Merge branch 'master' into dev/update_vignettes

DESCRIPTION

@@ -32,7 +32,8 @@ Imports:
  covr,
  rvest,
  memoise,
- janitor
+ janitor,
+ cranlogs
 RoxygenNote: 7.0.2
 Suggests:
  knitr,

NAMESPACE

@@ -12,6 +12,7 @@ S3method(as_pkg_ref,default)
 S3method(as_pkg_ref,pkg_ref)
 S3method(as_tibble,list_of_pkg_ref)
 S3method(as_tibble,pkg_ref)
+S3method(assess_downloads_1yr,pkg_ref)
 S3method(assess_export_help,pkg_install)
 S3method(assess_has_news,pkg_ref)
 S3method(assess_license,pkg_ref)
@@ -29,6 +30,7 @@ S3method(pillar_shaft,pkg_metric_error)
 S3method(print,dev_hint)
 S3method(print,pkg_ref)
 S3method(score,default)
+S3method(score,pkg_metric_downloads_1yr)
 S3method(score,pkg_metric_error)
 S3method(score,pkg_metric_export_help)
 S3method(score,pkg_metric_has_news)
@@ -43,6 +45,7 @@ export(.risk_weights)
 export(all_assessments)
 export(as_pkg_ref)
 export(assess)
+export(assess_downloads_1yr)
 export(assess_export_help)
 export(assess_has_news)
 export(assess_license)
@@ -60,6 +63,7 @@ export(score_error_NA)
 export(score_error_default)
 export(score_error_zero)
 export(summarize_risk)
+import(cranlogs)
 import(dplyr)
 import(janitor)
 import(memoise)

R/assess_downloads.r

@@ -0,0 +1,48 @@
+#' Assess a package for the number of downloads in the past year
+#' 
+#' @details The more times a package has been downloaded the more extensive the user testing and the greater chance there is of someone finding a bug and logging it.
+#'
+#' @eval assess_family_roxygen(
+#' "downloads_1yr",
+#' "a numeric value between [0,1] indicating the volume of downloads")
+#'
+#' @export
+assess_downloads_1yr <- function(x, ...){
+ UseMethod("assess_downloads_1yr")
+}
+# assign a friendly name for assess column
+attr(assess_downloads_1yr,"column_name") <- "downloads_1yr"
+attr(assess_downloads_1yr,"label") <- "number of downloads in the past year"
+
+pkg_ref_cache.downloads <- function(x, ...) {
+ cran_downloads(x$name, from=Sys.Date()-365, to=Sys.Date()) 
+}
+
+#' @import cranlogs
+#' @export
+assess_downloads_1yr.pkg_ref <- function(x, ...) {
+ downloads_1yr <- sum(x$downloads$count)
+ pkg_metric(downloads_1yr, class = "pkg_metric_downloads_1yr")
+}
+
+# Defining an Assessment Scoring Function
+#' Score a package for the number of downloads in the past year
+#'
+#' Convert the number of downloads \code{x} in the past year into a validation score [0,1] 
+#' \deqn{ 1 - 150,000 / (x + 150,000) }
+#' 
+#' @details The scoring function is a simplification of the classic logistic curve
+#' \deqn{ 1 / (1 + exp(-k(x-x[0])) }
+#' with a log scale for the number of downloads \eqn{x = log(x)}, 
+#' sigmoid midpoint is 1000 downloads, ie. \eqn{x[0] = log(1,000)}, 
+#' and logistic growth rate of \eqn{k = 0.5}.
+# #' \deqn{ 1 - 1 / (1 + exp(log(x)-log(1.5e5))) = 1 - 150,000 / (x + 150,000) }
+#'
+#' @eval score_family_roxygen("downloads_1yr")
+#' @return numeric value between \code{0} (low) and \code{1} (high download volume) converting the number of downloads. 
+#'
+#' @export
+score.pkg_metric_downloads_1yr <- function(x, ...) {
+ # simplification from logistic: 1 - 1 / (1 + exp(log(x)-log(1.5e5)))
+ 1 - 1.5e5 / (x + 1.5e5) 
+}

README.md

@@ -19,17 +19,25 @@ exploring the heterogeneity of code quality, and begin a broader conversation
 about the validation of R packages. Primarily, this effort aims to provide some
 context for validation within regulated industries.
 
-## Quick Start
+We sperate three steps in the workflow to assess the risk of an R package using `riskmetric`:
 
-### Installation
+1. **Finding a source for package information (installed package or CRAN/git source)** `pkg_ref()`
+1. **Assessing the package under validation criteria** `assess()` 
+1. **Scoring assessment criteria** `score()`
+1. **Summarize scores into an aggregate risk metric** `summarize_risk()`
+
+The results will be a datasets of validation criteria and its overall risk score for each package as
+showin in the example below. 
+
+## Installation
 
 `riskmetric` is not yet on CRAN. Until it is, install using `devtools`.
 
 ```r
 devtools::install_github("pharmaR/riskmetric")
 ```
 
-### Example
+## Example
 
 Scrape metadata locally or remotely, then assess that metadata and score it to
 estimate risk. For each package, derive a composite measure of risk, or a
@@ -49,10 +57,11 @@ pkg_ref(c("riskmetric", "utils", "tools")) %>%
 
 ## Get Involved
 
-We had a bi-weekly sprint meeting for developer to discuss the progress. 
+We had a bi-weekly sprint meeting for developer to discuss the progress.
 
-* Frequecy: every two weeks
-* Starting Time: 2019/11/06 12:00 PM - 12:30 PM
+* Contact `[email protected]` to add into the meeting invitation. 
+* Date: 1st and 3rd Wednesday of the month.
+* Meeting Time: 12:00PM - 12:30PM EST
 * [Project Planning Meeting Structure](https://github.com/pharmaR/riskmetric/issues/57) 
 * [Milestone](https://github.com/pharmaR/riskmetric/milestones)
 * [Meeting Room](https://merck.webex.com/join/zhanyilo)