ERGtools2
The ERGtools2 package is an environment for working with electroretinogram data. It contains an import method for Diagnosys Espion data, but allows reading in of data coming in other formats with limited coding effort. Standard procedures like averaging, sub-setting an visualization of individual exams are supported.
Installation
You can install the development version of ERGtools2 from GitHub with:
if (!requireNamespace("remotes", quietly = TRUE)){
install.packages("remotes")
}
remotes::install_github("moritzlindner/ERGtools2")Note that ERGtools2 depends on the github-deposited R Packages EPhysData and EPhysMethods. Installation usually works automatically. Updating, however may fail. If this is the case, update manually using the following line of code:
remotes::install_github("moritzlindner/EPhysData")
remotes::install_github("moritzlindner/EPhysMethods")Example
This is a basic example which shows you how to solve a common problem:
library(ERGtools2)
## a typical workflow
data(ERG) # load example data, to import own data, see the examples provided for newERGExam and ImportEspion
StimulusTable(ERG) # have a look whats inside
#> Step Description Intensity Background Type
#> 1 1 DA 0 01 cd s m 0.01 DA Flash
#> 2 2 DA 1 cd s m 1.00 DA Flash
#> 3 3 DA 3 cd s m 3.00 DA Flash
Metadata(ERG)
#> Step Channel Result Eye Channel_Name Recording
#> 1 1 ERG 1 RE ERG 1
#> 2 1 ERG 1 LE ERG 2
#> 3 1 OP 1 RE OP 3
#> 4 1 OP 1 LE OP 4
#> 5 2 ERG 1 RE ERG 5
#> 6 2 ERG 1 LE ERG 6
#> 7 2 OP 1 RE OP 7
#> 8 2 OP 1 LE OP 8
#> 9 3 ERG 1 RE ERG 9
#> 10 3 ERG 1 LE ERG 10
#> 11 3 OP 1 RE OP 11
#> 12 3 OP 1 LE OP 12
ERG<-ClearMeasurements(ERG) # Clear Measuremnts that migth be alredy in object
ERG<-SetStandardFunctions(ERG)
ggERGTrace(ERG, where = list( Step = as.integer(3), Eye = "RE", Channel ="ERG", Result = as.integer(1))) # pick one and have a look at the traces as imported
ERG <- AutoPlaceMarkers(ERG, Channel.names = pairlist(ERG = "ERG")) # automatically place markers
#> =======================================================================================================================
Measurements(ERG)
#> =======================================================================================================================
#> Recording Step Description Channel Result Eye Name Relative Time Voltage Channel_Name Recording.y
#> 1 1 1 DA 0 01 cd s m ERG 1 RE a <NA> 0.0315 [s] -53.17071 [uV] ERG 1
#> 2 1 1 DA 0 01 cd s m ERG 1 RE B a 0.0515 [s] 346.34079 [uV] ERG 1
#> 3 2 1 DA 0 01 cd s m ERG 1 LE a <NA> 0.0310 [s] -85.88321 [uV] ERG 2
#> 4 2 1 DA 0 01 cd s m ERG 1 LE B a 0.0505 [s] 310.38093 [uV] ERG 2
#> 5 5 2 DA 1 cd s m ERG 1 RE a <NA> 0.0125 [s] -206.37706 [uV] ERG 5
#> 6 5 2 DA 1 cd s m ERG 1 RE B a 0.0355 [s] 547.86889 [uV] ERG 5
#> 7 6 2 DA 1 cd s m ERG 1 LE a <NA> 0.0130 [s] -209.66536 [uV] ERG 6
#> 8 6 2 DA 1 cd s m ERG 1 LE B a 0.0355 [s] 491.97428 [uV] ERG 6
#> 9 9 3 DA 3 cd s m ERG 1 RE a <NA> 0.0090 [s] -233.89249 [uV] ERG 9
#> 10 9 3 DA 3 cd s m ERG 1 RE B a 0.0345 [s] 587.60032 [uV] ERG 9
#> 11 10 3 DA 3 cd s m ERG 1 LE a <NA> 0.0095 [s] -240.61577 [uV] ERG 10
#> 12 10 3 DA 3 cd s m ERG 1 LE B a 0.0345 [s] 568.70641 [uV] ERG 10
ggERGTrace(ERG, where = list( Step = as.integer(3), Eye = "RE", Channel ="ERG", Result = as.integer(1))) # pick one and have a look at the traces as imported
#> =======================================================================================================================
#> =======================================================================================================================