Comparing branches

git package

tempDir <- tempdir()
pathToRepo <- file.path(tempDir, "CDMConnector")

git2r::clone(
  url = "https://github.com/darwin-eu/CDMConnector.git",
  local_path = pathToRepo
)

## cloning into 'C:\Users\MVANKE~1\AppData\Local\Temp\RtmpE9RQLo/CDMConnector'...
## Receiving objects:   1% (86/8529),  124 kb
## Receiving objects:  11% (939/8529), 1436 kb
## Receiving objects:  21% (1792/8529), 4350 kb
## Receiving objects:  31% (2644/8529), 6896 kb
## Receiving objects:  41% (3497/8529), 7064 kb
## Receiving objects:  51% (4350/8529), 8713 kb
## Receiving objects:  61% (5203/8529), 10370 kb
## Receiving objects:  71% (6056/8529), 13115 kb
## Receiving objects:  81% (6909/8529), 16268 kb
## Receiving objects:  91% (7762/8529), 16381 kb
## Receiving objects: 100% (8529/8529), 29661 kb, done.

## Local:    main C:/Users/mvankessel/AppData/Local/Temp/RtmpE9RQLo/CDMConnector
## Remote:   main @ origin (https://github.com/darwin-eu/CDMConnector.git)
## Head:     [af064fc] 2024-11-13: V1.6 cran release (#514)

Objects

Repository

repo <- PaRe::Repository$new(pathToRepo)

Git management

repo$gitCheckout("main")
repo$gitPull()

dev <- repo$clone()
dev$gitCheckout("75e7333cb2d9f8ec7f7a77ae21fb611f8141ef0e")

## Switched to: 75e7333cb2d9f8ec7f7a77ae21fb611f8141ef0e

## Re-initializing

Repository properties

repo$getPath()

## [1] "C:\\Users\\mvankessel\\AppData\\Local\\Temp\\RtmpE9RQLo\\CDMConnector"

repo$getName()

## [1] "CDMConnector"

repo$getDescription()

## Package: CDMConnector
## Title: Connect to an OMOP Common Data Model
## Version: 1.6.0
## Authors@R (parsed):
##     * Adam Black <black@ohdsi.org> [aut, cre] (<https://orcid.org/0000-0001-5576-8701>)
##     * Artem Gorbachev <artem.gorbachev@odysseusinc.com> [aut]
##     * Edward Burn <edward.burn@ndorms.ox.ac.uk> [aut]
##     * Marti Catala Sabate <marti.catalasabate@ndorms.ox.ac.uk> [aut]
## Description: Provides tools for working with observational health
##     data in the Observational Medical Outcomes Partnership (OMOP) Common
##     Data Model format with a pipe friendly syntax.  Common data model
##     database table references are stored in a single compound object along
##     with metadata.
## License: Apache License (>= 2)
## URL: https://darwin-eu.github.io/CDMConnector/,
##     https://github.com/darwin-eu/CDMConnector
## BugReports: https://github.com/darwin-eu/CDMConnector/issues
## Depends:
##     R (>= 4.0)
## Imports:
##     checkmate,
##     cli,
##     DBI (>= 0.3.0),
##     dbplyr (>= 2.5.0),
##     dplyr,
##     fs,
##     generics,
##     glue,
##     jsonlite,
##     lifecycle,
##     methods,
##     omopgenerics (>= 0.1.2),
##     purrr,
##     readr,
##     rlang,
##     stringi,
##     stringr,
##     tidyr,
##     tidyselect,
##     waldo,
##     withr
## Suggests:
##     bigrquery,
##     CirceR,
##     clock,
##     covr,
##     DatabaseConnector,
##     duckdb,
##     ggplot2,
##     knitr,
##     lubridate,
##     odbc,
##     palmerpenguins,
##     pool,
##     rJava,
##     rmarkdown,
##     RPostgres,
##     RSQLite,
##     snakecase,
##     SqlRender,
##     testthat (>= 3.0.0),
##     tibble,
##     tictoc
## Enhances:
##     arrow
## VignetteBuilder:
##     knitr
## Config/testthat/edition: 3
## Config/testthat/parallel: false
## Encoding: UTF-8
## Roxygen: list(markdown = TRUE)
## RoxygenNote: 7.3.2
## Collate:
##     'CDMConnector-package.R'
##     'Eunomia.R'
##     'benchmarkCDMConnector.R'
##     'cdm.R'
##     'cdmSubset.R'
##     'cdm_from_environment.R'
##     'cohortTransformations.R'
##     'cohort_ddl.R'
##     'compute.R'
##     'copy_cdm_to.R'
##     'dateadd.R'
##     'dbSource.R'
##     'reexports-omopgenerics.R'
##     'generateCohortSet.R'
##     'generateConceptCohortSet.R'
##     'summariseQuantile.R'
##     'utils.R'
##     'validate.R'
##     'zzz-deprecated.R'

