New main features into refac

.github/ISSUE_TEMPLATE/bug_report.md

@@ -10,7 +10,7 @@ assignees: ''
 Please place an "x" in all the boxes that apply
 ---------------------------------------------
 
-- [ ] I have the most recent version of linelist and R
+- [ ] I have the most recent version of vaccineff and R
 - [ ] I have found a bug
 - [ ] I have a [reproducible example](http://reprex.tidyverse.org/articles/reprex-dos-and-donts.html)
 - [ ] I want to request a new feature

DESCRIPTION

@@ -2,18 +2,29 @@ Package: vaccineff
 Title: Estimate Vaccine Effectiveness Based on Different Study Designs
 Version: 0.0.1
 Authors@R: c(
-    person(given = "Zulma M.", family = "Cucunubá", email = "zulma.cucunuba@javeriana.edu.co", role = c("aut", "cre"),
-        comment = c(ORCID = "0000-0002-8165-3198")),
     person(given = "David Santiago", family = "Quevedo", email = "ex-dsquevedo@javeriana.edu.co", role = c("aut"),
         comment = c(ORCID = "0000-0003-1583-4262")),
-    person(given = "Santiago", family = "Loaiza", email = "santiago.loaiza@javeriana.edu.co", role = c("aut"),
-        comment = c(ORCID = "0000-0002-2092-3262")),
+    person(given = "Zulma M.", family = "Cucunubá", email = "zulma.cucunuba@javeriana.edu.co", role = c("aut", "cre"),
+        comment = c(ORCID = "0000-0002-8165-3198")),
+    person("International Development Research Center (IDRC)", role = c("fnd")),
     person(given = "Geraldine", family = "Gómez Millán", email = "geralidine.gomez@javeriana.edu.co", role = c("ctb"),
         comment = c(ORCID = "0009-0007-8701-0568")),
     person(given = "Pratik", family = "Gupte", email = "pratik.gupte@lshtm.ac.uk", role = c("ctb"), 
-           comment = c(ORCID = "0000-0001-5294-7819"))
+        comment = c(ORCID = "0000-0001-5294-7819")),
+    person(given = "Érika J", family = "Cantor", email = "erika.cantor@javeriana.edu.co", role = c("ctb"), 
+        comment = c(ORCID = "0000-0003-3320-6032")),
+    person(given = "Santiago", family = "Loaiza", email = "santiago.loaiza@javeriana.edu.co", role = c("ctb"),
+        comment = c(ORCID = "0000-0002-2092-3262")),
+    person(given = "Jaime", family = "Pavlich-Mariscal", email = "jpavlich@javeriana.edu.co", role = c("ctb"),
+           comment = c(ORCID = "0000-0002-3892-6680")),
+    person(given = "Hugo", family = "Gruson", email = "hugo.gruson@data.org", role = c("ctb"),
+           comment = c(ORCID = "0000-0002-4094-1476")),
+    person(given = "Chris", family = "Hartgerink", email = "chris@data.org", role = "ctb",
+           comment = c(ORCID = "0000-0003-1050-6809")),
+    person(given = "Felipe Segundo", family = "Abril", email = "fsabrilb@unal.edu.co", role = "ctb",
+           comment = c(ORCID = "0000-0002-2512-4929"))
   )
-Description: Estimate vaccine effectiveness based on different observational study designs, as discussed in Torvaldsen and McIntyre (2020) <doi:10.3316/informit.511798489353134>.
+Description: R package with tools for estimating vaccine effectiveness and vaccine related metrics.
 URL: https://github.com/epiverse-trace/vaccineff, https://epiverse-trace.github.io/vaccineff/
 BugReports: https://github.com/epiverse-trace/vaccineff/issues
 License: MIT + file LICENSE

