Installation and initialization of the package

To install UnitEvents, you need to download the archive package and to install the package as a usual package. For example, using the command line, for version 0.0.1

install.packages('UnitEvents_0.0.1.tar.gz', repos=NULL, type="source")

The $\textrm{neuro-stat}$ code is downloaded and compiled during the installation process. $\textit{Subversion}$, $\textit{git}$, $\textit{CMake}$ and a C++ compiler are required. The compilation of $\textrm{neuro-stat}$ on Mac OS should complete despite several warnings.

To initialize the package, do as usual for an R package

library('UnitEvents')

Time windows

Creation of time windows

The time windows of reference examples in papers (Albert et al. 2016) and (Tuleau-Malot et al. 2014) are defined by the $\textit{compute_windows}$ function for Neurons 13 and 40 as follows

$\textit{compute_time_windows}$ function is the main function to create time windows.

TW1 = compute_time_windows(0, 2.05, 0.1, 0.05)
print(TW1$len)

## [1] 40

print(TW1$A[,c(1:5,36:40)])

##      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
## [1,]  0.0 0.05  0.1 0.15  0.2 1.75  1.8 1.85  1.9  1.95
## [2,]  0.1 0.15  0.2 0.25  0.3 1.85  1.9 1.95  2.0  2.05

Representation of time windows

$\textit{draw_windows}$ function allows to represent time windows.

draw_windows(TW1, yrange=c(-0.5,0), density=c(0), col='black')

Time windows for interval $[0,2]$ from compute_time_windows function

MTGAUE tests

Some results are presented here for MTGAUE (Multiple Tests based on a Gaussian Approximation of the Unitary Events method with delayed coincidence count) (see (Tuleau-Malot et al. 2014)).

MTGAUE tests with neuro-stat code

Neuron 13

Result for $\simeq$ 40 time windows

TW = compute_time_windows(0, 2.05, duration=0.1, spacing=0.05)
removefirstandlast7col <- function(v) { return(v[-c(1,(length(v)-6):length(v))])}
scaling <- 1/10000
fNeur1_13 <- system.file("extdata", "Neur1_c13.txt", package="UnitEvents")
fNeur2_13 <- system.file("extdata", "Neur2_c13.txt", package="UnitEvents")
DN13 = DNeur(list(fNeur1_13, fNeur2_13),
                listOptions=list('removeCols'=removefirstandlast7col, 'scaling'=c(scaling)))

## [1] ""
## [1] "The neuron file is /home/gscarella/R/x86_64-redhat-linux-gnu-library/3.4/UnitEvents/extdata/Neur1_c13.txt"
## [1] ""
## [1] "The neuron file is /home/gscarella/R/x86_64-redhat-linux-gnu-library/3.4/UnitEvents/extdata/Neur2_c13.txt"

xns = UnitEvents(delay=0.02, TW=TW, DataNeur=DN13, DName="Neur_c13")

## Figure title is
## Raster plot for Neur_c13
## type = MTGAUE, delay=0.02, level=0.05, nw=40, Rtest=all

## [1] ""
## [1] "The value of delay for coincidences (denoted by delta in MTGAUE paper) is 0.02"
## [1] "The level value in Benjamini-Hochberg procedure is 0.05"
## [1] ""
## [1] "Plotting figures ..."

## [1] ""
## [1] "WINK: Loading ~/R/x86_64-redhat-linux-gnu-library/3.4/UnitEvents/neuro-stat/v3/src/wink_mam4//wink.so"
## [1] ""
## [1] "There are 40 time windows"
## [1] "Both upper and lower tests"

$MTGAUE test for neuro-stat code. Neuron 13 - 40 time windows, $\delta=0.02$$

MTGAUE test for neuro-stat code. Neuron 13 - 40 time windows, $\delta=0.02$

save(xns, file='MTGAUE-nw=40-ns.RData')

Result for $\simeq$ 2000 time windows

TW = compute_time_windows(a=0.001, b=1.973, duration=0.1, spacing=0.001)
xns_nw2000 = UnitEvents(delay=0.02, TW=TW, DataNeur=DN13, DName="Neur_c13")

## Figure title is
## Raster plot for Neur_c13
## type = MTGAUE, delay=0.02, level=0.05, nw=1873, Rtest=all

## [1] ""
## [1] "The value of delay for coincidences (denoted by delta in MTGAUE paper) is 0.02"
## [1] "The level value in Benjamini-Hochberg procedure is 0.05"
## [1] ""
## [1] "Plotting figures ..."

