot;]] # 1
h[[&quot;b&quot;]] # 2
# Add new elements
h[[&quot;d&quot;]] &lt;- 4
h[[&quot;z&quot;]]
Key
Data
# Existence check with has.key()
has.key(&quot;a&quot;, h) # TRUE
has.key(&quot;x&quot;, h) # FALSE
# Safe lookup: return NA if not exist
k &lt;- &quot;x&quot;
if (has.key(k, h)) {
print(h[[k]])
} else {
print(NA)
}
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hash
# Lookup Table（Country Code, Country Name）
lookup &lt;- data.frame(
code = c(&quot;JP&quot;, &quot;US&quot;, &quot;FR&quot;),
name = c(&quot;Japan&quot;, &quot;United States&quot;, &quot;France&quot;)
)
# Target Dataset
df &lt;- data.frame(
subject = 1:5,
code = c(&quot;JP&quot;, &quot;US&quot;, &quot;CN&quot;, &quot;FR&quot;, &quot;JP&quot;)
)
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hash
library(hash)
# Create Hash
h &lt;- hash(keys = lookup$code, values = lookup$name)
df$name &lt;- vapply(df$code,
function(k) if (has.key(k, h)) h[[k]] else NA_character_,
FUN.VALUE = character(1))
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hash
Summary of the R hash package
• Fundamentally, it is a dictionary structure of “one key → one value.”
• While the value can be a vector or a list, it is not natural to define multiple variables as keys or
to manage multiple variables together as data.
• Therefore, unlike the SAS hash object, it does not support something like defineKey /
defineData method with multiple variables.
• Intuitively, its behavior is closer to a proc format lookup table in SAS (mapping a code to a
label).
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data.table
https://github.com/Rdatatable/data.table?tab=readme-ov-file
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data.table
Key Features of data.table in R
High Performance
• Extremely fast operations even with tens of millions of rows.
• Optimized algorithms for joins and aggregation.
• Reference-based operations minimize memory consumption.
Concise Syntax ([i, j, by])
Core structure: DT[i, j, by]
i: row filtering (similar to SQL WHERE)
j: column operations or aggregations (similar to SQL SELECT)
by: grouping (similar to SQL GROUP BY)
Enables SQL-like data manipulation in a very compact form.
Flexible and Fast Joins
Key-based joins with on= are highly efficient.
Supports equi-joins, non-equi joins, rolling joins, and multi-key joins.
Can reproduce INNER, LEFT, and FULL OUTER JOIN behavior.
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data.table
library(data.table)
dt51 &lt;- data.table(id = c(1,2,3), val1 = c(&quot;A&quot;,&quot;B&quot;,&quot;C&quot;))
dt52 &lt;- data.table(id = c(2,3,4), val2 = c(10,20,30))
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Inner &amp; Left Outer Join - data.table
#Inner Join
dt_out1 &lt;- dt51[dt52, on = .(id), nomatch=0]
#Left Outer Join (dt51 on the left side as the reference)
dt_out2 &lt;- dt52[dt51, on = .(id)]
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Full Outer &amp; Cross Join - data.table
#Full Outer Join
dt_out3 &lt;- merge(dt51, dt52, by=&quot;id&quot;, all=TRUE)
data.table::merge.data.table(dt51, dt52, by = &quot;id&quot;, all = TRUE)
#Cross Join
dt51_ &lt;- dt51[, key := 1]
dt52_ &lt;- dt52[, key := 1]
dt_out4 &lt;- dt51_[dt52_, on=.(key)
, allow.cartesian=TRUE][, key := NULL]
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Rolling Join - data.table
#Rolling Join
dt_query &lt;- data.table(time = c(2,6,9))
dt_time &lt;- data.table(time = c(1,5,10)
, value = c(&quot;a&quot;,&quot;b&quot;,&quot;c&quot;))
#Join the most recent past value
dt_out5 &lt;- dt_time[dt_query, on=.(time), roll=TRUE]
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Rolling Join - data.table
Rolling join is an ordered join that fills in matches using the closest previous
(or next) key value, when an exact match is not found.
