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-[{"path":"/articles/extending-riskmetric.html","id":"package-classes","dir":"Articles","previous_headings":"","what":"Package Classes","title":"Extending riskmetric","text":"can assess package first need represent package data. refer collection package metadata “package reference” - way referring related information ’ve able pull together package. represented pkg_ref class object. dimensions risk assessed, data needed evaluate terms cached within object, building small store information package assessments can refer build . Importantly, references packages equal. can collect information given source code, locally installed package scraping data package web. ’s hierarchy subclasses encapsulate disparate use cases. subclasses direct behavior downstream operations provides flexibility bucket implementations similar data can collected number potential sources. example, determine author package easiest look package’s DESCRIPTION file content maintained. However, without access source installed files, one find information CRAN package webpage. Using subclasses, appropriate method collecting data can selected.","code":"pkg_ref ├─ pkg_source ├─ pkg_install └─ pkg_remote ├─ pkg_cran_remote └─ pkg_bioc_remote"},{"path":"/articles/extending-riskmetric.html","id":"adding-an-assessment","dir":"Articles","previous_headings":"","what":"Adding an Assessment","title":"Extending riskmetric","text":"Assessments atomic unit riskmetric package, used kick individual metric evaluation. assessment generic function starting assess_ prefix, can dispatch based subclass pkg_ref object.","code":""},{"path":"/articles/extending-riskmetric.html","id":"assessment-example","dir":"Articles","previous_headings":"Adding an Assessment","what":"Assessment Example","title":"Extending riskmetric","text":"example, take look assess_has_news implemented. ’ll focus just generic pkg_install functions: couple things note. First, S3 system used dispatch functionality appropriate package reference class. Since way ’d assess inclusion NEWS file might different installed package remotely sourced metadata, may separate functions process datatypes distinct ways. Second, assessment, pkg_metric object returned. stores atomic data pertaining metric importantly adopts unique subclass assessment function. Finally, cosmetic \"column_name\" attribute tagged function. used calling assess function. assess verb convenience function steps available assessments returning tibble assessment outputs. \"column_name\" provides user-friendly label assessment tibble.","code":"#> assess_has_news <- function (x, ...) #> { #> UseMethod(\"assess_has_news\") #> } #> attr(,\"column_name\") #> [1] \"has_news\" #> attr(,\"label\") #> [1] \"number of discovered NEWS files\" #> #> assess_has_news.pkg_install <- NULL"},{"path":"/articles/extending-riskmetric.html","id":"writing-a-new-assessment","dir":"Articles","previous_headings":"Adding an Assessment","what":"Writing a New Assessment","title":"Extending riskmetric","text":"Now ’ll write assessment. Eventually want consider package high risk name start “r”. ’ll need make pkg_metric object containing first letter name.","code":"assess_name_first_letter <- function(x, ...) { UseMethod(\"assess_name_first_letter\") } attr(assess_name_first_letter, \"column_name\") <- \"name_first_letter\" assess_name_first_letter.pkg_ref <- function(x, ...) { pkg_metric(substr(x$name, 0, 1), class = \"pkg_metric_name_first_letter\") }"},{"path":"/articles/extending-riskmetric.html","id":"adding-pkg_ref-metadata","dir":"Articles","previous_headings":"","what":"Adding pkg_ref Metadata","title":"Extending riskmetric","text":"Perhaps want reuse metadata used assessing first letter can reused assessments. particularly taxing metadata, metadata requires query public API, scraping web page large data download, ’s important store assessment functions reuse. handle , define function pkg_ref_cache dispatch .","code":""},{"path":"/articles/extending-riskmetric.html","id":"example-metadata-caching","dir":"Articles","previous_headings":"Adding pkg_ref Metadata","what":"Example Metadata Caching","title":"Extending riskmetric","text":"riskmetric package handles parsing DESCRIPTION file can feed downstream assessments without re-parse file time copy code . defined, ’ll automatically called field first accessed pkg_ref object, stored downstream uses. Notice upon initialization, description field indicates hasn’t yet evaluated trailing ... name. accessed, object call caching function go grab package metadata return newly derived value. pkg_ref object stores environment, caching value makes available future attempts access field. helpful , developers package, don’t need think critically order assessments performed, allows users redefine order assessments without worry metadata acquired.","code":"#> pkg_ref_cache.description <- function (x, name, ...) #> { #> UseMethod(\"pkg_ref_cache.description\") #> } #> #> pkg_ref_cache.description.pkg_install <- function (x, name, ...) #> { #> read.dcf(file.path(x$path, \"DESCRIPTION\")) #> } library(riskmetric) package <- pkg_ref(\"riskmetric\") #>
riskmetric v0.2.4.9000 #> $path #> [1] \"/home/user/username/R/4.4/Resources/library/riskmetric\" #> $source #> [1] \"pkg_install\" #> $version #> [1] '0.2.4.9000' #> $name #> [1] \"riskmetric\" #> $bug_reports... #> $bug_reports_host... #> $bug_reports_url... #> $description... #> $downloads... #> $examples... #> $help... #> $help_aliases... #> $license... #> $maintainer... #> $news... #> $r_cmd_check... #> $release_date... #> $remote_checks... #> $source_control_url... #> $vignettes... #> $website_urls... package$description"},{"path":"/articles/extending-riskmetric.html","id":"writing-a-metadata-cache","dir":"Articles","previous_headings":"Adding pkg_ref Metadata","what":"Writing a Metadata Cache","title":"Extending riskmetric","text":"Now, new metric, want cache package name’s first letter. need add new pkg_ref_cache function field. Thankfully, subclass pkg_ref can access first letter way, just need one function. adding caching function, need make small modification assess_name_first_letter.pkg_ref order use newly cached value. Let’s try !","code":"pkg_ref_cache.name_first_letter <- function(x, name, ...) { substr(x$name, 0, 1) } assess_name_first_letter.pkg_ref <- function(x, ...) { pkg_metric(x$name_first_letter, class = \"pkg_metric_name_first_letter\") } package$name #> [1] \"riskmetric\" package$name_first_letter #> [1] \"r\""},{"path":"/articles/extending-riskmetric.html","id":"defining-an-assessment-scoring-function","dir":"Articles","previous_headings":"","what":"Defining an Assessment Scoring Function","title":"Extending riskmetric","text":"Next, need function scoring assessment output. case, output pkg_metric object whose data first letter package name. ’ll add dispatched function score function. convention, functions return numeric value representing well package conforms best practices values 0 (poor practice) 1 (best practice).","code":"metric_score.pkg_metric_name_first_letter <- function(x, ...) { as.numeric(x == \"r\") }"},{"path":"/articles/extending-riskmetric.html","id":"adding-our-assessment-to-the-pkg_assess-verb","dir":"Articles","previous_headings":"","what":"Adding our Assessment to the pkg_assess() Verb","title":"Extending riskmetric","text":"assess function accepts list functions apply. riskmetric provides shorthand, all_assessments(), collect included assessment functions, ’re free add list customize assessment toolkit. scoring function automatically get picked used score method. can define summarizing weights passing named list pkg_score. course can downstream processing resulting tibble ’d like fine-tune summarization using nonlinear function.","code":"library(dplyr) pkg_ref(c(\"riskmetric\", \"utils\", \"tools\")) %>% as_tibble() %>% pkg_assess(c(all_assessments(), assess_name_first_letter)) #> # A tibble: 3 × 23 #> package version pkg_ref covr_coverage has_news remote_checks #> #> 1 riskmetric 0.2.4.9000 riskmetric NA 1 NA #> 2 utils 4.4.0 utils NA 0 NA #> 3 tools 4.4.0 tools NA 0 NA #> # ℹ 17 more variables: news_current , r_cmd_check , #> # exported_namespace , has_vignettes , #> # export_help , has_website , has_maintainer , #> # bugs_status , size_codebase , #> # has_source_control , has_bug_reports_url , #> # downloads_1yr , reverse_dependencies , #> # has_examples , dependencies , license , … pkg_ref(c(\"riskmetric\", \"utils\", \"tools\")) %>% as_tibble() %>% pkg_assess(c(all_assessments(), assess_name_first_letter)) %>% pkg_score() #> # A tibble: 3 × 24 #> package version pkg_ref pkg_score covr_coverage has_news #> #> 1 riskmetric 0.2.4.9000 riskmetric 0.547 NA 1 #> 2 utils 4.4.0 utils 0.703 NA 0 #> 3 tools 4.4.0 tools 0.748 NA 0 #> # ℹ 18 more variables: remote_checks , news_current , #> # r_cmd_check , exported_namespace , #> # has_vignettes , export_help , has_website , #> # has_maintainer , bugs_status , #> # size_codebase , has_source_control , #> # has_bug_reports_url , downloads_1yr , #> # reverse_dependencies , has_examples , … pkg_ref(c(\"riskmetric\", \"utils\", \"tools\")) %>% as_tibble() %>% pkg_assess(c(all_assessments(), assess_name_first_letter)) %>% pkg_score(weights = c(has_news = 1, name_first_letter = 1)) #> # A tibble: 3 × 24 #> package version pkg_ref pkg_score covr_coverage has_news #> #> 1 riskmetric 0.2.4.9000 riskmetric 0 NA 1 #> 2 utils 4.4.0 utils 1 NA 0 #> 3 tools 4.4.0 tools 1 NA 0 #> # ℹ 18 more variables: remote_checks , news_current , #> # r_cmd_check , exported_namespace , #> # has_vignettes , export_help , has_website , #> # has_maintainer , bugs_status , #> # size_codebase , has_source_control , #> # has_bug_reports_url , downloads_1yr , #> # reverse_dependencies , has_examples , …"},{"path":"/articles/extending-riskmetric.html","id":"how-you-can-help","dir":"Articles","previous_headings":"","what":"How you can help…","title":"Extending riskmetric","text":"riskmetric package designed easily extensible. can develop dispatched functions development environment, hone well formed assessments contribute back core riskmetric package ’re done. ’d like feedback embarking developing new metric, please feel free file issue riskmetric GitHub.","code":""},{"path":"/articles/riskmetric.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Get Started","text":"riskmetric provides workflow evaluate quality set R packages involves five major steps. workflow can help users choose high quality R packages, improve package reliability prove validity R packages regulated industry. concept, steps include:","code":""},{"path":"/articles/riskmetric.html","id":"finding-a-source-for-package-information","dir":"Articles","previous_headings":"Introduction","what":"1. Finding a source for package information","title":"Get Started","text":"First need identify source package metadata. number places one may want look information, source code directory, local package library remote package repository. find source package data, begin collect package reference (pkg_ref) object. Learn : ?pkg_ref","code":""},{"path":"/articles/riskmetric.html","id":"caching-package-metadata","dir":"Articles","previous_headings":"Introduction","what":"2. Caching package metadata","title":"Get Started","text":"information needed perform given risk assessment, use metadata already continue search fine-grained information package. example, location locally installed package, can use path search package’s DESCRIPTION file, read DESCRIPTION contents. avoid repeatedly processing metadata, intermediate results cached within pkg_ref object can used derivation mulitple risk metrics. Learn : ?pkg_ref_cache","code":""},{"path":"/articles/riskmetric.html","id":"assess-this-metadata-against-a-risk-criterion","dir":"Articles","previous_headings":"Introduction","what":"3. Assess this metadata against a risk criterion","title":"Get Started","text":"measure risk, first try boil measure fundamental nugget package metadata comparable across packages sources information. cross-comparable result assessing package way refer package metric (pkg_metric). example, DESCRIPTION file content, might look whether maintainer identified authors list. ensure can easily compare information packages use Authors field Authors@R field, boil information just single logical value indicating whether maintainer identified. Learn : ?pkg_assess","code":""},{"path":"/articles/riskmetric.html","id":"score-our-metrics","dir":"Articles","previous_headings":"Introduction","what":"4. Score our metrics","title":"Get Started","text":"atomic representations metrics, want score can meaningfully compared one another. practice just embeds means converting datatype metric numeric value fixed scale 0 (worst) 1 (best). Given maintainer metric example, might rate package 1 (great) maintainer identified 0 (poor) maintainer found. Learn : ?pkg_score","code":""},{"path":"/articles/riskmetric.html","id":"summarizing-across-metric-scores","dir":"Articles","previous_headings":"Introduction","what":"5. Summarizing across metric scores","title":"Get Started","text":"Finally, may want look scores individual metrics sort aggregate risk score. Naturally, metric scores may warrant weight. scores normalized fixed range allows us define summarizing algorithm consistently assess compare packages. Notably, risk inverse scale metric scores. High metric scores favorable, whereas high risk scores unfavorable. Learn : ?summarize_scores","code":""},{"path":"/articles/riskmetric.html","id":"the-riskmetric-workflow","dir":"Articles","previous_headings":"","what":"The riskmetric Workflow","title":"Get Started","text":"five steps broken just handful primary functions.","code":""},{"path":"/articles/riskmetric.html","id":"creating-a-package-reference-object","dir":"Articles","previous_headings":"The riskmetric Workflow","what":"Creating a package reference object","title":"Get Started","text":"First, create package reference class object using pkg_ref constructor function. object contain metadata ’s collected various risk assessments. see riskmetric pkg_ref object actually subclassed pkg_install. hierarchy pkg_ref object classes including pkg_source source code directories, pkg_install locally installed packages pkg_remote references package information pulled internet including pkg_cran_remote pkg_bioc_remote CRAN Bioconductor hosted packages respectively. Throughout riskmetric, S3 classes used extensively make use generic functions divergent, reference mechanism dependent behaviors caching metadata, assessing packages scoring metrics. Likewise, fields trailing ... indicating haven’t yet computed, reference type knowledge go grab information field requested. Behind scenes, done using pkg_ref_cache function, S3 generic, using name field pkg_ref class dispatch appropriate functions retrieving metadata.","code":"library(riskmetric) riskmetric_pkg_ref <- pkg_ref(\"riskmetric\") print(riskmetric_pkg_ref) #> riskmetric v0.2.4.9000 #> $path #> [1] \"/home/user/username/R/4.4/Resources/library/riskmetric\" #> $source #> [1] \"pkg_install\" #> $version #> [1] '0.2.4.9000' #> $name #> [1] \"riskmetric\" #> $bug_reports... #> $bug_reports_host... #> $bug_reports_url... #> $description... #> $downloads... #> $examples... #> $help... #> $help_aliases... #> $license... #> $maintainer... #> $news... #> $r_cmd_check... #> $release_date... #> $remote_checks... #> $source_control_url... #> $vignettes... #> $website_urls..."