Burton P, Wilson R, Butters O, Ryser-Welch P, Westerberg A, Abarrategui L, Villegas-Diaz R, Avraam D, Marcon Y, Wheater S (2025). -dsBase: DataSHIELD Server Site Base Functions. +dsBase: 'DataSHIELD' Server Site Base Functions. R package version 6.3.3.
@Manual{,
- title = {dsBase: DataSHIELD Server Site Base Functions},
+ title = {dsBase: 'DataSHIELD' Server Site Base Functions},
author = {Paul Burton and Rebecca Wilson and Olly Butters and Patricia Ryser-Welch and Alex Westerberg and Leire Abarrategui and Roberto Villegas-Diaz and Demetris Avraam and Yannick Marcon and Stuart Wheater},
year = {2025},
note = {R package version 6.3.3},
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 5c084b52..ca6da52a 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -2,4 +2,4 @@ pandoc: 3.1.3
pkgdown: 2.1.3
pkgdown_sha: ~
articles: {}
-last_built: 2025-07-01T22:30Z
+last_built: 2025-07-16T10:31Z
diff --git a/docs/reference/BooleDS.html b/docs/reference/BooleDS.html
index 452f7f13..03e2b322 100644
--- a/docs/reference/BooleDS.html
+++ b/docs/reference/BooleDS.html
@@ -81,8 +81,7 @@ Arguments
A character string taking values 'NA', '1' or '0'. If 'NA' then any NA values in the input vector remain as NAs in the output vector. If '1' or '0' NA values in the -input vector are -all converted to 1 or 0 respectively.#' @return the levels of the input variable.
the levels of the input variable.
+The function converts the input vector into Boolean indicators.
diff --git a/docs/reference/asFactorDS2.html b/docs/reference/asFactorDS2.html index 839d0522..a3ebf298 100644 --- a/docs/reference/asFactorDS2.html +++ b/docs/reference/asFactorDS2.html @@ -69,7 +69,7 @@a boolean that determines whether the new object will be represented as a vector or as a matrix of dummy variables indicating the factor level of each data point. -If this argyment is set to FALSE (default) then the input variable is converted to a factor and +If this argument is set to FALSE (default) then the input variable is converted to a factor and assigned as a vector. If is set to TRUE then the input variable is converted to a factor but assigned as a matrix of dummy variables.
This serverside function check that the server is running in "permissive" privacy control level.
+This server-side function check that the server is running in "permissive" privacy control level.
is a vector of strings which contains the privacy control level names which are permitted by the calling method.
No return value, called for side effects
+Tests whether the R option "datashield.privacyControlLevel" is set to "permissive", if it isn't @@ -63,7 +67,7 @@
a list that includes a matrix with elements the sum of products between each two variables, a matrix with
elements the sum of the values of each variable, a matrix with elements the number of complete cases in each
pair of variables, a list with the number of missing values in each variable separately (columnwise) and the number
-of missing values casewise or pairwise depending on the arqument use, and an error message which indicates
+of missing values casewise or pairwise depending on the argument use, and an error message which indicates
whether or not the input variables pass the disclosure controls. The first disclosure control checks that the number
of variables is not bigger than a percentage of the individual-level records (the allowed percentage is pre-specified
by the 'nfilter.glm'). The second disclosure control checks that none of them is dichotomous with a level having fewer
diff --git a/docs/reference/glmDS1.html b/docs/reference/glmDS1.html
index 38a6a16c..80525b07 100644
--- a/docs/reference/glmDS1.html
+++ b/docs/reference/glmDS1.html
@@ -1,5 +1,5 @@
-
This is the first serverside aggregate function called by ds.glm
+This is the first server-side aggregate function called by ds.glm
List with values from GLM model.
+It is an diff --git a/docs/reference/glmDS2.html b/docs/reference/glmDS2.html index 2cefd28f..0f9df3f4 100644 --- a/docs/reference/glmDS2.html +++ b/docs/reference/glmDS2.html @@ -1,5 +1,5 @@ -
This is the second serverside aggregate function called by ds.glm.
+This is the second server-side aggregate function called by ds.glm.
List with values from GLM model
+It is an aggregate function that uses the model structure and starting diff --git a/docs/reference/heatmapPlotDS.html b/docs/reference/heatmapPlotDS.html index eb3715fa..cf9941b6 100644 --- a/docs/reference/heatmapPlotDS.html +++ b/docs/reference/heatmapPlotDS.html @@ -60,7 +60,7 @@
the number of the nearest neghbours for which their centroid is calculated if the +
the number of the nearest neighbours for which their centroid is calculated if the
method.indicator is equal to 1 (i.e. deterministic method).
The first serverside function called by ds.lexis.
