diff --git a/apple-touch-icon-120x120.png b/apple-touch-icon-120x120.png index 3b550e769..74b86372e 100644 Binary files a/apple-touch-icon-120x120.png and b/apple-touch-icon-120x120.png differ diff --git a/apple-touch-icon-152x152.png b/apple-touch-icon-152x152.png index dc481cdb5..b880cdf67 100644 Binary files a/apple-touch-icon-152x152.png and b/apple-touch-icon-152x152.png differ diff --git a/apple-touch-icon-180x180.png b/apple-touch-icon-180x180.png index 6636caf7a..877e20792 100644 Binary files a/apple-touch-icon-180x180.png and b/apple-touch-icon-180x180.png differ diff --git a/apple-touch-icon-60x60.png b/apple-touch-icon-60x60.png index 4784362b0..77dd3b551 100644 Binary files a/apple-touch-icon-60x60.png and b/apple-touch-icon-60x60.png differ diff --git a/apple-touch-icon-76x76.png b/apple-touch-icon-76x76.png index 872605cf0..3d5b3e4cf 100644 Binary files a/apple-touch-icon-76x76.png and b/apple-touch-icon-76x76.png differ diff --git a/apple-touch-icon.png b/apple-touch-icon.png index ad0101a08..c5fbf5189 100644 Binary files a/apple-touch-icon.png and b/apple-touch-icon.png differ diff --git a/articles/data_protocol.html b/articles/data_protocol.html index 10458e45e..5ea0825c2 100644 --- a/articles/data_protocol.html +++ b/articles/data_protocol.html @@ -136,7 +136,7 @@

Scope of packageThe epiparameter package spans a range of infectious diseases, including several distributions for each disease when available. The pathogens and diseases that are currently systematically searched for and included in the package library are:

#> Returning 122 results that match the criteria (99 are parameterised). 
 #> Use subset to filter by entry variables or single_epidist to return a single entry. 
-#> To retrieve the short citation for each use the 'get_citation' function
+#> To retrieve the citation for each use the 'get_citation' function @@ -636,7 +636,7 @@

Scope of packageThe distributions currently included in the literature search for each pathogen/disease are:

#> Returning 122 results that match the criteria (99 are parameterised). 
 #> Use subset to filter by entry variables or single_epidist to return a single entry. 
-#> To retrieve the short citation for each use the 'get_citation' function
+#> To retrieve the citation for each use the 'get_citation' function

Disease
diff --git a/articles/epiparameter.html b/articles/epiparameter.html index 6b0e749aa..0bb8ae45e 100644 --- a/articles/epiparameter.html +++ b/articles/epiparameter.html @@ -136,7 +136,7 @@

Library of epidemiological parame epi_dist_db <- epidist_db() #> Returning 122 results that match the criteria (99 are parameterised). #> Use subset to filter by entry variables or single_epidist to return a single entry. -#> To retrieve the short citation for each use the 'get_citation' function +#> To retrieve the citation for each use the 'get_citation' function epi_dist_db #> List of <epidist> objects #> Number of entries in library: 122 @@ -223,7 +223,7 @@

Single set of epidemiological #> meta-analysis of observational research." _BMJ Open_. #> doi:10.1136/bmjopen-2020-039652 #> <https://doi.org/10.1136/bmjopen-2020-039652>.. -#> To retrieve the short citation use the 'get_citation' function +#> To retrieve the citation use the 'get_citation' function covid_incubation #> Disease: COVID-19 #> Pathogen: SARS-CoV-2 @@ -294,7 +294,7 @@

Subsetting database) #> Returning 3 results that match the criteria (3 are parameterised). #> Use subset to filter by entry variables or single_epidist to return a single entry. -#> To retrieve the short citation for each use the 'get_citation' function +#> To retrieve the citation for each use the 'get_citation' function #> [[1]] #> Disease: COVID-19 #> Pathogen: SARS-CoV-2 @@ -371,7 +371,7 @@

Distribution functions#> Epidemic after One Year — Slowing but Not Yet under Control." _The New #> England Journal of Medicine_. doi:10.1056/NEJMc1414992 #> <https://doi.org/10.1056/NEJMc1414992>.. -#> To retrieve the short citation use the 'get_citation' function +#> To retrieve the citation use the 'get_citation' function density(ebola_incubation, at = 0.5) #> [1] 0.03608013 @@ -380,8 +380,8 @@

Distribution functionsquantile(ebola_incubation, p = 0.5) #> [1] 8.224347 generate(ebola_incubation, times = 10) -#> [1] 17.9089729 3.1294561 11.0474087 2.3899915 6.8530911 3.6977050 -#> [7] 8.9236888 13.9665572 0.3544369 15.3587828 +#> [1] 2.720139 12.634015 1.511021 3.599137 8.979791 16.778460 5.858835 +#> [8] 7.139121 11.758976 16.724751
diff --git a/articles/extract_convert.html b/articles/extract_convert.html index 13f3420a6..fc0b10de9 100644 --- a/articles/extract_convert.html +++ b/articles/extract_convert.html @@ -512,7 +512,7 @@

Extraction#> Stochastic numerical optimisation used. #> Rerun function multiple times to check global optimum is found #> shape scale -#> 3.358202 1.284185

+#> 3.358206 1.284185

In the above example we estimate parameters of the gamma distribution, but extraction is also implemented for the lognormal, normal and Weibull distributions, but specifying "lnorm", "norm" or "weibull".