R/coh_matching.R

@@ -173,27 +173,21 @@ get_censoring_date_match <- function(data,
     data,
     min.rows = 1L
   )
+
+  # check for string type
+  checkmate::assert_string(outcome_date_col)
+  checkmate::assert_string(censoring_date_col)
+
   # check for names in data
   checkmate::assert_names(
     colnames(data),
-    must.include = c(outcome_date_col, censoring_date_col)
-  )
-  # check for subclass
-  checkmate::expect_names(
-    colnames(data),
-    must.include = "subclass",
-    info = "'subclass' column from match must be included in 'data' to \
-      identify matched couples."
+    must.include = c(outcome_date_col, censoring_date_col, "subclass")
   )
 
   # check for date type
   checkmate::assert_date(data[[outcome_date_col]])
   checkmate::assert_date(data[[censoring_date_col]])
 
-  # check for string type
-  checkmate::assert_string(outcome_date_col)
-  checkmate::assert_string(censoring_date_col)
-
   # create censoring date for every couple indexed by subclass
   censoring_date <- unlist(
     tapply(data[[censoring_date_col]],

README.Rmd

@@ -29,15 +29,11 @@ knitr::opts_chunk$set(
 
 <!-- badges: end -->
 
-*{{ packagename }}* is an R package that offers tools for estimating the
-vaccine effectiveness, using a series of epidemiological designs including cohort studies, test-negative case-control, and screening
-methods [@torvaldsen2020]. The package provides a set of features for preparing the data,
-to analyze different study designs and for assessing the performance of
-the models.
-
 *{{ packagename }}* is developed at [Pontificia Universidad Javeriana](https://www.javeriana.edu.co/inicio) as part of the
 [Epiverse-TRACE initiative](https://data.org/initiatives/epiverse/).
 
+*{{ packagename }}* is an R package that offers tools for estimating vaccine effectiveness, using a series of epidemiological designs including cohort studies, test-negative case-control, and screening methods [@torvaldsen2002]. The current version of the package provides a set of features for preparing, visualizing, and managing cohort data, estimating vaccine effectiveness, and assessing the performance of the models. Test-negative design and screening method will be included in future versions.
+
 ## Installation
 
 The current development version of _{{ packagename }}_ can be installed from [GitHub](https://github.com/) using the `pak` package.
@@ -53,8 +49,8 @@ pak::pak("{{ gh_repo }}")
 library(vaccineff)
 ```
 
-*{{ packagename }}* provides minimal datasets that can be used to test out
-each design `(cohortdata, testnegdata, screeningdata)`
+*{{ packagename }}* provides a minimal cohort dataset that can be used to test out
+the models.
 
 ```{r example, include = TRUE, echo = TRUE}
 # Load example `cohortdata` included in the package
@@ -74,25 +70,16 @@ To report a bug or to request a new feature please open an [issue](https://githu
 
 Contributions to _{{ packagename }}_ are welcomed. Please follow the [package contributing guide](https://github.com/{{ gh_repo }}/blob/main/.github/CONTRIBUTING.md).
 
-## Code of conduct
-
-Please note that the _{{ packagename }}_ project is released with a [Contributor Code of Conduct](https://github.com/epiverse-trace/.github/blob/main/CODE_OF_CONDUCT.md). By contributing to this project, you agree to abide by its terms.
-
-## Contributions
-
 Contributors to the project include:
 
--   [David Santiago Quevedo](https://github.com/davidsantiagoquevedo)
-    (author)
+**Authors**: [David Santiago Quevedo](https://github.com/davidsantiagoquevedo) and [Zulma M. Cucunubá](https://github.com/zmcucunuba) (maintainer)
 
--   [Zulma M. Cucunubá](https://github.com/zmcucunuba) (author)
+**Contributors**:
+[Geraldine Gómez](https://github.com/GeraldineGomez), [Pratik Gupte](https://github.com/pratikunterwegs), [Érika J. Cantor](https://github.com/ErikaCantor), [Santiago Loaiza](https://github.com/santilo9513), [Jaime A. Pavlich-Mariscal](https://github.com/jpavlich), [Hugo Gruson](https://github.com/Bisaloo), [Chris Hartgerink](https://github.com/chartgerink), [Felipe Segundo Abril-Bermúdez](https://github.com/fsabrilb)
 
--   [Santiago Loaiza](https://github.com/santilo9513) (author)
 
--   [Geraldine Gómez](https://github.com/GeraldineGomez) (contributor)
-
--   [Jaime A. Pavlich-Mariscal](https://github.com/jpavlich) (contributor)
+## Code of conduct
 
--   [Pratik Gupte](https://github.com/pratikunterwegs) (contributor)
+Please note that the _{{ packagename }}_ project is released with a [Contributor Code of Conduct](https://github.com/epiverse-trace/.github/blob/main/CODE_OF_CONDUCT.md). By contributing to this project, you agree to abide by its terms.
 
