Lindner Lab
ERGtools2
Package details, installation notes, and examples.
ERGtools2
Description
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")
Examples
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 Repeat 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", Repeat = 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 Repeat 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", Repeat = as.integer(1))) # pick one and have a look at the traces as imported
#> ========================================================================================================================================================================================================================
#> ========================================================================================================================================================================================================================
