set-up tests

diff --git a/pkg/tests/testthat/test.computeFilaments.R b/pkg/tests/testthat/test.computeFilaments.R
index 9de6274..46f2e3f 100644 (file)
--- a/pkg/tests/testthat/test.computeFilaments.R
+++ b/pkg/tests/testthat/test.computeFilaments.R
@@ -1,36 +1,51 @@
-#TODO: toy dataset, check that indices returned are correct + colors
+context("Check that computeFilaments behaves as expected")

 
 

-context("Check that getParamsDirs behaves as expected")
-
-test_that("on input of sufficient size, beta is estimated accurately enough", {
-       n = 100000
-       d = 2
-       K = 2
-       Pr = c(0.5, 0.5)
-
-       betas_ref = array( c(1,0,0,1 , 1,-2,3,1), dim=c(2,2,2) )
-       for (i in 1:(dim(betas_ref)[3]))
+test_that("output is as expected on simulated series",
+{
+       x = seq(0,10,0.1)
+       L = length(x)
+       s1 = cos(x)
+       s2 = sin(x)
+       s3 = c( s1[1:(L%/%2)] , s2[(L%/%2+1):L] )
+       #sum((s1-s2)^2) == 97.59381
+       #sum((s1-s3)^2) == 57.03051
+       #sum((s2-s3)^2) == 40.5633
+       s = list( s1, s2, s3 )
+       n = 150
+       series = list()
+       for (i in seq_len(n))

        {
        {

-               beta_ref = betas_ref[,,i]
-               #all parameters are supposed to be of norm 1: thus, normalize beta_ref
-               norm2 = sqrt(colSums(beta_ref^2))
-               beta_ref = beta_ref / norm2[col(beta_ref)]
-
-               io = generateSampleIO(n, d, K, Pr, beta_ref)
-               beta = getParamsDirs(io$X, io$Y, K)
-               betas = .labelSwitchingAlign(
-                       array( c(beta_ref,beta), dim=c(d,K,2) ), compare_to="first", ls_mode="exact")
-
-               #Some traces: 0 is not well estimated, but others are OK
-               cat("\n\nReference parameter matrix:\n")
-               print(beta_ref)
-               cat("Estimated parameter matrix:\n")
-               print(betas[,,2])
-               cat("Difference norm (Matrix norm ||.||_1, max. abs. sum on a column)\n")
-               diff_norm = norm(beta_ref - betas[,,2])
-               cat(diff_norm,"\n")
-
-               #NOTE: 0.5 is loose threshold, but values around 0.3 are expected...
-               expect_that( diff_norm, is_less_than(0.5) )
+               index = (i%%3) + 1
+               level = mean(s[[index]])
+               serie = s[[index]] - level + rnorm(L,sd=0.05)
+               # 10 series with NAs for index 2
+               if (index == 2 && i >= 60 && i<= 90)
+                       serie[sample(seq_len(L),1)] = NA
+               series[[i]] = list("level"=level,"serie"=serie) #no need for more

        }
        }

+       data = new("Data", data=series)
+
+       # index 142 : serie type 2
+       f2 = computeFilaments(data, 142, limit=60, plot=FALSE)
+       # Expected output: 22 series of type 3 (closer), then 50-2-10 series of type 2
+       #
+       #
+       #
+       #
+       #
+       #
+       # Simulate shift at origin when predict_at > 0
+       series[2:(n+1)] = series[1:n]
+       series[[1]] = list("level"=0, "serie"=s[[1]][1:(L%/%2)])
+       # index 143 : serie type 3
+       f3 = computeFilaments(data, 143, limit=70, plot=FALSE)
+       # Expected output: 22 series of type 2 (closer) then 50-2 series of type 3
+       # ATTENTION au shift
+       #
+       #
+       # index 144 : serie type 1
+       f1 = computeFilaments(data, 144, limit=50, plot=FALSE)
+       # Expected output: 2 series of type 3 (closer), then 50-2 series of type 1
+       #
+       expect_that( diff_norm, is_less_than(0.5) )

 })
 })

diff --git a/pkg/tests/testthat/test.dateIndexToInteger.R b/pkg/tests/testthat/test.dateIndexToInteger.R
index fb4c8e4..9786097 100644 (file)
--- a/pkg/tests/testthat/test.dateIndexToInteger.R
+++ b/pkg/tests/testthat/test.dateIndexToInteger.R
@@ -1,69 +1,26 @@
-context("Check that getParamsDirs behaves as expected")
+context("Check that dateIndexToInteger behaves as expected")

 
 

-test_that("on input of sufficient size, beta is estimated accurately enough", {
-       n = 100000
-       d = 2
-       K = 2
-       Pr = c(0.5, 0.5)
+test_that("integer index matches date in data",
+{

 
 

-       betas_ref = array( c(1,0,0,1 , 1,-2,3,1), dim=c(2,2,2) )
-       for (i in 1:(dim(betas_ref)[3]))
-       {
-               beta_ref = betas_ref[,,i]
-               #all parameters are supposed to be of norm 1: thus, normalize beta_ref
-               norm2 = sqrt(colSums(beta_ref^2))
-               beta_ref = beta_ref / norm2[col(beta_ref)]

 
 

-               io = generateSampleIO(n, d, K, Pr, beta_ref)
-               beta = getParamsDirs(io$X, io$Y, K)
-               betas = .labelSwitchingAlign(
-                       array( c(beta_ref,beta), dim=c(d,K,2) ), compare_to="first", ls_mode="exact")