## [1] ""
## [1] "WINK: Loading ~/R/x86_64-redhat-linux-gnu-library/3.4/UnitEvents/neuro-stat/v3/src/wink_mam4//wink.so"
## [1] ""
## [1] "There are 1873 time windows"
## [1] "Both upper and lower tests"

$MTGAUE test for neuro-stat code. Neuron 13 - $\simeq 2000$ time windows, $\delta=0.02$$

MTGAUE test for neuro-stat code. Neuron 13 - $\simeq 2000$ time windows, $\delta=0.02$

save(xns_nw2000, file='MTGAUE-nw=2000-ns.RData')

Neuron 40

Result for 40 time windows and upper test only

TW = compute_time_windows(0, 2.05, 0.1, 0.05)
fNeur1_40 <- system.file("extdata", "Neur1_c40.txt", package="UnitEvents")
fNeur2_40 <- system.file("extdata", "Neur2_c40.txt", package="UnitEvents")
DN40 = DNeur(list(fNeur1_40, fNeur2_40),
                listOptions=list('removeCols'=removefirstandlast7col,'scaling'=c(scaling)))

## [1] ""
## [1] "The neuron file is /home/gscarella/R/x86_64-redhat-linux-gnu-library/3.4/UnitEvents/extdata/Neur1_c40.txt"
## [1] ""
## [1] "The neuron file is /home/gscarella/R/x86_64-redhat-linux-gnu-library/3.4/UnitEvents/extdata/Neur2_c40.txt"

xns_nw40_up = UnitEvents(delay=0.02, TW=TW, Rtest="upper", DataNeur=DN40, DName="Neur_c40")

## Figure title is
## Raster plot for Neur_c40
## type = MTGAUE, delay=0.02, level=0.05, nw=40, Rtest=upper

## [1] ""
## [1] "The value of delay for coincidences (denoted by delta in MTGAUE paper) is 0.02"
## [1] "The level value in Benjamini-Hochberg procedure is 0.05"
## [1] ""
## [1] "Plotting figures ..."

## [1] ""
## [1] "WINK: Loading ~/R/x86_64-redhat-linux-gnu-library/3.4/UnitEvents/neuro-stat/v3/src/wink_mam4//wink.so"
## [1] ""
## [1] "There are 40 time windows"
## [1] "upper test with neuro-stat code"

$MTGAUE test for neuro-stat code. Neuron 40 - 40 time windows, upper test, $\delta=0.02$$

MTGAUE test for neuro-stat code. Neuron 40 - 40 time windows, upper test, $\delta=0.02$

save(xns_nw40_up, file='MTGAUE-nw=40-ns-up_40.RData')

Result for 40 time windows and lower test only

TW = compute_time_windows(0, 2.05, 0.1, 0.05)
xns_nw40_lo = UnitEvents(delay=0.02, TW=TW, Rtest="lower", DataNeur=DN40, DName="Neur_c40")

## Figure title is
## Raster plot for Neur_c40
## type = MTGAUE, delay=0.02, level=0.05, nw=40, Rtest=lower

## [1] ""
## [1] "The value of delay for coincidences (denoted by delta in MTGAUE paper) is 0.02"
## [1] "The level value in Benjamini-Hochberg procedure is 0.05"
## [1] ""
## [1] "Plotting figures ..."

## [1] ""
## [1] "WINK: Loading ~/R/x86_64-redhat-linux-gnu-library/3.4/UnitEvents/neuro-stat/v3/src/wink_mam4//wink.so"
## [1] ""
## [1] "There are 40 time windows"
## [1] "lower test with neuro-stat code"

$MTGAUE test for neuro-stat code. Neuron 40 - 40 time windows, lower test, $\delta=0.02$$

MTGAUE test for neuro-stat code. Neuron 40 - 40 time windows, lower test, $\delta=0.02$

save(xns_nw40_lo, file='MTGAUE-nw=40-ns-lo_40.RData')

Result for 40 time windows both upper and lower test

TW = compute_time_windows(0, 2.05, 0.1, 0.05)
xns_nw40_40 = UnitEvents(delay=0.02, TW=TW, DataNeur=DN40, DName="Neur_c40")

## Figure title is
## Raster plot for Neur_c40
## type = MTGAUE, delay=0.02, level=0.05, nw=40, Rtest=all

## [1] ""
## [1] "The value of delay for coincidences (denoted by delta in MTGAUE paper) is 0.02"
## [1] "The level value in Benjamini-Hochberg procedure is 0.05"
## [1] ""
## [1] "Plotting figures ..."

