Merge branch 'version-comparison' into 'master'

Version comparison

See merge request aspree/aspree-r-package!33

DESCRIPTION

@@ -22,5 +22,6 @@ Imports:
     reshape2,
     tidyr,
     e1071,
-    ggplot2
+    ggplot2,
+    compareDF (>= 1.8.0)
 RoxygenNote: 6.1.1

NAMESPACE

 # Generated by roxygen2: do not edit by hand
 
 export(ASPREEDb)
+export(CalculateQueryRanges)
+export(CalculateXTQueryRanges)
+export(CombinedPathologyAU)
+export(CombinedPathologyUS)
+export(CombinedPhysicalMeasures)
 export(CommentaryCodeSummary)
 export(CommentaryCodesAsFactor)
 export(CreateKeyPair)
+export(DatasetComparison)
 export(DecryptData)
 export(DeriveSharedSecret)
 export(EncryptData)
@@ -36,5 +42,6 @@ export(extract_DeathDate)
 export(extract_XT_End)
 export(get_endpoints)
 import(dplyr)
+import(ggplot2)
 import(haven)
 import(lubridate)

R/data_quality.R

@@ -228,3 +228,49 @@ CalculateXTQueryRanges <- function(con, cutoff_sd = 3) {
                           )))$cutoffs
   )
 }
+
+#' Dataset comparison report
+#'
+#' Generates a difference report comparing two versions of a dataset
+#'
+#' @param dataset_version1 the version number of the older dataset
+#' @param dataset_version2 the version number of the newer dataset
+#' @param section_name the name of the section to compare
+#' @param html_output_location if provided, the html output will be saved here
+#' @param id_column the name of the column containing SubjectIDs
+#' @param max_html_table_length the maximum number of rows in the HTML version of the diff
+#' @return summary of changes between versions
+#' @examples
+#' diff <- DatasetComparison(1, 2, "SectionA1")
+#' @export
+DatasetComparison <- function(dataset_version1, dataset_version2, section_name, html_output_location = NA, id_column = "SubjectID", max_html_table_length = 1000) {
+  # Load dataset if version is a name, keep original value if it's a data frame
+  if (inherits(dataset_version1, "data.frame") | inherits(dataset_version1, "tbl")) {
+    dataset1 <- dataset_version1
+  } else {
+    dataset1 <- read.csv(SDrivePaths(ver = dataset_version1)[[section_name]])
+  }
+  if (inherits(dataset_version2, "data.frame") | inherits(dataset_version2, "tbl")) {
+    dataset2 <- dataset_version2
+  } else {
+    dataset2 <- read.csv(SDrivePaths(ver = dataset_version2)[[section_name]])
+  }
+
+  # Identify common, deleted and added columns
+  cols <- intersect(colnames(dataset1), colnames(dataset2))
+  cols_added <- setdiff(colnames(dataset2), colnames(dataset1))
+  cols_deleted <- setdiff(colnames(dataset1), colnames(dataset2))
+
+  # Calculate diff, add in column addition and deletion information
+  diff <- compareDF::compare_df(dataset2[,cols], dataset1[,cols], group_col = id_column, keep_unchanged_cols = FALSE, limit_html = max_html_table_length)
+  diff$cols_added <- cols_added
+  diff$cols_deleted <- cols_deleted
+
+  if (!is.na(html_output_location)) {
+    html_output_file <- file(html_output_location)
+    writeLines(diff$html_output, html_output_file)
+    close(html_output_file)
+  }
+
+  return(diff)
+}

