From a PAFitData object, which contains summary statistics summerized from the dataset, PAFit estimates the attachment function *A_k* and node fitness *η_i* by penalized log-likelihood maximization. It also calculates confidence intervals for *A_k* and *η_i*. Estimation of the attachment function in isolation (while fixing *η_i = 1*) can be specified by setting only_PA = TRUE. Estimation of node fitness in isolation (fixing either *A_k = k* or *A_k = 1*) can be specified by setting only_f = TRUE.

1 2 3 4 5 6 7 | ```
PAFit (data, only_PA = FALSE, only_f = FALSE,
mode_f = c("Linear_PA", "Constant_PA","Log_linear"),
true_A = NULL, true_f = NULL, s = 1, auto_lambda = TRUE,
r = 0.01, lambda = 1, weight_PA_mode = 1, auto_stop = TRUE,
stop_cond = 10^-6, iteration = 20, max_iter = 1000,
debug = FALSE, alpha_start = 1, normalized_f = FALSE,
interpolate = TRUE, ...)
``` |

`data` |
An object of class "PAFitData" containing all the summary statistics summerized from the data by the function GetStatistics |

`only_PA` |
Logical. TRUE means that the attachment function |

`only_f` |
Logical. TRUE means that the fitness function is estimated in isolation. Default is FALSE. |

`mode_f` |
String. Only effective when only_f == TRUE. If mode_f == "Linear_PA" then |

`true_A` |
Numeric vector. If the true_A is supplemented, then only fitness is estimated. |

`true_f` |
Numeric vector. If the true_f is supplemented, then only PA is estimated. |

`s` |
Numeric. The regularization parameter |

`auto_lambda` |
Logical. If auto_lambda == TRUE, lambda will be determined automatically from the data. Default is TRUE. |

`r` |
Numeric. The regularization parameter |

`lambda` |
Numeric. The strength of the regularization for PA function. Ignored when auto_lambda == TRUE. Default value is |

`weight_PA_mode` |
Integer. Indicates how the regularization terms for |

`auto_stop` |
Logical. Indicates whether the algorithm stop automatically or not. Default is TRUE |

`stop_cond` |
Numeric. If |

`iteration` |
Numeric. The number of iterations. Ignored if auto_stop == TRUE. Default value is |

`max_iter` |
Numeric. The maximum number of iterations. Regardless of other settings, the algorithm will stop once the number of iterations reaches this threshold. Default value is |

`debug` |
Logical. if debug == TRUE, the value of the objective function |

`alpha_start` |
Numeric. The starting value for alpha when we use the model |

`normalized_f` |
Logical. Indicates whether we should normalize the estimated value of |

`interpolate` |
Logical. Indicates whether we should perform interpolation for the missing values of the estimated |

`...` |

an object of class "PAFit", which is a list. Some important fields of this object:

`A ` |
The estimated attachment function |

`k` |
The corresponding degree |

`var_A` |
Variances of the estimated A |

`linear_fit` |
Result of fitting the log-linear model |

`alpha` |
The estimated attachment exponent of the log-linear model |

`weight_of_A` |
The number of A in each bin |

`var_logA` |
Variances of log(A) |

`upper_A` |
The upper value of the 2-sigma confidence interval of A |

`lower_A` |
The lower value of the 2-sigma confidence interval of A |

`center_k` |
The logarithmic center of the bins |

`theta` |
Attachment value of the bins (before converting back to |

`upper_bin` |
The upper value of the 2-sigma confidence interval of theta |

`lower_bin` |
The lower value of the 2-sigma confidence interval of theta |

`f` |
The estimated node fitnesses |

`var_f` |
Variances of the estimated node fitnesses |

`upper_f` |
The upper value of the 2-sigma confidence interval of |

`lower_f` |
The lower value of the 2-sigma confidence interval of |

`objective_value` |
Values of the objective function |

Thong Pham thongpham@thongpham.net

1. Pham, T., Sheridan, P. & Shimodaira, H. (2016). Nonparametric Estimation of the Preferential Attachment Function in Complex Networks: Evidence of Deviations from Log Linearity, Proceedings of ECCS 2014, 141-153 (Springer International Publishing) (http://dx.doi.org/10.1007/978-3-319-29228-1_13).

2. Pham, T., Sheridan, P. & Shimodaira, H. (2015). PAFit: A Statistical Method for Measuring Preferential Attachment in Temporal Complex Networks. PLoS ONE 10(9): e0137796. doi:10.1371/journal.pone.0137796 (http://dx.doi.org/10.1371/journal.pone.0137796).

3. Pham, T., Sheridan, P. & Shimodaira, H. (2016). Joint Estimation of Preferential Attachment and Node Fitness in Growing Complex Networks. Scientific Reports 6, Article number: 32558. doi:10.1038/srep32558 (www.nature.com/articles/srep32558).

1 2 3 4 | ```
library("PAFit")
data <- GenerateNet(N = 100,m = 1, mode = 1, alpha = 1, shape = 5, rate = 5)
stats <- GetStatistics(data$graph)
result <- PAFit(stats,stop_cond = 10^-3)
``` |

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