## [1] ""
## [1] "WINK: Loading ~/R/x86_64-redhat-linux-gnu-library/3.4/UnitEvents/neuro-stat/v3/src/wink_mam4//wink.so"
## [1] ""
## [1] "There are 40 time windows"
## [1] "Both upper and lower tests"

$MTGAUE test for neuro-stat code. Neuron 40 - 40 time windows, $\delta=0.02$$

MTGAUE test for neuro-stat code. Neuron 40 - 40 time windows, $\delta=0.02$

save(xns_nw40_40, file='MTGAUE-nw=40-ns_40.RData')

Result for $\simeq$ 2000 time windows, upper test

TW = compute_time_windows(a=0.001, b=1.997, duration=0.1, spacing=0.001)
xns_nw2000_40_up = UnitEvents(delay=0.02, TW=TW, Rtest="upper", DataNeur=DN40, DName="Neur_c40")

## Figure title is
## Raster plot for Neur_c40
## type = MTGAUE, delay=0.02, level=0.05, nw=1897, Rtest=upper

## [1] ""
## [1] "The value of delay for coincidences (denoted by delta in MTGAUE paper) is 0.02"
## [1] "The level value in Benjamini-Hochberg procedure is 0.05"
## [1] ""
## [1] "Plotting figures ..."

## [1] ""
## [1] "WINK: Loading ~/R/x86_64-redhat-linux-gnu-library/3.4/UnitEvents/neuro-stat/v3/src/wink_mam4//wink.so"
## [1] ""
## [1] "There are 1897 time windows"
## [1] "upper test with neuro-stat code"

$MTGAUE test for neuro-stat code. Neuron 40 - $\simeq 2000$ time windows, upper test, $\delta=0.02$$

MTGAUE test for neuro-stat code. Neuron 40 - $\simeq 2000$ time windows, upper test, $\delta=0.02$

save(xns_nw2000_40_up, file='MTGAUE-nw=2000-ns-up_40.RData')

Result for $\simeq$ 2000 time windows, lower test

TW = compute_time_windows(a=0.001, b=1.997, duration=0.1, spacing=0.001)
xns_nw2000_40_lo = UnitEvents(delay=0.02, TW=TW, Rtest="lower", DataNeur=DN40, DName="Neur_c40")

## Figure title is
## Raster plot for Neur_c40
## type = MTGAUE, delay=0.02, level=0.05, nw=1897, Rtest=lower

## [1] ""
## [1] "The value of delay for coincidences (denoted by delta in MTGAUE paper) is 0.02"
## [1] "The level value in Benjamini-Hochberg procedure is 0.05"
## [1] ""
## [1] "Plotting figures ..."

$MTGAUE test for neuro-stat code. Neuron 40 - $\simeq 2000$ time windows, lower test, $\delta=0.02$$

MTGAUE test for neuro-stat code. Neuron 40 - $\simeq 2000$ time windows, lower test, $\delta=0.02$

## [1] ""
## [1] "WINK: Loading ~/R/x86_64-redhat-linux-gnu-library/3.4/UnitEvents/neuro-stat/v3/src/wink_mam4//wink.so"
## [1] ""
## [1] "There are 1897 time windows"
## [1] "lower test with neuro-stat code"
## [1] "k==0"

save(xns_nw2000_40_lo, file='MTGAUE-nw=2000-ns-lo_40.RData')

Result for $\simeq$ 2000 time windows, both upper and lower test

TW = compute_time_windows(a=0.001, b=1.997, duration=0.1, spacing=0.001)
xns_nw2000_40 = UnitEvents(delay=0.02, TW=TW, DataNeur=DN40, DName="Neur_c40")

## Figure title is
## Raster plot for Neur_c40
## type = MTGAUE, delay=0.02, level=0.05, nw=1897, Rtest=all

## [1] ""
## [1] "The value of delay for coincidences (denoted by delta in MTGAUE paper) is 0.02"
## [1] "The level value in Benjamini-Hochberg procedure is 0.05"
## [1] ""
## [1] "Plotting figures ..."

