+1 195662009 Acute viral pharyngitis
+2 444814009 Viral sinusitis
+```
+
+Please note that in this example both the input and output are R data frames,
+even though internally they were processed as Spark/Sparklyr data frames.
+
+To find out about other Pathling capabilities please explore the examples in
+the help topics for `pathling` functions. In particular these are some good
+starting points:
+
+- `?pathling_connect` for information about creating and configuring Pathling
+ contexts.
+- `?tx_display` and `?tx_to_snomed_coding` for terminology functions.
+- `?ds_aggregate` and `?ds_extract` for pathling queries.
+- `?pathling_encode` for encoding of FHIR resources into data frames.
+- `?pathling_read_ndjson` and `?ds_write_ndjson` for reading and writing FHIR
+ resources in various formats.
+
+## Developer notes (MacOS)
+
+The following packages are needed to generate pdf manuals:
+
+ brew install basictex
+ brew install freetype
+
+Then run the following to install the `inconsolata` fonts used in R manuals:
+
+ # Install texlive packages needed to build R package vignettes
+ sudo tlmgr update --self
+ sudo tlmgr update --all
+ sudo tlmgr install titling framed inconsolata
+ sudo tlmgr install collection-fontsrecommended
+
+The following packages may be needed to build the dependencies of `devtools`.
+
+ brew install harfbuzz fribidi
+ brew install libjpeg
+ brew install libtiff
+ brew install libgit2
+
+
+To setup the dev environment, run the following commands:
+
+Use miniconda to install R in the activated dev environment:
+
+ # run 'conda activate your-dev-env-name' first
+ conda install -y -c conda-forge r-base=4.1.3
+
+Install the `devtools` R package:
+
+ Rscript --vanilla -e 'install.packages("devtools", repos="https://cloud.r-project.org/")'
+
+Pathling is copyright © 2018-2023, Commonwealth Scientific and Industrial
+Research Organisation
+(CSIRO) ABN 41 687 119 230. Licensed under
+the [Apache License, version 2.0](https://www.apache.org/licenses/LICENSE-2.0).
diff --git a/lib/R/data/conditions.rda b/lib/R/data/conditions.rda
new file mode 100644
index 0000000000..a8ddcd279e
Binary files /dev/null and b/lib/R/data/conditions.rda differ
diff --git a/lib/R/examples/aggregate.R b/lib/R/examples/aggregate.R
new file mode 100644
index 0000000000..1423204245
--- /dev/null
+++ b/lib/R/examples/aggregate.R
@@ -0,0 +1,15 @@
+library(sparklyr)
+library(pathling)
+
+pc <- pathling_connect()
+
+data_source <- pc %>% pathling_read_ndjson(pathling_examples('ndjson'))
+
+result <- data_source %>% ds_aggregate('Patient',
+ aggregations = c(patientCount='count()', 'id.count()'),
+ groupings = c('gender', givenName='name.given')
+ )
+
+result %>% show()
+
+pc %>% pathling_disconnect()
diff --git a/lib/R/examples/encode_resources.R b/lib/R/examples/encode_resources.R
new file mode 100644
index 0000000000..bebd464b0d
--- /dev/null
+++ b/lib/R/examples/encode_resources.R
@@ -0,0 +1,12 @@
+library(sparklyr)
+library(pathling)
+
+pc <- pathling_connect()
+
+json_resources <- pathling_spark(pc) %>% spark_read_text(pathling_examples('ndjson'))
+
+pc %>% pathling_encode(json_resources, 'Condition') %>% show()
+
+pc %>% pathling_disconnect()
+
+
diff --git a/lib/R/examples/member_of.R b/lib/R/examples/member_of.R
new file mode 100644
index 0000000000..35ddb8c4fb
--- /dev/null
+++ b/lib/R/examples/member_of.R
@@ -0,0 +1,22 @@
+library(sparklyr)
+library(pathling)
+
+pc <- pathling_connect()
+
+
+VIRAL_DISEASE_ECL <- '<< 64572001|Disease| : (
+ << 370135005|Pathological process| = << 441862004|Infectious process|,
+ << 246075003|Causative agent| = << 49872002|Virus|
