gfpop Vignette

Vincent Runge

LaMME, Evry University

March 2, 2022

Quick Start

Some examples

Graph construction

Supplementary R functions

Quick Start

we present a basic use of the main functions of the gfpop package. More details about the theory of graph-cosntrained multiple change-point detection can be found here

We install the package from Github:

#devtools::install_github("vrunge/gfpop")
library(gfpop)

We simulate some univariate gaussian data (n = 1000 points) with relative change-point positions 0.1, 0.3, 0.5, 0.8, 1 and means 1, 2, 1, 3, 1 with a variance equal to 1.

n <- 1000
myData <- dataGenerator(n, c(0.1,0.3,0.5,0.8,1), c(1,2,1,3,1), sigma = 1)

We define the graph of constraints to use for the dynamic programming algorithm. A simple case is the up-down constraint with a penalty here equal to a classic 2 log(n).

myGraph <- graph(penalty = 2*log(n), type = "updown")

The gfpop function gives the result of the segmentation using myData and myGraph as parameters. We choose a gaussian cost.

gfpop(data = myData, mygraph = myGraph, type = "mean")
## $changepoints
## [1]  100  298  500  800 1000
## 
## $states
## [1] "Dw" "Up" "Dw" "Up" "Dw"
## 
## $forced
## [1] FALSE FALSE FALSE FALSE
## 
## $parameters
## [1] 1.0317856 1.9865414 0.9697470 3.0359938 0.8527903
## 
## $globalCost
## [1] 1010.133
## 
## attr(,"class")
## [1] "gfpop" "mean"

The vector changepoints gives the last index of each segment. It always ends with the length of the vector vectData.

The vector states contains the states in which lies each mean. The length of this vector is the same as the length of changepoint.

The vector forced is a boolean vector. A forced element means that two consecutive means have been forced to satisfy the constraint. For example, the “up” edge with parameter c is forced if m(i+1) - m(i) = c.

The vector parameters contains the inferred means/parameters of the successive segments.

The number globalCost is equal to the non-penalized cost, that is the value of the fit to the data ignoring the penalties for adding changes.

Some examples

Isotonic regression

The isotonic regression infers a sequence of nondecreasing means.

n <- 1000
mydata <- dataGenerator(n, c(0.1, 0.2, 0.3, 0.4, 0.6, 0.8, 1), c(0, 0.5, 1, 1.5, 2, 2.5, 3), sigma = 1)
myGraphIso <- graph(penalty = 2*log(n), type = "isotonic")
gfpop(data =  mydata, mygraph = myGraphIso, type = "mean")
## $changepoints
## [1]  186  361  713 1000
## 
## $states
## [1] "Iso" "Iso" "Iso" "Iso"
## 
## $forced
## [1] FALSE FALSE FALSE
## 
## $parameters
## [1] 0.1250638 1.2483475 2.1161519 2.8636266
## 
## $globalCost
## [1] 992.7441
## 
## attr(,"class")
## [1] "gfpop" "mean"

In this example, we use in gfpop function a robust biweight gaussian cost with K = 1 and the min parameter in order to infer means greater than 0.5.

Fixed number of change-points

This algorithm is called segment neighborhood in the change-point litterature. In this example, we fixed the number of segments at 3 with an isotonic constraint. The graph contains two “up” edges with no cycling.

n <- 1000
mydata <- dataGenerator(n, c(0.1, 0.2, 0.3, 0.4, 0.6, 0.8, 1), c(0, 0.5, 1, 1.5, 2, 2.5, 3), sigma = 1)
beta <- 0
myGraph <- graph(
  Edge(0, 1,"up", beta),
  Edge(1, 2, "up", beta),
  Edge(0, 0, "null"),
  Edge(1, 1, "null"),
  Edge(2, 2, "null"),
  StartEnd(start = 0, end = 2))

gfpop(data =  mydata, mygraph = myGraph, type = "mean")
## $changepoints
## [1]  323  705 1000
## 
## $states
## [1] "0" "1" "2"
## 
## $forced
## [1] FALSE FALSE
## 
## $parameters
## [1] 0.5031993 2.1549691 2.9441510
## 
## $globalCost
## [1] 1102.695
## 
## attr(,"class")
## [1] "gfpop" "mean"