## [1] ""
## [1] "WINK: Loading ~/R/x86_64-redhat-linux-gnu-library/3.4/UnitEvents/neuro-stat/v3/src/wink_mam4//wink.so"
## [1] ""
## [1] "There are 1897 time windows"
## [1] "Both upper and lower tests"

$MTGAUE test for neuro-stat code. Neuron 40 - $\simeq 2000$ time windows, $\delta=0.02$$

MTGAUE test for neuro-stat code. Neuron 40 - $\simeq 2000$ time windows, $\delta=0.02$

save(xns_nw2000_40, file='MTGAUE-nw=2000-ns_40.RData')

Tests with permutation method

Permutation with neuro-stat code

Neuron 13

Result for 40 time windows

ti = proc.time()
TW = compute_time_windows(0, 2.05, 0.1, 0.05)
xns_perm_nw40 = UnitEvents(delay=0.02, iperm=TRUE, TW=TW, DataNeur=DN13, DName="Neur_c13")

## Figure title is
## Raster plot for Neur_c13
## type = Perm, delay=0.02, level=0.05, nw=40, Rtest=all

## [1] ""
## [1] "The value of delay for coincidences (denoted by delta in MTGAUE paper) is 0.02"
## [1] "The level value in Benjamini-Hochberg procedure is 0.05"
## [1] ""
## [1] "Plotting figures ..."

## [1] ""
## [1] "WINK: Loading ~/R/x86_64-redhat-linux-gnu-library/3.4/UnitEvents/neuro-stat/v3/src/wink_mam4//wink.so"
## [1] ""
## [1] "There are 40 time windows"
## [1] "Both upper and lower tests"
##  WINK: Permutation[1 thread ]
##  WINK: Neuron 1 | #trials= 177 | max_tops=   91
##  WINK: Neuron 2 | #trials= 177 | max_tops=   91
##  WINK: #intervals  = 40
##  WINK: #bootstraps = 10000
##  WINK: <SERIAL CODE>

$Permutation for neuro-stat code. Neuron 13 - 40 time windows, $\delta=0.02$$

Permutation for neuro-stat code. Neuron 13 - 40 time windows, $\delta=0.02$

tf = (proc.time()-ti)[3]; print(paste('Computation time', as.character(tf)))

## [1] "Computation time 2.53300000000002"

save(xns_perm_nw40, file='Perm-nw=40-ns.RData')

Result for $\simeq$ 2000 time windows

ti = proc.time()
TW = compute_time_windows(a=0.001, b=1.973, duration=0.1, spacing=0.001)
xns_perm = UnitEvents(delay=0.02, TW=TW, iperm=TRUE, DataNeur=DN13, DName="Neur_c13")

## Figure title is
## Raster plot for Neur_c13
## type = Perm, delay=0.02, level=0.05, nw=1873, Rtest=all

## [1] ""
## [1] "The value of delay for coincidences (denoted by delta in MTGAUE paper) is 0.02"
## [1] "The level value in Benjamini-Hochberg procedure is 0.05"
## [1] ""
## [1] "Plotting figures ..."

## [1] ""
## [1] "WINK: Loading ~/R/x86_64-redhat-linux-gnu-library/3.4/UnitEvents/neuro-stat/v3/src/wink_mam4//wink.so"
## [1] ""
## [1] "There are 1873 time windows"
## [1] "Both upper and lower tests"
##  WINK: Permutation[1 thread ]
##  WINK: Neuron 1 | #trials= 177 | max_tops=   91
##  WINK: Neuron 2 | #trials= 177 | max_tops=   91
##  WINK: #intervals  = 1873
##  WINK: #bootstraps = 10000
##  WINK: <SERIAL CODE>

$Permutation for neuro-stat code. Neuron 13 - $\simeq 2000$ time windows, $\delta=0.02$$

Permutation for neuro-stat code. Neuron 13 - $\simeq 2000$ time windows, $\delta=0.02$

tf = (proc.time()-ti)[3]; print(paste('Computation time', as.character(tf)))

## [1] "Computation time 133.4"

save(xns_perm, file='Perm-nw=2000-ns.RData')

Neuron 40

Result for 40 time windows and upper test only

ti = proc.time()
TW = compute_time_windows(a=0, b=2.05, duration=0.1, spacing=0.05)
xns_perm_nw40_40_up = UnitEvents(delay=0.02, TW=TW, iperm=TRUE, 
                     DataNeur=DN40, Rtest="upper", DName="Neur_c40")

## Figure title is
## Raster plot for Neur_c40
## type = Perm, delay=0.02, level=0.05, nw=40, Rtest=upper

## [1] ""
## [1] "The value of delay for coincidences (denoted by delta in MTGAUE paper) is 0.02"
## [1] "The level value in Benjamini-Hochberg procedure is 0.05"
## [1] ""
## [1] "Plotting figures ..."

