Add example BAMA dataset from DataSpaceR

.gitignore

@@ -21,3 +21,6 @@ Meta
 /doc/
 /Meta/
 docs
+
+# Dataspace login
+.netrc

NEWS.md

@@ -1,5 +1,6 @@
 # VISCfunctions (development version)
 
+* Add `CAVD579_bama` to example datasets (#17)
 * Add `SampleSizes` output to `pairwise_test_bin()` (#130)
 * Minor updates to vignette (#141)
 * Update title and description in package DESCRIPTION file (#139)

R/CAVD579_bama.R

@@ -0,0 +1,30 @@
+#' CAVD579_bama dataset
+#'
+#' @description CAVD579 Binding antibody multiplex assay (BAMA) data. Descriptions
+#' accessed via DataSpaceR::connectDS()$getStudy('cvd579')$getDatasetDescription("BAMA")
+#'
+#' @format A data.frame with 1,717 rows and 18 variables:
+#' \describe{
+#'   \item{participant_id}{Subject identifier.}
+#'   \item{visit_day}{Target study day defined for a study visit. Study days are relative to Day 0, where Day 0 is typically defined as enrollment and/or first injection.}
+#'   \item{specimen_type}{The type of specimen used in the assay.}
+#'   \item{assay_identifier}{Name identifying assay.}
+#'   \item{antibody_isotype}{The binding anitbody isotype that is quantified by the assay.}
+#'   \item{antigen}{The name of the antigen being tested as reported by the lab in the assay dataset.}
+#'   \item{response_call}{Binary response call calculated using standard criteria across studies.}
+#'   \item{dilution}{Indicates the initial specimen dilution.}
+#'   \item{mfi_delta}{The difference between the Median Fluorescence Intensity (MFI) of antibody binding to antigen-conjugated beads adjusted to subtract background (Magnitude (mfi) - Background subtracted from raw) and the maximum MFI of antibody-binding to non-conjugated (blank) beads adjusted to subtract background (Magnitude (mfi)-Background subtracted from blank).}
+#'   \item{mfi_raw}{Median Fluorescence Intensity of antibody binding to antigen-conjugated beads.}
+#'   \item{mfi_blank}{Median Fluorescence Intensity of antibody-binding to non-conjugated (blank) beads.}
+#'   \item{mfi_bkgd}{Median Fluorescence Intensity of antibody binding to antigen-conjugated beads, adjusted to subtract background.}
+#'   \item{auc}{The area under the titration curve as calculated for VISC analysis. Method may vary across studies.}
+#'   \item{study_start_date}{The official study start date assigned by the network (e.g. date of study registration).}
+#'   \item{study_type}{Study classification indicating the type of trial design used in the study (e.g. preclinical, Phase I, or Phase II).}
+#'   \item{study_group}{A set of treatment arms grouped within a study as defined in the schema. Typcially, used to indicate the schedule of product administration, assessments, and other study procedures.}
+#'   \item{study_arm}{Treatment arm assigned to study subjects which indicates the visit schedule and specific product, doses, and routes to be administered during the study.}
+#'   \item{study_arm_summary}{A brief summary of information about the assigned treatment arm, including the study part, group, vaccinee/placebo, and products administered.}
+#'   \item{description}{Treatment description.}
+#' }
+#' @source Kim J, Taylor J, Miller H (2025). DataSpaceR: Interface to 'the CAVD DataSpace'.
+#' Rpackage version 0.7.7, <https://CRAN.R-project.org/package=DataSpaceR>.
+"CAVD579_bama"

data-raw/cds_datasets.R

@@ -15,3 +15,35 @@ CAVD812_mAB <- cvd812$getDataset("NAB Ig") |>
 
 usethis::use_data(CAVD812_mAB, overwrite = TRUE)
 
+# bama dataset
+cvd579 <- con$getStudy('cvd579')
+
+cvd579_trt <- cvd579$getDataset("Demographics") |>
+  left_join(cvd579$treatmentArm, join_by(study_arm == arm_name)) |>
+  select(participant_id,
+         study_start_date,
+         study_type,
+         study_group, #for blinded example code
+         study_arm, #for unblinded example code
+         study_arm_summary,
+         description)
+
+CAVD579_bama <- cvd579$getDataset("BAMA") |>
+  distinct(
+    participant_id,
+    visit_day,
+    specimen_type,
+    assay_identifier,
+    antibody_isotype,
+    antigen,
+    response_call,
+    dilution,
+    mfi_delta,
+    mfi_raw,
+    mfi_blank,
+    mfi_bkgd,
+    auc) |>
+  left_join(cvd579_trt, join_by(participant_id)) |>
+  as.data.frame()
+
+usethis::use_data(CAVD579_bama, overwrite = TRUE)

tests/testthat/test_CAVD579_bama.R

@@ -0,0 +1,27 @@
+context("check_CAVD579_bama")
+
+# test basic dataset details based on
+# https://dataspace.cavd.org/cds/CAVD/app.view#learn/learn/Study/label=CAVD%20579
+test_that("CAVD579_bama has expected ID, visit and antigen counts", {
+
+  # Participants were enrolled in two groups
+  expect_equal(length(unique(CAVD579_bama$study_group)),
+               2)
+
+  # Group 1: DCVax-001 prime/MVA-CMDR boost (n=8);
+  # Group 2: placebo/MVA-CMDR (n=6)
+  expect_equal(length(unique(CAVD579_bama$participant_id)),
+               14)
+
+  # Participants were administered 2 intramuscular injections of MVA-CMDR
+  # at weeks 0 and 12, and followed for 36 weeks after second immunization (week 48).
+  expect_equal(length(unique(CAVD579_bama$visit_day)),
+               3)
+
+  expect_equal(length(unique(CAVD579_bama$antibody_isotype)),
+               5)
+
+  expect_equal(length(unique(CAVD579_bama$antigen)),
+               9)
+
+  })