For each value in the query table, find the closest matching key in the source table
that does not exceed it (when roll=TRUE).
In data.table&#039;s Rolling Join, when there are duplicate key values,the row that is
matched depends on the mult argument:by default, the first matching row is used
(mult = &quot;first&quot;),while setting mult = &quot;last&quot; makes it use the last one.
Option
Description
roll = TRUE
Carry the most recent past value forward (LOCF)
roll = Inf
Carry the most recent past value forward (LOCF)
roll = -Inf
Carry the next future value backward (NOCB)
roll = &quot;nearest&quot;
Use whichever value is closest (past or future)
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Non-equi Join - data.table
# Non-equi Join (point-in-interval join)
dt_range &lt;- data.table(start = c(1,5), end = c(3,10),
label=c(&quot;low&quot;,&quot;high&quot;))
dt_point &lt;- data.table(x = 1:10)
# Combine elements where x is within the range start &lt;= x &lt;= end
dt_out6 &lt;- dt_range[dt_point, on=.(start &lt;= x, end &gt;= x), nomatch=0]
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Non-equi Join - data.table
# Non-equi Join
# Get the nearest previous or next value (without rolling)
X &lt;- data.table(time = c(1, 5, 10), value = c(&quot;a&quot;, &quot;b&quot;, &quot;c&quot;))
Y &lt;- data.table(time = c(2, 6, 9))
setkey(X, time)
# Nearest previous (time &lt; y)
prev &lt;- X[Y, on = .(time &lt; time), mult = &quot;last&quot;]
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Non-equi Join - data.table
# Non-equi Join
#Matching within a +-tolerance band
#Use non-equi conditions to find all matches inside [u − tol, u + tol],
#then pick the closest one (dist = abs(t − u)).
# Match within the tolerance band
X &lt;- data.table(id=1, t=c(1,5,9,12), val=c(&quot;A&quot;,&quot;B&quot;,&quot;C&quot;,&quot;D&quot;))
Y &lt;- data.table(id=1, u=c(2,6,11), tol=c(2,1,3))
setkey(X, id, t)
# Precompute join columns
Y[, lower := u - tol]
Y[, upper := u + tol]
# Now perform the join safely
hits &lt;- X[Y, on = .(id, t &gt;= lower, t &lt;= upper),
nomatch=0,.(id, u, tol, t, val, dist = abs(t - u))]
# Keep only the closest match per (id,u)
nearest &lt;- hits[order(id, u, dist)][, .SD[1], by=.(id, u)]
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data.table vs. dplyr
Aspect
dplyr::inner_join
data.table [i, on=]
Conceptual Model
SQL-like (declarative)
Hash / index-based
(imperative)
Implementation Algorithm
Hash-based (implemented in
C++) not sorted.
Hash join or key-based binary
search
Execution Environment
R + C++ (vctrs, dplyr)
C (datatable.c)
Key Features
Readability, strict type
consistency, tidyverse
integration
High speed, low memory
usage, supports non-equi joins
Translated to SQL via dbplyr
In-memory only (no direct SQL
translation)
Database Integration
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PharmaForest (SAS)
https://pharmaforest.github.io/
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Clinical Trial Data Handling
In clinical trial data programming, particularly in the creation of CDISC-compliant SDTM and
ADaM datasets, left joins account for the vast majority of data merge operations.Moreover, in
ADaM dataset derivations, it is extremely common to create flag variables (e.g., “Y/N”) indicating
whether a given key variable such as USUBJID exists in another dataset.