## [1] ""
## [1] "WINK: Loading ~/R/x86_64-redhat-linux-gnu-library/3.4/UnitEvents/neuro-stat/v3/src/wink_mam4//wink.so"
## [1] ""
## [1] "There are 40 time windows"
## [1] "upper test with neuro-stat code"
##  WINK: Permutation[1 thread ]
##  WINK: Neuron 1 | #trials= 141 | max_tops=  112
##  WINK: Neuron 2 | #trials= 141 | max_tops=  112
##  WINK: #intervals  = 40
##  WINK: #bootstraps = 10000
##  WINK: <SERIAL CODE>

$Permutation for neuro-stat code. Neuron 40 - 40 time windows, upper test, $\delta=0.02$$

Permutation for neuro-stat code. Neuron 40 - 40 time windows, upper test, $\delta=0.02$

tf = (proc.time()-ti)[3]; print(paste('Computation time', as.character(tf)))

## [1] "Computation time 2.25299999999993"

save(xns_perm_nw40_40_up, file='Perm-nw=40-ns_40_up.RData')

Result for 40 time windows and lower test only

ti = proc.time()
TW = compute_time_windows(a=0, b=2.05, duration=0.1, spacing=0.05)
xns_perm_nw40_40_lo = UnitEvents(delay=0.02, TW=TW, DataNeur=DN40,
            iperm=TRUE, Rtest="lower", DName="Neur_c40")

## Figure title is
## Raster plot for Neur_c40
## type = Perm, delay=0.02, level=0.05, nw=40, Rtest=lower

## [1] ""
## [1] "The value of delay for coincidences (denoted by delta in MTGAUE paper) is 0.02"
## [1] "The level value in Benjamini-Hochberg procedure is 0.05"
## [1] ""
## [1] "Plotting figures ..."

## [1] ""
## [1] "WINK: Loading ~/R/x86_64-redhat-linux-gnu-library/3.4/UnitEvents/neuro-stat/v3/src/wink_mam4//wink.so"
## [1] ""
## [1] "There are 40 time windows"
## [1] "lower test with neuro-stat code"
##  WINK: Permutation[1 thread ]
##  WINK: Neuron 1 | #trials= 141 | max_tops=  112
##  WINK: Neuron 2 | #trials= 141 | max_tops=  112
##  WINK: #intervals  = 40
##  WINK: #bootstraps = 10000
##  WINK: <SERIAL CODE>

$Permutation for neuro-stat code. Neuron 40 - 40 time windows, lower test, $\delta=0.02$$

Permutation for neuro-stat code. Neuron 40 - 40 time windows, lower test, $\delta=0.02$

tf = (proc.time()-ti)[3]; print(paste('Computation time', as.character(tf)))

## [1] "Computation time 2.15599999999995"

save(xns_perm_nw40_40_lo, file='Perm-nw=40-ns-lo_40.RData')

Result for 40 time windows both upper and lower test

ti = proc.time()
TW = compute_time_windows(a=0, b=2.05, duration=0.1, spacing=0.05)
xns_perm_nw40_40 = UnitEvents(delay=0.02, TW=TW, DataNeur=DN40, iperm=TRUE, DName="Neur_c40")

## Figure title is
## Raster plot for Neur_c40
## type = Perm, delay=0.02, level=0.05, nw=40, Rtest=all

## [1] ""
## [1] "The value of delay for coincidences (denoted by delta in MTGAUE paper) is 0.02"
## [1] "The level value in Benjamini-Hochberg procedure is 0.05"
## [1] ""
## [1] "Plotting figures ..."