A message is shown when running extract_param() to make the user aware that the estimates are not completely reliable due to the use of numerical optimisation. Rerunning the function to and finding the same parameters are returned indicates that they have successfully converged. This issue is mostly overcome by the internal setup of the extract_param() function which searches for convergence to consistent parameter estimates before returning these to the user.

The alternative extraction, by median and range, can be achieved by specifying type = "range" and using the samples argument instead of the percentiles argument. When using type = "percentiles" the samples argument is ignored and when using type = "range" the percentiles argument is ignored.

@@ -526,7 +526,7 @@

Extraction#> Stochastic numerical optimisation used. #> Rerun function multiple times to check global optimum is found #> meanlog sdlog -#> 2.302585 4.925233 +#> 2.302585 3.617866

In the above section it was mentioned that extract_param() has an internal mechanism to check that the parameters have consistently converged to the same estimates over several optimisation iterations. The tolerance of this convergence and number of times the optimisation can be repeated is specified in the control argument of extract_param(). This is set by default (tolerance = 1e-5 and max_iter = 1000), and thus does not need to be specified by the user (as shown in the above examples). In the case that the maximum number of optimisation iterations is reached, the calculation terminates returning the most recent optimisation result to the user along with a warning message.

Code
 # set seed to ensure warning is produced
diff --git a/favicon-16x16.png b/favicon-16x16.png
index d245950f3..d40d4cc1f 100644
Binary files a/favicon-16x16.png and b/favicon-16x16.png differ
diff --git a/favicon-32x32.png b/favicon-32x32.png
index 1e73fedf8..9687b0755 100644
Binary files a/favicon-32x32.png and b/favicon-32x32.png differ
diff --git a/news/index.html b/news/index.html
index f3a94849f..521b492b6 100644
--- a/news/index.html
+++ b/news/index.html
@@ -75,13 +75,14 @@ 
epiparameter
 
Initial release of {epiparameter}, an R package to work with epidemiological parameters and distributions, and contains a library of epidemiological parameters.

 

 
New features

-
  • A library of epidemiological parameters (parameters.json) stored as internal data (inst/extdata).
    • 
+
    • A library of 122 epidemiological parameter set from the epidemiological literature. This is accessible from the package as system data (sysdata.rda, as epiparameter::multi_epidist) or as internal data (inst/extdata/parameters.json).
      • 
+
    • The epidist_db() function loads epidemiological parameters from the library.
      • 
 
    • Distribution parameter conversion and extraction functions (convert_params_to_summary_stats() & convert_summary_stats_to_params(), and extract_param()).
      • 
-
    • S3 classes to work with parameters <epidist>, <epiparam> and <vb_epidist>. These classes are accompanied by S3 methods to aid users easily work with these data structures. These include printing, plotting, and distribution functions for PDF/PMF, CDF, random number generation and distribution quantiles. Each class has a constructor and a validator.
      • 
-
    • The package contains a few utility functions.
      • 
-
    • Four vignettes are included in this initial release. One as an introduction to the package (epiparameter.Rmd), one as an tutorial on converting and extracting parameters (extract_convert.Rmd), one on the protocol used to collect entries for the library of epidemiological parameters (data_protocol.Rmd) and a supplementary vignette which quantifies the bias from using the parameter extraction (extract_param()) from {epiparameter} (extract-bias.Rmd).
      • 
+
    • An S3 class to work with epidemiological parameters <epidist>. This class has S3 methods to aid users easily work with these data structures. These include printing, plotting, and distribution functions for PDF/PMF, CDF, random number generation and distribution quantiles. The <epidist> class has a constructor function, a validator function, accessors (get_*()), checkers (is_*()). There is also a <vb_epidist> S3 class for vector-borne parameters, and an internal <multi_epidist> class for improved printing of lists of <epidist> objects.
      • 
+
    • The package contains a few utility functions. list_distributions() is a helper function to provide information from a list of <epidist> objects in tabular form. calc_disc_dist_quantile() calculates the quantiles of a probability distribution based on the vector of probabilities and time data.
      • 
+
    • Five vignettes are included in this initial release. One as an introduction to the package (epiparameter.Rmd), one as an tutorial on converting and extracting parameters (extract_convert.Rmd), one on the protocol used to collect entries for the library of epidemiological parameters (data_protocol.Rmd), a design vignette (design_principles.Rmd), and a supplementary vignette which quantifies the bias from using the parameter extraction (extract_param()) from {epiparameter} (extract-bias.Rmd).
      • 
 
