---
title: "Introduction to metacor"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Introduction to metacor}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
library(metacor)
```

# metacor: Meta-analysis with correlated data

The `metacor` package provides tools for conducting meta-analyses when your effect sizes involve pre-post correlations, missing SDs, and flexible imputation methods. It is especially useful for single-group or controlled designs with incomplete data.

## Main Features

- Calculates multiple effect sizes (SMDpre, SMDchange, ScMDpooled, etc.)
- Handles missing correlations and SDs with advanced imputation methods
- Produces detailed imputation reports (Word)
- Flexible for intervention-only or control-intervention designs

## Quick Start Example

Let's illustrate a simple workflow with example data:

```{r}
library(metacor)

# Example dataset (for pre/post design only)
df <- data.frame(
  study_name = c("Study1", "Study2", "Study3", "Study4","Study5", "Study6", "Study7", "Study8", "Study9"),
  p_value_Int = c(1.038814e-07, NA, NA, NA, NA, 2.100000e-02, NA, NA, NA),
  n_Int = c(10, 10, 10, 10, 15, 15, 10, 10, 10),
  meanPre_Int = c(8.17, 10.09, 10.18, 9.85, 9.51,7.70, 10.00,  11.53, 11.20),
  meanPost_Int = c(10.12, 12.50, 12.56,10.41, 10.88, 9.20, 10.80,13.42,12.00),
  sd_pre_Int = c(1.83,0.67,0.66,0.90,0.62, 0.90, 0.70, 0.60, 1.90),
  sd_post_Int = c(1.85, 0.72, 0.97, 0.67, 0.76, 1.10, 0.70,0.80,1.80),
  upperCI_Int = c(NA, NA,NA, NA,NA, NA,NA, NA, NA),
  lowerCI_Int = c(NA, NA,NA, NA,NA, NA,NA, NA, NA))

results <- metacor_dual(df,
                        digits = 3,
                        method = "both",
                        apply_hedges = TRUE,
                        add_to_df = TRUE,
                        SMD_method = "SMDpre",
                        MeanDifferences = TRUE,
                        impute_method = "cv",
                        verbose = TRUE,
                        report_imputations = TRUE,
                        custom_sd_diff_int = NULL,
                        custom_sd_diff_con = NULL,
                        single_group = TRUE)
```

## Imputation and Reporting

If your dataset has missing values for correlations or SD differences, metacor_dual() will automatically perform imputations based on the method you choose (e.g., "direct", "mean", "cv"). You can also request a Word report with all imputations performed by setting the argument report_imputations = TRUE.

```{r}
result <- metacor_dual(df, report_imputations = TRUE)
```

The report will be saved as imputation_report.docx in your working directory.

## Advanced Usage

You can customise the imputation methods and other arguments. For more details, see the documentation:

```{r}
?metacor_dual

```

## References

Fu, R., Vandermeer, B. W., Shamliyan, T. A., O’Neil, M. E., Yazdi, F., Fox, S. H., & Morton, S. C. (2013). Handling Continuous Outcomes in Quantitative Synthesis. Methods Guide for Comparative Effectiveness Reviews. AHRQ Publication No. 13-EHC103-EF. Link

## Session info

```{r}
sessionInfo()
```


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