},{"path":"/articles/riskmetric.html","id":"assessing-a-package","dir":"Articles","previous_headings":"The riskmetric Workflow","what":"Assessing a package","title":"Get Started","text":"number prespecified assessments, prefixed convention assess_*. Every assessment function takes single argument, pkg_ref object produces pkg_metric object corresponding assess_* function applied. Every function assess_* family functions expected return basic measure package. case, return named logical vector indicating whether export function associated help document. return type also leaves trail assessment produced metric. addition pkg_metric class, now pkg_metric_export_help subclass used dispatching appropriate scoring method. ’s worth pointing act calling function side-effect mutating riskmetric_pkg_ref object. riskmetric_pkg_ref$help_aliases known value needed asses whether package documentation exports. note caching happens pkg_ref objects really just environments syntactic sugar, environments R always modified -reference. globally mutable behavior used operations performed one assessment can reused others. Likewise, computing one field may require previous field computed first, triggering chain metadata retrieval. case, $help_aliases required $path available. chaining behavior comes free implementing pkg_ref_cache caching function field. contributors, alleviates need remember order operations, users behavior means subsets assessments can run arbitrary order without pulling superfluous metadata, keeping track every-growing objects ensuring certain assessments get called others. addition metric-specific assess_* family functions, comprehensive pkg_assess function provided. Notably, pkg_assess accepts pkg_ref object list assessments apply, defaulting all_assessments(), returns list assess_* functions riskmetric namespace. Since lot take , pkg_assess also operates tibbles, returning cleaner output might easier sort assessing package.","code":"riskmetric_export_help_metric <- assess_export_help(riskmetric_pkg_ref) print(riskmetric_export_help_metric[1:5]) #> assess_covr_coverage assessment_error_as_warning #> TRUE TRUE #> as_pkg_metric assess_has_news #> TRUE TRUE #> score_error_zero #> TRUE riskmetric_pkg_ref #> riskmetric v0.2.4.9000 #> $help_aliases #> riskmetric-package %||% #> \"riskmetric\" \"if_not_null_else\" #> .tools allow_mutation #> \"dot-tools\" \"allow_mutation\" #> all_assessments assessment_error_as_warning #> \"all_assessments\" \"assessment_error_as_warning\" #> #> $path #> [1] \"/home/user/username/R/4.4/Resources/library/riskmetric\" #> $source #> [1] \"pkg_install\" #> $version #> [1] '0.2.4.9000' #> $name #> [1] \"riskmetric\" #> $bug_reports... #> $bug_reports_host... #> $bug_reports_url... #> $description... #> $downloads... #> $examples... #> $help... #> $license... #> $maintainer... #> $news... #> $r_cmd_check... #> $release_date... #> $remote_checks... #> $source_control_url... #> $vignettes... #> $website_urls... pkg_assess(riskmetric_pkg_ref) #> #> $covr_coverage #> [1] NA #> attr(,\"class\") #> [1] \"pkg_metric_na\" \"pkg_metric_condition\" #> [3] \"pkg_metric_covr_coverage\" \"pkg_metric\" #> [5] \"logical\" #> attr(,\"label\") #> [1] \"Package unit test coverage\" #> #> $has_news #> [1] 1 #> attr(,\"class\") #> [1] \"pkg_metric_has_news\" \"pkg_metric\" \"integer\" #> attr(,\"label\") #> [1] \"number of discovered NEWS files\" #> #> $remote_checks #> [1] NA #> attr(,\"class\") #> [1] \"pkg_metric_na\" \"pkg_metric_condition\" #> [3] \"pkg_metric_remote_checks\" \"pkg_metric\" #> [5] \"logical\" #> attr(,\"label\") #> [1] \"Number of OS flavors that passed/warned/errored on R CMD check\" #> #> $news_current #> [1] FALSE #> attr(,\"class\") #> [1] \"pkg_metric_news_current\" \"pkg_metric\" #> [3] \"logical\" #> attr(,\"label\") #> [1] \"NEWS file contains entry for current version number\" #> #> $r_cmd_check #> [1] NA #> attr(,\"class\") #> [1] \"pkg_metric_na\" \"pkg_metric_condition\" \"pkg_metric_r_cmd_check\" #> [4] \"pkg_metric\" \"logical\" #> attr(,\"label\") #> [1] \"Package check results\" #> #> $exported_namespace #> [1] \"assess_covr_coverage\" \"assessment_error_as_warning\" #> [3] \"as_pkg_metric\" \"assess_has_news\" #> [5] \"score_error_zero\" \"assess_remote_checks\" #> [7] \"pkg_metric\" \"assess_news_current\" #> [9] \"assess_r_cmd_check\" \"pkg_score\" #> [11] \"pkg_assess\" \"as_pkg_ref\" #> [13] \"score_error_NA\" \"metric_score\" #> [15] \"assess_exported_namespace\" \"assess_has_vignettes\" #> [17] \"assess_export_help\" \"assess_has_website\" #> [19] \"score_error_default\" \"assessment_error_throw\" #> [21] \"assess_has_maintainer\" \"assess_last_30_bugs_status\" #> [23] \"assess_size_codebase\" \"all_assessments\" #> [25] \"assess_has_source_control\" \"assess_has_bug_reports_url\" #> [27] \"assess_downloads_1yr\" \"assess_reverse_dependencies\" #> [29] \"get_assessments\" \"assess_has_examples\" #> [31] \"summarize_scores\" \"pkg_ref\" #> [33] \"assessment_error_empty\" \"assess_dependencies\" #> [35] \"assess_license\" #> #> $has_vignettes #> [1] 0 #> #> $export_help #> assess_covr_coverage assessment_error_as_warning #> TRUE TRUE #> as_pkg_metric assess_has_news #> TRUE TRUE #> score_error_zero assess_remote_checks #> TRUE TRUE #> pkg_metric assess_news_current #> TRUE TRUE #> assess_r_cmd_check pkg_score #> TRUE TRUE #> pkg_assess as_pkg_ref #> TRUE TRUE #> score_error_NA metric_score #> TRUE TRUE #> assess_exported_namespace assess_has_vignettes #> TRUE TRUE #> assess_export_help assess_has_website #> TRUE TRUE #> score_error_default assessment_error_throw #> TRUE TRUE #> assess_has_maintainer assess_last_30_bugs_status #> TRUE TRUE #> assess_size_codebase all_assessments #> TRUE TRUE #> assess_has_source_control assess_has_bug_reports_url #> TRUE TRUE #> assess_downloads_1yr assess_reverse_dependencies #> TRUE TRUE #> get_assessments assess_has_examples #> TRUE TRUE #> summarize_scores pkg_ref #> TRUE TRUE #> assessment_error_empty assess_dependencies #> TRUE TRUE #> assess_license #> TRUE #> #> $has_website #> [1] \"https://pharmar.github.io/riskmetric/\" #> [2] \"https://github.com/pharmaR/riskmetric\" #> #> $has_maintainer #> [1] \"Eli Miller \" #> #> $bugs_status #> [1] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE #> [13] TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE #> [25] TRUE TRUE TRUE FALSE FALSE FALSE #> #> $size_codebase #> #> #> $has_source_control #> [1] \"https://github.com/pharmaR/riskmetric\" #> #> $has_bug_reports_url #> [1] 1 #> attr(,\"class\") #> [1] \"pkg_metric_has_bug_reports_url\" \"pkg_metric\" #> [3] \"integer\" #> attr(,\"label\") #> [1] \"presence of a bug reports url in repository\" #> #> $downloads_1yr #> [1] 4193 #> #> $reverse_dependencies #> character(0) #> #> $has_examples #> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE #> [16] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE #> [31] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE #> [46] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE #> [61] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE #> [76] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE #> [91] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE #> [106] TRUE TRUE #> #> $dependencies #> package type #> 1 backports Imports #> 2 utils Imports #> 3 tools Imports #> 4 xml2 Imports #> 5 httr Imports #> 6 curl Imports #> 7 urltools Imports #> 8 memoise Imports #> 9 BiocManager Imports #> 10 cranlogs Imports #> 11 covr Imports #> 12 vctrs Imports #> 13 pillar Imports #> 14 tibble Imports #> 15 pkgload Imports #> 16 devtools Imports #> #> $license #> [1] \"MIT + file LICENSE\" pkg_assess(as_tibble(riskmetric_pkg_ref)) #> # A tibble: 1 × 22 #> package version pkg_ref covr_coverage has_news remote_checks #> #> 1 riskmetric 0.2.4.9000 riskmetric NA 1 NA #> # ℹ 16 more variables: news_current , r_cmd_check , #> # exported_namespace , has_vignettes , #> # export_help , has_website , has_maintainer , #> # bugs_status , size_codebase , #> # has_source_control , has_bug_reports_url , #> # downloads_1yr , reverse_dependencies , #> # has_examples , dependencies , license "},{"path":"/articles/riskmetric.html","id":"scoring-package-metrics","dir":"Articles","previous_headings":"The riskmetric Workflow","what":"Scoring package metrics","title":"Get Started","text":"metric collected, “score” metric convert quantified representation risk. single scoring function, metric_score, dispatches based class metric passed interpret atomic metric result. convenience, pkg_score provided convenience operate pkg_ref objects directly. can also operate tibble produced pkg_assess applied pkg_ref tibble, providing new tibble scored metrics. Note pkg_assess pkg_score accepts error_handler argument determines errors escalated communication. ’ve chosen default cautious, displaying warnings liberally ensure thorough documentation risk assessment process. warnings bothersome, alternative reporting schemes assessment_error_* score_error_* families functions.","code":"metric_score(riskmetric_export_help_metric) #> [1] 1 pkg_score(pkg_assess(as_tibble(pkg_ref(\"riskmetric\")))) #> # A tibble: 1 × 23 #> package version pkg_ref pkg_score covr_coverage has_news #> #> 1 riskmetric 0.2.4.9000 riskmetric 0.576 NA 1 #> # ℹ 17 more variables: remote_checks , news_current , #> # r_cmd_check , exported_namespace , #> # has_vignettes , export_help , has_website , #> # has_maintainer , bugs_status , #> # size_codebase , has_source_control , #> # has_bug_reports_url , downloads_1yr , #> # reverse_dependencies , has_examples , …"},{"path":"/articles/riskmetric.html","id":"cohort-assessments","dir":"Articles","previous_headings":"","what":"Cohort assessments","title":"Get Started","text":"Packages often part larger cohort, ’ve made sure accommodate assessments mulitple packages simultaneously.","code":""},{"path":"/articles/riskmetric.html","id":"creating-a-tibble-from-pkg_refs","dir":"Articles","previous_headings":"Cohort assessments","what":"Creating a tibble from pkg_refs","title":"Get Started","text":"start calling pkg_ref constructor function list vector. return list pkg_ref objects. list, can use tibble::as_tibble convert pkg_ref list tibble, automatically populating useful index columns like package version. clean things can use magrittr pipe (%>%) chain commands together.","code":"package_tbl <- pkg_ref(c(\"riskmetric\", \"utils\", \"tools\")) %>% as_tibble()"},{"path":"/articles/riskmetric.html","id":"the-riskmetric-workflow-on-multiple-packages","dir":"Articles","previous_headings":"Cohort assessments","what":"The riskmetric workflow on multiple packages","title":"Get Started","text":"pkg_assess pkg_score can operate tibbles, making easy simultaneously test entire cohort packages . Notice summary column, pkg_score, included addition metric scores. value shorthand aggregating weighted average risk scores across tibble columns using summarize_scores.","code":"package_tbl %>% pkg_assess() %>% pkg_score() #> # A tibble: 3 × 23 #> package version pkg_ref pkg_score covr_coverage has_news #> #> 1 riskmetric 0.2.4.9000 riskmetric 0.576 NA 1 #> 2 utils 4.4.0 utils 0.687 NA 0 #> 3 tools 4.4.0 tools 0.734 NA 0 #> # ℹ 17 more variables: remote_checks , news_current , #> # r_cmd_check , exported_namespace , #> # has_vignettes , export_help , has_website , #> # has_maintainer , bugs_status , #> # size_codebase , has_source_control , #> # has_bug_reports_url , downloads_1yr , #> # reverse_dependencies , has_examples , … package_tbl %>% pkg_assess() %>% pkg_score() %>% summarize_scores() #> [1] 0.5761911 0.6870599 0.7344892"},{"path":"/articles/riskmetric.html","id":"how-you-can-help","dir":"Articles","previous_headings":"","what":"How you can help…","title":"Get Started","text":"can see, package currently quite bare-bones nobody reasonably choose packages based solely existence NEWS file. priority far set extensible framework foundation community effort, ’s come ! things can get started. Propose new metric riskmetric GitHub Take part discussion metrics captured measured Check extending-riskmetric vignette see extend functionality metrics can discuss new metric proposals Help us develop new metrics package functionality","code":""},{"path":"/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"R Validation Hub. Author. Doug Kelkhoff. Author. Marly Gotti. Author. Eli Miller. Maintainer, author. Kevin K. Author. Yilong Zhang. Author. Eric Milliman. Author. Juliane Manitz. Author. Mark Padgham. Contributor. PSI special interest group Application Implementation Methodologies Statistics. Copyright holder.","code":""},{"path":"/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"R Validation Hub, Kelkhoff D, Gotti M, Miller E, K K, Zhang Y, Milliman E, Manitz J (2024). riskmetric: Risk Metrics Evaluating R Packages. R package version 0.2.4.9000, https://github.com/pharmaR/riskmetric, https://pharmar.github.io/riskmetric/.","code":"@Manual{, title = {riskmetric: Risk Metrics to Evaluating R Packages}, author = {{R Validation Hub} and Doug Kelkhoff and Marly Gotti and Eli Miller and Kevin K and Yilong Zhang and Eric Milliman and Juliane Manitz}, year = {2024}, note = {R package version 0.2.4.9000, https://github.com/pharmaR/riskmetric}, url = {https://pharmar.github.io/riskmetric/}, }"},{"path":"/index.html","id":"riskmetric-","dir":"","previous_headings":"","what":"Risk Metrics to Evaluating R Packages","title":"Risk Metrics to Evaluating R Packages","text":"riskmetric collection risk metrics evaluate quality R packages. package experimentation. 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metric_score.pkg_metric_downloads_1yr","title":"Defining an Assessment Scoring Function — metric_score.pkg_metric_downloads_1yr","text":"Score package number downloads past year regularized Convert number downloads x past year validation score [0,1] $$ 1 - 150,000 / (x + 150,000) $$","code":""},{"path":"/reference/metric_score.pkg_metric_downloads_1yr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Defining an Assessment Scoring Function — metric_score.pkg_metric_downloads_1yr","text":"","code":"# S3 method for pkg_metric_downloads_1yr metric_score(x, ...)"