 ## References

README.md

@@ -17,17 +17,19 @@ status](https://www.r-pkg.org/badges/version/vaccineff)](https://CRAN.R-project.
 
 <!-- badges: end -->
 
-*vaccineff* is an R package that offers tools for estimating the vaccine
-effectiveness, using a series of epidemiological designs including
-cohort studies, test-negative case-control, and screening methods
-([Torvaldsen and McIntyre 2020](#ref-torvaldsen2020)). The package
-provides a set of features for preparing the data, to analyze different
-study designs and for assessing the performance of the models.
-
 *vaccineff* is developed at [Pontificia Universidad
 Javeriana](https://www.javeriana.edu.co/inicio) as part of the
 [Epiverse-TRACE initiative](https://data.org/initiatives/epiverse/).
 
+*vaccineff* is an R package that offers tools for estimating vaccine
+effectiveness, using a series of epidemiological designs including
+cohort studies, test-negative case-control, and screening methods
+([Torvaldsen and McIntyre 2002](#ref-torvaldsen2002)). The current
+version of the package provides a set of features for preparing,
+visualizing, and managing cohort data, estimating vaccine effectiveness,
+and assessing the performance of the models. Test-negative design and
+screening method will be included in future versions.
+
 ## Installation
 
 The current development version of *vaccineff* can be installed from
@@ -40,19 +42,25 @@ pak::pak("epiverse-trace/vaccineff")
 
 ## Quick start
 
-*vaccineff* provides minimal datasets that can be used to test out each
-design `(cohortdata, testnegdata, screeningdata)`
+*vaccineff* provides a minimal cohort dataset that can be used to test
+out the models.
 
 ``` r
 # Load example `cohortdata` included in the package
 data("cohortdata")
 head(cohortdata, 5)
-#>   sex age subsidy death_date vaccine_date_1 vaccine_date_2 vaccine_1 vaccine_2
-#> 1   F   6       0       <NA>           <NA>           <NA>      <NA>      <NA>
-#> 2   M  79       0       <NA>     2044-03-31     2044-05-07    BRAND2    BRAND2
-#> 3   F  34       0       <NA>     2044-07-26     2044-09-03    BRAND2    BRAND2
-#> 4   M  26       0       <NA>           <NA>           <NA>      <NA>      <NA>
-#> 5   F  66       0       <NA>     2044-05-20     2044-06-17    BRAND2    BRAND2
+#>         id sex age death_date death_other_causes vaccine_date_1 vaccine_date_2
+#> 1 afade1b2   F  37       <NA>               <NA>           <NA>           <NA>
+#> 2 556c8c76   M  19       <NA>               <NA>           <NA>           <NA>
+#> 3 04edf85a   M  50       <NA>               <NA>           <NA>           <NA>
+#> 4 7e51a18e   F   8       <NA>               <NA>           <NA>           <NA>
+#> 5 c5a83f56   M  66       <NA>               <NA>           <NA>           <NA>
+#>   vaccine_1 vaccine_2
+#> 1      <NA>      <NA>
+#> 2      <NA>      <NA>
+#> 3      <NA>      <NA>
+#> 4      <NA>      <NA>
+#> 5      <NA>      <NA>
 ```
 
 ## Package vignettes
@@ -73,40 +81,39 @@ Contributions to *vaccineff* are welcomed. Please follow the [package
 contributing
 guide](https://github.com/epiverse-trace/vaccineff/blob/main/.github/CONTRIBUTING.md).
 
