From 1dc9f03f8d814263902dc1b2a8dff3c4b4db9ef5 Mon Sep 17 00:00:00 2001 From: joshwlambert Date: Thu, 28 Mar 2024 11:34:21 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20epiverse?= =?UTF-8?q?-trace/epiparameter@18e9dd866addf2c4168a007260fb6b0a99843738=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- apple-touch-icon-120x120.png | Bin 16870 -> 16870 bytes apple-touch-icon-152x152.png | Bin 22476 -> 22476 bytes apple-touch-icon-180x180.png | Bin 27397 -> 27397 bytes apple-touch-icon-60x60.png | Bin 6395 -> 6395 bytes apple-touch-icon-76x76.png | Bin 9023 -> 9023 bytes apple-touch-icon.png | Bin 27397 -> 27397 bytes articles/data_protocol.html | 4 +- articles/epiparameter.html | 12 +- articles/extract_convert.html | 4 +- favicon-16x16.png | Bin 1401 -> 1401 bytes favicon-32x32.png | Bin 2570 -> 2570 bytes news/index.html | 11 +- pkgdown.yml | 2 +- .../convert_params_to_summary_stats.html | 4 +- .../convert_summary_stats_to_params.html | 2 +- reference/epidist_db.html | 8 +- reference/get_citation.epidist.html | 4 +- reference/get_citation.multi_epidist.html | 132 +----------------- reference/get_parameters.epidist.html | 2 +- reference/is_parameterised.html | 2 +- reference/list_distributions.html | 4 +- reference/mean.epidist.html | 2 +- search.json | 2 +- 23 files changed, 38 insertions(+), 157 deletions(-) diff --git a/apple-touch-icon-120x120.png b/apple-touch-icon-120x120.png index 3b550e769978fc19f7788d77bf11d062cca2074d..74b86372ee6a403e238d1220b971b1546225703d 100644 GIT binary patch delta 95 zcmaFX%=oOCaY7Y`47Z$KeqN2|#-cndllA>l&eJkp8hSc5=C6J^+nn9H9UJ delta 95 zcmaFX%=oOCaY7Y`q>!QIt&Wv?8=E#bxSEC-T3DG_TA7+_8yHv_7({ob7&9<1sFt`! ll%yncndllA>l&eJ(7JM`e{#8FJ^-=S9Yg>C diff --git a/apple-touch-icon-152x152.png b/apple-touch-icon-152x152.png index dc481cdb53f01f3606fb33a6ceb1e17288eabc6a..b880cdf671aec6523138ffbb5baaf2bfd417f150 100644 GIT binary patch delta 71 zcmX@Jp7G3j#tBs%GTd_d5}7{tH#SWR6R`*}G_*1{ure{%HZZU+EjZNn>T`fWk4Xum~tV}Gl4GgS+Xjal51_lPz64!{5 kl*E!$tK9sQ%(O}dBLgE7T?1oXBXkYk$8RxAo|csl0Dv?co&W#< delta 95 zcmZp@#@Kp|aY7Y`q>vHAx&=i~H#VKmbTthzw6HQYure^vHUN>YLl<0TU|>)!ag8WR jNi0dV%FR#7OsixtGB7gHH89pSLf0^hLn43jw5)sp0WlrC diff --git a/apple-touch-icon-60x60.png b/apple-touch-icon-60x60.png index 4784362b0f7fe840624ae28075ad3a9d0257311a..77dd3b551ffe7a120a482b19b11e5ff84fc299b0 100644 GIT binary patch delta 69 zcmexu_}g$o6^9JBoK9ncZ0g3Qqv9eKA%=!l#s*d!LJSS9j180|) delta 69 zcmdn*w%=_+6^Epdp~c$%nL9Q%aVm+Jh8S8{nOItxnrRytSQ!}n{g>Z9dA^b?hD6We L>(-MmDCGkHGOQON diff --git a/apple-touch-icon.png b/apple-touch-icon.png index ad0101a08bceaff1036f0a114b2a9e2644eea601..c5fbf5189d6f284e78ed10031f881f4a504ca552 100644 GIT binary patch delta 95 zcmZp@#@Kp|aY7Y`47Z%&qqM?38=KB&x>|%78d@0}SeaOA8yHv_7|eN_$-%(DpjzS@ mQIe8al4_NkpOTqY$zWt)WTI;q8WtTP9D-$_D`AV;=JW delta 95 zcmZp@#@Kp|aY7Y`q>vHg&E-zT8=KB&x|)UVScope 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 d245950f388c820517c4bf5e5340e4ac7a7f8b2f..d40d4cc1f166e4cc5acaa2ecc3e81ba356245112 100644
GIT binary patch
delta 71
zcmey#^^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