v1.0.0

.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$
+^LICENSE\.md$
+^README\.Rmd$
+^data-raw$
+^doc$
+^Meta$
+^\.github$

.github/.gitignore

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+*.html

.github/workflows/R-CMD-check.yaml

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+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.gitignore

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+.Rproj.user
+.Rhistory
+inst/doc
+/doc/
+/Meta/
+.DS_Store
+# Payne dataset - do not git/bundle #
+PayneEtAl.zip
+fyp26zjgmj-1

DESCRIPTION

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+Package: chronogram
+Title: Chronogram: Adaptive Data Casting for Pandemic Data Analysis
+Version: 1.0.0
+Authors@R: c(
+    person("Edward", "Carr", email="[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0001-9343-4593")),
+    person("David", "Greenwood", email="[email protected]", role = c("aut")),
+    person("Marianne", "Shawe-Taylor", email="[email protected]", role = c("aut"))
+    )       
+Description: A system to "cast" laboratory and clinical data 
+    into a tidy-like data structure. 
+    This allows rapid, intuititive integration of different data 
+    sources - for example, PCR, viral sequencing and participant 
+    symptom diaries - and bridges the gap between a laboratory
+    information management system (LIMS) and a data structure to allow testing of biological hypotheses. 
+    A chronogram has a flexible design not limited to a particular
+    pathogen, vaccine schedule, or experimental assays.
+License: MIT + file LICENSE
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3
+Imports: 
+    DBI,
+    dbplyr,
+    dplyr,
+    gginnards,
+    ggplot2,
+    glue,
+    lobstr,
+    lubridate,
+    magrittr,
+    patchwork,    
+    purrr,
+    rlang (>= 0.4.11),
+    RSQLite,
+    stringr,
+    tibble,
+    tidyr,
+    vctrs
+Suggests: 
+    rmarkdown,
+    knitr,
+    testthat (>= 3.0.0),
+    roxygen2
+Config/testthat/edition: 3
+VignetteBuilder: knitr
+LazyData: true
+Depends: 
+    R (>= 2.10)

LICENSE

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+YEAR: 2023
+COPYRIGHT HOLDER: chronogram authors

LICENSE.md

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+# MIT License
+
+Copyright (c) 2023 chronogram authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+S3method("[",cg_tbl)
+S3method("[",grouped_cg_df)
+S3method("names<-",cg_tbl)
+S3method("names<-",grouped_cg_df)
+S3method(dplyr_col_modify,cg_tbl)
+S3method(dplyr_col_modify,grouped_cg_df)
+S3method(dplyr_reconstruct,cg_tbl)
+S3method(dplyr_reconstruct,grouped_cg_df)
+S3method(dplyr_row_slice,cg_tbl)
+S3method(dplyr_row_slice,grouped_cg_df)
+S3method(glimpse,cg_tbl)
+S3method(glimpse,grouped_cg_df)
+S3method(glimpse_experiment_data,cg_tbl)
+S3method(glimpse_metadata,cg_tbl)
+S3method(group_by,cg_tbl)
+S3method(print,cg_skl_tbl)
+S3method(print,cg_tbl)
+S3method(print,grouped_cg_df)
+S3method(ungroup,grouped_cg_df)
+export("%>%")
+export(":=")
+export(.data)
+export(as_label)
+export(as_name)
+export(cg_add_experiment)
+export(cg_add_treatment)
+export(cg_annotate_antigenic_history)
+export(cg_annotate_episodes_count)
+export(cg_annotate_episodes_fill)
+export(cg_annotate_episodes_find)
+export(cg_annotate_episodes_find_seroconversion)
+export(cg_annotate_exposures_count)
+export(cg_annotate_vaccines_count)
+export(cg_assemble)
+export(cg_load)
+export(cg_plot)
+export(cg_plot_meta)
+export(cg_save)
+export(cg_select_visit)
+export(cg_window_by_episode)
+export(cg_window_by_metadata)
+export(cg_window_by_visit)
+export(chronogram)
+export(chronogram_skeleton)
+export(enquo)
+export(enquos)
+export(glimpse_experiment_data)
+export(glimpse_metadata)
+export(group_data_trim)
+export(new_grouped_chronogram)
+export(new_tbl2chronogram)
+importFrom(dplyr,dplyr_col_modify)
+importFrom(dplyr,dplyr_reconstruct)
+importFrom(dplyr,dplyr_row_slice)
+importFrom(dplyr,glimpse)
+importFrom(dplyr,group_by)
+importFrom(dplyr,group_data)
+importFrom(dplyr,ungroup)
+importFrom(magrittr,"%>%")
+importFrom(rlang,":=")
+importFrom(rlang,.data)
+importFrom(rlang,as_label)
+importFrom(rlang,as_name)
+importFrom(rlang,enquo)
+importFrom(rlang,enquos)