+Contributors to the project include:
+
+**Authors**: [David Santiago
+Quevedo](https://github.com/davidsantiagoquevedo) and [Zulma M.
+Cucunubá](https://github.com/zmcucunuba) (maintainer)
+
+**Contributors**: [Geraldine Gómez](https://github.com/GeraldineGomez),
+[Pratik Gupte](https://github.com/pratikunterwegs), [Érika J.
+Cantor](https://github.com/ErikaCantor), [Santiago
+Loaiza](https://github.com/santilo9513), [Jaime A.
+Pavlich-Mariscal](https://github.com/jpavlich), [Hugo
+Gruson](https://github.com/Bisaloo), [Chris
+Hartgerink](https://github.com/chartgerink), [Felipe Segundo
+Abril-Bermúdez](https://github.com/fsabrilb)
+
 ## Code of conduct
 
 Please note that the *vaccineff* project is released with a [Contributor
 Code of
 Conduct](https://github.com/epiverse-trace/.github/blob/main/CODE_OF_CONDUCT.md).
 By contributing to this project, you agree to abide by its terms.
 
-## Contributions
-
-Contributors to the project include:
-
-- [David Santiago Quevedo](https://github.com/davidsantiagoquevedo)
-  (author)
-
-- [Zulma M. Cucunubá](https://github.com/zmcucunuba) (author)
-
-- [Santiago Loaiza](https://github.com/santilo9513) (author)
-
-- [Geraldine Gómez](https://github.com/GeraldineGomez) (contributor)
-
-- [Jaime A. Pavlich-Mariscal](https://github.com/jpavlich) (contributor)
-
-- [Pratik Gupte](https://github.com/pratikunterwegs) (contributor)
-
 ## References
 
-<div id="refs" class="references csl-bib-body hanging-indent">
+<div id="refs" class="references csl-bib-body hanging-indent"
+entry-spacing="0">
 
-<div id="ref-torvaldsen2020" class="csl-entry">
+<div id="ref-torvaldsen2002" class="csl-entry">
 
-Torvaldsen, S., and P. B. McIntyre. 2020. “Observational Methods in
+Torvaldsen, S., and P. B. McIntyre. 2002. “Observational Methods in
 Epidemiologic Assessment of Vaccine Effectiveness.” *Communicable
 Diseases Intelligence Quarterly Report* 26 (3).
-<https://doi.org/10.3316/informit.511798489353134>.
+<https://pubmed.ncbi.nlm.nih.gov/12416713/>.
 
 </div>
 

inst/WORDLIST

@@ -48,3 +48,7 @@ steelblue
 darkred
 coh
 MatchIt
+Bermúdez
+IDRC
+Érika
+funder

vignettes/references.json

@@ -1,3 +1,3 @@
 [
-  {"id":"torvaldsen2020","accessed":{"date-parts":[[2023,7,5]]},"author":[{"family":"Torvaldsen","given":"S."},{"family":"McIntyre","given":"P. B."}],"citation-key":"torvaldsen2020","container-title":"Communicable Diseases Intelligence Quarterly Report","DOI":"10.3316/informit.511798489353134","issue":"3","issued":{"date-parts":[[2020,8,23]]},"publisher":"Australian Government Department of Health","source":"search.informit.org (Atypon)","title":"Observational methods in epidemiologic assessment of vaccine effectiveness","type":"article-journal","URL":"https://search.informit.org/doi/abs/10.3316/INFORMIT.511798489353134","volume":"26"}
+  {"id":"torvaldsen2002","accessed":{"date-parts":[[2024,5,2]]},"author":[{"family":"Torvaldsen","given":"S."},{"family":"McIntyre","given":"P. B."}],"citation-key":"torvaldsen2002","container-title":"Communicable Diseases Intelligence Quarterly Report","issue":"3","issued":{"date-parts":[[2002,8,23]]},"publisher":"Australian Government Department of Health","source":"health.gov.au","title":"Observational methods in epidemiologic assessment of vaccine effectiveness","type":"article-journal","URL":"https://pubmed.ncbi.nlm.nih.gov/12416713/","volume":"26"}
 ]