Automatic report generation

The qcReport method generates report in various formats taking a QcMetrics instance as input. Each individual quality control item produces a section with description of the item and a assessment figure.

Details

The reporting functions take a QcMetrics instance as input, generate the source of the report and compile it into the final format that are currently available are reporting_pdf, reporting_tex, reporting_rmd and reporting_html. See qcto for details about the sectioning functions, that convert individual QcMetric objects into adequate report sections.

The package vignette documents the report generation in more details and describes possibilities for customisation.

Methods

signature( object = "QcMetrics", reportname = "character", type = "character", author = "character", title = "character", metadata = "logical", toc = "logical", summary = "logical", sessioninfo = "logical", clean = "logical", quiet = "logical", reporter, qcto, ...)

generates a report for the QcMetrics object. The report will be named according the reportname (default is qcreprt)and type, the latter defining the output format and the extension. Possible types are pdf (default), "tex", "Rmd", "html" (all generated using the package knitr). A custom title can be provided; default is "Quality control report generated with qcmetrics". If no author is provided, the default value (Sys.getenv("USER")) is used. The addition of a table of contents (default is FALSE), a metadata section, a summary section and the session information can be controlled with the toc, metadata, summary and sessioninformation arguments. The metadata section is added to the report when present and the other have TRUE as default.

Intermediate files are deleted, unless clean is set to FALSE and verbose output can be turned on by setting quiet to FALSE.

The reporter and qcto arguments are used to convert QcMetric and QcMetrics objects into report source. See Details and the package vignette for details.

Addition parameters can be passed to inner functions. For the pdf report, passed to texi2pdf; for html, passed to markdown::markdownToHTML.

The method invisibly returns the name of the report that was generated.

Examples

example(QcMetrics)
#> 
#> QcMtrc> example(QcMetric)
#> 
#> QcMtrc> (qc <- QcMetric())
#> Object of class "QcMetric"
#>  Name: A QcMetric prototype 
#>  Status: NA 
#>  Data: empty
#> 
#> QcMtrc> qcdata(qc)
#> character(0)
#> 
#> QcMtrc> try(qcdata(qc, "x"))
#> Error in qcdata(qc, "x") : No qcdata 'x' in object.
#> 
#> QcMtrc> x <- rnorm(10)
#> 
#> QcMtrc> qcdata(qc, "qc1") <- x
#> 
#> QcMtrc> qcdata(qc, "qc2") <- 1:10
#> 
#> QcMtrc> qcdata(qc)
#> [1] "qc1" "qc2"
#> 
#> QcMtrc> all.equal(qcdata(qc, "qc1"), x)
#> [1] TRUE
#> 
#> QcMtrc> all.equal(qcdata(qc, "qc2"), 1:10)
#> [1] TRUE
#> 
#> QcMtrc> name(qc) <- "My test QcMetric"
#> 
#> QcMtrc> description(qc) <- "This qc metric describes bla bla bla, indicating possible issues in the third step of protocol bla bla bla."
#> 
#> QcMtrc> status(qc) <- FALSE
#> 
#> QcMtrc> qc
#> Object of class "QcMetric"
#>  Name: My test QcMetric 
#>  Description:
#> This qc metric describes bla bla bla, indicating possible issues in the
#> third step of protocol bla bla bla.
#>  Status: FALSE 
#>  Data: qc1 qc2 
#> 
#> QcMtrc> ## or
#> QcMtrc> e <- new.env()
#> 
#> QcMtrc> e$qc1 <- rnorm(100)
#> 
#> QcMtrc> e$qc2 <- 1:100
#> 
#> QcMtrc> qcenv(qc) <- e
#> 
#> QcMtrc> length(qcdata(qc, "qc1"))
#> [1] 100
#> 
#> QcMtrc> head(qcdata(qc, "qc2"))
#> [1] 1 2 3 4 5 6
#> 
#> QcMtrc> show(qc)
#> Object of class "QcMetric"
#>  Name: My test QcMetric 
#>  Description:
#> This qc metric describes bla bla bla, indicating possible issues in the
#> third step of protocol bla bla bla.
#>  Status: FALSE 
#>  Data: qc1 qc2 
#> 
#> QcMtrc> show(qc) <- function(object) cat("Updated show method\n")
#> 
#> QcMtrc> show(qc)
#> Updated show method
#> 
#> QcMtrc> show(qc) <- qcshow
#> 
#> QcMtrc> qc
#> Object of class "QcMetric"
#>  Name: My test QcMetric 
#>  Description:
#> This qc metric describes bla bla bla, indicating possible issues in the
#> third step of protocol bla bla bla.
#>  Status: FALSE 
#>  Data: qc1 qc2 
#> 
#> QcMtrc> plot(qc)
#> Warning: No specific plot function defined
#> 
#> QcMtrc> plot(qc) <-
#> QcMtrc+     function(object, ...)
#> QcMtrc+         plot(qcdata(object, "qc2"),
#> QcMtrc+              qcdata(object, "qc1"),
#> QcMtrc+              xlab = "qc1",
#> QcMtrc+              ylab = "qc2",
#> QcMtrc+              ...)
#> 
#> QcMtrc> plot(qc)

