simulate_breathtest_data {breathtestcore} | R Documentation |

## Simulate 13C breath time series data

### Description

Generates simulated breath test data, optionally with errors. If none of the three
standard deviations `m_std, k_std, beta_std`

is given, an empirical covariance
matrix from USZ breath test data is used. If any of the standard deviations is given,
default values for the others will be used.

### Usage

```
simulate_breathtest_data(
n_records = 10,
m_mean = 40,
m_std = NULL,
k_mean = 0.01,
k_std = NULL,
beta_mean = 2,
beta_std = NULL,
noise = 1,
cov = NULL,
student_t_df = NULL,
missing = 0,
seed = NULL,
dose = 100,
first_minute = 5,
step_minute = 15,
max_minute = 155
)
```

### Arguments

`n_records` |
Number of records |

`m_mean` , `m_std` |
Mean and between-record standard deviation of parameter m giving metabolized fraction. |

`k_mean` , `k_std` |
Mean and between-record standard deviation of parameter k, in units of 1/minutes. |

`beta_mean` , `beta_std` |
Mean and between-record standard deviations of lag parameter beta |

`noise` |
Standard deviation of normal noise when |

`cov` |
Covariance matrix, default NULL, i.e. not used. If given, overrides standard deviation settings. |

`student_t_df` |
When NULL (default), Gaussian noise is added; when >= 2, Student_t distributed noise is added, which generates more realistic outliers. Values from 2 to 5 are useful, when higher values are used the result comes close to that of Gaussian noise. Values below 2 are truncated to 2. |

`missing` |
When 0 (default), all curves have the same number of data points. When > 0, this is the fraction of points that were removed randomly to simulate missing |

`seed` |
Optional seed; not set if seed = NULL (default) |

`dose` |
Octanoate/acetate dose, almost always 100 mg, which is also the default |

`first_minute` |
First sampling time. Do not use 0 here, some algorithms do not converge when data near 0 are passed. |

`step_minute` |
Inter-sample interval for breath test |

`max_minute` |
Maximal time in minutes. |

### Value

A list of class simulated_breathtest_data with 2 elements:

- record
Data frame with columns

`patient_id(chr), m, k, beta, t50`

giving the effective parameters for the individual patient record.- data
Data frame with columns

`patient_id(chr), minute(dbl), pdr(dbl)`

giving the time series and grouping parameters.

A comment is attached to the return value that can be used as a title for plotting.

### Examples

```
library(ggplot2)
pdr = simulate_breathtest_data(n_records = 4, seed = 4711, missing = 0.3,
student_t_df = 2, noise = 1.5) # Strong outliers
#
str(pdr, 1)
#
pdr$record # The "correct" parameters
#
# Explicit plotting
ggplot(pdr$data, aes(x = minute, y = pdr)) + geom_point() +
facet_wrap(~patient_id) + ggtitle(comment(pdr$data))
#
# Or use cleanup_data and null_fit for S3 plotting
plot(null_fit(cleanup_data(pdr$data)))
```

*breathtestcore*version 0.8.7 Index]