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PharmaForest
https://github.com/PharmaForest
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%kvlookup - Sashash Package
data dm;
length SUBJID SEX $20.;
SUBJID=&quot;A001&quot;;SEX=&quot;MALE&quot;;AGE=14;output;
SUBJID=&quot;A002&quot;;SEX=&quot;FEMALE&quot;;AGE=13;output;
SUBJID=&quot;B001&quot;;SEX=&quot;MALE&quot;;AGE=13;output;
run;
data wk1;
length SUBJID $20.;
SUBJID=&quot;A001&quot;;output;
SUBJID=&quot;A002&quot;;output;
SUBJID=&quot;A003&quot;;output;
SUBJID=&quot;B001&quot;;output;
run;
data out1;
set wk1;
%kvlookup(master=dm,key=SUBJID,var=SEX AGE);
run;
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Kvlookup_dt [R]
kvlookup_dt &lt;- function(x,
master,
key,
# character vector: key column names
var = NULL,
# character vector: variable names to retrieve (NULL = all columns except keys)
wh = NULL,
# character scalar: data.table expression applied to master (e.g., quote(Age &gt; 12) or &quot;Age &gt; 12&quot;)
warn = FALSE, # whether to issue a warning when lookup keys are not found
overwrite = TRUE # whether to overwrite existing columns in x if names overlap
){
stopifnot(requireNamespace(&quot;data.table&quot;, quietly = TRUE))
DTx &lt;- data.table::as.data.table(x)
# --- Add a matching flag to master (used to check hits after join) --DTm &lt;- data.table::as.data.table(master)
hit_col &lt;- &quot;__kv_hit__&quot;
while (hit_col %in% names(DTm)) hit_col &lt;- paste0(hit_col, &quot;_&quot;)
# --- Apply WHERE filter (wh) to master --DTm[, (hit_col) := TRUE]
if (!is.null(wh) &amp;&amp; nzchar(as.character(wh))) {
# Allow both character and expression inputs for evaluation
# --- Set key for faster join --if (is.character(wh)) {
data.table::setkeyv(DTm, key)
wh_expr &lt;- parse(text = wh)[[1]]
} else {
# --- Perform join (X[i] form; keep i = x to preserve its order and row count) --wh_expr &lt;- wh
# master[x, on=key] → keeps the number and order of i (=x) rows,
}
# with X (=master) columns first
DTm &lt;- DTm[eval(wh_expr)]
RES &lt;- DTm[DTx, on = key]
}
# --- Determine columns to keep (key + var) --if (is.null(var)) {
# If var is not specified, use all columns in master except keys
var &lt;- setdiff(names(DTm), key)
}
keep_cols &lt;- unique(c(key, var))
miss_cols &lt;- setdiff(keep_cols, names(DTm))
if (length(miss_cols)) {
stop(sprintf(&quot;The following columns do not exist in master: %s&quot;, paste(miss_cols, collapse = &quot;, &quot;)))
}
DTm &lt;- DTm[, ..keep_cols]
# --- Extract target columns (var) and merge them into x --# Handle name conflicts
dup_in_x &lt;- intersect(var, names(DTx))
if (length(dup_in_x) &amp;&amp; !overwrite) {
stop(sprintf(&quot;The following columns already exist in x (overwrite=FALSE): %s&quot;,
paste(dup_in_x, collapse = &quot;, &quot;)))
}
# Add new columns or overwrite existing ones (similar to SAS DATA step behavior)
for (vn in var) {
DTx[, (vn) := RES[[vn]]]
}
# --- Issue warnings (warn=TRUE when keys are non-NA but not found) --if (isTRUE(warn)) {
# &quot;matched&quot; = whether the master-side flag is TRUE
matched &lt;- isTRUE(RES[[hit_col]])
matched[is.na(matched)] &lt;- FALSE
# &quot;key_any_present&quot; = at least one key is non-missing
key_df &lt;- RES[, ..key]
key_any_present &lt;- apply(!is.na(as.data.frame(key_df)), 1, any)
not_found &lt;- (!matched) &amp; key_any_present
if (any(not_found)) {
# Log the missing key values
msg_keys &lt;- apply(as.data.frame(key_df[not_found]), 1, function(rw) {
paste(sprintf(&quot;%s=%s&quot;, names(key_df), ifelse(is.na(rw),
&quot;NA&quot;, as.character(rw))), collapse = &quot;, &quot;)
})
warning(sprintf(&quot;kvlookup_dt: %d key(s) not found in master. Examples:\n%s&quot;,
sum(not_found),
paste(utils::head(msg_keys, 5), collapse = &quot;\n&quot;)))
}
}
# --- Remove temporary working column --RES[, (hit_col) := NULL]
# The result is a data.table where var columns are added to x
return(DTx[])
}
Using data.table, I reproduced the behavior of SAS’s PharmaForest.sashash Package. kvlookup
macro — one of the most commonly used data-handling techniques in clinical trial programming —
with equivalent functionality in R.