Robust up-down with constrained starting and ending states

In presence of outliers we need a robust loss (biweight). We can also force the starting and ending state and a minimal gap between the means (here equal to 1)

n <- 1000
chgtpt <- c(0.1, 0.3, 0.5, 0.8, 1)
myData <- dataGenerator(n, chgtpt, c(0, 1, 0, 1, 0), sigma = 1)
myData <- myData + 5 * rbinom(n, 1, 0.05) - 5 * rbinom(n, 1, 0.05)
beta <- 2 * log(n)
myGraph <- graph(
         Edge("Dw", "Up", type = "up", penalty = beta, gap = 1, K = 3),
         Edge("Up", "Dw", type = "down", penalty = beta, gap = 1, K = 3),
         Edge("Dw", "Dw", type = "null", K = 3),
         Edge("Up", "Up", type = "null", K = 3),
         StartEnd(start = "Dw", end = "Dw"))
gfpop(data =  myData, mygraph = myGraph, type = "mean")
## $changepoints
## [1]  100  312  500  800 1000
## 
## $states
## [1] "Dw" "Up" "Dw" "Up" "Dw"
## 
## $forced
## [1]  TRUE FALSE FALSE FALSE
## 
## $parameters
## [1]  0.0456763883  1.0456763883 -0.0603308658  1.0383495117 -0.0003792976
## 
## $globalCost
## [1] 1110.176
## 
## attr(,"class")
## [1] "gfpop" "mean"

Robust up-down with constrained starting and ending states

In presence of outliers we need a robust loss (biweight). We can also force the starting and ending state and a minimal gap between the means (here equal to 1)

n <- 1000
chgtpt <- c(0.1, 0.3, 0.5, 0.8, 1)
myData <- dataGenerator(n, chgtpt, c(0, 1, 0, 1, 0), sigma = 1)
myData <- myData + 5 * rbinom(n, 1, 0.05) - 5 * rbinom(n, 1, 0.05)
beta <- 2 * log(n)
myGraph <- graph(
         Edge("Dw", "Up", type = "up", penalty = beta, gap = 1, K = 3),
         Edge("Up", "Dw", type = "down", penalty = beta, gap = 1, K = 3),
         Edge("Dw", "Dw", type = "null", K = 3),
         Edge("Up", "Up", type = "null", K = 3),
         StartEnd(start = "Dw", end = "Dw"))
gfpop(data =  myData, mygraph = myGraph, type = "mean")
## $changepoints
## [1]  113  300  500  796 1000
## 
## $states
## [1] "Dw" "Up" "Dw" "Up" "Dw"
## 
## $forced
## [1] FALSE FALSE  TRUE FALSE
## 
## $parameters
## [1] -0.17825898  1.09464865  0.00177342  1.00177342 -0.20725183
## 
## $globalCost
## [1] 1065.075
## 
## attr(,"class")
## [1] "gfpop" "mean"

If we skip all these constraints and use a standard fpop algorithm, the result is the following

