Nothing
## ----echo = FALSE, include = FALSE--------------------------------------------
library(knitr)
library(dplyr)
library(stringr)
opts_chunk$set(comment = NA, fig.width = 4, fig.height = 3)
knitr::opts_knit$set(unnamed.chunk.label = "btcore_data_")
options(digits = 3)
## -----------------------------------------------------------------------------
library(breathtestcore)
head(btcore_file())
btcore_file("Standard.TXT")
## -----------------------------------------------------------------------------
files = c(
btcore_file("IrisCSV.TXT"), # Wagner/IRIS format
btcore_file("350_20043_0_GER.txt") # BreathID
)
bt = read_any_breathtest(files)
# Returns a list of elements of class breathtest_data
str(bt, 1)
bt_df = cleanup_data(bt)
str(bt_df)
## ----nf, fig.height = 2, fig.width =4-----------------------------------------
nf = null_fit(bt_df)
str(nf)
plot(nf) # dispatches to plot.breathtestfit
## ----three, fig.height = 2.5, fig.width = 8-----------------------------------
files1 = c(
group_a = btcore_file("IrisCSV.TXT"), # Use only single file with grouping
group_a = btcore_file("Standard.TXT"),
group_b = btcore_file("350_20043_0_GER.txt")
)
# Alternative syntax using magrittr operator
suppressPackageStartupMessages(library(dplyr))
read_any_breathtest(files1) %>%
cleanup_data() %>%
null_fit() %>%
plot()
## ----simulated, fig.height = 5, fig.width = 6, fig.cap = "Example of a cross-over design with missing data, outliers and missing record in the red curve."----
set.seed(212)
data = list(meal_a = simulate_breathtest_data(n_records = 3, noise = 2,
student_t_df = 3, missing = 0.3),
meal_b = simulate_breathtest_data(n_records = 4))
data %>%
cleanup_data() %>%
nlme_fit() %>%
plot()
## ----fig.cap= "Function simulate_breathtest_data returns the values of the parameters used to generate the data. These can be used to check the results of the model prediction."----
data$meal_a$record
## -----------------------------------------------------------------------------
data("usz_13c")
cat("usz_13c has data from", length(unique(usz_13c$patient_id)), "patients with" ,
length(unique(usz_13c$group)), "different meals")
## ----fig.height = 3, include = FALSE------------------------------------------
knitr::include_graphics("breathtestshiny.png")
## ----echo = FALSE, include = FALSE--------------------------------------------
options(tibble.print_min= 4)
options(digits = 2)
## -----------------------------------------------------------------------------
(bt = read_breathtest_excel(btcore_file("ExcelSamples.xlsx"), "2col"))
## -----------------------------------------------------------------------------
(cbt = cleanup_data(bt))
## ----nlsfit, height = 3, width = 4--------------------------------------------
cbt %>% nls_fit() %>% plot()
## -----------------------------------------------------------------------------
(bt = read_breathtest_excel(btcore_file("ExcelSamples.xlsx"), "3col"))
## -----------------------------------------------------------------------------
(cbt = cleanup_data(bt))
## ----four_col "---------------------------------------------------------------
bt = read_breathtest_excel(btcore_file("ExcelSamples.xlsx"), "4col_2group") %>%
cleanup_data()
kable(sample_frac(bt, 0.08) %>% arrange(patient_id, group), caption = "A sample from a four-column format. See worksheet 4col_2group.")
## ----nlme_fit, fig.width = 7--------------------------------------------------
bt %>% nlme_fit() %>% plot()
## ----iriswagner, fig.cap = "IRIS/Wagner composite file. These data cannot be fitted successfully with the single-curve fit method, therefore only data are shown."----
read_iris(btcore_file("IrisMulti.TXT")) %>%
cleanup_data() %>%
null_fit() %>%
plot()
## ----iris_csv, fig.cap = "IRIS/Wagner CSV file"-------------------------------
read_iris_csv(btcore_file("Standard.TXT")) %>%
cleanup_data() %>%
nls_fit() %>%
plot()
## ----breathidc, fig.cap = "BreathID composite file"---------------------------
read_breathid(btcore_file("350_20043_0_GER.txt")) %>%
cleanup_data() %>%
nls_fit() %>%
plot()
## ----breathid_xml, fig.cap = "BreathID XML format"----------------------------
read_breathid_xml(btcore_file("NewBreathID_multiple.xml")) %>%
cleanup_data() %>%
nls_fit() %>%
plot()
## ----breathid_man, fig.cap = "BreathID XML format with manual grouping."------
# Could also use read_any_breathtest()
read_breathid_xml(btcore_file("NewBreathID_multiple.xml")) %>%
cleanup_data() %>%
mutate(
group = "New"
) %>%
nls_fit() %>%
plot()
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