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Update MIT badge URL #87

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Feb 23, 2024
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Update MIT badge URL #87

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e8604a3
update MIT badge URL
joshwlambert Feb 23, 2024
23e4277
Automatic readme update
actions-user Feb 23, 2024
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2 changes: 1 addition & 1 deletion README.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@ knitr::opts_chunk$set(
# _simulist_: Simulate line list data <img src="man/figures/logo.svg" align="right" width="120" />

<!-- badges: start -->
[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/license/mit/)
[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/license/mit)
[![R-CMD-check](https://github.com/{{ gh_repo }}/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/{{ gh_repo }}/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://codecov.io/gh/{{ gh_repo }}/branch/main/graph/badge.svg)](https://app.codecov.io/gh/{{ gh_repo }}?branch=main)
[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
Expand Down
142 changes: 71 additions & 71 deletions README.md
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Expand Up @@ -10,7 +10,7 @@
<!-- badges: start -->

[![License:
MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/license/mit/)
MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/license/mit)
[![R-CMD-check](https://github.com/epiverse-trace/simulist/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/epiverse-trace/simulist/actions/workflows/R-CMD-check.yaml)
[![Codecov test
coverage](https://codecov.io/gh/epiverse-trace/simulist/branch/main/graph/badge.svg)](https://app.codecov.io/gh/epiverse-trace/simulist?branch=main)
Expand Down Expand Up @@ -125,20 +125,20 @@ linelist <- sim_linelist(
onset_to_death = onset_to_death
)
head(linelist)
#> id case_name case_type gender age date_onset date_admission
#> 1 1 Sabeeha el-Hannan probable f 28 2023-01-01 <NA>
#> 2 2 Jaedyn Robbins confirmed f 62 2023-01-02 2023-01-02
#> 5 5 Young Vu confirmed m 42 2023-01-01 <NA>
#> 6 6 Alyssa Gloyd probable f 60 2023-01-01 <NA>
#> 8 8 Sebastian Boden probable m 28 2023-01-02 2023-01-03
#> 9 9 Sierra Hernandez suspected f 78 2023-01-01 <NA>
#> date_death date_first_contact date_last_contact ct_value