},{"path":"/reference/metric_score.pkg_metric_downloads_1yr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Defining an Assessment Scoring Function — metric_score.pkg_metric_downloads_1yr","text":"x pkg_metric_downloads_1yr packge metric object ... additional arguments 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metric_score.pkg_metric_export_help","text":"","code":"if (FALSE) metric_score(assess_export_help(pkg_ref(\"riskmetric\")))"},{"path":"/reference/metric_score.pkg_metric_exported_namespace.html","id":null,"dir":"Reference","previous_headings":"","what":"Score a package for the number of exported objects — metric_score.pkg_metric_exported_namespace","title":"Score a package for the number of exported objects — metric_score.pkg_metric_exported_namespace","text":"Score package number exported objects ; regularized Convert number exported objects length(x) validation score [0,1] $$ 1 / (1 + exp(-0.5 * (sqrt(length(x)) + sqrt(5)))) $$","code":""},{"path":"/reference/metric_score.pkg_metric_exported_namespace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Score a package for the number of exported objects — metric_score.pkg_metric_exported_namespace","text":"","code":"# S3 method for pkg_metric_exported_namespace metric_score(x, 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the presence of a example or usage fields — metric_score.pkg_metric_has_examples","text":"","code":"if (FALSE) metric_score(assess_has_examples(pkg_ref(\"riskmetric\")))"},{"path":"/reference/metric_score.pkg_metric_has_maintainer.html","id":null,"dir":"Reference","previous_headings":"","what":"Score a package for inclusion of an associated maintainer — metric_score.pkg_metric_has_maintainer","title":"Score a package for inclusion of an associated maintainer — metric_score.pkg_metric_has_maintainer","text":"Coerce list maintainers numeric value indicating whether number listed maintainers greater 0.","code":""},{"path":"/reference/metric_score.pkg_metric_has_maintainer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Score a package for inclusion of an associated maintainer — metric_score.pkg_metric_has_maintainer","text":"","code":"# S3 method for pkg_metric_has_maintainer metric_score(x, 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metric_score(assess_has_maintainer(pkg_ref(\"riskmetric\")))"},{"path":"/reference/metric_score.pkg_metric_has_news.html","id":null,"dir":"Reference","previous_headings":"","what":"Score a package for the presence of a NEWS file — metric_score.pkg_metric_has_news","title":"Score a package for the presence of a NEWS file — metric_score.pkg_metric_has_news","text":"Coerce number news files binary indication valid NEWS files","code":""},{"path":"/reference/metric_score.pkg_metric_has_news.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Score a package for the presence of a NEWS file — metric_score.pkg_metric_has_news","text":"","code":"# S3 method for pkg_metric_has_news metric_score(x, ...)"},{"path":"/reference/metric_score.pkg_metric_has_news.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Score a package for the presence of a NEWS file — metric_score.pkg_metric_has_news","text":"x pkg_metric_has_news 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metric_score.pkg_metric_has_source_control","text":"Coerce list source control urls numeric value indicating whether number listed urls greater 0.","code":""},{"path":"/reference/metric_score.pkg_metric_has_source_control.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Score a package for inclusion of an associated source control url — metric_score.pkg_metric_has_source_control","text":"","code":"# S3 method for pkg_metric_has_source_control metric_score(x, ...)"},{"path":"/reference/metric_score.pkg_metric_has_source_control.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Score a package for inclusion of an associated source control url — metric_score.pkg_metric_has_source_control","text":"x pkg_metric_has_source_control packge metric object ... additional arguments 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metric_score.pkg_metric_has_vignettes","text":"Coerce number vignettes files binary indication valid Vignettes","code":""},{"path":"/reference/metric_score.pkg_metric_has_vignettes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Score a package for the presence of a Vignettes file — metric_score.pkg_metric_has_vignettes","text":"","code":"# S3 method for pkg_metric_has_vignettes metric_score(x, ...)"},{"path":"/reference/metric_score.pkg_metric_has_vignettes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Score a package for the presence of a Vignettes file — metric_score.pkg_metric_has_vignettes","text":"x pkg_metric_has_vignettes packge metric object ... additional arguments unused","code":""},{"path":"/reference/metric_score.pkg_metric_has_vignettes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Score a package for the presence of a Vignettes file — metric_score.pkg_metric_has_vignettes","text":"1 Vignettes files found, otherwise 0","code":""},{"path":"/reference/metric_score.pkg_metric_has_vignettes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Score a package for the presence of a Vignettes file — metric_score.pkg_metric_has_vignettes","text":"","code":"if (FALSE) metric_score(assess_has_vignettes(pkg_ref(\"riskmetric\")))"},{"path":"/reference/metric_score.pkg_metric_has_website.html","id":null,"dir":"Reference","previous_headings":"","what":"Score a package for inclusion of an associated website url — metric_score.pkg_metric_has_website","title":"Score a package for inclusion of an associated website url — metric_score.pkg_metric_has_website","text":"Coerce list website urls numeric value indicating whether number listed urls greater 0.","code":""},{"path":"/reference/metric_score.pkg_metric_has_website.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Score a package for inclusion of an associated website url — metric_score.pkg_metric_has_website","text":"","code":"# S3 method for pkg_metric_has_website metric_score(x, ...)"},{"path":"/reference/metric_score.pkg_metric_has_website.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Score a package for inclusion of an associated website url — metric_score.pkg_metric_has_website","text":"x pkg_metric_has_website packge metric object ... additional arguments unused","code":""},{"path":"/reference/metric_score.pkg_metric_has_website.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Score a package for inclusion of an associated website url — metric_score.pkg_metric_has_website","text":"1 website url provided, otherwise 0","code":""},{"path":"/reference/metric_score.pkg_metric_has_website.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Score a package for inclusion of an associated website url — metric_score.pkg_metric_has_website","text":"","code":"if (FALSE) metric_score(assess_has_website(pkg_ref(\"riskmetric\")))"},{"path":"/reference/metric_score.pkg_metric_last_30_bugs_status.html","id":null,"dir":"Reference","previous_headings":"","what":"Score a package for number of recently opened BugReports that are now closed — metric_score.pkg_metric_last_30_bugs_status","title":"Score a package for number of recently opened BugReports that are now closed — metric_score.pkg_metric_last_30_bugs_status","text":"Score package number recently opened BugReports now closed","code":""},{"path":"/reference/metric_score.pkg_metric_last_30_bugs_status.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Score a package for number of recently opened BugReports that are now closed — metric_score.pkg_metric_last_30_bugs_status","text":"","code":"# S3 method for pkg_metric_last_30_bugs_status metric_score(x, ...)"},{"path":"/reference/metric_score.pkg_metric_last_30_bugs_status.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Score a package for number of recently opened BugReports that are now closed — metric_score.pkg_metric_last_30_bugs_status","text":"x pkg_metric_last_30_bugs_status packge metric object ... additional arguments unused","code":""},{"path":"/reference/metric_score.pkg_metric_last_30_bugs_status.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Score a package for number of recently opened BugReports that are now closed — metric_score.pkg_metric_last_30_bugs_status","text":"fractional value indicating percentage last 30 bug reports now 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...)"},{"path":"/reference/metric_score.pkg_metric_license.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Score a package for acceptable license — metric_score.pkg_metric_license","text":"x pkg_metric_license packge metric object ... additional arguments unused","code":""},{"path":"/reference/metric_score.pkg_metric_license.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Score a package for acceptable license — metric_score.pkg_metric_license","text":"score metric license","code":""},{"path":"/reference/metric_score.pkg_metric_license.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Score a package for acceptable license — metric_score.pkg_metric_license","text":"","code":"if (FALSE) metric_score(assess_license(pkg_ref(\"riskmetric\")))"},{"path":"/reference/metric_score.pkg_metric_news_current.html","id":null,"dir":"Reference","previous_headings":"","what":"Score a package for NEWS files updated to current version — metric_score.pkg_metric_news_current","title":"Score a package for NEWS files updated to current version — metric_score.pkg_metric_news_current","text":"Coerce logical vector discovered --date NEWS metric score","code":""},{"path":"/reference/metric_score.pkg_metric_news_current.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Score a package for NEWS files updated to current version — metric_score.pkg_metric_news_current","text":"","code":"# S3 method for pkg_metric_news_current metric_score(x, ...)"},{"path":"/reference/metric_score.pkg_metric_news_current.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Score a package for NEWS files updated to current version — metric_score.pkg_metric_news_current","text":"x pkg_metric_news_current packge metric object ... additional arguments unused","code":""},{"path":"/reference/metric_score.pkg_metric_news_current.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Score a package for NEWS files updated to current version — metric_score.pkg_metric_news_current","text":"1 NEWS files --date, otherwise 0","code":""},{"path":"/reference/metric_score.pkg_metric_news_current.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Score a package for NEWS files updated to current version — metric_score.pkg_metric_news_current","text":"","code":"if (FALSE) metric_score(assess_news_current(pkg_ref(\"riskmetric\")))"},{"path":"/reference/metric_score.pkg_metric_r_cmd_check.html","id":null,"dir":"Reference","previous_headings":"","what":"Score a package based on R CMD check results run locally — metric_score.pkg_metric_r_cmd_check","title":"Score a package based on R CMD check results run locally — metric_score.pkg_metric_r_cmd_check","text":"scoring function weighted sum notes (0.1), errors (1) warnings (0.25), maximum score 1 (errors, notes warnings) minimum score 0. 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metric_score.pkg_metric_r_cmd_check","text":"weighted sum errors warnings tests preformed","code":""},{"path":"/reference/metric_score.pkg_metric_r_cmd_check.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Score a package based on R CMD check results run locally — metric_score.pkg_metric_r_cmd_check","text":"","code":"if (FALSE) metric_score(assess_r_cmd_check(pkg_ref(\"riskmetric\")))"},{"path":"/reference/metric_score.pkg_metric_remote_checks.html","id":null,"dir":"Reference","previous_headings":"","what":"Score a package based on R CMD check results run by BioC or CRAN — metric_score.pkg_metric_remote_checks","title":"Score a package based on R CMD check results run by BioC or CRAN — metric_score.pkg_metric_remote_checks","text":"scoring function number OS flavors passed OK NOTES + 0.5*number OS's produced WARNINGS divided number OS's 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percentage OS flavors produce error warning R CMD check","code":""},{"path":"/reference/metric_score.pkg_metric_remote_checks.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Score a package based on R CMD check results run by BioC or CRAN — metric_score.pkg_metric_remote_checks","text":"","code":"if (FALSE) metric_score(assess_remote_checks(pkg_ref(\"riskmetric\")))"},{"path":"/reference/metric_score.pkg_metric_reverse_dependencies.html","id":null,"dir":"Reference","previous_headings":"","what":"Scoring method for number of reverse dependencies a package has — metric_score.pkg_metric_reverse_dependencies","title":"Scoring method for number of reverse dependencies a package has — metric_score.pkg_metric_reverse_dependencies","text":"Score package number reverse dependencies ; regularized Convert number reverse dependencies length(x) validation score [0,1] $$ 1 / (1 + exp(-0.5 * (sqrt(length(x)) + sqrt(5)))) $$","code":""},{"path":"/reference/metric_score.pkg_metric_reverse_dependencies.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Scoring method for number of reverse dependencies a package has — metric_score.pkg_metric_reverse_dependencies","text":"","code":"# S3 method for pkg_metric_reverse_dependencies metric_score(x, ...)"},{"path":"/reference/metric_score.pkg_metric_reverse_dependencies.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Scoring method for number of reverse dependencies a package has — metric_score.pkg_metric_reverse_dependencies","text":"x pkg_metric_reverse_dependencies packge metric object ... additional arguments unused","code":""},{"path":"/reference/metric_score.pkg_metric_reverse_dependencies.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Scoring method for number of reverse dependencies a package has — metric_score.pkg_metric_reverse_dependencies","text":"numeric value 1 (high number reverse dependencies) 0 (low number reverse dependencies)","code":""},{"path":"/reference/metric_score.pkg_metric_reverse_dependencies.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Scoring method for number of reverse dependencies a package has — metric_score.pkg_metric_reverse_dependencies","text":"scoring function classic logistic curve $$ 1 / (1 + exp(-k(x-x[0])) $$ square root scale number reverse dependencies \\(x = sqrt(length(x))\\), sigmoid midpoint 5 reverse dependencies, ie. \\(x[0] = sqrt(5)\\), logistic growth rate \\(k = 0.5\\). $$ 1 / (1 + -0.5 * exp(sqrt(length(x)) - sqrt(5))) $$","code":""},{"path":"/reference/metric_score.pkg_metric_reverse_dependencies.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Scoring method for number of reverse dependencies a package has — metric_score.pkg_metric_reverse_dependencies","text":"","code":"if (FALSE) metric_score(assess_reverse_dependencies(pkg_ref(\"riskmetric\")))"},{"path":"/reference/metric_score.pkg_metric_size_codebase.html","id":null,"dir":"Reference","previous_headings":"","what":"Score a package for number of lines of code — metric_score.pkg_metric_size_codebase","title":"Score a package for number of lines of code — metric_score.pkg_metric_size_codebase","text":"Scores packages based codebase size, determined number lines code.","code":""},{"path":"/reference/metric_score.pkg_metric_size_codebase.