diff --git a/.Rbuildignore b/.Rbuildignore index 91114bf..4952b99 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,2 +1,3 @@ ^.*\.Rproj$ ^\.Rproj\.user$ +^docs$ diff --git a/DESCRIPTION b/DESCRIPTION index 3a79d25..b5d43a9 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: dsDanger Maintainer: DataSHIELD Developers Author: DataSHIELD Developers -Version: 6.3.0 +Version: 6.3.1 License: GPL-3 Title: DataSHIELD server side DANGER functions Description: DataSHIELD server side DANGER functions. @@ -18,5 +18,5 @@ AggregateMethods: DANGERvarsEXTRACTDS AssignMethods: Options: -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.2 Encoding: UTF-8 diff --git a/R/DANGERlistcodeDS.R b/R/DANGERlistcodeDS.R index 189619e..5821e42 100644 --- a/R/DANGERlistcodeDS.R +++ b/R/DANGERlistcodeDS.R @@ -1,6 +1,6 @@ #' @title lists the code for a function #' @description list the code for a named fucntion in a named package -#' @details Serverside aggregate function {DANGERsearchDS} called by clientside function +#' @details Serverside aggregate function \code{DANGERsearchDS} called by clientside function #' @param package.name a vector of character containing a package name #' @param function.name a vector of character containing a function name #' @return a vector of character containing the code for the function, or a stop error message diff --git a/R/DANGERpassPARSERDS.R b/R/DANGERpassPARSERDS.R index a9fde51..259b3fb 100644 --- a/R/DANGERpassPARSERDS.R +++ b/R/DANGERpassPARSERDS.R @@ -2,11 +2,11 @@ #' @description presents an R object or character string to the DataSHIELD R parser #' and determines whether it is passed by the parser and, if so, what form it #' takes after it has traversed the parser. -#' @details Serverside aggregate function {DANGERpassPARSERDS} called by clientside function -#' {ds.DANGERpassPARSER} which presents an R object or character string to the DataSHIELD R parser +#' @details Serverside aggregate function \code{DANGERpassPARSERDS} called by clientside function +#' \code{ds.DANGERpassPARSER} which presents an R object or character string to the DataSHIELD R parser #' and determines whether it is passed or blocked by the parser. If it passes, #' it then explores what form it takes after it has traversed the parser. For further details -#' see help for {ds.DANGERpassPARSER}. +#' see help for \code{ds.DANGERpassPARSER}. #' @param transmit.object fully specified by equivalent clientside argument. #' @return information about whether the input object/string gets blocked or passed #' by the parser. If it passes the parser, the object itself and a record of its class diff --git a/R/DANGERsearchDS.R b/R/DANGERsearchDS.R index 3affb7a..2a5472f 100644 --- a/R/DANGERsearchDS.R +++ b/R/DANGERsearchDS.R @@ -2,8 +2,8 @@ #' @title lists all environments on serverside #' @description creates a list of the names of all of the serverside #' environments -#' @details Serverside aggregate function {DANGERsearchDS} called by clientside function -#' {ds.DANGERsearch}. No arguments need to be specified +#' @details Serverside aggregate function \code{DANGERsearchDS} called by clientside function +#' \code{ds.DANGERsearch}. No arguments need to be specified #' @return a vector of character strings to the clientside giving the names of #' each of the R environments on the serverside in order of their numeric "pos" #' @author Paul Burton 2020 diff --git a/docs/404.html b/docs/404.html index 41747f9..278ca96 100644 --- a/docs/404.html +++ b/docs/404.html @@ -6,7 +6,7 @@ Page not found (404) • dsDanger - + @@ -18,7 +18,7 @@ - +
@@ -50,7 +50,7 @@
- +
@@ -78,16 +78,16 @@

Page not found (404)

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/authors.html b/docs/authors.html index dcdc69e..9fb31c0 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -1,9 +1,9 @@ -Authors and Citation • dsDangerAuthors and Citation • dsDanger - +
@@ -29,38 +29,38 @@
- +
- +
  • -

    DataSHIELD Developers. Maintainer. +

    DataSHIELD Developers. Maintainer.

