# LZeroSpikeInference v1.0.1

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## Exact Spike Train Inference via L0 Optimization

An implementation of algorithms described in Jewell and Witten (2017) <arXiv:1703.08644>.

## Readme

# LZeroSpikeInference: A package for estimating spike times from calcium imaging data using an L0 penalty

This package implements an algorithm for deconvolving calcium imaging data for a single neuron in order to estimate the times at which the neuron spikes.

This algorithm solves the optimization problems

### AR(1) model

minimize*{c1,...,cT} 0.5 sum*{t=1}^T ( y_t - c*t )^2 + lambda sum*{t=2}^T 1_{c*t neq gamma c*{t-1} }

for the global optimum, where y_t is the observed fluorescence at the tth timepoint.

### AR(1) with intercept

minimize*{c1,...,cT,b1,...,bT} 0.5 sum*{t=1}^T (y_t - c_t - b*t)^2 + lambda sum*{t=2}^T 1_{c*t neq gamma c*{t-1}, b*t neq b*{t-1} }

where the indicator variable 1_{(A,B)} equals 1 if the event A cup B holds, and equals zero otherwise.

## Install

If `devtools`

is installed type

```
devtools::install_github("jewellsean/LZeroSpikeInference")
```

## Usage

Once installed type

```
library(LZeroSpikeInference)
?LZeroSpikeInference
```

## Reference

See Jewell and Witten, Exact Spike Train Inference Via L0 Optimization (2017)

## Functions in LZeroSpikeInference

Name | Description | |

plot.estimatedSpikes | Plot the solution to an L0 segmentation problem | |

plot.simdata | Plot simulated data | |

estimateSpikes | Estimate spike train, underlying calcium concentration, and changepoints based on fluorescence | |

plot.cvSpike | Plot mean squared error vs. tuning parameter from the cross-validation output | |

print.cvSpike | Print CV results | |

print.estimatedSpikes | Print estimated spikes | |

LZeroSpikeInference | LZeroSpikeInference: LZeroSpikeInference: A package for estimating spike | |

cv.estimateSpikes | Cross-validate and optimize model parameters | |

print.simdata | Print simulated data | |

simulateAR1 | Simulate fluorescence trace based on simple AR(1) generative model | |

No Results! |

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