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Score a package for number of lines of code — metric_score.pkg_metric_size_codebase","text":"","code":"# S3 method for pkg_metric_size_codebase metric_score(x, ...)"},{"path":"/reference/metric_score.pkg_metric_size_codebase.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Score a package for number of lines of code — metric_score.pkg_metric_size_codebase","text":"x pkg_metric_size_codebase packge metric object ... additional arguments unused","code":""},{"path":"/reference/metric_score.pkg_metric_size_codebase.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Score a package for number of lines of code — metric_score.pkg_metric_size_codebase","text":"numeric value 0 (low) 1 (large number lines code) converting number downloads.","code":""},{"path":"/reference/metric_score.pkg_metric_size_codebase.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Score a package for number of lines of code — metric_score.pkg_metric_size_codebase","text":"","code":"if (FALSE) metric_score(assess_size_codebase(pkg_ref(\"riskmetric\")))"},{"path":"/reference/news_from_dir.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a list of NEWS files discovered within a given directory — news_from_dir","title":"Build a list of NEWS files discovered within a given directory — news_from_dir","text":"Build list NEWS files discovered within given directory","code":""},{"path":"/reference/news_from_dir.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a list of NEWS files discovered within a given directory — news_from_dir","text":"","code":"news_from_dir(path)"},{"path":"/reference/news_from_dir.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a list of NEWS files discovered within a given directory — news_from_dir","text":"path package directory path expected contain NEWS files","code":""},{"path":"/reference/news_from_dir.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build a list of NEWS files discovered within a given directory — news_from_dir","text":"list parsed NEWS files","code":""},{"path":"/reference/parse_dcf_dependencies.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse DCF of description file — parse_dcf_dependencies","title":"Parse DCF of description file — parse_dcf_dependencies","text":"Parse DCF description file","code":""},{"path":"/reference/parse_dcf_dependencies.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse DCF of description file — parse_dcf_dependencies","text":"","code":"parse_dcf_dependencies(path)"},{"path":"/reference/parse_dcf_dependencies.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse DCF of description file — parse_dcf_dependencies","text":"path pkg_ref path","code":""},{"path":"/reference/pkg_assess.html","id":null,"dir":"Reference","previous_headings":"","what":"Apply assess_* family of functions to a package reference — pkg_assess","title":"Apply assess_* family of functions to a package reference — pkg_assess","text":"default, use assess_* funtions riskmetric namespace produce tibble one column per assessment applied.","code":""},{"path":"/reference/pkg_assess.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Apply assess_* family of functions to a package reference — pkg_assess","text":"","code":"pkg_assess( x, assessments = all_assessments(), ..., error_handler = assessment_error_empty )"},{"path":"/reference/pkg_assess.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Apply assess_* family of functions to a package reference — pkg_assess","text":"x single pkg_ref object tibble package references assess assessments list assessment functions apply package reference. default, list exported assess_* functions riskmetric package. ... additional arguments unused error_handler function, accepts single parameter expecting raised error, called errors occur attempting apply assessment function.","code":""},{"path":"/reference/pkg_assess.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Apply assess_* family of functions to a package reference — pkg_assess","text":"Either list_of_pkg_metric object single pkg_ref object passed x, tibble metrics list_of_pkg_ref tibble passed x. tibble returned, one row per package reference new column per assessment function, cells column package metric objects returned assessment called associated pacakge reference.","code":""},{"path":"/reference/pkg_assess.html","id":"assessment-function-catalog","dir":"Reference","previous_headings":"","what":"Assessment function catalog","title":"Apply assess_* family of functions to a package reference — pkg_assess","text":"assess_last_30_bugs_status vector indicating whether BugReports status closed assess_covr_coverage Package unit test coverage assess_size_codebase number lines code base assess_export_help exported objects documentation assess_r_cmd_check Package check results assess_dependencies Package dependency footprint assess_reverse_dependencies List reverse dependencies package assess_license software released acceptable license assess_has_maintainer vector associated maintainers assess_remote_checks Number OS flavors passed/warned/errored R CMD check assess_exported_namespace Objects exported package assess_has_website vector associated website urls assess_downloads_1yr number downloads past year assess_has_news number discovered NEWS files assess_has_vignettes number discovered vignettes files assess_has_examples proportion discovered function files examples assess_has_source_control vector associated source control urls assess_has_bug_reports_url presence bug reports url repository assess_news_current NEWS file contains entry current version number","code":""},{"path":"/reference/pkg_metric.html","id":null,"dir":"Reference","previous_headings":"","what":"A helper for structuring assessment return objects for dispatch with the score function — pkg_metric","title":"A helper for structuring assessment return objects for dispatch with the score function — pkg_metric","text":"helper structuring assessment return objects dispatch score function","code":""},{"path":"/reference/pkg_metric.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A helper for structuring assessment return objects for dispatch with the score function — pkg_metric","text":"","code":"pkg_metric(x = NA, ..., class = c())"},{"path":"/reference/pkg_metric.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A helper for structuring assessment return objects for dispatch with the score function — pkg_metric","text":"x data store pkg_metric ... additional attributes bind pkg_metric object class subclass differentiate pkg_metric object","code":""},{"path":"/reference/pkg_metric.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A helper for structuring assessment return objects for dispatch with the score function — pkg_metric","text":"pkg_metric object","code":""},{"path":"/reference/pkg_metric_eval.html","id":null,"dir":"Reference","previous_headings":"","what":"Evaluate a metric — pkg_metric_eval","title":"Evaluate a metric — pkg_metric_eval","text":"Evalute code relevant metric, capturing evaluated code well messages, warnings errors thrown process.","code":""},{"path":"/reference/pkg_metric_eval.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Evaluate a metric — pkg_metric_eval","text":"","code":"pkg_metric_eval(expr, ..., class = c(), env = parent.frame())"},{"path":"/reference/pkg_metric_eval.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Evaluate a metric — pkg_metric_eval","text":"expr expression evaluate order calculate pkg_metric ... additional attributes bind pkg_metric object class subclass differentiate pkg_metric object env environment expr evaluated","code":""},{"path":"/reference/pkg_metric_eval.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Evaluate a metric — pkg_metric_eval","text":"pkg_metric object containing result expr","code":""},{"path":"/reference/pkg_ref.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a package reference — pkg_ref","title":"Create a package reference — pkg_ref","text":"Create package reference package name filepath, producing object package metadata collected risk assessments performed. Depending package found - whether found source code, local library remote host - S3 subclass given allow source-specific collection metadata. See 'Details' breakdown subclasses. Different sources can specified passing subclass arguemnt named 'source', see details.","code":""},{"path":"/reference/pkg_ref.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a package reference — pkg_ref","text":"","code":"pkg_ref(x, ...) pkg_install(x, lib.loc = NULL) pkg_source(x) pkg_cran(x, repos = getOption(\"repos\", \"https://cran.rstudio.com\")) pkg_bioc(x) pkg_missing(x) pkg_library(lib.loc) as_pkg_ref(x, ...)"},{"path":"/reference/pkg_ref.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a package reference — pkg_ref","text":"x singular character value, character vector list character values package names source code directory paths. ... Additional arguments passed methods. lib.loc path R library directory installed package. repos URL CRAN repository pull package metadata.","code":""},{"path":"/reference/pkg_ref.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a package reference — pkg_ref","text":"single value provided, single pkg_ref object returned, possibly subclass based package found. vector list provided, list_of_pkg_ref object constructed list_of returned, can considered analogous list. See 'Details' information pkg_ref subclasses.","code":""},{"path":"/reference/pkg_ref.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a package reference — pkg_ref","text":"Package reference objects used collect metadata pertaining given package. data needed assessing package's risk, metadata populates fields within package reference object. pkg_ref S3 subclasses used extensively divergent metadata collection behaviors dependent package discovered. , rich hierarchy subclasses articulate different ways package information can found. source argument can passed using `source` argument. override logic riskmetric determining package source. can useful scoring recent version present repository, testing specific library. pkg_ref default class general metadata collection. pkg_source reference source code directory. pkg_install reference package installation location package library. specific library can passed passing path library parameter `lib.loc` pkg_remote reference package metadata remote server. pkg_cran_remote reference package information pulled CRAN repository. pkg_bioc_remote reference package information pulled Bioconductor repository. pkg_git_remote reference package source code git repository. (yet implemented)","code":""},{"path":"/reference/pkg_ref.html","id":"package-cohorts","dir":"Reference","previous_headings":"","what":"Package Cohorts","title":"Create a package reference — pkg_ref","text":"*Experimental!* Package cohorts structures determine risk set packages. `pkg_library()` can called create object containing pkg_ref objects packages system library.","code":""},{"path":"/reference/pkg_ref.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a package reference — pkg_ref","text":"","code":"if (FALSE) { # riskmetric will check for installed packages by default ref_1 <- pkg_ref(\"utils\") ref_1$source # returns 'pkg_install' # lib.loc can be used to specify a library for pkg_install ref_3 <- pkg_ref(\"utils\", source = \"pkg_install\", lib.loc = .libPaths()[1]) # You can also override this behavior with a source argument ref_2 <- pkg_ref(\"utils\", source = \"pkg_cran_remote\") ref_2$source # returns 'pkg_cran_remote' }"},{"path":"/reference/pkg_ref_cache.bug_reports_host.default.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the host name of a BugReports url — pkg_ref_cache.bug_reports_host.default","title":"Get the host name of a BugReports url — pkg_ref_cache.bug_reports_host.default","text":"Get host name BugReports url","code":""},{"path":"/reference/pkg_ref_cache.bug_reports_host.default.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the host name of a BugReports url — pkg_ref_cache.bug_reports_host.default","text":"","code":"# S3 method for bug_reports_host.default pkg_ref_cache(x, ...)"},{"path":"/reference/pkg_ref_cache.bug_reports_host.default.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the host name of a BugReports url — pkg_ref_cache.bug_reports_host.default","text":"pkg_ref object","code":""},{"path":"/reference/pkg_ref_cache.bug_reports_url.pkg_source.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the BugReports url — pkg_ref_cache.bug_reports_url.pkg_source","title":"Get the BugReports url — pkg_ref_cache.bug_reports_url.pkg_source","text":"Get BugReports url","code":""},{"path":"/reference/pkg_ref_cache.bug_reports_url.pkg_source.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the BugReports url — pkg_ref_cache.bug_reports_url.pkg_source","text":"","code":"# S3 method for bug_reports_url.pkg_source pkg_ref_cache(x, ...)"},{"path":"/reference/pkg_ref_cache.bug_reports_url.pkg_source.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the BugReports url — pkg_ref_cache.bug_reports_url.pkg_source","text":"pkg_ref object","code":""},{"path":"/reference/pkg_ref_cache.covr_coverage.pkg_source.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve output of covr::package_coverage — pkg_ref_cache.covr_coverage.pkg_source","title":"Retrieve output of covr::package_coverage — pkg_ref_cache.covr_coverage.pkg_source","text":"Retrieve output covr::package_coverage","code":""},{"path":"/reference/pkg_ref_cache.covr_coverage.pkg_source.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve output of covr::package_coverage — pkg_ref_cache.covr_coverage.pkg_source","text":"","code":"# S3 method for covr_coverage.pkg_source pkg_ref_cache(x, ...)"},{"path":"/reference/pkg_ref_cache.covr_coverage.pkg_source.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve output of covr::package_coverage — pkg_ref_cache.covr_coverage.pkg_source","text":"pkg_ref object","code":""},{"path":"/reference/pkg_ref_cache.expression_coverage.pkg_source.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve output of covr::package_coverage, tallied by expression — pkg_ref_cache.expression_coverage.pkg_source","title":"Retrieve output of covr::package_coverage, tallied by expression — pkg_ref_cache.expression_coverage.pkg_source","text":"Retrieve output covr::package_coverage, tallied expression","code":""},{"path":"/reference/pkg_ref_cache.expression_coverage.pkg_source.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve output of covr::package_coverage, tallied by expression — pkg_ref_cache.expression_coverage.pkg_source","text":"","code":"# S3 method for expression_coverage.pkg_source pkg_ref_cache(x, ...)"