## [1] ""
## [1] "WINK: Loading ~/R/x86_64-redhat-linux-gnu-library/3.4/UnitEvents/neuro-stat/v3/src/wink_mam4//wink.so"
## [1] ""
## [1] "There are 40 time windows"
## [1] "Both upper and lower tests"
##  WINK: Permutation[1 thread ]
##  WINK: Neuron 1 | #trials= 141 | max_tops=  112
##  WINK: Neuron 2 | #trials= 141 | max_tops=  112
##  WINK: #intervals  = 40
##  WINK: #bootstraps = 10000
##  WINK: <SERIAL CODE>

$Permutation for neuro-stat code. Neuron 40 - 40 time windows, $\delta=0.02$$

Permutation for neuro-stat code. Neuron 40 - 40 time windows, $\delta=0.02$

tf = (proc.time()-ti)[3]; print(paste('Computation time', as.character(tf)))

## [1] "Computation time 2.12400000000002"

save(xns_perm_nw40_40, file='Perm-nw=40-ns_40.RData')

Result for $\simeq$ 2000 time windows, upper test

ti = proc.time()
TW = compute_time_windows(a=0.001, b=1.997, duration=0.1, spacing=0.001)
xns_perm_nw2000_40_up = UnitEvents(delay=0.02,  TW=TW, iperm=TRUE,
               DataNeur=DN40, Rtest="upper", DName="Neur_c40")

## Figure title is
## Raster plot for Neur_c40
## type = Perm, delay=0.02, level=0.05, nw=1897, Rtest=upper

## [1] ""
## [1] "The value of delay for coincidences (denoted by delta in MTGAUE paper) is 0.02"
## [1] "The level value in Benjamini-Hochberg procedure is 0.05"
## [1] ""
## [1] "Plotting figures ..."

$Permutation for neuro-stat code. Neuron 40 - $\simeq 2000$ time windows, upper test, $\delta=0.02$$

Permutation for neuro-stat code. Neuron 40 - $\simeq 2000$ time windows, upper test, $\delta=0.02$

## [1] ""
## [1] "WINK: Loading ~/R/x86_64-redhat-linux-gnu-library/3.4/UnitEvents/neuro-stat/v3/src/wink_mam4//wink.so"
## [1] ""
## [1] "There are 1897 time windows"
## [1] "upper test with neuro-stat code"
##  WINK: Permutation[1 thread ]
##  WINK: Neuron 1 | #trials= 141 | max_tops=  112
##  WINK: Neuron 2 | #trials= 141 | max_tops=  112
##  WINK: #intervals  = 1897
##  WINK: #bootstraps = 10000
##  WINK: <SERIAL CODE>
## [1] "k==0"

tf = (proc.time()-ti)[3]; print(paste('Computation time', as.character(tf)))

## [1] "Computation time 100.652"

save(xns_perm_nw2000_40_up, file='Perm-nw=2000-ns_40_up.RData')

Result for $\simeq$ 2000 time windows, lower test

ti = proc.time()
TW = compute_time_windows(a=0.001, b=1.997, duration=0.1, spacing=0.001)
xns_perm_nw2000_40_lo = UnitEvents(delay=0.02,  TW=TW, iperm=TRUE,
 DataNeur=DN40, Rtest="lower", DName="Neur_c40")

## Figure title is
## Raster plot for Neur_c40
## type = Perm, delay=0.02, level=0.05, nw=1897, Rtest=lower

## [1] ""
## [1] "The value of delay for coincidences (denoted by delta in MTGAUE paper) is 0.02"
## [1] "The level value in Benjamini-Hochberg procedure is 0.05"
## [1] ""
## [1] "Plotting figures ..."

## [1] ""
## [1] "WINK: Loading ~/R/x86_64-redhat-linux-gnu-library/3.4/UnitEvents/neuro-stat/v3/src/wink_mam4//wink.so"
## [1] ""
## [1] "There are 1897 time windows"
## [1] "lower test with neuro-stat code"
##  WINK: Permutation[1 thread ]
##  WINK: Neuron 1 | #trials= 141 | max_tops=  112
##  WINK: Neuron 2 | #trials= 141 | max_tops=  112
##  WINK: #intervals  = 1897
##  WINK: #bootstraps = 10000
##  WINK: <SERIAL CODE>

$Permutation for neuro-stat code. Neuron 40 - $\simeq 2000$ time windows, $\delta=0.02$, lower test$

Permutation for neuro-stat code. Neuron 40 - $\simeq 2000$ time windows, $\delta=0.02$, lower test

tf = (proc.time()-ti)[3]; print(paste('Computation time', as.character(tf)))

## [1] "Computation time 95.769"

save(xns_perm_nw2000_40_lo, file='Perm-nw=2000-ns_40_lo.RData')

Result for $\simeq$ 2000 time windows

ti = proc.time()
TW = compute_time_windows(a=0.001, b=1.997, duration=0.1, spacing=0.001)
xns_perm_nw2000_40 = UnitEvents(delay=0.02,  TW=TW, iperm=TRUE, DataNeur=DN40, DName="Neur_c40")

## Figure title is
## Raster plot for Neur_c40
## type = Perm, delay=0.02, level=0.05, nw=1897, Rtest=all

## [1] ""
## [1] "The value of delay for coincidences (denoted by delta in MTGAUE paper) is 0.02"
## [1] "The level value in Benjamini-Hochberg procedure is 0.05"
## [1] ""
## [1] "Plotting figures ..."