 
 

-               #Some traces: 0 is not well estimated, but others are OK
-               cat("\n\nReference parameter matrix:\n")
-               print(beta_ref)
-               cat("Estimated parameter matrix:\n")
-               print(betas[,,2])
-               cat("Difference norm (Matrix norm ||.||_1, max. abs. sum on a column)\n")
-               diff_norm = norm(beta_ref - betas[,,2])
-               cat(diff_norm,"\n")
+#TODO: with and without shift at origin (so series values at least forst ones are required)

 
 

-               #NOTE: 0.5 is loose threshold, but values around 0.3 are expected...
-               expect_that( diff_norm, is_less_than(0.5) )
-       }
-})
-dateIndexToInteger = function(index, data)
-{
-       index = index[1]
-       if (is.numeric(index))
-               index = as.integer(index)
-       if (is.integer(index))
-               return (index)
-       if (inherits(index, "Date") || is.character(index))
+
+       n = 1500
+       series = list()
+       for (i in seq_len(n))

        {
        {

-               tryCatch(dt <- as.POSIXct(index), error=function(e) stop("Unrecognized index format"))
-               #TODO: tz arg to difftime ?
-               integerIndex <- round( (as.numeric( difftime(dt, data$getTime(1)) ))[1] ) + 1
-               if (integerIndex > 0 && integerIndex <= data$getSize())
-               {
-                       #WARNING: if series start at date >0h, result must be shifted
-                       date1 = as.POSIXlt(data$getTime(1)[1])
-                       date2 = as.POSIXlt(data$getTime(2)[1])
-                       shift = (date1$year==date2$year && date1$mon==date2$mon && date1$mday==date2$mday)
-                       return (integerIndex + ifelse(shift,1,0))
-               }
-               stop("Date outside data range")
+               index = (i%%3) + 1
+               level = mean(s[[index]])
+               serie = s[[index]] - level + rnorm(L,sd=0.05)
+               # 10 series with NAs for index 2
+               if (index == 2 && i >= 60 && i<= 90)
+                       serie[sample(seq_len(L),1)] = NA
+               series[[i]] = list("level"=level,"serie"=serie) #no need for more :: si : time !!!

        }
        }

-       stop("Unrecognized index format")
-}
-
-#' @title integerIndexToDate
-#'
-#' @description Transform an integer index to date index (relative to data)
-#'
-#' @param index Date (or integer) index
-#' @param data Object of class \code{Data}
-#'
-#' @export
-integerIndexToDate = function(index, data)
+       data = new("Data", data=series)

 
 

+       dateIndexToInteger = function(index, data)
+})

diff --git a/pkg/tests/testthat/test.integerIndexToDate.R b/pkg/tests/testthat/test.integerIndexToDate.R
index 5f0008f..31cd740 100644 (file)
--- a/pkg/tests/testthat/test.integerIndexToDate.R
+++ b/pkg/tests/testthat/test.integerIndexToDate.R
@@ -1,34 +1,22 @@
-context("Check that getParamsDirs behaves as expected")
+context("Check that integerIndexToDate behaves as expected")

 
 

-test_that("on input of sufficient size, beta is estimated accurately enough", {
-       n = 100000
-       d = 2
-       K = 2
-       Pr = c(0.5, 0.5)
+test_that("date matches index in data",
+{
+       #TODO: with and without shift at origin (so series values at least forst ones are required)

 
 

-       betas_ref = array( c(1,0,0,1 , 1,-2,3,1), dim=c(2,2,2) )
-       for (i in 1:(dim(betas_ref)[3]))
+       n = 1500
+       series = list()
+       for (i in seq_len(n))

        {
        {

-               beta_ref = betas_ref[,,i]
-               #all parameters are supposed to be of norm 1: thus, normalize beta_ref
-               norm2 = sqrt(colSums(beta_ref^2))
-               beta_ref = beta_ref / norm2[col(beta_ref)]
-
-               io = generateSampleIO(n, d, K, Pr, beta_ref)
-               beta = getParamsDirs(io$X, io$Y, K)
-               betas = .labelSwitchingAlign(
-                       array( c(beta_ref,beta), dim=c(d,K,2) ), compare_to="first", ls_mode="exact")
-
-               #Some traces: 0 is not well estimated, but others are OK
-               cat("\n\nReference parameter matrix:\n")
-               print(beta_ref)
-               cat("Estimated parameter matrix:\n")
-               print(betas[,,2])
-               cat("Difference norm (Matrix norm ||.||_1, max. abs. sum on a column)\n")
-               diff_norm = norm(beta_ref - betas[,,2])
-               cat(diff_norm,"\n")
-
-               #NOTE: 0.5 is loose threshold, but values around 0.3 are expected...
-               expect_that( diff_norm, is_less_than(0.5) )
+               index = (i%%3) + 1
+               level = mean(s[[index]])
+               serie = s[[index]] - level + rnorm(L,sd=0.05)
+               # 10 series with NAs for index 2
+               if (index == 2 && i >= 60 && i<= 90)
+                       serie[sample(seq_len(L),1)] = NA
+               series[[i]] = list("level"=level,"serie"=serie) #no need for more :: si : time !!!

        }
        }

+       data = new("Data", data=series)
+
+       integerIndexToDate = function(index, data)

 })
 })