},{"path":"/reference/pkg_ref_cache.expression_coverage.pkg_source.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve output of covr::package_coverage, tallied by expression — pkg_ref_cache.expression_coverage.pkg_source","text":"pkg_ref object","code":""},{"path":"/reference/pkg_ref_cache.help.pkg_install.html","id":null,"dir":"Reference","previous_headings":"","what":"Cache a list of available help files as LaTeX objects — pkg_ref_cache.help.pkg_install","title":"Cache a list of available help files as LaTeX objects — pkg_ref_cache.help.pkg_install","text":"Cache list available help files LaTeX objects","code":""},{"path":"/reference/pkg_ref_cache.help.pkg_install.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cache a list of available help files as LaTeX objects — pkg_ref_cache.help.pkg_install","text":"","code":"# S3 method for help.pkg_install pkg_ref_cache(x, name, ...)"},{"path":"/reference/pkg_ref_cache.help.pkg_install.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cache a list of available help files as LaTeX objects — pkg_ref_cache.help.pkg_install","text":"pkg_ref object","code":""},{"path":"/reference/pkg_ref_cache.help.pkg_source.html","id":null,"dir":"Reference","previous_headings":"","what":"Cache a list of available help files as LaTeX objects — pkg_ref_cache.help.pkg_source","title":"Cache a list of available help files as LaTeX objects — pkg_ref_cache.help.pkg_source","text":"Cache list available help files LaTeX objects","code":""},{"path":"/reference/pkg_ref_cache.help.pkg_source.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cache a list of available help files as LaTeX objects — pkg_ref_cache.help.pkg_source","text":"","code":"# S3 method for help.pkg_source pkg_ref_cache(x, name, ...)"},{"path":"/reference/pkg_ref_cache.news.pkg_remote.html","id":null,"dir":"Reference","previous_headings":"","what":"Cache a list of NEWS files from a package reference — pkg_ref_cache.news.pkg_remote","title":"Cache a list of NEWS files from a package reference — pkg_ref_cache.news.pkg_remote","text":"Cache list NEWS files package reference","code":""},{"path":"/reference/pkg_ref_cache.news.pkg_remote.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cache a list of NEWS files from a package reference — pkg_ref_cache.news.pkg_remote","text":"","code":"# S3 method for news.pkg_remote pkg_ref_cache(x, name, ...)"},{"path":"/reference/pkg_ref_cache.news.pkg_remote.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cache a list of NEWS files from a package reference — pkg_ref_cache.news.pkg_remote","text":"pkg_ref object","code":""},{"path":"/reference/pkg_ref_class_hierarchy.html","id":null,"dir":"Reference","previous_headings":"","what":"The `pkg_ref` subclass hierarchy, used for pkg_ref object creation with a specified subclass — pkg_ref_class_hierarchy","title":"The `pkg_ref` subclass hierarchy, used for pkg_ref object creation with a specified subclass — pkg_ref_class_hierarchy","text":"`pkg_ref` subclass hierarchy, used pkg_ref object creation specified subclass","code":""},{"path":"/reference/pkg_ref_class_hierarchy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The `pkg_ref` subclass hierarchy, used for pkg_ref object creation with a specified subclass — pkg_ref_class_hierarchy","text":"","code":"pkg_ref_class_hierarchy"},{"path":"/reference/pkg_ref_class_hierarchy.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"The `pkg_ref` subclass hierarchy, used for pkg_ref object creation with a specified subclass — pkg_ref_class_hierarchy","text":"object class list length 1.","code":""},{"path":"/reference/pkg_ref_mutability_error.html","id":null,"dir":"Reference","previous_headings":"","what":"pretty printing for a pkg_ref mutability error caused by trying to do assignment within the pkg_ref without permission — pkg_ref_mutability_error","title":"pretty printing for a pkg_ref mutability error caused by trying to do assignment within the pkg_ref without permission — pkg_ref_mutability_error","text":"pretty printing pkg_ref mutability error caused trying assignment within pkg_ref without permission","code":""},{"path":"/reference/pkg_ref_mutability_error.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"pretty printing for a pkg_ref mutability error caused by trying to do assignment within the pkg_ref without permission — pkg_ref_mutability_error","text":"","code":"pkg_ref_mutability_error(name)"},{"path":"/reference/pkg_ref_mutability_error.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"pretty printing for a pkg_ref mutability error caused by trying to do assignment within the pkg_ref without permission — pkg_ref_mutability_error","text":"name name field mutation attempted","code":""},{"path":"/reference/pkg_ref_mutability_error.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"pretty printing for a pkg_ref mutability error caused by trying to do assignment within the pkg_ref without permission — pkg_ref_mutability_error","text":"simplError subclasses pkg_ref_mutability_error, pkg_ref_error","code":""},{"path":"/reference/pkg_score.html","id":null,"dir":"Reference","previous_headings":"","what":"Score a package assessment, collapsing results into a single numeric — pkg_score","title":"Score a package assessment, collapsing results into a single numeric — pkg_score","text":"pkg_score() calculates risk involved using package. Risk ranges 0 (low-risk) 1 (high-risk).","code":""},{"path":"/reference/pkg_score.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Score a package assessment, collapsing results into a single numeric — pkg_score","text":"","code":"pkg_score(x, ..., error_handler = score_error_default)"},{"path":"/reference/pkg_score.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Score a package assessment, collapsing results into a single numeric — pkg_score","text":"x pkg_metric object, whose subclass used choose appropriate scoring method atomic metric metadata. Optionally, tibble can provided, cases pkg_metric values scored. ... Additional arguments passed summarize_scores object class tbl_df provided, unused otherwise. error_handler Specify function called class identified. commonly occurs pkg_metric objects subclass pkg_metric_error, produced error encountered calculating associated assessment.","code":""},{"path":"/reference/pkg_score.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Score a package assessment, collapsing results into a single numeric — pkg_score","text":"numeric value single pkg_metric provided, tibble pkg_metric objects scored returned numeric values tibble provided.","code":""},{"path":[]},{"path":"/reference/pkg_score.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Score a package assessment, collapsing results into a single numeric — pkg_score","text":"","code":"if (FALSE) { # scoring a single assessment metric_score(assess_has_news(pkg_ref(\"riskmetric\"))) # scoring many assessments as a tibble library(dplyr) pkg_score(pkg_assess(as_tibble(pkg_ref(c(\"riskmetric\", \"riskmetric\"))))) }"},{"path":"/reference/print.with_eval_recording.html","id":null,"dir":"Reference","previous_headings":"","what":"Handle pretty printing of expression output — print.with_eval_recording","title":"Handle pretty printing of expression output — print.with_eval_recording","text":"Handle pretty printing expression output","code":""},{"path":"/reference/print.with_eval_recording.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Handle pretty printing of expression output — print.with_eval_recording","text":"","code":"# S3 method for with_eval_recording print(x, playback = FALSE, cr = TRUE, ..., sleep = 0)"},{"path":"/reference/print.with_eval_recording.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Handle pretty printing of expression output — print.with_eval_recording","text":"x expr_output print playback logical indicating whether evaluation output played back (FALSE), whether result value printed (TRUE, default) cr logical indicating whether carriage returns printed, possibly overwriting characters output. ... additional arguments unused sleep numeric indicating time sleep printing line console. can helpful original output overwrites valuable information log eventually overwritten like watch play formatted.","code":""},{"path":"/reference/print.with_eval_recording.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Handle pretty printing of expression output — print.with_eval_recording","text":"print message","code":""},{"path":"/reference/remove_base_packages.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to remove base and recommended packages — remove_base_packages","title":"Helper function to remove base and recommended packages — remove_base_packages","text":"Helper function remove base recommended packages","code":""},{"path":"/reference/remove_base_packages.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to remove base and recommended packages — remove_base_packages","text":"","code":"remove_base_packages(df)"},{"path":"/reference/remove_base_packages.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to remove base and recommended packages — remove_base_packages","text":"df Data frame dependencies package.","code":""},{"path":"/reference/require_cache_behaviors.html","id":null,"dir":"Reference","previous_headings":"","what":"Stop if a function requires disabled behaviors — require_cache_behaviors","title":"Stop if a function requires disabled behaviors — require_cache_behaviors","text":"Stop function requires disabled behaviors","code":""},{"path":"/reference/require_cache_behaviors.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Stop if a function requires disabled behaviors — require_cache_behaviors","text":"","code":"require_cache_behaviors(behaviors)"},{"path":"/reference/require_cache_behaviors.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Stop if a function requires disabled behaviors — require_cache_behaviors","text":"behaviors character vector behavior flags assert requirements metadata caching. values must entry found riskmetric:::cache_behaviors list","code":""},{"path":"/reference/require_cache_behaviors.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Stop if a function requires disabled behaviors — require_cache_behaviors","text":"boolean value","code":""},{"path":"/reference/riskmetric.html","id":null,"dir":"Reference","previous_headings":"","what":"riskmetric — riskmetric","title":"riskmetric — riskmetric","text":"Facilities assessing R packages number metrics help quantify robustness.","code":""},{"path":[]},{"path":"/reference/riskmetric.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"riskmetric — riskmetric","text":"Maintainer: Eli Miller eli.miller@atorusresearch.com Authors: R Validation Hub psi.aims.r.validation@gmail.com Doug Kelkhoff doug.kelkhoff@gmail.com Marly Gotti Kevin K Yilong Zhang Eric Milliman Juliane Manitz contributors: Mark Padgham [contributor] PSI special interest group Application Implementation Methodologies Statistics [copyright holder]","code":""},{"path":"/reference/riskmetric_metadata_caching.html","id":null,"dir":"Reference","previous_headings":"","what":"S3 generic to calculate a `pkg_ref` field — pkg_ref_cache","title":"S3 generic to calculate a `pkg_ref` field — pkg_ref_cache","text":"Reactively retrieve cache `pkg_ref` metadata","code":""},{"path":"/reference/riskmetric_metadata_caching.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S3 generic to calculate a `pkg_ref` field — pkg_ref_cache","text":"pkg_ref field","code":""},{"path":[]},{"path":"/reference/riskmetric_metadata_caching.html","id":"pkg-ref-class-fields","dir":"Reference","previous_headings":"","what":"pkg_ref class fields","title":"S3 generic to calculate a `pkg_ref` field — pkg_ref_cache","text":"pkg_ref class structures environment special handling indexing pkg_ref class using $ [[ operators. intents purposes, pkg_ref class works conceptually similar lazy, immutable list, uses pkg_ref_cache function internally lazily retrieve package reference fields.","code":""},{"path":"/reference/riskmetric_metadata_caching.html","id":"lazy-metadata-caching","dir":"Reference","previous_headings":"","what":"Lazy metadata caching","title":"S3 generic to calculate a `pkg_ref` field — pkg_ref_cache","text":"Laziness pkg_ref object refers delayed evaluation contents fields. Since metadata time computationally intensive retrieve, unnessary assessments, want avoid retrieval needed. first time field accessed within pkg_ref object x, corresponding pkg_ref_cache S3 generic called. example, x$description first accessed, pkg_ref object uses function pkg_ref_cache.description attempt retrieve contents corresponding DESCRIPTION file. Often, way data collected might different depending subclass pkg_ref. case description metadata, reference local install might able read local file directly, whereas reference remote source metadata might require first downloading file. reason, many pkg_ref_cache.* functions S3 generics dispatch class pkg_ref object, allowing divergent behaviors different source package metadata.","code":""},{"path":"/reference/riskmetric_metadata_caching.html","id":"pkg-ref-field-immutability","dir":"Reference","previous_headings":"","what":"pkg_ref field immutability","title":"S3 generic to calculate a `pkg_ref` field — pkg_ref_cache","text":"field calculated, value immutable. behavior chosen long time frame package metadata changes, rendering unnecessary continually reevaluate fields time accesssed. means within assessment, given field package ever calculated preserved downstream use.","code":""},{"path":"/reference/riskmetric_metadata_caching.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S3 generic to calculate a `pkg_ref` field — pkg_ref_cache","text":"","code":"if (FALSE) { # implementing a new field called \"first_letter\" that is consistently derived # across all pkg_ref objects: pkg_ref_cache.first_letter <- function(x, name, ...) { substring(x$name, 1, 1) } x <- pkg_ref(\"riskmetric\") x$first_letter # implementing a new field called \"subclass_enum\" that dispatches on # the subclass of the pkg_ref object: pkg_ref_cache.subclass_enum <- function(x, name, ...) { UseMethod(\"pkg_ref_cache.subclass_enum\") } pkg_ref_cache.subclass_enum.pkg_ref <- function(x, name, ...) { 0 } pkg_ref_cache.subclass_enum.pkg_install <- function(x, name, ...) { 1 } x$subclass_enum }"},{"path":"/reference/roxygen_assess_family.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper for creating a roxygen header from template for assess_* functions — roxygen_assess_family","title":"Helper for creating a roxygen header from template for assess_* functions — roxygen_assess_family","text":"Helper creating roxygen header template assess_* functions","code":""},{"path":"/reference/roxygen_assess_family.