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Kvlookup_dt [R]
dm &lt;- data.table(SUBJID =
c(&quot;A001&quot;,&quot;A002&quot;,&quot;B001&quot;),
AGE = c(14,13,13),
SEX = c(&quot;MALE&quot;,&quot;FEMALE&quot;,&quot;FEMALE&quot;))
wk1 &lt;- data.table(SUBJID =
c(&quot;A001&quot;,&quot;A002&quot;,&quot;A003&quot;,&quot;B001&quot;))
out &lt;- kvlookup_dt(
wk1, dm,
key = &quot;SUBJID&quot;,
var = c(&quot;AGE&quot;,&quot;SEX&quot;)
)
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Keycheck_dt [R]
keycheck_dt &lt;- function(x,
master,
key,
# character vector: key column names
wh = NULL,
# character or expression: filter applied to master (e.g., &quot;AGE &gt;= 15&quot;)
fl = &quot;exist_fl&quot;, # name of output flag column
cat = c(&quot;YN&quot;,&quot;NUM&quot;,&quot;Y&quot;) # &quot;YN&quot;=Y/N, &quot;NUM&quot;=1/0, &quot;Y&quot;=Y/&quot;&quot;
){
stopifnot(requireNamespace(&quot;data.table&quot;, quietly = TRUE))
cat &lt;- match.arg(cat)
DTx &lt;- data.table::as.data.table(x)
DTm &lt;- data.table::as.data.table(master)
# --- apply WHERE filter (wh) on master --if (!is.null(wh) &amp;&amp; nzchar(as.character(wh))) {
wh_expr &lt;- if (is.character(wh)) parse(text = wh)[[1]] else wh
DTm &lt;- DTm[eval(wh_expr)]
}
# --- keep only key columns, unique keys are enough for existence check --miss_cols &lt;- setdiff(key, names(DTm))
if (length(miss_cols)) {
stop(sprintf(&quot;Columns not found in master: %s&quot;, paste(miss_cols, collapse = &quot;, &quot;)))
}
DTm &lt;- unique(DTm[, ..key])
# --- prepare master with a hit flag for join result --hit_col &lt;- &quot;__key_hit__&quot;
while (hit_col %in% names(DTm)) hit_col &lt;- paste0(hit_col, &quot;_&quot;)
DTm[, (hit_col) := TRUE]
# --- set keys for fast join --data.table::setkeyv(DTm, key)
# --- left-join-like existence check against x (preserve x&#039;s order/rows) --RES &lt;- DTm[DTx, on = key]
# FIX: vectorized match flag
matched &lt;- RES[[hit_col]]
# logical vector: TRUE or NA
matched[is.na(matched)] &lt;- FALSE # NA -&gt; FALSE
# --- build the requested flag column on DTx --if (cat == &quot;YN&quot;) {
DTx[, (fl) := ifelse(matched, &quot;Y&quot;, &quot;N&quot;)]
} else if (cat == &quot;NUM&quot;) {
DTx[, (fl) := as.integer(matched)] # 1 if exists, 0 otherwise
} else if (cat == &quot;Y&quot;) {
DTx[, (fl) := ifelse(matched, &quot;Y&quot;, &quot;&quot;)]
}
It was also quite straightforward to reproduce
the behavior of SAS’s %keycheck() macro using
data.table in R.
