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Update {epiparameter} usage #106

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Oct 10, 2024
Merged

Update {epiparameter} usage #106

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2 changes: 1 addition & 1 deletion tests/testthat/test-probability_contain.R
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Original file line number Diff line number Diff line change
Expand Up @@ -96,7 +96,7 @@ test_that("probability_contain works with <epiparameter>", {
od <- suppressMessages(
epiparameter::epiparameter_db(
disease = "SARS",
epi_dist = "offspring distribution",
epi_name = "offspring distribution",
author = "Lloyd-Smith",
single_epiparameter = TRUE
)
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2 changes: 1 addition & 1 deletion tests/testthat/test-probability_epidemic.R
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Expand Up @@ -99,7 +99,7 @@ test_that("probability_epidemic works with <epiparameter>", {
od <- suppressMessages(
epiparameter::epiparameter_db(
disease = "SARS",
epi_dist = "offspring distribution",
epi_name = "offspring distribution",
author = "Lloyd-Smith",
single_epiparameter = TRUE
)
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2 changes: 1 addition & 1 deletion tests/testthat/test-proportion_cluster_size.R
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Expand Up @@ -89,7 +89,7 @@ test_that("proportion_cluster_size works with <epiparameter>", {
od <- suppressMessages(
epiparameter::epiparameter_db(
disease = "SARS",
epi_dist = "offspring distribution",
epi_name = "offspring distribution",
author = "Lloyd-Smith",
single_epiparameter = TRUE
)
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2 changes: 1 addition & 1 deletion tests/testthat/test-proportion_transmission.R
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Expand Up @@ -183,7 +183,7 @@ test_that("proportion_transmission works with <epiparameter>", {
od <- suppressMessages(
epiparameter::epiparameter_db(
disease = "SARS",
epi_dist = "offspring distribution",
epi_name = "offspring distribution",
author = "Lloyd-Smith",
single_epiparameter = TRUE
)
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4 changes: 2 additions & 2 deletions tests/testthat/test-utils.R
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Expand Up @@ -2,7 +2,7 @@ if (requireNamespace("epiparameter", quietly = TRUE)) {
od <- suppressMessages(
epiparameter::epiparameter_db(
disease = "SARS",
epi_dist = "offspring distribution",
epi_name = "offspring distribution",
author = "Lloyd-Smith",
single_epiparameter = TRUE
)
Expand All @@ -29,7 +29,7 @@ test_that("get_param fails as expected with incorrect parameters", {
od <- suppressMessages(
epiparameter::epiparameter_db(
disease = "COVID-19",
epi_dist = "incubation period",
epi_name = "incubation period",
author = "Linton",
single_epiparameter = TRUE
)
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2 changes: 1 addition & 1 deletion vignettes/proportion_transmission.Rmd
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Expand Up @@ -88,7 +88,7 @@ To show the proportion of transmission using both methods we can load the estima
```{r, load-offspring-dist}
library(epiparameter)
offspring_dists <- epiparameter_db(
epi_dist = "offspring distribution"
epi_name = "offspring distribution"
)
```

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4 changes: 2 additions & 2 deletions vignettes/superspreading.Rmd
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Expand Up @@ -119,12 +119,12 @@ diseases and evaluate how likely they are to cause epidemics.
```{r, epiparam}
sars <- epiparameter_db(
disease = "SARS",
epi_dist = "offspring distribution",
epi_name = "offspring distribution",
single_epiparameter = TRUE
)
evd <- epiparameter_db(
disease = "Ebola Virus Disease",
epi_dist = "offspring distribution",
epi_name = "offspring distribution",
single_epiparameter = TRUE
)
```
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