Citation

- +
-

Developers D (2023). +

Developers D (2024). dsDanger: DataSHIELD server side DANGER functions. -R package version 6.3.0. +R package version 6.3.1.

@Manual{,
   title = {dsDanger: DataSHIELD server side DANGER functions},
   author = {DataSHIELD Developers},
-  year = {2023},
-  note = {R package version 6.3.0},
+  year = {2024},
+  note = {R package version 6.3.1},
 }
@@ -74,15 +74,15 @@

Citation

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/index.html b/docs/index.html index fc05d35..0a127a6 100644 --- a/docs/index.html +++ b/docs/index.html @@ -6,7 +6,7 @@ DataSHIELD server side DANGER functions • dsDanger - + @@ -19,7 +19,7 @@ - +
@@ -51,7 +51,7 @@
- +
@@ -98,16 +98,16 @@

Developers

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 8add9cf..f746d8c 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,6 +1,5 @@ pandoc: 2.9.2.1 -pkgdown: 2.0.7 +pkgdown: 2.1.1 pkgdown_sha: ~ articles: {} -last_built: 2023-02-21T14:29Z - +last_built: 2024-09-30T11:08Z diff --git a/docs/reference/DANGERc2sMATDFDS.html b/docs/reference/DANGERc2sMATDFDS.html index 1bf520b..817e551 100644 --- a/docs/reference/DANGERc2sMATDFDS.html +++ b/docs/reference/DANGERc2sMATDFDS.html @@ -1,9 +1,9 @@ -DANGER FUNCTION copying clientside matrix to serverside — DANGERc2sMATDFDS • dsDangerDANGER FUNCTION copying clientside matrix to serverside — DANGERc2sMATDFDS • dsDanger - +
@@ -29,13 +29,13 @@
- +
@@ -58,61 +58,61 @@

DANGER FUNCTION copying clientside matrix to serverside

Arguments

-
mdata.transmit
+ + +
mdata.transmit

is a character string in a format that can pass through the DataSHIELD R parser which specifies the name of the matrix or data.frame to be copied from the clientside to the serverside.

-
from
+
from

a character string specifying the source and nature of <mdata>. Fixed by clientside function to "clientside.matdf".

-
nrows.transmit
+
nrows.transmit

specifies the number of rows in the matrix to be created in a format that can pass through the DataSHIELD R parser. Fixed by the clientside function as equal to the number of rows in the clientside matrix to be transferred

-
ncols.transmit
+
ncols.transmit

specifies the number of columns in the matrix to be created in a format that can pass through the DataSHIELD R parser. Fixed by the clientside function as equal to the number of columns in the clientside matrix to be transferred

-
colnames.transmit
+
colnames.transmit

a transmissable vector specifying the name of each column in the matrix or data.frame being transferred from clientside to serverside. Generated automatically by clientside function.

-
colclass.transmit
+
colclass.transmit

a transmissable vector specifying the class of the vector representing each column in the matrix or data.frame being transferred from clientside to serverside. Generated automatically by clientside function. This allows the transmission of data.frames containing data of multiple classes.

-
byrow
+
byrow

a logical value specifying whether the matrix created on the serverside should be filled row by row or column by column fixed by the clientside function as FALSE (fill column by column).

-
dimnames
+
dimnames

A dimnames attribute for the matrix: NULL or a list of length 2 giving the row and column names respectively. An empty list is treated as NULL, and a list of length one as row names only. If NULL (the default) the column names -of the original <mdata> data.frame or matrix are taken across to specify the +of the original <mdata> data.frame or matrix are taken across to specify the column names of the serverside matrix

Value

- - -

the object specified by the <newobj> argument (or default name "new_matrix") +

the object specified by the <newobj> argument (or default name "new_matrix") which is written as a data.frame to the serverside. In addition, two validity messages are returned indicating whether <newobj> has been created in each data source and if so whether it is in a valid form.

