ds.scatterPlot: Generates non-disclosive scatter plots
In datashield/dsBaseClient: DataSHIELD Client Functions
View source: R/ds.scatterPlot.R
ds.scatterPlot R Documentation
Generates non-disclosive scatter plots
Description
This function uses two disclosure control methods to generate non-disclosive
scatter plots of two server-side continuous variables.
Usage
ds.scatterPlot(
x = NULL,
y = NULL,
method = "deterministic",
k = 3,
noise = 0.25,
type = "split",
return.coords = FALSE,
datasources = NULL
)
Arguments
x
a character string specifying the name of the explanatory variable, a numeric vector.
y
a character string specifying the name of the response variable, a numeric vector.
method
a character string that specifies the
method that is used to generated non-disclosive
coordinates to be displayed in a scatter plot.
This argument can be set as 'deteministic' or 'probabilistic'.
Default 'deteministic'.
For more information see Details.
k
the number of the nearest neighbors for which their centroid is calculated.
Default 3.
For more information see Details.
noise
the percentage of the initial variance that is used as the variance of the embedded
noise if the argument method is set to 'probabilistic'.
For more information see Details.
type
a character that represents the type of graph to display.
This can be set as 'combine' or 'split'.
Default 'split'.
For more information see Details.
return.coords
a logical. If TRUE the coordinates of the anonymised data points are return
to the Console. Default value is FALSE.
datasources
a list of DSConnection-class objects obtained after login.
If the datasources argument is not specified
the default set of connections will be used: see datashield.connections_default.
Details
As the generation of a scatter plot from original data is disclosive and is not
permitted in DataSHIELD, this function allows the user to plot non-disclosive scatter plots.
If the argument method is set to 'deterministic', the server-side function searches
for the k-1 nearest neighbors of each single data point and calculates the centroid
of such k points.
The proximity is defined by the minimum Euclidean distances of z-score transformed data.
When the coordinates of all centroids are estimated the function applies scaling to expand the
centroids back to the dispersion of the original data. The scaling is achieved by multiplying
the centroids with a scaling factor that is equal to the ratio between the standard deviation of
the original variable and the standard deviation of the calculated centroids. The coordinates of
the scaled centroids are then returned to the client-side.
The value of k is specified by the user.
The suggested and default value is equal to 3 which is also
the suggested minimum threshold that is used to prevent disclosure which is specified in the
protection filter nfilter.kNN. When the value of k increases,
the disclosure risk decreases but the utility loss increases.
The value of k is used only
if the argument method is set to 'deterministic'.
Any value of k is ignored if the
argument method is set to 'probabilistic'.
If the argument method is set to 'probabilistic',
the server-side function generates a random normal noise of zero mean
and variance equal to 10% of the variance of each x and y variable.
The noise is added to each x and y variable and the disturbed by the addition of
noise data are returned to the client-side. Note that the seed random number generator is fixed to a
specific number generated from the data and therefore the user gets the same figure every time
that chooses the probabilistic method in a given set of variables.
The value of noise is used only if the argument method is set to 'probabilistic'.
Any value of noise is ignored if
the argument method is set to 'deterministic'.
In type argument can be set two graphics to display:
(1) If type = 'combine' a scatter plot for
combined data is generated.
(2) If type = 'split' one scatter plot for each
study is generated.
Server function called: scatterPlotDS
Value
ds.scatterPlot returns to the client-side one or more scatter
plots depending on the argument type.
Author(s)
DataSHIELD Development Team
Examples
## Not run:
## Version 6, for version 5 see the Wiki
# Connecting to the Opal servers
require('DSI')
require('DSOpal')
require('dsBaseClient')
builder <- DSI::newDSLoginBuilder()
builder$append(server = "study1",
url = "http://192.168.56.100:8080/",
user = "administrator", password = "datashield_test&",
table = "CNSIM.CNSIM1", driver = "OpalDriver")
builder$append(server = "study2",
url = "http://192.168.56.100:8080/",
user = "administrator", password = "datashield_test&",
table = "CNSIM.CNSIM2", driver = "OpalDriver")
builder$append(server = "study3",
url = "http://192.168.56.100:8080/",
user = "administrator", password = "datashield_test&",
table = "CNSIM.CNSIM3", driver = "OpalDriver")
logindata <- builder$build()
# Log onto the remote Opal training servers
connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D")
#Example 1: generate a scatter plot for each study separately
#Using the default deterministic method and k = 10
ds.scatterPlot(x = "D$PM_BMI_CONTINUOUS",
y = "D$LAB_GLUC_ADJUSTED",
method = "deterministic",
k = 10,
type = "split",
datasources = connections)
#Example 2: generate a combined scatter plot with the probabilistic method
#and noise of variance 0.5% of the variable's variance, and display the coordinates
# of the anonymised data points to the Console
ds.scatterPlot(x = "D$PM_BMI_CONTINUOUS",
y = "D$LAB_GLUC_ADJUSTED",
method = "probabilistic",
noise = 0.5,
type = "combine",
datasources = connections)
#Clear the Datashield R sessions and logout
datashield.logout(connections)
## End(Not run)
datashield/dsBaseClient documentation built on Nov. 16, 2024, 2:07 p.m.