#> 1 <NA> <NA> <NA> NA
#> 2 <NA> 2023-01-02 2023-01-05 25.1
#> 5 <NA> 2023-01-03 2023-01-04 25.1
#> 6 <NA> 2023-01-02 2023-01-04 NA
#> 8 <NA> 2023-01-01 2023-01-03 NA
#> 9 <NA> 2022-12-29 2023-01-04 NA
#> id case_name case_type sex age date_onset date_admission date_death
#> 1 1 Macella Moreland confirmed f 28 2023-01-01 <NA> <NA>
#> 2 2 Kayla Ellerman confirmed f 62 2023-01-02 2023-01-02 <NA>
#> 3 5 Matthew Biggerstaff confirmed m 42 2023-01-01 <NA> <NA>
#> 4 6 Vanessa Sihombing probable f 60 2023-01-01 <NA> <NA>
#> 5 8 Ross Mcclintock suspected m 28 2023-01-02 2023-01-03 <NA>
#> 6 9 Danielle Medero confirmed f 78 2023-01-01 <NA> <NA>
#> date_first_contact date_last_contact ct_value
#> 1 <NA> <NA> 23.6
#> 2 2023-01-02 2023-01-05 23.6
#> 3 2023-01-03 2023-01-04 23.6
#> 4 2023-01-02 2023-01-04 NA
#> 5 2023-01-01 2023-01-03 NA
#> 6 2022-12-29 2023-01-04 23.6
```

In this example, the line list is simulated using the default values
Expand All @@ -158,20 +158,20 @@ linelist <- sim_linelist(
outbreak_start_date = as.Date("2019-12-01")
)
head(linelist)
#> id case_name case_type gender age date_onset date_admission
#> 1 1 Aaren-Matthew Deguzman probable m 65 2019-12-01 <NA>
#> 2 2 Thaamira el-Yusuf confirmed f 61 2019-12-01 <NA>
#> 3 3 Hector Hickman suspected m 56 2019-12-01 <NA>
#> 4 4 Zuhriyaa al-Saleem probable f 36 2019-12-01 <NA>
#> 5 5 Chisa Xiong confirmed f 20 2019-12-01 <NA>
#> 6 6 Tre-Shawn Williams confirmed m 85 2019-12-02 2019-12-06
#> date_death date_first_contact date_last_contact ct_value
#> 1 <NA> <NA> <NA> NA
#> 2 <NA> 2019-11-26 2019-12-06 25.3
#> 3 <NA> 2019-11-28 2019-12-03 NA
#> 4 <NA> 2019-11-28 2019-12-02 NA
#> 5 <NA> 2019-11-28 2019-12-02 25.3
#> 6 <NA> 2019-12-01 2019-12-04 25.3
#> id case_name case_type sex age date_onset date_admission date_death
#> 1 1 Dakota Herman probable m 11 2019-12-01 <NA> <NA>
#> 2 5 Jose Dick confirmed m 20 2019-12-01 <NA> <NA>
#> 3 6 Fredric Mosley suspected m 38 2019-12-01 <NA> <NA>
#> 4 7 Ediht Valero-Zarate suspected f 71 2019-12-01 <NA> <NA>
#> 5 8 Kia Ouellette probable f 29 2019-12-01 <NA> <NA>
#> 6 10 Mukhtaar al-Samad probable m 8 2019-12-01 2019-12-07 <NA>
#> date_first_contact date_last_contact ct_value
#> 1 <NA> <NA> NA
#> 2 2019-12-03 2019-12-04 25.7
#> 3 2019-11-29 2019-12-01 NA
#> 4 2019-11-26 2019-12-03 NA
#> 5 2019-12-01 2019-12-07 NA
#> 6 2019-12-06 2019-12-07 NA
```