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper for creating a roxygen header from template for assess_* functions — roxygen_assess_family","text":"","code":"roxygen_assess_family( name, return_type = \"an atomic assessment result\", dontrun = TRUE )"},{"path":"/reference/roxygen_assess_family.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper for creating a roxygen header from template for assess_* functions — roxygen_assess_family","text":"name name assessment, assuming naming conventions followed return_type optional added commentary return type assessment function dontrun logical indicating whether examples wrapped dontrun block. particularly useful assessments may require internet connection.","code":""},{"path":"/reference/roxygen_assess_family.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper for creating a roxygen header from template for assess_* functions — roxygen_assess_family","text":"roxygen section template assess family functions","code":""},{"path":"/reference/roxygen_assess_family.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper for creating a roxygen header from template for assess_* functions — roxygen_assess_family","text":"","code":"if (FALSE) { #' @eval roxygen_assess_family( #' \"has_news\", #' \"an integer value indicating the number of discovered NEWS files\") }"},{"path":"/reference/roxygen_assess_family_catalog.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper for creating a roxygen itemized list for assess_* functions — roxygen_assess_family_catalog","title":"Helper for creating a roxygen itemized list for assess_* functions — roxygen_assess_family_catalog","text":"Helper creating roxygen itemized list assess_* functions","code":""},{"path":"/reference/roxygen_assess_family_catalog.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper for creating a roxygen itemized list for assess_* functions — roxygen_assess_family_catalog","text":"","code":"roxygen_assess_family_catalog()"},{"path":"/reference/roxygen_assess_family_catalog.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper for creating a roxygen itemized list for assess_* functions — roxygen_assess_family_catalog","text":"roxygen section template assess family function catalog","code":""},{"path":"/reference/roxygen_assess_family_catalog.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper for creating a roxygen itemized list for assess_* functions — roxygen_assess_family_catalog","text":"","code":"if (FALSE) { #' @eval assess_family_catalog_roxygen() }"},{"path":"/reference/roxygen_cache_behaviors.html","id":null,"dir":"Reference","previous_headings":"","what":"Document both declare_cache_behavior parameters and options list — roxygen_cache_behaviors","title":"Document both declare_cache_behavior parameters and options list — roxygen_cache_behaviors","text":"Document declare_cache_behavior parameters options list","code":""},{"path":"/reference/roxygen_cache_behaviors.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Document both declare_cache_behavior parameters and options list — roxygen_cache_behaviors","text":"","code":"roxygen_cache_behaviors( fmt = \"%s: %s\", name_fmt = \"%s\", annotation_fmt = \"%s\", wrap_fmt = \"%s\", collapse = \"\\n\" )"},{"path":"/reference/roxygen_cache_behaviors.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Document both declare_cache_behavior parameters and options list — roxygen_cache_behaviors","text":"fmt format cache behavior entries name_fmt special formating name (first) component annotation_fmt special formating annotation (second) component wrap_fmt wrapper entirety roxygen entries collapse passed paste","code":""},{"path":"/reference/roxygen_cache_behaviors.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Document both declare_cache_behavior parameters and options list — roxygen_cache_behaviors","text":"string","code":""},{"path":"/reference/roxygen_score_family.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper for creating a roxygen header from template for score.* functions — roxygen_score_family","title":"Helper for creating a roxygen header from template for score.* functions — roxygen_score_family","text":"Helper creating roxygen header template score.* functions","code":""},{"path":"/reference/roxygen_score_family.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper for creating a roxygen header from template for score.* functions — roxygen_score_family","text":"","code":"roxygen_score_family(name, dontrun = TRUE)"},{"path":"/reference/roxygen_score_family.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper for creating a roxygen header from template for score.* functions — roxygen_score_family","text":"name name scoring function, assuming naming conventions followed dontrun logical indicating whether examples wrapped dontrun block. particularly useful assessments may require internet connection.","code":""},{"path":"/reference/roxygen_score_family.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper for creating a roxygen header from template for score.* functions — roxygen_score_family","text":"roxygen section template score family functions","code":""},{"path":"/reference/roxygen_score_family.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper for creating a roxygen header from template for score.* functions — roxygen_score_family","text":"","code":"if (FALSE) { #' @eval roxygen_score_family(\"has_news\") }"},{"path":"/reference/score_error_NA.html","id":null,"dir":"Reference","previous_headings":"","what":"Score error handler to silently return NA — score_error_NA","title":"Score error handler to silently return NA — score_error_NA","text":"Score error handler silently return NA","code":""},{"path":"/reference/score_error_NA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Score error handler to silently return NA — score_error_NA","text":"","code":"score_error_NA(...)"},{"path":"/reference/score_error_NA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Score error handler to silently return NA — score_error_NA","text":"... Additional arguments unused","code":""},{"path":"/reference/score_error_NA.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Score error handler to silently return NA — score_error_NA","text":"value package score","code":""},{"path":"/reference/score_error_default.html","id":null,"dir":"Reference","previous_headings":"","what":"Default score error handling, emitting a warning and returning 0 — score_error_default","title":"Default score error handling, emitting a warning and returning 0 — score_error_default","text":"Default score error handling, emitting warning returning 0","code":""},{"path":"/reference/score_error_default.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Default score error handling, emitting a warning and returning 0 — score_error_default","text":"","code":"score_error_default(x, ...)"},{"path":"/reference/score_error_default.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Default score error handling, emitting a warning and returning 0 — score_error_default","text":"x pkg_metric_* class object score ... Additional arguments unused","code":""},{"path":"/reference/score_error_default.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Default score error handling, emitting a warning and returning 0 — score_error_default","text":"value package score","code":""},{"path":"/reference/score_error_zero.html","id":null,"dir":"Reference","previous_headings":"","what":"Score error handler to silently return 0 — score_error_zero","title":"Score error handler to silently return 0 — score_error_zero","text":"Score error handler silently return 0","code":""},{"path":"/reference/score_error_zero.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Score error handler to silently return 0 — score_error_zero","text":"","code":"score_error_zero(...)"},{"path":"/reference/score_error_zero.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Score error handler to silently return 0 — score_error_zero","text":"... Additional arguments unused","code":""},{"path":"/reference/score_error_zero.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Score error handler to silently return 0 — score_error_zero","text":"value package score","code":""},{"path":"/reference/sub-sub-.pkg_ref.html","id":null,"dir":"Reference","previous_headings":"","what":"Lazily instantiated, immutable metadata access — [[.pkg_ref","title":"Lazily instantiated, immutable metadata access — [[.pkg_ref","text":"errors thrown upon instantiation, saved rethrown time value attempted accessed. propegate assessment scoring functions affect downstream metrics.","code":""},{"path":"/reference/sub-sub-.pkg_ref.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lazily instantiated, immutable metadata access — [[.pkg_ref","text":"","code":"# S3 method for pkg_ref [[(x, name, ...)"},{"path":"/reference/sub-sub-.pkg_ref.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Lazily instantiated, immutable metadata access — [[.pkg_ref","text":"x pkg_ref object extract metadata name name metadata field extract ... additional arguments used extract internal environment","code":""},{"path":"/reference/sub-sub-.pkg_ref.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Lazily instantiated, immutable metadata access — [[.pkg_ref","text":"pkg_ref object","code":""},{"path":"/reference/summarize_scores.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize a default set of assessments into a single risk score — summarize_scores","title":"Summarize a default set of assessments into a single risk score — summarize_scores","text":"function serves example risk score might derived. Assuming assessments provided riskmetric available dataset, function can used calculate vector risks.","code":""},{"path":"/reference/summarize_scores.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarize a default set of assessments into a single risk score — summarize_scores","text":"","code":"summarize_scores(data, weights = NULL)"},{"path":"/reference/summarize_scores.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarize a default set of assessments into a single risk score — summarize_scores","text":"data tibble scored assessments whose column names match provided riskmetric's pkg_assess function. weights optional vector non-negative weights assigned assessment.","code":""},{"path":"/reference/summarize_scores.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarize a default set of assessments into a single risk score — summarize_scores","text":"numeric vector risk scores","code":""},{"path":"/reference/summarize_scores.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Summarize a default set of assessments into a single risk score — summarize_scores","text":"","code":"if (FALSE) { library(dplyr) summarize_scores(pkg_score(pkg_assess(as_tibble(pkg_ref(\"riskmetric\"))))) library(dplyr) pkg_ref(\"riskmetric\") %>% pkg_assess() %>% pkg_score() %>% summarize_scores() }"},{"path":"/reference/suppressMatchingConditions.html","id":null,"dir":"Reference","previous_headings":"","what":"Suppress messages and warnings based on one or more regex matches — suppressMatchingConditions","title":"Suppress messages and warnings based on one or more regex matches — suppressMatchingConditions","text":"Suppress messages warnings based one regex matches","code":""},{"path":"/reference/suppressMatchingConditions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Suppress messages and warnings based on one or more regex matches — suppressMatchingConditions","text":"","code":"suppressMatchingConditions(expr, ..., .opts = list(), .envir = parent.frame())"},{"path":"/reference/suppressMatchingConditions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Suppress messages and warnings based on one or more regex matches — suppressMatchingConditions","text":"expr expression evaluate ... Named parameters, name indicates class conditions capture value vector regular expressions , matched respective condition message, suppress condition. .opts named list arguments pass grepl .envir environment expr evaluated","code":""},{"path":"/reference/suppressMatchingConditions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Suppress messages and warnings based on one or more regex matches — suppressMatchingConditions","text":"message printed console","code":""},{"path":"/reference/use_assessments_column_names.html","id":null,"dir":"Reference","previous_headings":"","what":"reassign assignment list names with column_name attribute if available — use_assessments_column_names","title":"reassign assignment list names with column_name attribute if available — use_assessments_column_names","text":"reassign assignment list names column_name attribute available","code":""},{"path":"/reference/use_assessments_column_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"reassign assignment list names with column_name attribute if available — use_assessments_column_names","text":"","code":"use_assessments_column_names(x)"},{"path":"/reference/use_assessments_column_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"reassign assignment list names with column_name attribute if available — use_assessments_column_names","text":"x list columns consider friendly column name attributes","code":""},{"path":"/reference/use_assessments_column_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"reassign assignment list names with column_name attribute if available — use_assessments_column_names","text":"vector friendly column names available","code":""},{"path":"/reference/verify_pkg_source.html","id":null,"dir":"Reference","previous_headings":"","what":"Verify a pkg_source when one is manually specified by the user — verify_pkg_source","title":"Verify a pkg_source when one is manually specified by the user — verify_pkg_source","text":"Verify pkg_source one manually specified user","code":""},{"path":"/reference/verify_pkg_source.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Verify a pkg_source when one is manually specified by the user — verify_pkg_source","text":"","code":"verify_pkg_source(x, source, repos)"},{"path":"/reference/verify_pkg_source.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Verify a pkg_source when one is manually specified by the user — verify_pkg_source","text":"string package source","code":""},{"path":"/reference/vignettes_from_dir.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a List of Vignettes Files Discovered Within a Given Directory — vignettes_from_dir","title":"Build a List of Vignettes Files Discovered Within a Given Directory — vignettes_from_dir","text":"Build List Vignettes Files Discovered Within Given Directory","code":""},{"path":"/reference/vignettes_from_dir.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a List of Vignettes Files Discovered Within a Given Directory — vignettes_from_dir","text":"","code":"vignettes_from_dir(path)"},{"path":"/reference/vignettes_from_dir.