myGraphStd <- graph(penalty = 2*log(n), type = "std")
gfpop(data =  myData, mygraph = myGraphStd, type = "mean")
## $changepoints
##  [1]   29   30   51   56   58   65   66   99  101  143  144  145  197  199  207
## [16]  208  242  245  246  282  283  306  307  350  351  356  357  378  379  392
## [31]  393  426  427  429  430  446  447  494  496  509  510  529  530  556  557
## [46]  570  571  575  577  605  606  616  617  620  621  676  677  718  722  723
## [61]  746  747  769  770  780  781  821  822  829  830  892  893  898  899  908
## [76]  909  912  913  914  921  926  930  931  975  977  998 1000
## 
## $states
##  [1] "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std"
## [14] "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std"
## [27] "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std"
## [40] "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std"
## [53] "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std"
## [66] "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std"
## [79] "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std" "Std"
## 
## $forced
##  [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [14] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [27] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [40] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [53] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [66] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [79] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## 
## $parameters
##  [1]  0.013157272  5.852235983  0.397219746 -2.487036978  4.306750060 -0.459086261
##  [7] -6.020547264 -0.580351710  5.041691711  0.767738682  5.961869168 -4.888515188
## [13]  1.104751718  6.573977997  0.319794566 -4.738167431  0.833793130 -2.899282191
## [19]  6.688410838  1.228639284 -4.269924074  0.404707460 -6.793861272  0.003291056
## [25]  6.506591287  0.629007228 -5.756058094 -0.259927168 -5.736196028  0.362430172
## [31]  5.983851635 -0.083938587 -6.728110389 -0.201933380 -5.596212715  0.515240779
## [37] -5.724921497 -0.233094949 -3.954707046  1.376006649  6.850232664  0.807237359
## [43] -4.772661389  1.572871812  7.044477776  0.419697210  6.576539303  0.668004319
## [49] -4.089779401  1.165036227  6.569345168  0.950959210  6.681891964  1.106775879
## [55]  7.174884098  0.932498620  7.593847560  0.593401906  3.024204730 -4.575301756
## [61]  1.347643390 -4.167946713  0.779419604  6.188344490  1.295509948  6.468646144
## [67]  0.008155765  5.288100272 -0.317542994  5.547977558  0.073240269  5.784884068
## [73]  0.018864107 -5.515696794  0.218333250 -6.987266782  0.513760015 -5.093780701
## [79]  5.643352084 -0.154778961 -4.128204915 -0.544777860  5.729519458 -0.404145572
## [85]  3.440665204  0.088765491  2.860110512
## 
## $globalCost
## [1] 1467.21
## 
## attr(,"class")
## [1] "gfpop" "mean"

abs edge

With a unique "abs" edge, we impose a difference between the means of size at least 1.

n <- 10000
myData <- dataGenerator(n, c(0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1), c(0, 1, 0, 2, 1, 2, 0, 1, 0, 1), sigma = 0.5)
beta <- 2*log(n)
myGraph <- graph(
  Edge(0, 0,"abs", penalty = beta, gap = 1),
  Edge(0, 0,"null"))
gfpop(data =  myData, mygraph = myGraph, type = "mean")
## $changepoints
##  [1]   999  2000  3000  4000  4999  6000  7000  8000  8999 10000
## 
## $states
##  [1] "0" "0" "0" "0" "0" "0" "0" "0" "0" "0"
## 
## $forced
## [1]  TRUE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE  TRUE
## 
## $parameters
##  [1] -0.001621797  0.998378203 -0.001621797  2.018687659  1.000371240  2.000371240
##  [7]  0.007557667  1.039364965 -0.007114006  0.992885994
## 
## $globalCost
## [1] 2417.046
## 
## attr(,"class")
## [1] "gfpop" "mean"

Notice that some of the edges are forced, the vector forced contains non-zero values.

Exponential decay

The null edge corresponds to an exponential decay state if its parameter is not equal to 1.

n <- 1000
mydata <- dataGenerator(n, c(0.2, 0.5, 0.8, 1), c(5, 10, 15, 20), sigma = 1, gamma = 0.966)
beta <- 2*log(n)
myGraphDecay <- graph(
  Edge(0, 0, "up", penalty = beta),
  Edge(0, 0, "null", 0, decay = 0.966)
  )
g <- gfpop(data =  mydata, mygraph = myGraphDecay, type = "mean")
g
## $changepoints
## [1]  200  322  500  800 1000
## 
## $states
## [1] "0" "0" "0" "0" "0"
## 
## $forced
## [1] FALSE FALSE FALSE FALSE
## 
## $parameters
## [1] 0.0049454559 0.1510457319 0.0028802127 0.0004721947 0.0194129929
## 
## $globalCost
## [1] 976.4308
## 
## attr(,"class")
## [1] "gfpop" "mean"

and we plot the result

gamma <- 0.966
len <- diff(c(0, g$changepoints))
signal <- NULL
for(i in length(len):1)
  {signal <- c(signal, g$parameters[i]*c(1, cumprod(rep(1/gamma,len[i]-1))))}
signal <- rev(signal)

ylimits <- c(min(mydata), max(mydata))
plot(mydata, type ='p', pch ='+', ylim = ylimits)
par(new = TRUE)
plot(signal, type ='l', col = 4, ylim = ylimits, lwd = 3)
plot of chunk unnamed-chunk-12