$Permutation for neuro-stat code. Neuron 40 - $\simeq 2000$ time windows, $\delta=0.02$$

Permutation for neuro-stat code. Neuron 40 - $\simeq 2000$ time windows, $\delta=0.02$

## [1] ""
## [1] "WINK: Loading ~/R/x86_64-redhat-linux-gnu-library/3.4/UnitEvents/neuro-stat/v3/src/wink_mam4//wink.so"
## [1] ""
## [1] "There are 1897 time windows"
## [1] "Both upper and lower tests"
##  WINK: Permutation[1 thread ]
##  WINK: Neuron 1 | #trials= 141 | max_tops=  112
##  WINK: Neuron 2 | #trials= 141 | max_tops=  112
##  WINK: #intervals  = 1897
##  WINK: #bootstraps = 10000
##  WINK: <SERIAL CODE>
## [1] "k==0"

tf = (proc.time()-ti)[3]; print(paste('Computation time', as.character(tf)))

## [1] "Computation time 92.825"

save(xns_perm_nw2000_40, file='Perm-nw=2000-ns_40.RData')

TODO

Amélioration de la représentation graphique des fenêtres en temps (rug)
Le bug dans neuro-stat est toujours présent (si un spike correspond exactement à la fin d’une fenêtre en temps, il n’est pas pris en compte par neuro-stat, certaines fois)
La démo que le test “symétrique” (pour MTGAUE) est identique à l’union des tests “upper” et “lower” n’est pas claire pour moi.
Que sont les tests “upper” et “lower” pour la méthode des permutations?
Y-a-t-il une différence entre “méthode des permutations” et “trial shuffling”. Il semble que oui dans l’article ….
Pour la méthode des permutations, il faut répéter l’expérience un certain nombre de fois? Pas encore dans le code.
Ecrire une documentation mathématique donnant explicitement les formules.
Améliorer les sorties de la fonction MulTestsBH (stat MTGAUE, stat centrée ou pas pour les permutations)

References

Albert, Mélisande, Yann Bouret, Magalie Fromont, and Patricia Reynaud-Bouret. 2016. “Surrogate Data Methods Based on a Shuffling of the Trials for Synchrony Detection: The Centering Issue.” Neural Computation 28 (11): 2352–2392. doi:10.1162/neco_a_00839. https://hal.archives-ouvertes.fr/hal-01154918.

Tuleau-Malot, Christine, Amel Rouis, Franck Grammont, and Patricia Reynaud-Bouret. 2014. “Multiple Tests Based on a Gaussian Approximation of the Unitary Events Method with Delayed Coincidence Count.” Neural Computation 26 (7) (July): 1408–1454. doi:10.1162/NECO_a_00604. https://hal.archives-ouvertes.fr/hal-00757323.

Tests for the UnitEvents package

2018-02-06

Installation and initialization of the package

Time windows

Creation of time windows

Representation of time windows

MTGAUE tests

MTGAUE tests with neuro-stat code

Neuron 13

Result for \(\simeq\) 40 time windows

Result for \(\simeq\) 2000 time windows

Neuron 40

Result for 40 time windows and upper test only

Result for 40 time windows and lower test only

Result for 40 time windows both upper and lower test

Result for \(\simeq\) 2000 time windows, upper test

Result for \(\simeq\) 2000 time windows, lower test

Result for \(\simeq\) 2000 time windows, both upper and lower test

Tests with permutation method

Permutation with neuro-stat code

Neuron 13

Result for 40 time windows

Result for \(\simeq\) 2000 time windows

Neuron 40

Result for 40 time windows and upper test only

Result for 40 time windows and lower test only

Result for 40 time windows both upper and lower test

Result for \(\simeq\) 2000 time windows, upper test

Result for \(\simeq\) 2000 time windows, lower test

Result for \(\simeq\) 2000 time windows

TODO

References