#> 
#> QcMtrc> plot(qc, col = "red", pch = 19)
#> 
#> QcMtrc> show(qc)
#> Object of class "QcMetric"
#>  Name: My test QcMetric 
#>  Description:
#> This qc metric describes bla bla bla, indicating possible issues in the
#> third step of protocol bla bla bla.
#>  Status: FALSE 
#>  Data: qc1 qc2 
#> 
#> QcMtrc> qc2 <- QcMetric(name = "My other metric", status = TRUE)
#> 
#> QcMtrc> qcdata(qc2, "x") <- rnorm(100)
#> 
#> QcMtrc> qcdata(qc2, "k") <- rep(LETTERS[1:2], 50)
#> 
#> QcMtrc> plot(qc2) <- function(object, ...) {
#> QcMtrc+     require("lattice")
#> QcMtrc+     d <- data.frame(x = qcdata(object, "x"),
#> QcMtrc+                     k = qcdata(object, "k"))
#> QcMtrc+     bwplot(x ~ k, data = d)
#> QcMtrc+ }
#> 
#> QcMtrc> qcm <- QcMetrics(qcdata = list(qc, qc2))
#> 
#> QcMtrc> qcm
#> Object of class "QcMetrics"
#>  containing 2 QC metrics.
#>  and no metadata variables.
#> 
#> QcMtrc> qcm[1] ## a QcMetrics instance
#> Object of class "QcMetrics"
#>  containing 1 QC metrics.
#>  and no metadata variables.
#> 
#> QcMtrc> qcm[[1]] ## a single QcMetric
#> Object of class "QcMetric"
#>  Name: My test QcMetric 
#>  Description:
#> This qc metric describes bla bla bla, indicating possible issues in the
#> third step of protocol bla bla bla.
#>  Status: FALSE 
#>  Data: qc1 qc2 
#> 
#> QcMtrc> metadata(qcm)
#> list()
#> 
#> QcMtrc> metadata(qcm) <- QcMetadata(list(name = "Prof. Who",
#> QcMtrc+                                  lab = "Cabin University"))
#> 
#> QcMtrc> ## or, shorter but equivalent
#> QcMtrc> metadata(qcm) <- list(name = "Prof. Who",
#> QcMtrc+                       lab = "Cabin University")
#> 
#> QcMtrc> metadata(qcm) ## or mdata(qcm)
#> $name
#> [1] "Prof. Who"
#> 
#> $lab
#> [1] "Cabin University"
#> 
#> 
#> QcMtrc> ## update metadata
#> QcMtrc> metadata(qcm) <- list(lab = "Big lab", ## updated
#> QcMtrc+                       uni = "Cabin University") ## added
#> 
#> QcMtrc> mdata(qcm)
#> $name
#> [1] "Prof. Who"
#> 
#> $lab
#> [1] "Big lab"
#> 
#> $uni
#> [1] "Cabin University"
#> 
show(qcm)
#> Object of class "QcMetrics"
#>  containing 2 QC metrics.
#>  and 3 metadata variables.

destdir <- tempdir()
(report <- file.path(destdir, "testQCReport"))
#> [1] "/tmp/Rtmp0j7VNf/testQCReport"


if (FALSE) {
  ## pdf report
  qcReport(qcm, reportname = report)
  ## use pdflatex to generate the pdf file
  qcReport(qcm, reportname = report, texi2dvi = "pdflatex")
}

## default html report
html <- qcReport(qcm, reportname = report, type = "html")
#> Report written to /tmp/Rtmp0j7VNf/testQCReport.html

html
#> [1] "/tmp/Rtmp0j7VNf/testQCReport.html"
if (interactive())
    browseURL(html)