man/CalculateQueryRanges.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data_quality.R
+\name{CalculateQueryRanges}
+\alias{CalculateQueryRanges}
+\title{Calculate data query ranges}
+\usage{
+CalculateQueryRanges(con, av_start, av_end, cutoff_sd = 3,
+  make_plots = TRUE, tables_and_fields = list())
+}
+\arguments{
+\item{con}{a database connection using the DBI package or \code{ASPREEDb()}}
+
+\item{av_start}{the first timepoint from which to calculate the longitudinal change or a function that filters the data appropriately.
+If the function returns multiple records per participant, the maximum AV per participant is used.}
+
+\item{cutoff_sd}{the z-score either side of the mean outside of which queries should be raised}
+
+\item{tables_and_fields}{a list of tables and columns to retrieve. Omitting the columns will retrieve all columns.
+A data frame or table of data may also be provided}
+
+\item{av_stop}{the last timepoint from which to calculate the longitudinal change or a function that filters the data appropriately.
+If the function returns multiple records per participant, the maximum AV per participant is used.}
+}
+\description{
+Calculates the data query ranges based on a z-score cutoff along with some diagnostics
+}

man/CalculateXTQueryRanges.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data_quality.R
+\name{CalculateXTQueryRanges}
+\alias{CalculateXTQueryRanges}
+\title{Calculate XT data query ranges}
+\usage{
+CalculateXTQueryRanges(con, cutoff_sd = 3)
+}
+\arguments{
+\item{con}{a database connection using the DBI package or \code{ASPREEDb()}}
+}
+\description{
+Calculates the XT data query ranges based on a z-score cutoff along with some diagnostics
+}

man/CombinedPathologyAU.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data_access.R
+\name{CombinedPathologyAU}
+\alias{CombinedPathologyAU}
+\title{Get a combined view of the pre-XT and XT pathology tables for Australian participants}
+\usage{
+CombinedPathologyAU(con, measures = NULL)
+}
+\arguments{
+\item{con}{a database connection using the DBI package or \code{ASPREEDb()}}
+}
+\value{
+the combined data
+}
+\description{
+Queries the database for the union of tblPathologyAU and xt_PathologyAU
+}

man/CombinedPathologyUS.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data_access.R
+\name{CombinedPathologyUS}
+\alias{CombinedPathologyUS}
+\title{Get a combined view of the pre-XT and XT pathology tables for USA participants}
+\usage{
+CombinedPathologyUS(con, measures = NULL)
+}
+\arguments{
+\item{con}{a database connection using the DBI package or \code{ASPREEDb()}}
+}
+\value{
+the combined data
+}
+\description{
+Queries the database for the union of tblPathologyUS and xt_PathologyUS
+}

man/CombinedPhysicalMeasures.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data_access.R
+\name{CombinedPhysicalMeasures}
+\alias{CombinedPhysicalMeasures}
+\title{Get a combined view of the pre-XT and XT physicsl measures}
+\usage{
+CombinedPhysicalMeasures(con, measures = NULL)
+}
+\arguments{
+\item{con}{a database connection using the DBI package or \code{ASPREEDb()}}
+}
+\value{
+the combined data
+}
+\description{
+Queries the database for the union of tblAnnualVisits and xt_PhysExam for physical measures
+}

man/DatasetComparison.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data_quality.R
+\name{DatasetComparison}
+\alias{DatasetComparison}
+\title{Dataset comparison report}
+\usage{
+DatasetComparison(dataset_version1, dataset_version2, section_name,
+  html_output_location = NA, id_column = "SubjectID",
+  max_html_table_length = 1000)
+}
+\arguments{
+\item{dataset_version1}{the version number of the older dataset}
+
+\item{dataset_version2}{the version number of the newer dataset}
+
+\item{section_name}{the name of the section to compare}
+
+\item{html_output_location}{if provided, the html output will be saved here}
+
+\item{id_column}{the name of the column containing SubjectIDs}
+
+\item{max_html_table_length}{the maximum number of rows in the HTML version of the diff}
+}
+\value{
+summary of changes between versions
+}
+\description{
+Generates a difference report comparing two versions of a dataset
+}
+\examples{
+diff <- DatasetComparison(1, 2, "SectionA1")
+}

man/GetDataBySubjectID.Rd

@@ -12,7 +12,9 @@ GetDataBySubjectID(con, tables_and_fields = list(),
 \item{con}{a database connection using the DBI package or \code{ASPREEDb()}}
 
