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fix methodology citations #360

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merged 4 commits into from
Feb 2, 2025
Merged

fix methodology citations #360

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ab4b861
try
d-morrison Feb 2, 2025
ea9d4f0
Increment version number to 1.3.0.9009
d-morrison Feb 2, 2025
c486f6c
news
d-morrison Feb 2, 2025
a43d5e4
Merge branch 'main' into fix-methodology
d-morrison Feb 2, 2025
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Type: Package
Package: serocalculator
Title: Estimating Infection Rates from Serological Data
Version: 1.3.0.9011
Version: 1.3.0.9012
Authors@R: c(
person("Peter", "Teunis", , "[email protected]", role = c("aut", "cph"),
comment = "Author of the method and original code."),
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2 changes: 2 additions & 0 deletions NEWS.md
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Expand Up @@ -2,6 +2,8 @@

## New features

* Fixed citations in `methodology.qmd` article (#360)

* Added outline to pkgdown website (#353)

* Added verbose option for `summary.seroincidence()` and
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1 change: 1 addition & 0 deletions vignettes/methodology.qmd
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Expand Up @@ -4,6 +4,7 @@
%\VignetteIndexEntry{Methodology}
%\VignetteEngine{quarto::html}
%\VignetteEncoding{UTF-8}
bibliography: references.bib
---

{{< include articles/_macros.qmd >}}
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library(dplyr)
# Import longitudinal antibody parameters from OSF
curves <-
"https://osf.io/download/rtw5k/" %>%

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file=vignettes/methodology.qmd,line=193,col=36,[pipe_consistency_linter] Use the |> pipe operator instead of the %>% pipe operator.
load_curve_params() %>%

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file=vignettes/methodology.qmd,line=194,col=23,[pipe_consistency_linter] Use the |> pipe operator instead of the %>% pipe operator.
filter(iter < 50)

# Import cross-sectional data from OSF and rename required variables:
xs_data <-
"https://osf.io/download//n6cp3/" %>%

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file=vignettes/methodology.qmd,line=199,col=37,[pipe_consistency_linter] Use the |> pipe operator instead of the %>% pipe operator.
load_pop_data()

noise <- url("https://osf.io/download//hqy4v/") %>% readRDS()

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file=vignettes/methodology.qmd,line=202,col=49,[pipe_consistency_linter] Use the |> pipe operator instead of the %>% pipe operator.
```

```{r}
#| fig-cap: "Example log(likelihood) curves"
#| label: fig-loglik
lik_HlyE_IgA <- graph_loglik(

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file=vignettes/methodology.qmd,line=208,col=1,[object_name_linter] Variable and function name style should match snake_case or symbols.
pop_data = xs_data,
curve_params = curves,
noise_params = noise,
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log_x = TRUE
)

lik_HlyE_IgG <- graph_loglik(

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file=vignettes/methodology.qmd,line=216,col=1,[object_name_linter] Variable and function name style should match snake_case or symbols.
previous_plot = lik_HlyE_IgA,
pop_data = xs_data,
curve_params = curves,
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