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Pre process parameter dataframes for meta analysis of proportions #31

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ebdedbc
new function to pre process parameter dataframes for meta analysis of…
annecori Apr 26, 2024
5761f47
bump epireview version
annecori Apr 29, 2024
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4 changes: 4 additions & 0 deletions priority-pathogens.Rproj
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Expand Up @@ -11,3 +11,7 @@ Encoding: UTF-8

RnwWeave: Sweave
LaTeX: pdfLaTeX

BuildType: Package
PackageUseDevtools: Yes
PackageInstallArgs: --no-multiarch --with-keep.source
10 changes: 3 additions & 7 deletions shared/lassa_functions.R
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Expand Up @@ -232,13 +232,9 @@ metaprop_wrap <- function(dataframe, subgroup,
plot_pooled, sort_by_subg, plot_study, digits, colour,
width, height, resolution){

stopifnot(length(unique(dataframe$parameter_unit[!is.na(dataframe$parameter_unit)])) == 1)#values must have same units

dataframe <- dataframe %>% filter(!is.na(cfr_ifr_denominator)) %>%
filter(!(is.na(cfr_ifr_numerator)&is.na(parameter_value))) %>%
mutate(cfr_ifr_numerator = case_when(
is.na(cfr_ifr_numerator) & !is.na(parameter_value) ~ round((parameter_value/100)*cfr_ifr_denominator),
TRUE ~ cfr_ifr_numerator))
dataframe <- epireview::filter_df_for_metaprop(dataframe,
num_col = "cfr_ifr_numerator",
denom_col = "cfr_ifr_denominator")

mtan <- metaprop(data = dataframe,
studlab = refs,
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6 changes: 6 additions & 0 deletions src/lassa_severity/orderly.R
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Expand Up @@ -17,6 +17,12 @@ library(png)
library(grid)
library(patchwork)
library(gridExtra)
if(packageVersion("epireview") < "1.1.3") {
error_msg <-
paste("Please download the latest development version of epireview using:",
"devtools::install_github('mrc-ide/epireview@develop')")
stop(error_msg)
}

#orderly preparation
orderly_strict_mode()
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