library(metapsyData)
library(metapsyTools)
library(tidyverse)

d <- getData("psychosis-psyctr", version = "23.0.4")
dat <- d$data

# Clear study labels, variable labels
dat %>%
    mutate(
        study = recode(study,
            `Färdig 2011` = "Färdig 2011",
            `Jørgensen  2015` = "Jørgensen 2015",
            `Jørgensen 2015` = "Jørgensen 2015",
            `SaÌ<81>nchez 2013` = "Sánchez 2013"),
        stage = replace_na(stage, "Unspecified"),
        clinical_picture = replace_na(clinical_picture, "Unspecified")
    ) -> dat

# Run combined MA for total symptom data
filterPoolingData(
  dat, symptom_domain  == "total") %>%
  runMetaAnalysis(which.run = "combined",
                  rho.within.study = 0.5,
                  which.combine = "arms") %>%
  {.$model.combined$data$N =
    .$model.combined$data$totaln_arm1 +
    .$model.combined$data$totaln_arm2;
    .$model.combined$data$rob = floor(.$model.combined$data$rob);
  .$model.combined$data} -> total

# Run combined MA for positive data
filterPoolingData(
  dat, symptom_domain  == "positive") %>%
  runMetaAnalysis(which.run = "combined",
                  rho.within.study = 0.5,
                  which.combine = "arms") %>%
  {.$model.combined$data$N =
    .$model.combined$data$totaln_arm1 +
    .$model.combined$data$totaln_arm2;
    .$model.combined$data$rob = floor(.$model.combined$data$rob);
  .$model.combined$data} -> positive


# Run combined MA for negative symptom data
filterPoolingData(
  dat, symptom_domain == "negative") %>%
  runMetaAnalysis(which.run = "combined",
                  rho.within.study = 0.5,
                  which.combine = "arms") %>%
  {.$model.combined$data$N =
   .$model.combined$data$totaln_arm1 +
   .$model.combined$data$totaln_arm2;
   .$model.combined$data$rob = floor(.$model.combined$data$rob);
   .$model.combined$data} -> negative

# Combine and save
list(total = total,
     positive = positive,
     negative = negative,
     metadata = d$returnMetadata()) -> PsychosisPsyCtrDB

save(PsychosisPsyCtrDB,
     file="www/data/PsychosisPsyCtrDB.rda")