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a List of Vignettes Files Discovered Within a Given Directory — vignettes_from_dir","text":"path package directory path expected contain Vignettes files","code":""},{"path":"/reference/vignettes_from_dir.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build a List of Vignettes Files Discovered Within a Given Directory — vignettes_from_dir","text":"vector parsed Vignettes files","code":""},{"path":"/reference/vignettes_from_html.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a List of Vignettes Files Discovered Within a Package Website — vignettes_from_html","title":"Build a List of Vignettes Files Discovered Within a Package Website — vignettes_from_html","text":"Build List Vignettes Files Discovered Within Package Website","code":""},{"path":"/reference/vignettes_from_html.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a List of Vignettes Files Discovered Within a Package Website — vignettes_from_html","text":"","code":"vignettes_from_html(x)"},{"path":"/reference/vignettes_from_html.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a List of Vignettes Files Discovered Within a Package Website — vignettes_from_html","text":"x pkg_ref object","code":""},{"path":"/reference/vignettes_from_html.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build a List of Vignettes Files Discovered Within a Package Website — vignettes_from_html","text":"vector Vignettes files","code":""},{"path":"/reference/with.pkg_ref.html","id":null,"dir":"Reference","previous_headings":"","what":"Evaluate an expression in the context of a pkg_ref — with.pkg_ref","title":"Evaluate an expression in the context of a pkg_ref — with.pkg_ref","text":"pkg_ref objects environments can passed much way. specialized function makes sure fields within pkg_ref appropriately evaluated trying execute expression.","code":""},{"path":"/reference/with.pkg_ref.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Evaluate an expression in the context of a pkg_ref — with.pkg_ref","text":"","code":"# S3 method for pkg_ref with(data, expr, ...)"},{"path":"/reference/with.pkg_ref.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Evaluate an expression in the context of a pkg_ref — with.pkg_ref","text":"data data use constructing environment. default method may environment, list, data frame, integer sys.call. within, can list data frame. expr expression evaluate; particularly within() often “compound” expression, .e., form ... arguments passed (future) methods.","code":"{ a <- somefun() b <- otherfun() ..... rm(unused1, temp) }"},{"path":"/reference/with.pkg_ref.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Evaluate an expression in the context of a pkg_ref — with.pkg_ref","text":"value evaluated expr.","code":""},{"path":"/reference/with_unclassed_to.html","id":null,"dir":"Reference","previous_headings":"","what":"Evaluate an expression after first removing a range of S3 classes — with_unclassed_to","title":"Evaluate an expression after first removing a range of S3 classes — with_unclassed_to","text":"Evaluate expression first removing range S3 classes","code":""},{"path":"/reference/with_unclassed_to.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Evaluate an expression after first removing a range of S3 classes — with_unclassed_to","text":"","code":"with_unclassed_to(x, .class = 1:length(class(x)), expr, envir = parent.frame())"},{"path":"/reference/with_unclassed_to.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Evaluate an expression after first removing a range of S3 classes — with_unclassed_to","text":"x structured S3-classed object .class class unclass object expr expression evaluate, avoiding parent classs dispatch envir environment expression evaluated","code":""},{"path":"/reference/with_unclassed_to.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Evaluate an expression after first removing a range of S3 classes — with_unclassed_to","text":"result expr","code":""},{"path":"/news/index.html","id":"riskmetric-024","dir":"Changelog","previous_headings":"","what":"riskmetric 0.2.4","title":"riskmetric 0.2.4","text":"CRAN release: 2024-01-09 Fix CRAN errors.","code":""},{"path":"/news/index.html","id":"riskmetric-023","dir":"Changelog","previous_headings":"","what":"riskmetric 0.2.3","title":"riskmetric 0.2.3","text":"CRAN release: 2023-08-31 Fix issue CRAN package documentation flags. (#311)","code":""},{"path":"/news/index.html","id":"riskmetric-022","dir":"Changelog","previous_headings":"","what":"riskmetric 0.2.2","title":"riskmetric 0.2.2","text":"CRAN release: 2023-06-29 Fix bug reporting number downloads.","code":""},{"path":"/news/index.html","id":"riskmetric-021","dir":"Changelog","previous_headings":"","what":"riskmetric 0.2.1","title":"riskmetric 0.2.1","text":"CRAN release: 2023-03-10 Updates S3 Method consistancy vec_cast pillar_shift per CRAN comments.","code":""},{"path":"/news/index.html","id":"riskmetric-020","dir":"Changelog","previous_headings":"","what":"riskmetric 0.2.0","title":"riskmetric 0.2.0","text":"CRAN release: 2023-02-22 now Hex Logo! #233. Thanks @AARON-CLARK. Number download assessment can now take specified number days. #258. Thanks @parmsam-pfizer. new assessment added determining size codebase. #66. Thanks @shengwei66. Fixed issue scores returning negative numbers instead values [0,1]. Thanks @emilliman5. new assessment added presens bug report URL package. Thanks @kimjj93. new assessment added score dependency footprint package. Thanks @emilliman5.","code":""},{"path":"/news/index.html","id":"riskmetric-012","dir":"Changelog","previous_headings":"","what":"riskmetric 0.1.2","title":"riskmetric 0.1.2","text":"CRAN release: 2022-01-28 Hotfix release correct testing suite tests less continent assumptions locally installed packages, addressing build issues CRAN builders. (#223, @elimillera)","code":""},{"path":"/news/index.html","id":"riskmetric-011","dir":"Changelog","previous_headings":"","what":"riskmetric 0.1.1","title":"riskmetric 0.1.1","text":"CRAN release: 2021-07-29 Fixing bug subclassing pkg_ref objects using new concrete constructors. (#208, @dgkf)","code":""},{"path":"/news/index.html","id":"riskmetric-010","dir":"Changelog","previous_headings":"","what":"riskmetric 0.1.0","title":"riskmetric 0.1.0","text":"CRAN release: 2021-05-13 Initial version. Added NEWS.md file track changes package.","code":""}]
+[{"path":"/articles/extending-riskmetric.html","id":"package-classes","dir":"Articles","previous_headings":"","what":"Package Classes","title":"Extending riskmetric","text":"can assess package first need represent package data. refer collection package metadata “package reference” - way referring related information ’ve able pull together package. represented pkg_ref class object. dimensions risk assessed, data needed evaluate terms cached within object, building small store information package assessments can refer build . Importantly, references packages equal. can collect information given source code, locally installed package scraping data package web. ’s hierarchy subclasses encapsulate disparate use cases. subclasses direct behavior downstream operations provides flexibility bucket implementations similar data can collected number potential sources. example, determine author package easiest look package’s DESCRIPTION file content maintained. However, without access source installed files, one find information CRAN package webpage. Using subclasses, appropriate method collecting data can selected.","code":"pkg_ref ├─ pkg_source ├─ pkg_install └─ pkg_remote ├─ pkg_cran_remote └─ pkg_bioc_remote"},{"path":"/articles/extending-riskmetric.html","id":"adding-an-assessment","dir":"Articles","previous_headings":"","what":"Adding an Assessment","title":"Extending riskmetric","text":"Assessments atomic unit riskmetric package, used kick individual metric evaluation. assessment generic function starting assess_ prefix, can dispatch based subclass pkg_ref object.","code":""},{"path":"/articles/extending-riskmetric.html","id":"assessment-example","dir":"Articles","previous_headings":"Adding an Assessment","what":"Assessment Example","title":"Extending riskmetric","text":"example, take look assess_has_news implemented. ’ll focus just generic pkg_install functions: couple things note. First, S3 system used dispatch functionality appropriate package reference class. Since way ’d assess inclusion NEWS file might different installed package remotely sourced metadata, may separate functions process datatypes distinct ways. Second, assessment, pkg_metric object returned. stores atomic data pertaining metric importantly adopts unique subclass assessment function. Finally, cosmetic \"column_name\" attribute tagged function. used calling assess function. assess verb convenience function steps available assessments returning tibble assessment outputs. \"column_name\" provides user-friendly label assessment tibble.","code":"#> assess_has_news <- function (x, ...) #> { #> UseMethod(\"assess_has_news\") #> } #> attr(,\"column_name\") #> [1] \"has_news\" #> attr(,\"label\") #> [1] \"number of discovered NEWS files\" #> #> assess_has_news.pkg_install <- NULL"},{"path":"/articles/extending-riskmetric.html","id":"writing-a-new-assessment","dir":"Articles","previous_headings":"Adding an Assessment","what":"Writing a New Assessment","title":"Extending riskmetric","text":"Now ’ll write assessment. Eventually want consider package high risk name start “r”. ’ll need make pkg_metric object containing first letter name.","code":"assess_name_first_letter <- function(x, ...) { UseMethod(\"assess_name_first_letter\") } attr(assess_name_first_letter, \"column_name\") <- \"name_first_letter\" assess_name_first_letter.pkg_ref <- function(x, ...) { pkg_metric(substr(x$name, 0, 1), class = \"pkg_metric_name_first_letter\") }"},{"path":"/articles/extending-riskmetric.html","id":"adding-pkg_ref-metadata","dir":"Articles","previous_headings":"","what":"Adding pkg_ref Metadata","title":"Extending riskmetric","text":"Perhaps want reuse metadata used assessing first letter can reused assessments. particularly taxing metadata, metadata requires query public API, scraping web page large data download, ’s important store assessment functions reuse. handle , define function pkg_ref_cache dispatch .","code":""},{"path":"/articles/extending-riskmetric.html","id":"example-metadata-caching","dir":"Articles","previous_headings":"Adding pkg_ref Metadata","what":"Example Metadata Caching","title":"Extending riskmetric","text":"riskmetric package handles parsing DESCRIPTION file can feed downstream assessments without re-parse file time copy code . defined, ’ll automatically called field first accessed pkg_ref object, stored downstream uses. Notice upon initialization, description field indicates hasn’t yet evaluated trailing ... name. accessed, object call caching function go grab package metadata return newly derived value. pkg_ref object stores environment, caching value makes available future attempts access field. helpful , developers package, don’t need think critically order assessments performed, allows users redefine order assessments without worry metadata acquired.","code":"#> pkg_ref_cache.description <- function (x, name, ...) #> { #> UseMethod(\"pkg_ref_cache.description\") #> } #> #> pkg_ref_cache.description.pkg_install <- function (x, name, ...) #> { #> read.dcf(file.path(x$path, \"DESCRIPTION\")) #> } library(riskmetric) package <- pkg_ref(\"riskmetric\") #> riskmetric v0.2.4.9000 #> $path #> [1] \"/home/user/username/R/4.4/Resources/library/riskmetric\" #> $source #> [1] \"pkg_install\" #> $version #> [1] '0.2.4.9000' #> $name #> [1] \"riskmetric\" #> $bug_reports... #> $bug_reports_host... #> $bug_reports_url... #> $description... #> $downloads... #> $examples... #> $help... #> $help_aliases... #> $license... #> $maintainer... #> $news... #> $r_cmd_check... #> $release_date... #> $remote_checks... #> $source_control_url... #> $vignettes... #> $website_urls... package$description"},{"path":"/articles/extending-riskmetric.html","id":"writing-a-metadata-cache","dir":"Articles","previous_headings":"Adding pkg_ref Metadata","what":"Writing a Metadata Cache","title":"Extending riskmetric","text":"Now, new metric, want cache package name’s first letter. need add new pkg_ref_cache function field. Thankfully, subclass pkg_ref can access first letter way, just need one function. adding caching function, need make small modification assess_name_first_letter.pkg_ref order use newly cached value. Let’s try !","code":"pkg_ref_cache.name_first_letter <- function(x, name, ...) { substr(x$name, 0, 1) } assess_name_first_letter.pkg_ref <- function(x, ...) { pkg_metric(x$name_first_letter, class = \"pkg_metric_name_first_letter\") } package$name #> [1] \"riskmetric\" package$name_first_letter #> [1] \"r\""},{"path":"/articles/extending-riskmetric.html","id":"defining-an-assessment-scoring-function","dir":"Articles","previous_headings":"","what":"Defining an Assessment Scoring Function","title":"Extending riskmetric","text":"Next, need function scoring assessment output. case, output pkg_metric object whose data first letter package name. ’ll add dispatched function score function. convention, functions return numeric value representing well package conforms best practices values 0 (poor practice) 1 (best practice).","code":"metric_score.pkg_metric_name_first_letter <- function(x, ...) { as.numeric(x == \"r\") }"},{"path":"/articles/extending-riskmetric.html","id":"adding-our-assessment-to-the-pkg_assess-verb","dir":"Articles","previous_headings":"","what":"Adding our Assessment to the pkg_assess() Verb","title":"Extending riskmetric","text":"assess function accepts list functions apply. riskmetric provides shorthand, all_assessments(), collect included assessment functions, ’re free add list customize assessment toolkit. scoring function automatically get picked used score method. can define summarizing weights passing named list pkg_score. course can downstream processing resulting tibble ’d like fine-tune summarization using nonlinear function.","code":"library(dplyr) pkg_ref(c(\"riskmetric\", \"utils\", \"tools\")) %>% as_tibble() %>% pkg_assess(c(all_assessments(), assess_name_first_letter)) #> # A tibble: 3 × 23 #> package version pkg_ref covr_coverage has_news remote_checks #> #> 1 riskmetric 0.2.4.9000 riskmetric NA 1 NA #> 2 utils 4.4.0 utils NA 0 NA #> 3 tools 4.4.0 tools NA 0 NA #> # ℹ 17 more variables: news_current , r_cmd_check , #> # exported_namespace , has_vignettes , #> # export_help , has_website , has_maintainer , #> # bugs_status , size_codebase , #> # has_source_control , has_bug_reports_url , #> # downloads_1yr , reverse_dependencies , #> # has_examples , dependencies , license , … pkg_ref(c(\"riskmetric\", \"utils\", \"tools\")) %>% as_tibble() %>% pkg_assess(c(all_assessments(), assess_name_first_letter)) %>% pkg_score() #> # A tibble: 3 × 24 #> package version pkg_ref pkg_score covr_coverage has_news #> #> 1 riskmetric 0.2.4.9000 riskmetric 0.547 NA 1 #> 2 utils 4.4.0 utils 0.703 NA 0 #> 3 tools 4.4.0 tools 0.748 NA 0 #> # ℹ 18 more variables: remote_checks , news_current , #> # r_cmd_check , exported_namespace , #> # has_vignettes , export_help , has_website , #> # has_maintainer , bugs_status , #> # size_codebase , has_source_control , #> # has_bug_reports_url , downloads_1yr , #> # reverse_dependencies , has_examples , … pkg_ref(c(\"riskmetric\", \"utils\", \"tools\")) %>% as_tibble() %>% pkg_assess(c(all_assessments(), assess_name_first_letter)) %>% pkg_score(weights = c(has_news = 1, name_first_letter = 1)) #> # A tibble: 3 × 24 #> package version pkg_ref pkg_score covr_coverage has_news #> #> 1 riskmetric 0.2.4.9000 riskmetric 0 NA 1 #> 2 utils 4.4.0 utils 1 NA 0 #> 3 tools 4.4.0 tools 1 NA 0 #> # ℹ 18 more variables: remote_checks , news_current , #> # r_cmd_check , exported_namespace , #> # has_vignettes , export_help , has_website , #> # has_maintainer , bugs_status , #> # size_codebase , has_source_control , #> # has_bug_reports_url , downloads_1yr , #> # reverse_dependencies , has_examples , …"},{"path":"/articles/extending-riskmetric.html","id":"how-you-can-help","dir":"Articles","previous_headings":"","what":"How you can help…","title":"Extending riskmetric","text":"riskmetric package designed easily extensible. can develop dispatched functions development environment, hone well formed assessments contribute back core riskmetric package ’re done. ’d like feedback embarking developing new metric, please feel free file issue riskmetric GitHub.","code":""},{"path":"/articles/riskmetric.