 \item{tables_and_fields}{a list of tables and columns to retrieve, e.g. \code{list("tblAnnualVisits" = c("Wt", "Ht"))}
-omitting the columns will retrieve all columns}
+omitting the columns will retrieve all columns.
+Custom data can be provided instead of column names, e.g. \code{list("pathology" = tbl(sql("SELECT * FROM someTable"))}.
+In this case, the names used in the list are not used.}
 
 \item{include_visit_time}{TRUE if the tables to be merged include visit time}
 

tests/testthat/test-data_access.R

-context("Generate longitudinal dataset file paths")
-library(aspree)
-
-test_that("sensible file paths are generated by default for Windows", {
-  file_paths <- SDrivePaths()
-  sapply(file_paths, FUN = function(path) {
-    expect_true(startsWith(path, "S:/MNHS-SPHPM-EPM"))
-  })
-  sapply(file_paths, FUN = function(path) {
-    expect_true(endsWith(path, ".csv") || endsWith(path, ".dta"))
-  })
-})
-
-test_that("providing a prefix produces sensible file paths", {
-  prefix <- "/Volumes/shared/MNHS-SPHPM-EPM/ASPREE-Data/ASPREE Longitudinal Data Set/LOCKED/"
-  file_paths <- SDrivePaths(prefix)
-  sapply(file_paths, FUN = function(path) {
-    expect_true(startsWith(path, prefix))
-  })
-  sapply(file_paths, FUN = function(path) {
-    expect_true(endsWith(path, ".csv") || endsWith(path, ".dta"))
-  })
-})
-
-test_that("there are 20 sections", {
-  file_paths <- SDrivePaths()
-  expect_equal(length(file_paths), 20)
-})

tests/testthat/test-data_quality.R

+context("Ensure the quality of generated datasets")
+library(aspree)
+
+dummy_dataset_1_tmp_file <- tempfile()
+dummy_dataset_2_tmp_file <- tempfile()
+dataset_1 <- data.frame(SubjectID = c(1,2,3,4), ColumnA = c(5,6,7,8))
+dataset_2 <- data.frame(SubjectID = c(1,2,3,4), ColumnA = c(50,6,7,8), ColumnB = c(9, 10, 11, 12))
+setup({
+  write.csv(dataset_1, dummy_dataset_1_tmp_file)
+  write.csv(dataset_2, dummy_dataset_2_tmp_file)
+})
+
+teardown({
+  unlink(dummy_dataset_1_tmp_file)
+  unlink(dummy_dataset_2_tmp_file)
+})
+
+test_that("an expected diff is generated for two versions of a dataset read from file", {
+
+  local_mock(SDrivePaths = function(ver) {
+    if (ver == 1) {
+      return(list(SectionA1 = dummy_dataset_1_tmp_file))
+    } else {
+      return(list(SectionA1 = dummy_dataset_2_tmp_file))
+    }
+  })
+
+  diff <- DatasetComparison(1, 2, "SectionA1")
+  expect_true(all(diff$comparison_df == data.frame(SubjectID = c(1,1), chng_type = c("+", "-"), ColumnA = c(50, 5))))
+
+})
+
+test_that("an expected diff is generated for two versions of a dataset, one read from file and the other in memory", {
+
+  local_mock(SDrivePaths = function(ver) {
+    if (ver == 1) {
+      return(list(SectionA1 = dummy_dataset_1_tmp_file))
+    } else {
+      return(list(SectionA1 = dummy_dataset_2_tmp_file))
+    }
+  })
+
+  diff <- DatasetComparison(1, dataset_2, "SectionA1")
+  expect_true(all(diff$comparison_df == data.frame(SubjectID = c(1,1), chng_type = c("+", "-"), ColumnA = c(50, 5))))
+
+  diff <- DatasetComparison(dataset_1, 2, "SectionA1")
+  expect_true(all(diff$comparison_df == data.frame(SubjectID = c(1,1), chng_type = c("+", "-"), ColumnA = c(50, 5))))
+
+})