comparison.Rmd

# Comparison # 

## Data Summary ##

```{r}
comp <- read_xls(params$file, sheet = sheets$comp)
comp$GSP <- gsub(pattern="<|>",replacement="", x=comp$GSP, perl = TRUE) ## remove <,>
comp$GSP <- as.numeric(comp$GSP)
comp %<>%
##    na.omit() %>%
    filter(GSP >= info$lower & GSP <= info$upper & design == "p")

pander::pander(summary(comp[, c("AD", "GSP")]), caption = "\\label{tb:comp}Summary of Method Comparison Values")
```

```{r, fig.cap="\\label{fig:dens}Density plot for the method comparison"}
  comp %>%
      gather(method, result, AD:GSP) %>%
      ggplot(aes(result, fill = method)) +
      geom_density(alpha = 0.5) +
      xlab(paste(params$analyte, info$units)) +
      scale_fill_discrete(name = "Method")
```


```{r, fig.cap="\\label{fig:dens_inst}Density plot for the method comparison by instrument"}
comp %>%
      gather(method, result, AD:GSP) %>%
      ggplot(aes(result, fill = method)) +
      geom_density(alpha = 0.5) +
      facet_grid(instrument ~.) +
      xlab(paste(params$analyte, info$units)) +
      scale_fill_discrete(name = "Method")
ggsave("density.pdf")
``` 
\FloatBarrier

### Paired T-test ###

```{r}
pander::pander(t.test(comp$AD, comp$GSP, paired = TRUE),
                   caption = "\\label{tab:paired}Paired T-test")
```

### Regression Analysis ###

```{r, fig.cap="\\label{fig:dem}Deming regression"}
comp.deming <- mcreg(x = comp$AD, y =comp$GSP, error.ratio = 1, alpha = 0.05,
                     mref.name = "AD", mtest.name = "GSP", sample.names = NULL,
                     method.reg = "Deming", method.ci = "bootstrap",
                     method.bootstrap.ci = "BCa",
                     nsamples = 999, rng.seed = NULL, rng.kind = "Mersenne-Twister", iter.max = 30,
                     threshold = 1e-06, na.rm = TRUE, NBins = 1e+06)

plot(comp.deming, x.lab = "AD", y.lab = "GSP", main=paste("Pooled", params$analyte,"Method Comparision"))
```

```{r, fig.cap="\\label{fig:dem_inst}Deming regression by instrument"}
for (inst in c(344, 348, 349)){
    comp_inst<- comp %>%
        filter(instrument == inst)

    comp_inst.deming <- mcreg(x = comp_inst$AD, y =comp_inst$GSP, error.ratio = 1, alpha = 0.05,
                              mref.name = "AD", mtest.name = "GSP", sample.names = NULL,
                              method.reg = "Deming", method.ci = "bootstrap",
                              method.bootstrap.ci = "BCa",
                              nsamples = 999, rng.seed = NULL, rng.kind = "Mersenne-Twister", iter.max = 30,
                              threshold = 1e-06, na.rm = TRUE, NBins = 1e+06)

    plot(comp_inst.deming, x.lab = "AD", y.lab = "GSP", main=paste(inst, params$analyte, "Method Comparision" ))
}
```

\FloatBarrier