File

files <- repo$getFiles()
files

## $R
## $R[[1]]
## <File> <Code> <R6>
## Name: benchmarkCDMConnector.R
## # Lines: 138
## $R[[2]]
## <File> <Code> <R6>
## Name: cdm.R
## # Lines: 971
## $R[[3]]
## <File> <Code> <R6>
## Name: cdm_from_environment.R
## # Lines: 196
## $R[[4]]
## <File> <Code> <R6>
## Name: CDMConnector-package.R
## # Lines: 14
## $R[[5]]
## <File> <Code> <R6>
## Name: cdmSubset.R
## # Lines: 520
## $R[[6]]
## <File> <Code> <R6>
## Name: cohort_ddl.R
## # Lines: 126
## $R[[7]]
## <File> <Code> <R6>
## Name: cohortTransformations.R
## # Lines: 380
## $R[[8]]
## <File> <Code> <R6>
## Name: compute.R
## # Lines: 360
## $R[[9]]
## <File> <Code> <R6>
## Name: copy_cdm_to.R
## # Lines: 103
## $R[[10]]
## <File> <Code> <R6>
## Name: dateadd.R
## # Lines: 260
## $R[[11]]
## <File> <Code> <R6>
## Name: dbSource.R
## # Lines: 281
## $R[[12]]
## <File> <Code> <R6>
## Name: Eunomia.R
## # Lines: 406
## $R[[13]]
## <File> <Code> <R6>
## Name: generateCohortSet.R
## # Lines: 983
## $R[[14]]
## <File> <Code> <R6>
## Name: generateConceptCohortSet.R
## # Lines: 452
## $R[[15]]
## <File> <Code> <R6>
## Name: reexports-omopgenerics.R
## # Lines: 95
## $R[[16]]
## <File> <Code> <R6>
## Name: summariseQuantile.R
## # Lines: 146
## $R[[17]]
## <File> <Code> <R6>
## Name: utils.R
## # Lines: 280
## $R[[18]]
## <File> <Code> <R6>
## Name: validate.R
## # Lines: 246
## $R[[19]]
## <File> <Code> <R6>
## Name: zzz-deprecated.R
## # Lines: 121
## 
## $cpp
## list()
## 
## $o
## list()
## 
## $h
## list()
## 
## $java
## list()
## 
## $sql
## list()

file <- files$R[[1]]
file

## <File> <Code> <R6>
## Name: benchmarkCDMConnector.R
## # Lines: 138

File properties

file$getName()

## [1] "benchmarkCDMConnector.R"

file$getNLines()

## [1] 138

file$getType()

## [1] "R"

head(file$getLines())

## [1] "# Copyright 2024 DARWIN EU®"                                        
## [2] "#"                                                                  
## [3] "# This file is part of CDMConnector"                                
## [4] "#"                                                                  
## [5] "# Licensed under the Apache License, Version 2.0 (the \"License\");"
## [6] "# you may not use this file except in compliance with the License."

tail(file$getLines())

## [1] "                    dplyr::count() %>%"
## [2] "                    dplyr::pull())"    
## [3] ""                                      
## [4] ""                                      
## [5] "  return(timings)"                     
## [6] "}"

file$getFunctionTable()

##                    name lineStart lineEnd nArgs cycloComp
## 1 benchmarkCDMConnector        33     138     1         1

Function

functions <- file$getFunctions()
functions

## [[1]]
## <Function> <Code> <R6>
## Name: benchmarkCDMConnector
## # Lines: 106

funs <- unlist(lapply(files$R, function(file) {
  file$getFunctions()
}))

fun <- funs[[1]]
fun

## <Function> <Code> <R6>
## Name: benchmarkCDMConnector
## # Lines: 106

Function properties

fun$getName()

## [1] "benchmarkCDMConnector"

fun$getNLines()

## [1] 106

fun$getFunction()

##                    name lineStart lineEnd nArgs cycloComp
## 1 benchmarkCDMConnector        33     138     1         1

head(fun$getLines())

## [1] "benchmarkCDMConnector <- function(cdm) {"        
## [2] ""                                                
## [3] "  checkmate::assertClass(cdm, \"cdm_reference\")"
## [4] ""                                                
## [5] "  # will add timings to list"                    
## [6] "  timings <- list()"

tail(fun$getLines())

## [1] "                    dplyr::count() %>%"
## [2] "                    dplyr::pull())"    
## [3] ""                                      
## [4] ""                                      
## [5] "  return(timings)"                     
## [6] "}"

ComPaRing main to develop

dplyr::bind_rows(
  PaRe::countPackageLines(repo) %>% mutate(branch = "main"),
  PaRe::countPackageLines(dev) %>% mutate(branch = "V0.1.0")
)

## # A tibble: 2 × 7
##       R   cpp     o     h  java   sql branch
##   <int> <int> <int> <int> <int> <int> <chr> 
## 1  6078     0     0     0     0     0 main  
## 2  2628     0     0     0     0     0 V0.1.0

PaRe::pkgDiagram(repo)

