Merge pull request #4 from intervene-EU-H2020/update_metrics

add label for continuous phenotypes
intervene-EU-H2020 · Sep 13, 2023 · ac640af · ac640af
2 parents 41f060b + c6d0da0
commit ac640af
Show file tree

Hide file tree

Showing 6 changed files with 23 additions and 20 deletions.
diff --git a/R/dst.R b/R/dst.R
@@ -1,7 +1,5 @@
 #' Pairwise comparisons of polygenic risk score development methods
 #'
-#' A subset of data from... (science stuff here)
-#'
 #' @format
 #' A data frame with 11374 rows and 35 columns:
 #' \describe{

diff --git a/R/metrics.R b/R/metrics.R
@@ -1,9 +1,7 @@
 #' Polygenic risk score performance metrics table for single biobanks
 #'
-#' A subset of data from... (science stuff here)
-#'
 #' @format
-#' A data frame with 950 rows and 49 columns:
+#' A data frame with 950 rows and 50 columns:
 #' \describe{
 #'   \item{predictor}{unique score identifier}
 #'   \item{BETA}{linear/logistic regression coef}
@@ -66,6 +64,8 @@
 #'
 #'   \item{N_CAS}{number of cases for binary endpoints}
 #'   \item{N_CON}{number of controls for binary endpoints}
+#'
+#'   \item{is_continuous}{phenotype is continuous (TRUE) or binary (FALSE)}
 #' }
 #' @source <https://link/to/paper>
 "metrics"
diff --git a/data-raw/metrics.R b/data-raw/metrics.R
@@ -508,6 +508,9 @@ metrics <- metrics[!(bbid == 'ukbb' & phenotype == 'Alzheimers_disease' & ancest
 metrics <- rename_phenotypes(metrics)
 metrics$method <- adjust_methods_levels(metrics$method)
 
+# label continuous / binary traits
+metrics$is_continuous <- ifelse(is.na(metrics$AUC_MEDIAN), TRUE, FALSE)
+
 # export processed data --------------------------------------------------------
 # let R pick the best compression scheme
 # tools::resaveRdaFiles("data/", compress="auto")

diff --git a/data/metrics.rda b/data/metrics.rda
diff --git a/man/metrics.Rd b/man/metrics.Rd
diff --git a/renv/profiles/dev/renv.lock b/renv/profiles/dev/renv.lock
@@ -37,13 +37,13 @@
     },
     "askpass": {
       "Package": "askpass",
-      "Version": "1.1",
+      "Version": "1.2.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "sys"
       ],
-      "Hash": "e8a22846fff485f0be3770c2da758713"
+      "Hash": "cad6cf7f1d5f6e906700b9d3e718c796"
     },
     "cli": {
       "Package": "cli",
@@ -80,7 +80,7 @@
     },
     "credentials": {
       "Package": "credentials",
-      "Version": "1.3.2",
+      "Version": "2.0.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -90,17 +90,17 @@
         "openssl",
         "sys"
       ],
-      "Hash": "93762d0a34d78e6a025efdbfb5c6bb41"
+      "Hash": "c7844b32098dcbd1c59cbd8dddb4ecc6"
     },
     "curl": {
       "Package": "curl",
-      "Version": "5.0.1",
+      "Version": "5.0.2",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R"
       ],
-      "Hash": "2118af9cb164c8d2dddc7b89eaf732d9"
+      "Hash": "511bacbfa153a15251166b463b4da4f9"
     },
     "data.table": {
       "Package": "data.table",
@@ -129,18 +129,18 @@
     },
     "fs": {
       "Package": "fs",
-      "Version": "1.6.2",
+      "Version": "1.6.3",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "RSPM",
       "Requirements": [
         "R",
         "methods"
       ],
-      "Hash": "94af08e0aa9675a16fadbb3aaaa90d2a"
+      "Hash": "47b5f30c720c23999b913a1a635cf0bb"
     },
     "gert": {
       "Package": "gert",
-      "Version": "1.9.2",
+      "Version": "1.9.3",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -151,7 +151,7 @@
         "sys",
         "zip"
       ],
-      "Hash": "9122b3958e749badb5c939f498038b57"
+      "Hash": "b544c397820e05a97d391b2d614a921a"
     },
     "gh": {
       "Package": "gh",
@@ -331,13 +331,13 @@
     },
     "openssl": {
       "Package": "openssl",
-      "Version": "2.0.6",
+      "Version": "2.1.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "askpass"
       ],
-      "Hash": "0f7cd2962e3044bb940cca4f4b5cecbe"
+      "Hash": "273a6bb4a9844c296a459d2176673270"
     },
     "pbapply": {
       "Package": "pbapply",
@@ -352,7 +352,7 @@
     },
     "purrr": {
       "Package": "purrr",
-      "Version": "1.0.1",
+      "Version": "1.0.2",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -363,7 +363,7 @@
         "rlang",
         "vctrs"
       ],
-      "Hash": "d71c815267c640f17ddbf7f16144b4bb"
+      "Hash": "1cba04a4e9414bdefc9dcaa99649a8dc"
     },
     "rappdirs": {
       "Package": "rappdirs",