+ )'
+
+
+pc %>% pathling_example_resource('Condition') %>% mutate(
+ CONDITION_ID = id,
+ IS_VIRAL_DISEASE = !!tx_member_of(code[['coding']], !!tx_to_ecl_value_set(VIRAL_DISEASE_ECL)),
+ .keep="none"
+ ) %>% show()
+
+pc %>% pathling_disconnect()
+
+
+
diff --git a/lib/R/examples/member_of_R_dataframe.R b/lib/R/examples/member_of_R_dataframe.R
new file mode 100644
index 0000000000..6846597401
--- /dev/null
+++ b/lib/R/examples/member_of_R_dataframe.R
@@ -0,0 +1,30 @@
+library(sparklyr)
+library(pathling)
+
+# create a default pathling context
+pc <- pathling_connect()
+
+# copy the R data frame to the spark data frame
+conditions_sdf <- pc %>%
+ pathling_spark() %>%
+ copy_to(conditions, overwrite = TRUE)
+
+
+# define an ECL expression for viral diseases
+VIRAL_DISEASE_ECL <- '<< 64572001|Disease| : (
+ << 370135005|Pathological process| = << 441862004|Infectious process|,
+ << 246075003|Causative agent| = << 49872002|Virus|
+ )'
+
+# use pathling terminology functions and dplr verbs to find codes for viral diseases and obtain their display names
+result <- conditions_sdf %>%
+ filter(!!tx_member_of(!!tx_to_snomed_coding(CODE), !!tx_to_ecl_value_set(VIRAL_DISEASE_ECL))) %>%
+ mutate(DISPLAY_NAME = !!tx_display(!!tx_to_snomed_coding(CODE))) %>%
+ select(CODE, DISPLAY_NAME) %>% distinct() %>%
+ collect()
+
+# disconnect from the pathling context
+pc %>% pathling_disconnect()
+
+# as we used `collect()` `result` is the R data frame
+result %>% show()
diff --git a/lib/R/inst/CITATION b/lib/R/inst/CITATION
new file mode 100644
index 0000000000..23197b29c9
--- /dev/null
+++ b/lib/R/inst/CITATION
@@ -0,0 +1,17 @@
+bibentry(
+ bibtype = "article",
+ author = c(
+ person("John", "Grimes"),
+ person("Piotr", "Szul"),
+ person("Alejandro", "Metke-Jimenez"),
+ person("Michael", "Lawley"),
+ person("Kylynn", "Loi")
+ ),
+ title = "Pathling: analytics on FHIR",
+ journal = "Journal of Biomedical Semantics",
+ year = 2022,
+ volume = 13,
+ number = 1,
+ pages = "23",
+ publisher = "Springer"
+)
diff --git a/lib/R/inst/extdata/bundle-xml/Bennett146_Swaniawski813_704c9750-f6e6-473b-ee83-fbd48e07fe3f.xml b/lib/R/inst/extdata/bundle-xml/Bennett146_Swaniawski813_704c9750-f6e6-473b-ee83-fbd48e07fe3f.xml
new file mode 100644
index 0000000000..79f94c62ca
--- /dev/null
+++ b/lib/R/inst/extdata/bundle-xml/Bennett146_Swaniawski813_704c9750-f6e6-473b-ee83-fbd48e07fe3f.xml
@@ -0,0 +1,17372 @@
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Synthea.Version identifier: v2.4.0-373-g9417ce01\n . Person seed: -1116549638004693619 Population seed: 1567659637983
Generated by
Synthea.Version identifier: v2.4.0-373-g9417ce01\n . Person seed: 2489887534555043489 Population seed: 1567659637983
Generated by
Synthea.Version identifier: v2.4.0-373-g9417ce01\n . Person seed: -4398174870245759556 Population seed: 1567659637983
Generated by
Synthea.Version identifier: v2.4.0-373-g9417ce01\n . Person seed: 346614667352111003 Population seed: 1567659637983
Generated by
Synthea.Version identifier: v2.4.0-373-g9417ce01\n . Person seed: -8938394749892435555 Population seed: 1567659637983
Generated by
Synthea.Version identifier: v2.4.0-373-g9417ce01\n . Person seed: -8922649844579538715 Population seed: 1567659637983
Generated by
Synthea.Version identifier: v2.4.0-373-g9417ce01\n . Person seed: 2253619407104150534 Population seed: 1567659637983
Generated by
Synthea.Version identifier: v2.4.0-373-g9417ce01\n . Person seed: 7586416063432214179 Population seed: 1567659637983
Generated by
Synthea.Version identifier: v2.4.0-373-g9417ce01\n . Person seed: -9085673012511978392 Population seed: 1567659637983