PaRe::pkgDiagram(dev)

mainFunUse <- PaRe::getFunctionUse(repo) %>%
  mutate(branch = "main")

devFunUse <- PaRe::getFunctionUse(dev) %>%
  mutate(branch = "V0.1.0")

pkgUse <- dplyr::bind_rows(
  mainFunUse,
  devFunUse
) %>%
  group_by(pkg, branch) %>%
  tally()

library(ggplot2)

ggplot(data = pkgUse, mapping = aes(x = pkg, y = n, fill = branch)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme_bw() +
  theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1))

mainFuns <- PaRe::getDefinedFunctions(repo)
devFuns <- PaRe::getDefinedFunctions(dev)

defFuns <- bind_rows(
  mainFuns %>% mutate(branch = "main"),
  devFuns %>% mutate(branch = "V0.1.0")
)

ggplot(data = defFuns, mapping = aes(y = cycloComp, x = name, fill = branch)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme_bw() +
  theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1)) +
  labs(title = "Cyclomatic Complexity per Function", x = "Function", y = "Cyclomatic Complexity")

ggplot(data = defFuns, mapping = aes(y = lineEnd - lineStart + 1, x = name, fill = branch)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme_bw() +
  theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1)) +
  labs(title = "Number of Lines per Function", y = "Number of Lines", x = "Function")

effectiveCode <- defFuns %>%
  group_by(fileName, branch) %>%
  summarise(n = sum(lineEnd - lineStart + 1)) %>%
  ungroup()

## `summarise()` has grouped output by 'fileName'. You can override using the
## `.groups` argument.

ggplot(data = effectiveCode, mapping = aes(y = n, x = fileName, fill = branch)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme_bw() +
  theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1)) +
  labs(title = "Functional code increase", y = "Number of Lines", x = "File")

mainGraph <- PaRe::getGraphData(repo)

## ✔ Updated metadata database: 5.54 MB in 15 files.
## ℹ Updating metadata database✔ Updating metadata database ... done

## Warning in getParDeps(pkgs = deps, nThreads = nThreads): Could not fetch
## dependencies for package: `methods`

devGraph <- PaRe::getGraphData(dev)

## Warning in getParDeps(pkgs = deps, nThreads = nThreads): Could not fetch
## dependencies for package: `methods`

library(igraph)

## 
## Attaching package: 'igraph'
## 
## The following objects are masked from 'package:dplyr':
## 
##     as_data_frame, groups, union
## 
## The following objects are masked from 'package:stats':
## 
##     decompose, spectrum
## 
## The following object is masked from 'package:base':
## 
##     union

data.frame(
  branch = c("main", "V0.1.0"),
  countVertices = c(length(igraph::V(mainGraph)), length(igraph::V(devGraph))),
  countEdges = c(length(igraph::E(mainGraph)), length(igraph::E(devGraph))),
  meanDegree = c(round(mean(igraph::degree(mainGraph)), 2), round(mean(igraph::degree(devGraph)), 2)),
  meanDistance = c(round(mean(igraph::distances(mainGraph)), 2), round(mean(igraph::distances(devGraph)), 2))
)

##   branch countVertices countEdges meanDegree meanDistance
## 1   main            45        526      23.38         2.15
## 2 V0.1.0            43        348      16.19         2.15

messages <- PaRe::lintRepo(repo)
messages2 <- PaRe::lintRepo(dev)
head(messages)

##                  filename line_number column_number  type
## 1 benchmarkCDMConnector.R         110            81 style
## 2                   cdm.R          21            81 style
## 3                   cdm.R          23            81 style
## 4                   cdm.R          25            81 style
## 5                   cdm.R          27            81 style
## 6                   cdm.R          30            81 style
##                                                                    message
## 1 Lines should not be more than 80 characters. This line is 82 characters.
## 2 Lines should not be more than 80 characters. This line is 89 characters.
## 3 Lines should not be more than 80 characters. This line is 91 characters.
## 4 Lines should not be more than 80 characters. This line is 92 characters.
## 5 Lines should not be more than 80 characters. This line is 85 characters.
## 6 Lines should not be more than 80 characters. This line is 85 characters.
##                                                                                           line
## 1             task <- "summary of observation period start and end dates by gender concept id"
## 2    #' @param cdm_schema,cdmSchema The schema where the OMOP CDM tables are located. Defaults
## 3  #' @param write_schema,writeSchema An optional schema in the CDM database that the user has
## 4 #' @param cohort_tables,cohortTables A character vector listing the cohort table names to be
## 5        #' @param cdm_version,cdmVersion The version of the OMOP CDM: "5.3" (default), "5.4",
## 6        #' @param cdm_name,cdmName The name of the CDM. If NULL (default) the cdm_source_name
##               linter
## 1 line_length_linter
## 2 line_length_linter
## 3 line_length_linter
## 4 line_length_linter
## 5 line_length_linter
## 6 line_length_linter

bind_rows(
  PaRe::lintScore(repo, messages) %>% mutate(branch = "main"),
  PaRe::lintScore(dev, messages) %>% mutate(branch = "v0.1.0")
)

## # A tibble: 4 × 3
##   type      pct branch
##   <chr>   <dbl> <chr> 
## 1 style   14.9  main  
## 2 warning  3.37 main  
## 3 style   34.4  v0.1.0
## 4 warning  7.8  v0.1.0

Maarten van Kessel

2024-11-28

git package

Objects

Repository

Git management

Repository properties

File

File properties

Function

Function properties

ComPaRing main to develop