+The first server-side function called by ds.lexis.
a character string specifying the variable holding the time that each individual is censored or fails
List with `max.time`
+This is an aggregate function. diff --git a/docs/reference/lexisDS2.html b/docs/reference/lexisDS2.html index 39b99d50..89ebeabf 100644 --- a/docs/reference/lexisDS2.html +++ b/docs/reference/lexisDS2.html @@ -78,7 +78,7 @@
a clientside generated character string specifying the variable -holding the IDs of indivuals in the data set to be expanded
List with `expanded.table`
+This is the assign @@ -111,7 +115,7 @@
lexisDS3()Data frame with `messageobj` object
+This is an assign function that simplifies the diff --git a/docs/reference/listDisclosureSettingsDS.html b/docs/reference/listDisclosureSettingsDS.html index 10134413..549c94e3 100644 --- a/docs/reference/listDisclosureSettingsDS.html +++ b/docs/reference/listDisclosureSettingsDS.html @@ -49,6 +49,10 @@
listDisclosureSettingsDS()List with DataSHIELD disclosure settings
+For more details see the extensive header for ds.listDisclosureSettings
diff --git a/docs/reference/matrixMultDS.html b/docs/reference/matrixMultDS.html index 6af3ff82..c782eaac 100644 --- a/docs/reference/matrixMultDS.html +++ b/docs/reference/matrixMultDS.html @@ -69,7 +69,7 @@Undertakes standard matrix multiplication where with input matrices A and B with -dimensions A: mxn and B: nxp the output C has dimensions mxp and each elemnt C[i,j] has +dimensions A: mxn and B: nxp the output C has dimensions mxp and each element C[i,j] has value equal to the dot product of row i of A and column j of B where the dot product is obtained as sum(A[i,1]*B[1,j] + A[i,2]*B[2,j] + .... + A[i,n]*B[n,j]). This calculation is only valid if the number of columns of A is the same as the number of rows of B
diff --git a/docs/reference/meanSdGpDS.html b/docs/reference/meanSdGpDS.html index d60d33d7..7e902552 100644 --- a/docs/reference/meanSdGpDS.html +++ b/docs/reference/meanSdGpDS.html @@ -1,5 +1,5 @@ -Serverside function called by ds.meanSdGp
+Server-side function called by ds.meanSdGp
a clientside supplied character string identifying the variable for which +
a client-side supplied character string identifying the variable for which means/SDs are to be calculated
a clientside supplied character string identifying the factor across +
a client-side supplied character string identifying the factor across which means/SDs are to be calculated
List with results from the group statistics
+Computes the mean and standard deviation across groups defined by one diff --git a/docs/reference/scatterPlotDS.html b/docs/reference/scatterPlotDS.html index b1298f5d..2e3d5407 100644 --- a/docs/reference/scatterPlotDS.html +++ b/docs/reference/scatterPlotDS.html @@ -68,7 +68,7 @@
the number of the nearest neghbours for which their centroid is calculated if the +
the number of the nearest neighbours for which their centroid is calculated if the deterministic method is selected.
The function uses the R classical subsetting with squared brackets '[]' and allows also to -subset using a logical oprator and a threshold. The object to subset from must be a vector (factor, numeric -or charcater) or a table (data.frame or matrix).
+subset using a logical operator and a threshold. The object to subset from must be a vector (factor, numeric +or character) or a table (data.frame or matrix).a character, if the input data is a table, if this parameter is provided along with the 'logical' and 'threshold' -parameters, a subtable is based the threshold applied to the speicified variable. This parameter is however ignored if the parameter +parameters, a subtable is based the threshold applied to the specified variable. This parameter is however ignored if the parameter 'rows' and/or 'cols' are provided.
a subset of the vector, matric or dataframe as specified is stored on the server side
+a subset of the vector, matrix or dataframe as specified is stored on the server side
If the input data is a table: The user specifies the rows and/or columns to include in the subset if the input -object is a table; the columns can be refered to by their names. The name of a vector (i.e. a variable) can also be provided +object is a table; the columns can be referred to by their names. The name of a vector (i.e. a variable) can also be provided with a logical operator and a threshold (see example 3). If the input data is a vector: when the parameters 'rows', 'logical' and 'threshold' are all provided the last two are ignored ( 'rows' has precedence over the other two parameters then). diff --git a/docs/reference/table1DDS.html b/docs/reference/table1DDS.html index 6796312e..82d157f7 100644 --- a/docs/reference/table1DDS.html +++ b/docs/reference/table1DDS.html @@ -65,7 +65,7 @@
It generates a 1-dimensional tables where valid (non-disclosive) 1-dimensional tables are defined -as data from sources where no table cells have counts between 1 and the set threshold. When the ouput table +as data from sources where no table cells have counts between 1 and the set threshold. When the output table is invalid all cells but the total count are replaced by missing values. Only the total count is visible on the table returned to the client site. A message is also returned with the 1-dimensional; the message says "invalid table - invalid counts present" if the table is invalid and 'valid table' otherwise.
diff --git a/docs/reference/table2DDS.html b/docs/reference/table2DDS.html index 501a2273..0b5f74e1 100644 --- a/docs/reference/table2DDS.html +++ b/docs/reference/table2DDS.html @@ -69,7 +69,7 @@It generates 2-dimensional contingency tables where valid (non-disclosive) tables are defined -as those where none of their cells have counts between 1 and the set threshold "nfilter.tab". When the ouput table +as those where none of their cells have counts between 1 and the set threshold "nfilter.tab". When the output table is invalid all cells except the total counts are replaced by missing values. Only the total counts are visible on the table returned to the client side. A message is also returned with the 2-dimensional table; the message says "invalid table - invalid counts present" if the table is invalid and 'valid table' otherwise.
diff --git a/docs/reference/testObjExistsDS.html b/docs/reference/testObjExistsDS.html index 09cb4b5f..a0246beb 100644 --- a/docs/reference/testObjExistsDS.html +++ b/docs/reference/testObjExistsDS.html @@ -1,5 +1,5 @@ -The serverside function called by ds.testObjExists
+The server-side function called by ds.testObjExists
List with `test.obj.exists` and `test.obj.class`
+Tests whether a given object exists in