The package includes a report template that may help you generate a
report for a given assessment. This is installed as a file
report_assessment.Rmd in a directory markdown,
so to use it, you’ll need to use system.file() to find the
template file.
You can use this report tempate in two different ways:
Through report_assessment
The easiest way to generate reports is in bulk, as follows:
## Do whatever you need to get the assessment object
...
assessment <- run_assessment(timeseries)
report_assessment(
biota_assessment,
subset = NULL,
output_dir = my_output_dir
)This will generate all the reports, although you can pass a
subsetting expression (just like with plot_assessment) to
select which individual assessments you want reports on. The reports are
written as HTML files into the given output directory.
Directly through R Markdown
In this case, your usage will typically look a bit like this:
library(rmarkdown)
## Do whatever you need to get the assessment object
...
assessment <- run_assessment(timeseries)
## Locate the report file
package_dir = system.file(package = "harsat")
template_dir = file.path(package_dir, "markdown")
report_file <- file.path(template_dir, "report_assessment.Rmd")
## Create a new filename for the output file, here we just
## put it in a temporary file, but you'll usually want something
## more persistent.
output_file <- tempfile("plot", fileext = c(".htm"))
## Choose what you want to report. Pick the series you want to
## report like this.
params = list(
assessment_object = assessment,
series = 'A902 PFOA Globicephala melas LI JV'
)
## Generate the report -- note the use of `new.env()` to make a
## nice clean enviroment containing only the parameters you pass,
## as above.
rmarkdown::render(
report_file,
output_file = output_file,
params = params,
envir = new.env()
)Note that because this is R Markdown, you can do this as a child document from another template. You can also control the output format, generating PDF, for example.