inst/doc/ir-class.R

In ir: Functions to Handle and Preprocess Infrared Spectra

## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.align = "center",
  fig.width = 6.5,
  fig.height = 3.5
)

## ----load-package-ir----------------------------------------------------------
library(ir)

## ---- results='hide'----------------------------------------------------------
ir_sample_data

## ---- echo=FALSE--------------------------------------------------------------
rmarkdown::paged_table(ir_sample_data)

## -----------------------------------------------------------------------------
head(ir_sample_data$spectra[[1]])

## ---- results='hide'----------------------------------------------------------
d <- ir_sample_data
d$spectra[[1]] <- d$spectra[[1]][0, ]
d$spectra[[1]]

ir_normalize(d, method = "area")

## ---- echo=FALSE--------------------------------------------------------------
d <- ir_sample_data
d$spectra[[1]] <- d$spectra[[1]][0, ]
d$spectra[[1]]

rmarkdown::paged_table(ir_normalize(d, method = "area"))

## -----------------------------------------------------------------------------
methods(class = "ir")

## ---- results='hide'----------------------------------------------------------
ir_sample_data[5:10, ]

## ---- echo=FALSE--------------------------------------------------------------
rmarkdown::paged_table(ir_sample_data[5:10, ])

## -----------------------------------------------------------------------------
d1 <- ir_sample_data

class(d1[, setdiff(colnames(d), "id_sample")])

d1$spectra <- NULL
class(d1)

## -----------------------------------------------------------------------------
d2 <- ir_sample_data
d2$spectra[[1]] <- rep(d2$spectra[[1]], 2)
class(d2)

d3 <- ir_sample_data
colnames(d3$spectra[[1]]) <- c("a", "b")
class(d3)

## ---- results='hide'----------------------------------------------------------
library(dplyr)

d <- ir_sample_data

d <- 
  d %>%
  mutate(a = rnorm(n = nrow(.)))
  
head(ir_sample_data)

## ---- echo=FALSE--------------------------------------------------------------
library(dplyr)

d <- ir_sample_data

d1 <- 
  d %>%
  mutate(a = rnorm(n = nrow(.)))
  
rmarkdown::paged_table(head(ir_sample_data))

## -----------------------------------------------------------------------------
library(purrr)
library(ggplot2)

d2 <- 
  d %>%
  group_by(sample_type) %>%
  summarize(
    spectra = {
      res <- map_dfc(spectra, function(.x) .x[, 2, drop = TRUE])
      spectra[[1]] %>%
        dplyr::mutate(
          y =
            res %>%
            rowwise() %>%
            mutate(y = max(c_across(everything()))) %>%
            pull(y)
        ) %>%
        list()
    },
    .groups = "drop"
  )

plot(d2) + 
  facet_wrap(~ sample_type)

## ---- results='hide'----------------------------------------------------------
ir_sample_data %>%
  slice(2) %>%
  rep(20)

## ---- echo=FALSE--------------------------------------------------------------
ir_sample_data %>%
  slice(2) %>%
  rep(20) %>%
  rmarkdown::paged_table()

## -----------------------------------------------------------------------------
ir_sample_data %>%
  slice(2) %>%
  ir_subtract(y = ir_sample_data[3, ]) %>%
  dplyr::mutate(id_sample = "subtraction_result") %>%
  rbind(ir_sample_data[2:3, ]) %>%
  plot() + facet_wrap(~ id_sample)

## ---- error=TRUE--------------------------------------------------------------
# This will not work
ir_sample_data %>%
  slice(6) %>%
  ir_add(y = ir_sample_data[3:4, ])

# but this will
ir_sample_data %>%
  slice(2:6) %>%
  ir_add(y = ir_sample_data[3, ]) 

## -----------------------------------------------------------------------------
ir_sample_data[2, ] + ir_sample_data[3, ]
ir_sample_data[2, ] - ir_sample_data[3, ]
ir_sample_data[2, ] * ir_sample_data[3, ]
ir_sample_data[2, ] / ir_sample_data[3, ]

## ---- echo=FALSE--------------------------------------------------------------
sessionInfo()