PumasReports
Docstrings
PumasReports.PumasReports
— ModuleTools for working with, and generating, static reports based on Pumas data
PlottingUtilities.report
— Methodreport(
fitted_models;
output,
title,
version,
date,
author,
categorical,
force,
inspect,
infer,
clean,
header,
footer,
plot_fontsize,
plot_resolution
)
Create a PDF report based on the provided fitted_models
.
fitted_models
can be provided as one of several different inputs:
A single fitted model result from fit
.
fit_result = fit(...)
report(fit_result)
Note that ...
in these examples is not real syntax and is used in these examples to illustrate unimportant details.
A vector of fitted model results from fit
.
fit_1 = fit(...)
fit_2 = fit(...)
report([fit_1, fit_2])
The above two calls will result in fitted models named 1 to N. If you wish to provide named fitted models in the resulting report then pass in a NamedTuple
instead of a single fit
result or vector:
my_named_fit = fit(...)
report((; my_named_fit))
fit_1 = fit(...)
fit_2 = fit(...)
report((; fit_1, fit_2))
Note the leading ;
, which is standard Julia syntax and required for naming your fitted models.
Other computed results can also be included alongside your fit
results, namely inspect
, infer
, and vpc
results. Any number of vpc
results can be included, while only one of each of inspect
and infer
may be included. To include associated results along with the fitted model use Julia's tuple syntax, i.e. (a, b, c)
:
fit_1 = fit(...)
ins_1 = inspect(fit_1, ...)
inf_1 = infer(fit_1, ...)
vpc_1 = vpc(fit_1, ...)
vpc_2 = vpc(fit_1, ...)
report((; my_model = (fit_1, ins_1, inf_1, vpc_1, vpc_2)))
Keywords
output
: directory into which the final report files will be saved.title
: a title for the final report that will appear on the title page and be used for the name of the finished PDF.version
: the version of the document, given as av"..."
string.date
: the date of the report, given as aDate
value.author
: the name of the author of the document.categorical
: a vector ofSymbol
s for covariates that should be treated as categorical in all plots of the report.force
: (defaulttrue
) remove all contents ofoutput
(if it exists) before generating a new report.inspect
: (defaulttrue
) shouldinspect
be called automatically on fitted models if noinspect
result is already provided. The call toinspect
does not pass any additional arguments and so if customizedinspect
calls are required, for example when using NPDE, a pre-computedinspect
result should be passed in instead of relying of the automatic behaviour.infer
: (defaultfalse
) shouldinfer
be called automatically on fitted models if noinfer
result is already provided.clean
: (defaulttrue
) only include the final PDF document in theoutput
folder rather than all intermediate files as well.header
: custom text to be added to the header section of each page.footer
: custom text to be added to the footer section of each page.plot_fontsize
: set the font size for all plots in the report. Default is16
.plot_resolution
: set the resolution for all plots in the report. Default is(960, 540)
.
Examples
The following will generate a report based on objects fpm1
and fpm2
, which are FittedPumasModel
s. It will automatically call inspect
and infer
for each.
report((; fpm1, fpm2))
The names of the models in the reports will be the same as the variable names. To change the names pass a different key name in the NamedTuple
syntax passed to report
.
Report-level metadata that should be included in the generated report can be passed in via the keyword arguments title
and version
, others to be added later.
The name of the resulting PDF file can be given with output = "NAME.pdf
.
PumasReports._user_name
— FunctionReturn a valid "username" as defined in either "USER", "USERNAME", "USERNAME", "JULIAHUBUSERNAME", or "JULIAHUBUSERFULL_NAME" to cover the differences on unix, windows, and juliahub.
PumasReports.coefficients_table
— Functioncoefficients_table(fitted_model; ...)
coefficients_table(
fitted_model,
inference;
digits,
sigdigits,
latex
)
Presents the fitted_model
coefficients in a formatted DataFrame
for use in reporting. When the second argument inference
is provided then that is used for calculation of table values.
Keywords
digits = 3
the number of significant digits to format number to.latex = false
whether to display parameter names using$
for use in LaTeX tables.
PumasReports.compare_estimates
— Methodcompare_estimates(; fitted_models...)
Compare estimates for the given fitted_models
.
Examples
compare_estimates(; fit_1, fit_2, fit_3)
PumasReports.metrics_table
— Methodmetrics_table(fitted_model; digits, sigdigits, latex)
Presents the fitted_model
metrics in a formatted DataFrame
for use in reporting.
Keywords
digits = 3
the number of significant digits to format number to.latex = false
whether to display parameter names using$
for use in LaTeX tables.