Description Usage Arguments Details Examples
plots FROC curves, AFROC curves and FPF and TPF.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 | DrawCurves(
StanS4class,
modalityID,
readerID,
title = TRUE,
type_to_be_passed_into_plot = "l",
indexCFPCTP = FALSE,
upper_x,
upper_y,
lower_X = 0,
lower_y = 0,
new.imaging.device = TRUE,
Colour = TRUE,
DrawFROCcurve = TRUE,
DrawAFROCcurve = FALSE,
DrawAUC = TRUE,
DrawCFPCTP = TRUE,
Draw.Flexible.upper_y = TRUE,
Draw.Flexible.lower_y = TRUE,
summary = TRUE,
type = 4,
color_is_changed_by_each_reader = FALSE,
Draw.inner.circle.for.CFPCTPs = TRUE
)
|
StanS4class |
An S4 object of class To be passed to |
modalityID |
A positive integer vector indicating modalityID. If it is not given, then the first modality is chosen. |
readerID |
A positive integer vector indicating readerID. If it is not given, then the first reader is chosen. |
title |
Logical: |
type_to_be_passed_into_plot |
"l" or "p". |
indexCFPCTP |
TRUE of FALSE. If TRUE, then the cumulative false and hits are specified with its confidence level. |
upper_x |
A non-negative real number. This is a upper bound for the axis of the horisontal coordinate of FROC curve. |
upper_y |
A non-negative real number. This is a upper bound for the axis of the vertical coordinate of FROC curve. |
lower_X |
A non-negative real number. This is a lower bound for the axis of the horisontal coordinate of FROC curve. |
lower_y |
A non-negative real number. This is a lower bound for the axis of the vertical coordinate of FROC curve. |
new.imaging.device |
Logical: |
Colour |
Logical: |
DrawFROCcurve |
Logical: |
DrawAFROCcurve |
Logical: |
DrawAUC |
TRUE of FALSE. If TRUE then area under the AFROC curves are painted. |
DrawCFPCTP |
Logical: |
Draw.Flexible.upper_y |
Logical: |
Draw.Flexible.lower_y |
Logical: |
summary |
Logical: |
type |
An integer, for the color of background and etc. |
color_is_changed_by_each_reader |
A logical, if |
Draw.inner.circle.for.CFPCTPs |
TRUE or FALSE. If true, then to plot the cumulative false positives and true positives the plot points is depicted by two way, one is a large circle and one is a small circle. By see the small circle, user can see the more precise position of these points. |
plots of the FROC curves and AFROC curves for user's specified modality and user's specified reader. Using this function repeatedly, we can draw the different reader and modality in a same plane simultaneously. So, we can visualize the difference of modality ( or reader).
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 | #================The first example=======================================================
## Not run:
# 1) Fit a model to data by the following:
fit <- fit_Bayesian_FROC(
BayesianFROC::dataList.Chakra.Web, # data to which fit the model
ite=1111 # iteration of MCMC is too small
)
# Note that the return value "fit" is an object of an inherited S4 class from stanfit
# 2)
# With the above S4 class object, we plot the curves.
DrawCurves(
fit,
modality = 1,
reader = 4)
# From this code, an FROC curve is plotted
# for the first modality and the fourth reader.
#3)
# By changing, e.g., the modality, in the above,
# we can draw the curves for different modalities.
# This shows the comparison of modalites.
# In the following,
# the first script plots a curve for the 2 nd modality and the fourth reader,
# and the second script plots a curve for the 3rd modality and the 4 th reader,
# respectively.
DrawCurves(fit,modality = 2,reader = 4)
DrawCurves(fit,modality = 3,reader = 4)
# Curves are overwritten in a single imaging device for the comparison.
#4) By applying the function with respect to different modalities
# in this manner, we can draw AFROC (FROC) curves in the same plain.
#5) If you want to draw the FROC curves
#for reader ID =1,2,3,4 and modality ID =1,2, then the code is as follows;
DrawCurves(
fit,
modalityID = c(1,2,3,4),
readerID = c(1,2)
)
# Each color of curves corresponds to the modality ID.
# So, the curves of "different" readers will have the "same" color,
# if their modalities are "same".
# 6) To show only data points, i.e. FPF and TPF,
# use DrawFROCcurve = F as follows;
DrawCurves(fit,
DrawCFPCTP = TRUE, # This implies data points are ploted.
DrawFROCcurve = FALSE, # From this, the curves are not drawn.
modalityID = c(1,2,3,4),
readerID = c(1)
)
#7) If you use the plot in submission and it is not allowed to use color, then
# by Colour = FALSE, you can get black and white plots, e.g.,
DrawCurves(fit,
DrawCFPCTP = TRUE,
DrawFROCcurve = TRUE,
modalityID = c(1,2,3,4),
readerID = c(1),
Colour = FALSE # From this, you can get plots without colors.
)
#8) For AFROC, use DrawAFROCcurve = T
DrawCurves(fit,
DrawFROCcurve = FALSE,
DrawAFROCcurve = TRUE,
modalityID = c(1,2,3,4),
readerID = c(1)
)
#9)
# In order to compare modality, we draw curves by each modality
# The 1-st modality with all readers 1,2,3,4:
DrawCurves(fit,modalityID = 1,readerID = 1:4, new.imaging.device = TRUE)
#The 2-nd modality with all readers 1,2,3,4:
DrawCurves(fit,modalityID = 2,readerID = 1:4, new.imaging.device = FALSE)
#The 3-rd modality with all readers 1,2,3,4:
DrawCurves(fit,modalityID = 3,readerID = 1:4, new.imaging.device = FALSE)
#The 4-th modality with all readers 1,2,3,4:
DrawCurves(fit,modalityID = 4,readerID = 1:4, new.imaging.device = FALSE)
#The 5-th modality with all readers 1,2,3,4:
DrawCurves(fit,modalityID = 5,readerID = 1:4, new.imaging.device = FALSE)
# Draw for all pairs of modalities and readers:
DrawCurves(
modalityID = 1:fit@dataList$M,
readerID = 1:fit@dataList$Q,
StanS4class = fit
)
# Changes the color by
DrawCurves(fit, type = 2)
DrawCurves(fit, type = 3)
DrawCurves(fit, type = 4)
DrawCurves(fit, type = 5)
DrawCurves(fit, type = 6)
DrawCurves(fit, type = 7)
#================The Second Example======================================================
# This function is available in the case of a single reader and a single modality.
# The reason why the maintainer separate the function for two processes, one is
# the fitting and the second is to plot curves is, in MRMC case,
# it tooks a time to drawing, but in the a single reader and a single modality case, drawing
# the curve is very fast, so in fitting process the curves are also depicted, however
# by this function user can draw the FROC curves.
#First, we prepare the data endowed with this package.
dat <- get(data("dataList.Chakra.1"))
#Second, we fit a model to data named "dat"
fit <- fit_srsc(dat)
# Drawing the curves by
DrawCurves(fit)
# Changes the color by
DrawCurves(fit, type = 2)
DrawCurves(fit, type = 3)
DrawCurves(fit, type = 4)
DrawCurves(fit, type = 5)
DrawCurves(fit, type = 6)
DrawCurves(fit, type = 7)
# Close the graphic device to avoid errors in R CMD check.
Close_all_graphic_devices() # 2020 August
## End(Not run)# dottest
|
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