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View source: R/ds.scatterPlot.R
| ds.scatterPlot | R Documentation |
Generates non-disclosive scatter plots
Description
This function uses two disclosure control methods to generate non-disclosive scatter plots of two server-side continuous variables.
Usage
ds.scatterPlot(
x = NULL,
y = NULL,
method = "deterministic",
k = 3,
noise = 0.25,
type = "split",
return.coords = FALSE,
datasources = NULL
)
Arguments
x |
a character string specifying the name of the explanatory variable, a numeric vector. |
y |
a character string specifying the name of the response variable, a numeric vector. |
method |
a character string that specifies the
method that is used to generated non-disclosive
coordinates to be displayed in a scatter plot.
This argument can be set as |
k |
the number of the nearest neighbors for which their centroid is calculated. Default 3. For more information see Details. |
noise |
the percentage of the initial variance that is used as the variance of the embedded
noise if the argument |
type |
a character that represents the type of graph to display.
This can be set as |
return.coords |
a logical. If TRUE the coordinates of the anonymised data points are return to the Console. Default value is FALSE. |
datasources |
a list of |
Details
As the generation of a scatter plot from original data is disclosive and is not permitted in DataSHIELD, this function allows the user to plot non-disclosive scatter plots.
If the argument method is set to 'deterministic', the server-side function searches
for the k-1 nearest neighbors of each single data point and calculates the centroid
of such k points.
The proximity is defined by the minimum Euclidean distances of z-score transformed data.
When the coordinates of all centroids are estimated the function applies scaling to expand the centroids back to the dispersion of the original data. The scaling is achieved by multiplying the centroids with a scaling factor that is equal to the ratio between the standard deviation of the original variable and the standard deviation of the calculated centroids. The coordinates of the scaled centroids are then returned to the client-side.
The value of k is specified by the user.
The suggested and default value is equal to 3 which is also
the suggested minimum threshold that is used to prevent disclosure which is specified in the
protection filter nfilter.kNN. When the value of k increases,
the disclosure risk decreases but the utility loss increases.
The value of k is used only
if the argument method is set to 'deterministic'.
Any value of k is ignored if the
argument method is set to 'probabilistic'.
If the argument method is set to 'probabilistic',
the server-side function generates a random normal noise of zero mean
and variance equal to 10% of the variance of each x and y variable.
The noise is added to each x and y variable and the disturbed by the addition of
noise data are returned to the client-side. Note that the seed random number generator is fixed to a
specific number generated from the data and therefore the user gets the same figure every time
that chooses the probabilistic method in a given set of variables.
The value of noise is used only if the argument method is set to 'probabilistic'.
Any value of noise is ignored if
the argument method is set to 'deterministic'.
In type argument can be set two graphics to display:
(1) If type = 'combine' a scatter plot for
combined data is generated.
(2) If type = 'split' one scatter plot for each
study is generated.
Server function called: scatterPlotDS
Value
ds.scatterPlot returns to the client-side one or more scatter
plots depending on the argument type.
Author(s)
DataSHIELD Development Team
Examples
## Not run:
## Version 6, for version 5 see the Wiki
# Connecting to the Opal servers
require('DSI')
require('DSOpal')
require('dsBaseClient')
builder <- DSI::newDSLoginBuilder()
builder$append(server = "study1",
url = "http://192.168.56.100:8080/",
user = "administrator", password = "datashield_test&",
table = "CNSIM.CNSIM1", driver = "OpalDriver")
builder$append(server = "study2",
url = "http://192.168.56.100:8080/",
user = "administrator", password = "datashield_test&",
table = "CNSIM.CNSIM2", driver = "OpalDriver")
builder$append(server = "study3",
url = "http://192.168.56.100:8080/",
user = "administrator", password = "datashield_test&",
table = "CNSIM.CNSIM3", driver = "OpalDriver")
logindata <- builder$build()
# Log onto the remote Opal training servers
connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D")
#Example 1: generate a scatter plot for each study separately
#Using the default deterministic method and k = 10
ds.scatterPlot(x = "D$PM_BMI_CONTINUOUS",
y = "D$LAB_GLUC_ADJUSTED",
method = "deterministic",
k = 10,
type = "split",
datasources = connections)
#Example 2: generate a combined scatter plot with the probabilistic method
#and noise of variance 0.5% of the variable's variance, and display the coordinates
# of the anonymised data points to the Console
ds.scatterPlot(x = "D$PM_BMI_CONTINUOUS",
y = "D$LAB_GLUC_ADJUSTED",
method = "probabilistic",
noise = 0.5,
type = "combine",
datasources = connections)
#Clear the Datashield R sessions and logout
datashield.logout(connections)
## End(Not run)
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