Vignette Video Download |BEST|
Maarit Hibbits
This requires some intention, because unlike tests, by default, a vignette is rendered using the currently installed version of your package, not with the current source package, thanks to the initial call to library(yourpackage).
output: this specifies the output format. There are many options that are useful for regular reports (including html, pdf, slideshows, etc.), but rmarkdown::html_vignette has been specifically designed for this exact purpose. See ?rmarkdown::html_vignette for more details.
vignette: this is a block of special metadata needed by R. Here, you can see the legacy of LaTeX vignettes: the metadata looks like LaTeX comments. The only entry you might need to modify is the \VignetteIndexEntry. This is how the vignette appears in the vignette index and it should match the title. Leave the other two lines alone. They tell R to use knitr to process the file and that the file is encoded in UTF-8 (the only encoding you should ever use for a vignette).
Automatic links are generated for functions in the host package, namespace-qualified functions in another package, vignettes, and more. Here are the two most important examples of automatically linked text:
An external file that could be useful to users or elsewhere in the package (not just in vignettes): Put such a file in inst/ (Section 8.2), perhaps in inst/extdata/ (Section 7.3), and refer to it with system.file() or fs::path_package() (Section 7.3.1). Example from vignette("sf2", package = "sf"):
An external graphics file: put it in vignettes/, refer to it with a filepath that is relative to vignettes/ and use knitr::include_graphics() inside a code chunk. Example from vignette("sheet-geometry", package = "readxl"):
Any package used in a vignette must be a formal dependency, i.e. it must be listed in Imports or Suggests in DESCRIPTION. Similar to our stance in tests (Section 11.5.2), our policy is to write vignettes under the assumption that suggested packages will be installed in any context where the vignette is being built (Section 11.5.3). We generally use suggested packages unconditionally in vignettes. But, as with tests, if a package is particularly hard to install, we might make an exception and take extra measures to guard its use.
In vignettes, we use the eval option in a similar way as @examplesIf in examples (Section 16.5.4). If the code can only be run under specific conditions, you must find a way to to check for those pre-conditions programmatically at runtime and use the result to set the eval option.
Here are the first few chunks in a vignette from googlesheets4, which wraps the Google Sheets API. The vignette code can only be run if we are able to decrypt a token that allows us to authenticate with the API. That fact is recorded in can_decrypt, which is then set as the vignette-wide default for eval.
It can be helpful to appreciate the big difference between the workflow for function documentation and vignettes. The source of function documentation is stored in roxygen comments in .R files below R/. We use devtools::document() to generate .Rd files below man/. These man/*.Rd files are part of the source package. The official R machinery cares only about the .Rd files.
Vignettes are very different because the .Rmd source is considered part of the source package and the official machinery (R CMD build and check) interacts with vignette source and built vignettes in many ways. The result is that the vignette workflow feels more constrained, since the official tooling basically treats vignettes somewhat like tests, instead of documentation.
The key takeaway from the above is that it is awkward to keep rendered vignettes in a source package and this has implications for the vignette development workflow. It is tempting to fight this (and many have tried), but based on years of experience and discussion, the devtools philosophy is to accept this reality.
Active, iterative work on your vignettes: Use your usual interactive .Rmd workflow (such as the button) or devtools::build_rmd("vignettes/my-vignette.Rmd") to render a vignette to .html in the vignettes/ directory. Regard the .html as a disposable preview. (If you initiate vignettes with use_vignette(), this .html will already be gitignored.)
We highly recommend treating inst/doc/ as a strictly machine-writable directory for vignettes. We recommend that you do not take advantage of the fact that you can place arbitrary pre-built documentation in inst/doc/. This opinion permeates the devtools ecosystem which, by default, cleans out inst/doc/ during various development tasks, to combat the problem of stale documentation.
@Multi4G I have been trying very unsuccessfully for several hours to achieve this effect, and have now given up. Each time I follow the steps exactly, and on the screen the image with the new vignette looks perfect. But then when I try to print the image, I get a dark rectangle superimposed on the image (per the attached). Can you give me a clue to why this is not working? I did it perfectly using Photo v. 1.8.3, but yesterday upgraded to v. 1.8.4. Think that is the problem? (Images were printed, then scanned then converted to JPGs. Sorry they are so fuzzy.)
I've never tried this method to create vignettes - nor do I mess about with printers (I find the whole experience painful...ha!), but if I didn't know better I would say that the adjustment layer is smaller than the image size. The effect I'm seeing is exactly the same if that were the case. Have you tried checking the move tool on the vignette layer in question to see whether the bounding box covers the entire image?
We next use the count matrix to create a Seurat object. The object serves as a container that contains both data (like the count matrix) and analysis (like PCA, or clustering results) for a single-cell dataset. For more information, check out our [Seurat object interaction vignette], or our GitHub Wiki. For example, in Seurat v5, the count matrix is stored in pbmc[["RNA"]]$counts.
While this method of normalization is standard and widely used in scRNA-seq analysis, global-scaling relies on an assumption that each cell originally contains the same number of RNA molecules. We and others have developed alternative workflows for the single cell preprocessing that do not make these assumptions. For users who are interested, please check out our SCTransform() normalization workflow. The method is described in ourpaper, with a separate vignette using Seurat here. The use of SCTransform replaces the need to run NormalizeData, FindVariableFeatures, or ScaleData (described below.)
In Macosko et al, we implemented a resampling test inspired by the JackStraw procedure. While still available in Seurat (see previous vignette), this is a slow and computationally expensive procedure, and we is no longer routinely used in single cell analysis.
You must display the sticker on the inside of the windshield of your vehicle as you enter Austria. Please note, the vignette must be stuck to your windshield in order to be valid. Failure to do so will mean a heavy, on-the-spot fine.
This requires a build/vignettes.rds or Meta/vignettes.rds file. This file is automatically generated by devtools. Please make sure that you do not delete it or list it in .Rbuildignore (check for a line containing build Meta or ^build/vignettes.rds$ ^Meta/vignettes.rds$ and delete it from the file).
First, I made changes to the vignette: specification in the header so that it now reads as follows (note the difference in the encoding specification line, from %\usepackage[utf8]inputenc to %\VignetteEncodingUTF-8, which matches the directions in -package-vignette.html which seem to have changed)
I wrote an R package for internal purposes and also added some vignettes. When I use devtools::install(build_vignettes = TRUE), all vignettes are installed properly on my machine. But in order to distribute the package to colleages, I would like to generate a windows binary.
But when I use Build binary package from the RStudio Build pane, the vignettes will not show up when the package is installed from the generated binary. I figured that I could move the vignettes from doc to inst/doc before building the binary package, but this needs to be done manually whenever a vignette changes.
in the last month my new X100F has started showing a permanent vignette on all my photos. It shows in the viewfinder (both optical & electronic) as well as on the finished photo. I've googled and can't work out what I have done. The camera hasn't been dropped, but i have read the manual cover to cover & set the camera up the way i like, so am wondering if this is a setting i have somehow applied... Help - all the pics look terrible! The below is from a sunny day.
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