To simulate a table of contacts of cases (i.e. to reflect a contact
Expand All @@ -185,20 +185,20 @@ contacts <- sim_contacts(
prob_infect = 0.5
)
head(contacts)
#> from to age gender date_first_contact
#> 2 James Padilla Miranda Blanco 69 f 2022-12-31
#> 3 James Padilla Allan Bunge 83 m 2023-01-05
#> 4 Allan Bunge Nicholas Rabia 18 m 2023-01-02
#> 5 Allan Bunge Unais al-Shabazz 85 m 2023-01-04
#> 6 Nicholas Rabia Apiluck Chong 84 m 2022-12-30
#> 7 Nicholas Rabia Rachel Tyler 90 f 2023-01-02
#> date_last_contact was_case status
#> 2 2023-01-03 N unknown
#> 3 2023-01-05 Y case
#> 4 2023-01-05 Y case
#> 5 2023-01-06 Y case
#> 6 2023-01-02 N under_followup
#> 7 2023-01-04 Y case
#> from to age sex date_first_contact date_last_contact
#> 1 Hannah Johnson Amie Ismail 15 f 2023-01-01 2023-01-04
#> 2 Hannah Johnson Dravon Snell 13 m 2023-01-01 2023-01-04
#> 3 Hannah Johnson Travis Terry 34 m 2022-12-31 2023-01-06
#> 4 Hannah Johnson Marilyn Harling 56 f 2022-12-31 2023-01-03
#> 5 Travis Terry Daniel Laima 3 m 2023-01-06 2023-01-09
#> 6 Travis Terry Sean Brendle 84 m 2023-01-03 2023-01-06
#> was_case status
#> 1 Y case
#> 2 N under_followup
#> 3 Y case
#> 4 Y case
#> 5 Y case
#> 6 N lost_to_followup
```

If both the line list and contacts table are required, they can be
Expand All @@ -216,35 +216,35 @@ outbreak <- sim_outbreak(
onset_to_death = onset_to_death
)
head(outbreak$linelist)
#> id case_name case_type gender age date_onset date_admission
#> 1 1 Katherin Trancoso confirmed f 2 2023-01-01 <NA>
#> 4 4 E-Shaw Allen confirmed f 47 2023-01-01 <NA>
#> 5 5 Madison Moltrer suspected f 8 2023-01-01 <NA>
#> 8 8 Christopher Richter confirmed m 18 2023-01-02 2023-01-08
#> 11 11 Elias Mckenzie confirmed m 4 2023-01-01 <NA>
#> 12 12 Elaine Nguyen confirmed f 60 2023-01-02 <NA>
#> date_death date_first_contact date_last_contact ct_value
#> 1 <NA> <NA> <NA> 24.5
#> 4 <NA> 2023-01-02 2023-01-06 24.5
#> 5 <NA> 2022-12-31 2023-01-03 NA
#> 8 <NA> 2023-01-02 2023-01-03 24.5
#> 11 <NA> 2023-01-04 2023-01-06 24.5
#> 12 <NA> 2023-01-07 2023-01-09 24.5
#> id case_name case_type sex age date_onset date_admission date_death
#> 1 1 Y Nhi Eisele confirmed f 24 2023-01-01 <NA> <NA>
#> 2 3 Rorie Lawrence probable f 43 2023-01-01 2023-01-06 <NA>
#> 3 4 Wahida Bui probable f 16 2023-01-03 <NA> <NA>
#> 4 5 Navya Smalldon probable f 17 2023-01-01 <NA> <NA>
#> 5 8 Sebastian Padilla suspected m 88 2023-01-02 <NA> <NA>
#> 6 9 Lizzelle Schoon confirmed f 40 2023-01-01 <NA> <NA>
#> date_first_contact date_last_contact ct_value
#> 1 <NA> <NA> 24.2
#> 2 2023-01-01 2023-01-04 NA
#> 3 2022-12-30 2023-01-03 NA
#> 4 2023-01-02 2023-01-07 NA
#> 5 2022-12-31 2023-01-02 NA
#> 6 2022-12-29 2023-01-02 24.2
head(outbreak$contacts)
#> from to age gender date_first_contact
#> 2 Katherin Trancoso David Mcafee 46 m 2023-01-02
#> 3 Katherin Trancoso Firdaus al-Hamidi 68 f 2022-12-30
#> 4 Katherin Trancoso E-Shaw Allen 47 f 2023-01-02
#> 5 Katherin Trancoso Madison Moltrer 8 f 2022-12-31
#> 6 E-Shaw Allen Tyko Pahang 24 m 2023-01-05
#> 7 Madison Moltrer Bryan Rodriguez 67 m 2022-12-31
#> date_last_contact was_case status
#> 2 2023-01-02 N lost_to_followup
#> 3 2023-01-02 N under_followup
#> 4 2023-01-06 Y case
#> 5 2023-01-03 Y case
#> 6 2023-01-05 N lost_to_followup
#> 7 2023-01-02 N under_followup
#> from to age sex date_first_contact date_last_contact
#> 1 Y Nhi Eisele Najwa el-Mohammed 49 f 2023-01-03 2023-01-04
#> 2 Y Nhi Eisele Rorie Lawrence 43 f 2023-01-01 2023-01-04
#> 3 Y Nhi Eisele Wahida Bui 16 f 2022-12-30 2023-01-03
#> 4 Y Nhi Eisele Navya Smalldon 17 f 2023-01-02 2023-01-07
#> 5 Y Nhi Eisele Cole Batmanglidj 42 m 2022-12-29 2023-01-02
#> 6 Rorie Lawrence Aerika White Bear 74 f 2023-01-03 2023-01-05
#> was_case status
#> 1 N under_followup
#> 2 Y case
#> 3 Y case
#> 4 Y case
#> 5 N under_followup
#> 6 N lost_to_followup
```

## Help
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