    • Unit tests and documentation files.
      • 
-
    • Continuous integration workflows for R package checks, rendering the README.md, calculating test coverage, deploying the pkgdown website, updates the package citation, and validating the parameter library JSON file.
      • 
+
    • Continuous integration workflows for R package checks, rendering the README.md, calculating test coverage, deploying the pkgdown website, updates the package citation, linting package code, checking package or system dependency changes, updating copyright year, and validating the parameter library JSON file.
      • 
 

 

 
Breaking changes

diff --git a/pkgdown.yml b/pkgdown.yml
index 00c30e95b..c9755a557 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -7,7 +7,7 @@ articles:
   epiparameter: epiparameter.html
   extract-bias: extract-bias.html
   extract_convert: extract_convert.html
-last_built: 2024-03-25T18:50Z
+last_built: 2024-03-28T11:30Z
 urls:
   reference: https://epiverse-trace.github.io/epiparameter/reference
   article: https://epiverse-trace.github.io/epiparameter/articles
diff --git a/reference/convert_params_to_summary_stats.html b/reference/convert_params_to_summary_stats.html
index 84d41dc1d..d72bede1a 100644
--- a/reference/convert_params_to_summary_stats.html
+++ b/reference/convert_params_to_summary_stats.html
@@ -213,7 +213,7 @@ 
Examples#> Epidemic after One Year — Slowing but Not Yet under Control.” _The New
 #> England Journal of Medicine_. doi:10.1056/NEJMc1414992
 #> <https://doi.org/10.1056/NEJMc1414992>.. 
-#> To retrieve the short citation use the 'get_citation' function
+#> To retrieve the citation use the 'get_citation' function
 convert_params_to_summary_stats(epidist)
 #> $mean
 #> [1] 8.2
@@ -248,7 +248,7 @@ 
Examples)
 #> Returning 4 results that match the criteria (3 are parameterised). 
 #> Use subset to filter by entry variables or single_epidist to return a single entry. 
-#> To retrieve the short citation for each use the 'get_citation' function
+#> To retrieve the citation for each use the 'get_citation' function
 convert_params_to_summary_stats(epidist[[2]], shape = 1, scale = 1)
 #> $mean
 #> [1] 1
diff --git a/reference/convert_summary_stats_to_params.html b/reference/convert_summary_stats_to_params.html
index d4fdf1641..2bba473b4 100644
--- a/reference/convert_summary_stats_to_params.html
+++ b/reference/convert_summary_stats_to_params.html
@@ -170,7 +170,7 @@ 
Examples#> Epidemic after One Year — Slowing but Not Yet under Control.” _The New
 #> England Journal of Medicine_. doi:10.1056/NEJMc1414992
 #> <https://doi.org/10.1056/NEJMc1414992>.. 
-#> To retrieve the short citation use the 'get_citation' function
+#> To retrieve the citation use the 'get_citation' function
 convert_summary_stats_to_params(epidist)
 #> $shape
 #> [1] 1.641602
diff --git a/reference/epidist_db.html b/reference/epidist_db.html
index 246387253..bbd4cc27c 100644
--- a/reference/epidist_db.html
+++ b/reference/epidist_db.html
@@ -211,7 +211,7 @@ 
Examples
epidist_db(disease = "influenza", epi_dist = "serial_interval")
 #> Returning 1 results that match the criteria (1 are parameterised). 
 #> Use subset to filter by entry variables or single_epidist to return a single entry. 
-#> To retrieve the short citation for each use the 'get_citation' function
+#> To retrieve the citation for each use the 'get_citation' function
 #> Disease: Influenza
 #> Pathogen: Influenza-A-H1N1Pdm
 #> Epi Distribution: serial interval
@@ -234,7 +234,7 @@ 
Examples)
 #> Returning 1 results that match the criteria (1 are parameterised). 
 #> Use subset to filter by entry variables or single_epidist to return a single entry. 
-#> To retrieve the short citation for each use the 'get_citation' function
+#> To retrieve the citation for each use the 'get_citation' function
 
 # example using functional subsetting
 eparam <- epidist_db(
@@ -244,7 +244,7 @@ 
Examples)
 #> Returning 11 results that match the criteria (11 are parameterised). 
 #> Use subset to filter by entry variables or single_epidist to return a single entry. 
-#> To retrieve the short citation for each use the 'get_citation' function
+#> To retrieve the citation for each use the 'get_citation' function
 
 # example forcing a single <epidist> to be returned
 eparam <- epidist_db(
@@ -255,7 +255,7 @@ 
Examples#> Using Lloyd-Smith J, Schreiber S, Kopp P, Getz W (2005). “Superspreading and
 #> the effect of individual variation on disease emergence.” _Nature_.
 #> doi:10.1038/nature04153 <https://doi.org/10.1038/nature04153>.. 
-#> To retrieve the short citation use the 'get_citation' function
+#> To retrieve the citation use the 'get_citation' function

Epidemiological Distribution