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Get Started","text":"riskmetric provides workflow evaluate quality set R packages involves five major steps. workflow can help users choose high quality R packages, improve package reliability prove validity R packages regulated industry. concept, steps include:","code":""},{"path":"/articles/riskmetric.html","id":"finding-a-source-for-package-information","dir":"Articles","previous_headings":"Introduction","what":"1. Finding a source for package information","title":"Get Started","text":"First need identify source package metadata. number places one may want look information, source code directory, local package library remote package repository. find source package data, begin collect package reference (pkg_ref) object. Learn : ?pkg_ref","code":""},{"path":"/articles/riskmetric.html","id":"caching-package-metadata","dir":"Articles","previous_headings":"Introduction","what":"2. Caching package metadata","title":"Get Started","text":"information needed perform given risk assessment, use metadata already continue search fine-grained information package. example, location locally installed package, can use path search package’s DESCRIPTION file, read DESCRIPTION contents. avoid repeatedly processing metadata, intermediate results cached within pkg_ref object can used derivation mulitple risk metrics. Learn : ?pkg_ref_cache","code":""},{"path":"/articles/riskmetric.html","id":"assess-this-metadata-against-a-risk-criterion","dir":"Articles","previous_headings":"Introduction","what":"3. Assess this metadata against a risk criterion","title":"Get Started","text":"measure risk, first try boil measure fundamental nugget package metadata comparable across packages sources information. cross-comparable result assessing package way refer package metric (pkg_metric). example, DESCRIPTION file content, might look whether maintainer identified authors list. ensure can easily compare information packages use Authors field Authors@R field, boil information just single logical value indicating whether maintainer identified. Learn : ?pkg_assess","code":""},{"path":"/articles/riskmetric.html","id":"score-our-metrics","dir":"Articles","previous_headings":"Introduction","what":"4. Score our metrics","title":"Get Started","text":"atomic representations metrics, want score can meaningfully compared one another. practice just embeds means converting datatype metric numeric value fixed scale 0 (worst) 1 (best). Given maintainer metric example, might rate package 1 (great) maintainer identified 0 (poor) maintainer found. Learn : ?pkg_score","code":""},{"path":"/articles/riskmetric.html","id":"summarizing-across-metric-scores","dir":"Articles","previous_headings":"Introduction","what":"5. Summarizing across metric scores","title":"Get Started","text":"Finally, may want look scores individual metrics sort aggregate risk score. Naturally, metric scores may warrant weight. scores normalized fixed range allows us define summarizing algorithm consistently assess compare packages. Notably, risk inverse scale metric scores. High metric scores favorable, whereas high risk scores unfavorable. Learn : ?summarize_scores","code":""},{"path":"/articles/riskmetric.html","id":"the-riskmetric-workflow","dir":"Articles","previous_headings":"","what":"The riskmetric Workflow","title":"Get Started","text":"five steps broken just handful primary functions.","code":""},{"path":"/articles/riskmetric.html","id":"creating-a-package-reference-object","dir":"Articles","previous_headings":"The riskmetric Workflow","what":"Creating a package reference object","title":"Get Started","text":"First, create package reference class object using pkg_ref constructor function. object contain metadata ’s collected various risk assessments. see riskmetric pkg_ref object actually subclassed pkg_install. hierarchy pkg_ref object classes including pkg_source source code directories, pkg_install locally installed packages pkg_remote references package information pulled internet including pkg_cran_remote pkg_bioc_remote CRAN Bioconductor hosted packages respectively. Throughout riskmetric, S3 classes used extensively make use generic functions divergent, reference mechanism dependent behaviors caching metadata, assessing packages scoring metrics. Likewise, fields trailing ... indicating haven’t yet computed, reference type knowledge go grab information field requested. Behind scenes, done using pkg_ref_cache function, S3 generic, using name field pkg_ref class dispatch appropriate functions retrieving metadata.","code":"library(riskmetric) riskmetric_pkg_ref <- pkg_ref(\"riskmetric\") print(riskmetric_pkg_ref) #> riskmetric v0.2.4.9000 #> $path #> [1] \"/home/user/username/R/4.4/Resources/library/riskmetric\" #> $source #> [1] \"pkg_install\" #> $version #> [1] '0.2.4.9000' #> $name #> [1] \"riskmetric\" #> $bug_reports... #> $bug_reports_host... #> $bug_reports_url... #> $description... #> $downloads... #> $examples... #> $help... #> $help_aliases... #> $license... #> $maintainer... #> $news... #> $r_cmd_check... #> $release_date... #> $remote_checks... #> $source_control_url... #> $vignettes... #> $website_urls..."},{"path":"/articles/riskmetric.html","id":"assessing-a-package","dir":"Articles","previous_headings":"The riskmetric Workflow","what":"Assessing a package","title":"Get Started","text":"number prespecified assessments, prefixed convention assess_*. Every assessment function takes single argument, pkg_ref object produces pkg_metric object corresponding assess_* function applied. Every function assess_* family functions expected return basic measure package. case, return named logical vector indicating whether export function associated help document. return type also leaves trail assessment produced metric. addition pkg_metric class, now pkg_metric_export_help subclass used dispatching appropriate scoring method. ’s worth pointing act calling function side-effect mutating riskmetric_pkg_ref object. riskmetric_pkg_ref$help_aliases known value needed asses whether package documentation exports. note caching happens pkg_ref objects really just environments syntactic sugar, environments R always modified -reference. globally mutable behavior used operations performed one assessment can reused others. Likewise, computing one field may require previous field computed first, triggering chain metadata retrieval. case, $help_aliases required $path available. chaining behavior comes free implementing pkg_ref_cache caching function field. contributors, alleviates need remember order operations, users behavior means subsets assessments can run arbitrary order without pulling superfluous metadata, keeping track every-growing objects ensuring certain assessments get called others. addition metric-specific assess_* family functions, comprehensive pkg_assess function provided. Notably, pkg_assess accepts pkg_ref object list assessments apply, defaulting all_assessments(), returns list assess_* functions riskmetric namespace. Since lot take , pkg_assess also operates tibbles, returning cleaner output might easier sort assessing package.","code":"riskmetric_export_help_metric <- assess_export_help(riskmetric_pkg_ref) print(riskmetric_export_help_metric[1:5]) #> assess_covr_coverage assessment_error_as_warning #> TRUE TRUE #> as_pkg_metric assess_has_news #> TRUE TRUE #> score_error_zero #> TRUE riskmetric_pkg_ref #> riskmetric v0.2.4.9000 #> $help_aliases #> riskmetric-package %||% #> \"riskmetric\" \"if_not_null_else\" #> .tools allow_mutation #> \"dot-tools\" \"allow_mutation\" #> all_assessments assessment_error_as_warning #> \"all_assessments\" \"assessment_error_as_warning\" #> #> $path #> [1] \"/home/user/username/R/4.4/Resources/library/riskmetric\" #> $source #> [1] \"pkg_install\" #> $version #> [1] '0.2.4.9000' #> $name #> [1] \"riskmetric\" #> $bug_reports... #> $bug_reports_host... #> $bug_reports_url... #> $description... #> $downloads... #> $examples... #> $help... #> $license... #> $maintainer... #> $news... #> $r_cmd_check... #> $release_date... #> $remote_checks... #> $source_control_url... #> $vignettes... #> $website_urls... pkg_assess(riskmetric_pkg_ref) #> #> $covr_coverage #> [1] NA #> attr(,\"class\") #> [1] \"pkg_metric_na\" \"pkg_metric_condition\" #> [3] \"pkg_metric_covr_coverage\" \"pkg_metric\" #> [5] \"logical\" #> attr(,\"label\") #> [1] \"Package unit test coverage\" #> #> $has_news #> [1] 1 #> attr(,\"class\") #> [1] \"pkg_metric_has_news\" \"pkg_metric\" \"integer\" #> attr(,\"label\") #> [1] \"number of discovered NEWS files\" #> #> $remote_checks #> [1] NA #> attr(,\"class\") #> [1] \"pkg_metric_na\" \"pkg_metric_condition\" #> [3] \"pkg_metric_remote_checks\" \"pkg_metric\" #> [5] \"logical\" #> attr(,\"label\") #> [1] \"Number of OS flavors that passed/warned/errored on R CMD check\" #> #> $news_current #> [1] FALSE #> attr(,\"class\") #> [1] \"pkg_metric_news_current\" \"pkg_metric\" #> [3] \"logical\" #> attr(,\"label\") #> [1] \"NEWS file contains entry for current version number\" #> #> $r_cmd_check #> [1] NA #> attr(,\"class\") #> [1] \"pkg_metric_na\" \"pkg_metric_condition\" \"pkg_metric_r_cmd_check\" #> [4] \"pkg_metric\" \"logical\" #> attr(,\"label\") #> [1] \"Package check results\" #> #> $exported_namespace #> [1] \"assess_covr_coverage\" \"assessment_error_as_warning\" #> [3] \"as_pkg_metric\" \"assess_has_news\" #> [5] \"score_error_zero\" \"assess_remote_checks\" #> [7] \"pkg_metric\" \"assess_news_current\" #> [9] \"assess_r_cmd_check\" \"pkg_score\" #> [11] \"pkg_assess\" \"as_pkg_ref\" #> [13] \"score_error_NA\" \"metric_score\" #> [15] \"assess_exported_namespace\" \"assess_has_vignettes\" #> [17] \"assess_export_help\" \"assess_has_website\" #> [19] \"score_error_default\" \"assessment_error_throw\" #> [21] \"assess_has_maintainer\" \"assess_last_30_bugs_status\" #> [23] \"assess_size_codebase\" \"all_assessments\" #> [25] \"assess_has_source_control\" \"assess_has_bug_reports_url\" #> [27] \"assess_downloads_1yr\" \"assess_reverse_dependencies\" #> [29] \"get_assessments\" \"assess_has_examples\" #> [31] \"summarize_scores\" \"pkg_ref\" #> [33] \"assessment_error_empty\" \"assess_dependencies\" #> [35] \"assess_license\" #> #> $has_vignettes #> [1] 0 #> #> $export_help #> assess_covr_coverage assessment_error_as_warning #> TRUE TRUE #> as_pkg_metric assess_has_news #> TRUE TRUE #> score_error_zero assess_remote_checks #> TRUE TRUE #> pkg_metric assess_news_current #> TRUE TRUE #> assess_r_cmd_check pkg_score #> TRUE TRUE #> pkg_assess as_pkg_ref #> TRUE TRUE #> score_error_NA metric_score #> TRUE TRUE #> assess_exported_namespace assess_has_vignettes #> TRUE TRUE #> assess_export_help assess_has_website #> TRUE TRUE #> score_error_default assessment_error_throw #> TRUE TRUE #> assess_has_maintainer assess_last_30_bugs_status #> TRUE TRUE #> assess_size_codebase all_assessments #> TRUE TRUE #> assess_has_source_control assess_has_bug_reports_url #> TRUE TRUE #> assess_downloads_1yr assess_reverse_dependencies #> TRUE TRUE #> get_assessments assess_has_examples #> TRUE TRUE #> summarize_scores pkg_ref #> TRUE TRUE #> assessment_error_empty assess_dependencies #> TRUE TRUE #> assess_license #> TRUE #> #> $has_website #> [1] \"https://pharmar.github.io/riskmetric/\" #> [2] \"https://github.com/pharmaR/riskmetric\" #> #> $has_maintainer #> [1] \"Eli Miller \" #> #> $bugs_status #> [1] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE #> [13] FALSE TRUE TRUE FALSE TRUE TRUE TRUE FALSE FALSE FALSE TRUE FALSE #> [25] FALSE TRUE FALSE FALSE FALSE TRUE #> #> $size_codebase #> #> #> $has_source_control #> [1] \"https://github.com/pharmaR/riskmetric\" #> #> $has_bug_reports_url #> [1] 1 #> attr(,\"class\") #> [1] \"pkg_metric_has_bug_reports_url\" \"pkg_metric\" #> [3] \"integer\" #> attr(,\"label\") #> [1] \"presence of a bug reports url in repository\" #> #> $downloads_1yr #> [1] 4172 #> #> $reverse_dependencies #> character(0) #> #> $has_examples #> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE #> [16] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE #> [31] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE #> [46] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE #> [61] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE #> [76] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE #> [91] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE #> [106] TRUE TRUE #> #> $dependencies #> package type #> 1 backports Imports #> 2 utils Imports #> 3 tools Imports #> 4 xml2 Imports #> 5 httr Imports #> 6 curl Imports #> 7 urltools Imports #> 8 memoise Imports #> 9 BiocManager Imports #> 10 cranlogs Imports #> 11 covr Imports #> 12 vctrs Imports #> 13 pillar Imports #> 14 tibble Imports #> 15 pkgload Imports #> 16 devtools Imports #> #> $license #> [1] \"MIT + file LICENSE\" pkg_assess(as_tibble(riskmetric_pkg_ref)) #> # A tibble: 1 × 22 #> package version pkg_ref covr_coverage has_news remote_checks #> #> 1 riskmetric 0.2.4.9000 riskmetric NA 1 NA #> # ℹ 16 more variables: news_current , r_cmd_check , #> # exported_namespace , has_vignettes , #> # export_help , has_website , has_maintainer , #> # bugs_status , size_codebase , #> # has_source_control , has_bug_reports_url , #> # downloads_1yr , reverse_dependencies