ae &lt;- data.table(USUBJID = c(&quot;A001&quot;,&quot;A001&quot;,&quot;A003&quot;),
AETERM = c(&quot;AE 1&quot;, &quot;AE 2&quot;, &quot;AE 1&quot;))
dm &lt;- data.table(USUBJID = c(&quot;A001&quot;,&quot;A002&quot;,&quot;A003&quot;,&quot;A004&quot;))
out1 &lt;- keycheck_dt(dm, ae, key=&quot;USUBJID&quot;, fl=&quot;AEFL&quot;, cat=&quot;YN&quot;)
invisible(DTx[])
}
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Pharmaverse
https://pharmaverse.org/
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Representative join-related functions
in the {admiral} package
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Representative join-related functions
in the {admiral} package
derive_vars_merged()
library(admiral)
adae &lt;- tibble(USUBJID = c(&quot;A001&quot;,&quot;A001&quot;,&quot;A003&quot;),
AETERM = c(&quot;AE 1&quot;, &quot;AE 2&quot;, &quot;AE 1&quot;))
adsl &lt;- tibble(
USUBJID = c(&quot;A001&quot;,&quot;A002&quot;,&quot;A003&quot;,&quot;A004&quot;),
TRTSDT = as.IDate(c(&quot;2024-01-10&quot;,&quot;2024-01-12&quot;,&quot;2024-01-15&quot;,&quot;2024-01-18&quot;))
)
adae_1 &lt;- derive_vars_merged(
dataset = adae,
dataset_add = adsl,
by_vars = exprs(USUBJID),
new_vars = exprs(TRTSDT)
)
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Representative join-related functions in the {admiral} package
derive_var_merged_exist_flag()
adsl_1 &lt;- derive_var_merged_exist_flag(
dataset = adsl,
dataset_add = adae,
by_vars = exprs(USUBJID),
condition = TRUE,
new_var = AEFL,
true_value = &quot;Y&quot;,
false_value = &quot;N&quot; ,
missing_value= &quot;N&quot;
)
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Pharmaforest {Adamski} package
In the current PharmaForest adamski
package project,we are gradually
working on reproducing the functionality
of pharmaverse’s admiral in
SAS,inspired by the concepts and
design of admiral.
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sdtm.oak
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Final Comparison and Summary
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Summary Notes
Common but Subtle Differences in Join Behavior Across R Frameworks
Aspect
base::merge
dplyr::left_join
data.table X[i, on=]
hash package
Preserves order of i (right
Not applicable
operand)
Supported (on=.(a &lt;= b,
Non-equi Join
Not supported
Not supported
Not applicable
...))
Supported (roll=TRUE /
Rolling / Nearest Join
Not supported
Not supported
Not applicable
mult)
Explicit reference with i.
Column Name Conflicts Managed via suffixes
Appends .x / .y
Not applicable
(overwrite using :=)
Expands all combinations
Assumes one-to-one
Many-to-Many Handling Expands all combinations Expands all combinations (requires unique() /
mapping
aggregation if undesired)
△–○ Moderate (can
Performance on Large
◎ Excellent (in-memory ○ Good (limited by
△ Slow
leverage databases via
Data
optimized)
single-key design)
dbplyr)
Default Sorting
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Yes (sort=TRUE)
No (preserves left table
order)
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Summary Notes
• base::merge() is simple and reliable but can reorder rows and is memory-heavy.
• dplyr::xxxx_join() emphasizes readability and consistency, suitable for tidy workflows
and moderate datasets.
• data.table joins are the most efficient and flexible, supporting non-equi and rolling logic
ideal for clinical data (e.g., SDTM/ADaM period merges).
• The hash package provides ultra-fast one-to-one lookups, best for code mapping or
format-like replacements.
• In CDISC workflows, it is also recommended to use the built-in join functions provided by
Admiral or oak, as they help standardize and simplify data merge management across
ADaM and SDTM process
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I’m still learning R, so there might be a few mistakes in my slides.I’ll post any updates or
corrections on GitHub or LinkedIn later.If you have any questions or comments, please feel
free to contact me there.
[mail]
morioka.yutaka038@eps.co.jp
[Github]
https://github.com/Morioka-Yutaka
https://github.com/Morioka-Yutaka/RinPharma/tree/main/2025
[Linkdin]
morioka
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森岡 yutaka 裕
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The above kanji is a motto of a professional Shogi (Japanese chess) player,meaning
“Always try a new move.”
I’ve long been passionate about pioneering new techniques in SAS, and now, I’m ready to do the same
with R.
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