Graph construction

In the gfpop package, graphs are represented by a dataframe with 9 features and build with the R functions Edge, Node, StartEnd and graph.

emptyGraph <- graph()
emptyGraph
## [1] state1    state2    type      parameter penalty   K         a        
## [8] min       max      
## <0 lignes> (ou 'row.names' de longueur nulle)

state1 is the starting node of an edge, state2 its ending node. type is one of the available edge type ("null", "std", "up", "down", "abs"). penalty is a nonnegative parameter: the additional cost \(\beta_i\) to consider when we move within the graph using a edge (or stay on the same node). parameter is annother nonnegative parameter, a characteristics of the edge, depending of its type (it is a decay if type is “null” and a gap otherwise). K and a are robust parameters. min and max are used to constrain the rang of value for the node parameter.

We add edges into a graph as follows

myGraph <- graph(
  Edge("E1", "E1", "null"),
  Edge("E1", "E2", "down", 3.1415, gap = 1.5)
)
myGraph
##   state1 state2 type parameter penalty   K a min max
## 1     E1     E1 null       1.0       0 Inf 0  NA  NA
## 2     E1     E2 down       1.5       0 Inf 0  NA  NA

we can only add edges to this dataframe using the object Edge.

The graph can contain information on the starting and/or ending edge to use with the StartEnd function.

beta <- 2 * log(1000)
myGraph <- graph(
  Edge("Dw", "Dw", "null"),
  Edge("Up", "Up", "null"),
  Edge("Dw", "Up", "up", penalty = beta, gap = 1),
  Edge("Dw", "Dw", "down", penalty = beta),
  Edge("Up", "Dw", "down", penalty = beta),
  StartEnd(start = "Dw", end = "Dw"))
myGraph
##   state1 state2  type parameter  penalty   K  a min max
## 1     Dw     Dw  null         1  0.00000 Inf  0  NA  NA
## 2     Up     Up  null         1  0.00000 Inf  0  NA  NA
## 3     Dw     Up    up         1 13.81551 Inf  0  NA  NA
## 4     Dw     Dw  down         0 13.81551 Inf  0  NA  NA
## 5     Up     Dw  down         0 13.81551 Inf  0  NA  NA
## 6     Dw   <NA> start        NA       NA  NA NA  NA  NA
## 7     Dw   <NA>   end        NA       NA  NA NA  NA  NA

Some graphs are often used: they are defined by default in the graph function. To use these graphs, we specify a string type equal to "std", "isotonic", "updown" or "relevant". For example,

myGraphIso <- graph(penalty = 12, type = "isotonic")
myGraphIso
##   state1 state2 type parameter penalty   K a min max
## 1    Iso    Iso null         1       0 Inf 0  NA  NA
## 2    Iso    Iso   up         0      12 Inf 0  NA  NA

The function Node can be used to restrict the range of value for parameter associated to a node (called also a vertex). For example the following graph is an isotonic graph with inferred parameters between 0 et 1 only.

myGraph <- graph(
  Edge("Up", "Up", "up", penalty = 3.1415),
  Edge("Up", "Up"),
  Node("Up", min = 0, max = 1)
  )
myGraph
##   state1 state2 type parameter penalty   K  a min max
## 1     Up     Up   up         0  3.1415 Inf  0  NA  NA
## 2     Up     Up null         1  0.0000 Inf  0  NA  NA
## 3     Up     Up node        NA      NA  NA NA   0   1

Supplementary R functions

Data generator function

the dataGenerator function is used to simulate n data-points from a distribution of type equal to "mean", "poisson", "exp", "variance" or "negbin". Standard deviation parameter sigma and decay gamma are specific to the Gaussian mean model. size is linked to the R rnbinom function from R stats package.

Standard deviation estimation

We often need to estimate the standard deviation from the observed data to normalize the data or choose the edge penalties. The sdDiff returns such an estimation with the default HALL method [Hall et al., 1990] well suited for time series with change-points.

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