Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ---- eval = F----------------------------------------------------------------
# install.packages("rPACI", dependencies = TRUE)
# library("rPACI")
## ---- echo = F, warning = F, message=F----------------------------------------
library("rPACI")
## ---- eval = T----------------------------------------------------------------
dataset1 = readCSO(filepath = system.file("extdata","N01.txt", package="rPACI"))
## ---- eval = T----------------------------------------------------------------
head(dataset1)
## ---- eval = F----------------------------------------------------------------
# dataset2 = readrPACI(filepath = system.file("extdata","ds1.txt", package="rPACI"))
## ---- eval = T----------------------------------------------------------------
dataset3 = readFile(filepath = system.file("extdata","N01.txt", package="rPACI"))
head(dataset3)
## ---- eval = F----------------------------------------------------------------
# # Simulating an elliptic dataset, with ellipses axis ratio of 0.8 and an orientation of 45 degrees.
# dataset = simulateData(rings = 18, pointsPerRing = 300, ellipticAxesRatio = 0.8, ellipticRotation = 45)
#
# # Now the dataset can be saved to file using 'writerPACI' (check the working directory before saving):
# writerPACI(dataset, "datasetFile.txt")
## ---- eval = T----------------------------------------------------------------
results_N = computePlacidoIndices(dataset1)
results_N
## ---- eval = T, fig.width = 7, fig.height = 4---------------------------------
plotSingleCornea(dataset1, results_N, filename = "N01.txt")
## ---- eval = T, fig.width = 7, fig.height = 4---------------------------------
res_K = analyzeFile(system.file("extdata","K01.txt", package="rPACI"), drawplot=TRUE)
res_K
## ---- eval = T, fig.width = 7, fig.height = 4---------------------------------
# Generate a sample dataset
dataset = simulateData(rings = 12, maximumMireDisplacement = 0.2, mireDisplacementAngle = 50)
# Analyze the dataset
res_dataset = analyzeDataset(dataset = dataset)
res_dataset
## ---- eval = T, fig.width = 7, fig.height = 4---------------------------------
resultsAll = analyzeFolder(path = system.file("extdata", package="rPACI"), individualPlots = T, summaryPlot = T)
resultsAll
## ---- eval = T----------------------------------------------------------------
resultsAll[,c(13,1)]
## ---- eval = F, fig.width = 7, fig.height = 4---------------------------------
# # Simulate the patient's measures over time
# dataT1 = simulateData(rings = 12, maximumMireDisplacement = 0.15, mireDisplacementAngle = 10)
# dataT2 = simulateData(rings = 12, maximumMireDisplacement = 0.15, mireDisplacementAngle = 45)
# dataT3 = simulateData(rings = 12, maximumMireDisplacement = 0.2, mireDisplacementAngle = 50)
#
# # Create a list containing the data
# data = list(
# dataT1 = dataT1,
# dataT2 = dataT2,
# dataT3 = dataT3
# )
#
# # Analyze the data over time
# analyzeEvolution(data = data)
## ---- eval = T, fig.width = 7, fig.height = 4---------------------------------
# Specify a folder path to analyze a patient's evolution over time
analyzeEvolution(data = system.file("extdata/evolution/", package="rPACI"), fileExtension = 'txt')
## ---- echo = F, eval = F, fig.width = 4, fig.height = 4-----------------------
# # library(DiagrammeR)
# # DiagrammeR::grViz("digraph {
# #
# # graph [layout = dot]
# #
# # # define the global styles of the nodes. We can override these in box if we wish
# # node [shape = rounded, style = filled, fillcolor = Pink]
# #
# # step1 [label = 'How many patients?', fillcolor = Beige]
# # step2 [label = 'How many measures?', fillcolor = Beige]
# # step3 [label = 'Data on file or \n data.frame?', fillcolor = Beige]
# # leaf1 [label = 'analyzeFile()']
# # leaf2 [label= 'analyzeDataset()']
# # leaf3 [label = 'analyzeEvolution()']
# # leaf4 [label = 'analyzeFolder()']
# #
# #
# # # edge definitions with the node IDs
# # step1 -> step2 [label='One']
# # step1 -> leaf4 [label='Several']
# # step2 -> step3 [label='Single']
# # step2 -> leaf3 [label='Repeated']
# # step3 -> leaf2 [label='Data loaded in \nglobal environment']
# # step3 -> leaf1 [label='External \nfile']
# # }")
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