@@ -129,7 +129,7 @@

Details

This DANGER function was created from the ds.matrix function. A number of the parameters specifying the matrix to be generated are fixed by the nature of the clientside matrix -itself rather than by explicitly stating them as arguments. In consequence, +itself rather than by explicitly stating them as arguments. In consequence, they have been removed from the list of arguments and are instead given invariant values in the first few lines of code. These include: from<-"clientside.matdf", nrows.scalar=NULL, ncols.scalar=NULL, byrow = FALSE. The <from> argument @@ -157,15 +157,15 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/DANGERdfEXTRACTDS.html b/docs/reference/DANGERdfEXTRACTDS.html index 48e3593..76e5e48 100644 --- a/docs/reference/DANGERdfEXTRACTDS.html +++ b/docs/reference/DANGERdfEXTRACTDS.html @@ -1,11 +1,9 @@ -DANGER function returning data.frame (df) from processing servers to -clientside - *** DEPRECATED DANGERdmtEXTRACTDS *** — DANGERdfEXTRACTDS • dsDangerDANGER function returning data.frame (df) from processing servers to clientside - *** DEPRECATED DANGERdmtEXTRACTDS *** — DANGERdfEXTRACTDS • dsDanger - +
@@ -31,14 +29,13 @@
- +
@@ -52,16 +49,16 @@

DANGER function returning data.frame (df) from processing servers to

Arguments

-
dataframeName
-

character string that specifies the name of the df + + +

dataframeName
+

character string that specifies the name of the df to be copied from the serverside to the clientside

Value

- - -

the serverside df specified by name dataframeName as a +

the serverside df specified by name dataframeName as a data.frame/matrix/tibble on the clientside.

@@ -85,15 +82,15 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/DANGERdmtEXTRACTDS.html b/docs/reference/DANGERdmtEXTRACTDS.html index 1b5c166..6b6dfc4 100644 --- a/docs/reference/DANGERdmtEXTRACTDS.html +++ b/docs/reference/DANGERdmtEXTRACTDS.html @@ -1,11 +1,9 @@ -DANGER function returning data.frame, Matrix or tibble (DMT) from -processing servers to clientside — DANGERdmtEXTRACTDS • dsDangerDANGER function returning data.frame, Matrix or tibble (DMT) from processing servers to clientside — DANGERdmtEXTRACTDS • dsDanger - +
@@ -31,14 +29,13 @@
- +
@@ -52,17 +49,17 @@

DANGER function returning data.frame, Matrix or tibble (DMT) from

Arguments

-
dfName
-

is a character string that specifies the name of the DMT + + +

dfName
+

is a character string that specifies the name of the DMT to be copied from the serverside to the clientside. Fully speciifed by <dfName> argument in ds.DANGERdmtEXTRACT

Value

- - -

the serverside dmt specified by name dfName as a +

the serverside dmt specified by name dfName as a data.frame/matrix/tibble on the clientside.

@@ -90,15 +87,15 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/DANGERlistcodeDS.html b/docs/reference/DANGERlistcodeDS.html index e620d6c..d0dae18 100644 --- a/docs/reference/DANGERlistcodeDS.html +++ b/docs/reference/DANGERlistcodeDS.html @@ -1,9 +1,9 @@ -lists the code for a function — DANGERlistcodeDS • dsDangerlists the code for a function — DANGERlistcodeDS • dsDanger - +
@@ -29,13 +29,13 @@
- +
@@ -49,23 +49,23 @@

lists the code for a function

Arguments

-
package.name
+ + +
package.name

a vector of character containing a package name

-
function.name
+
function.name

a vector of character containing a function name

Value

- - -

a vector of character containing the code for the function, or a stop error message

+

a vector of character containing the code for the function, or a stop error message

Details

-

Serverside aggregate function DANGERsearchDS called by clientside function

+

Serverside aggregate function DANGERsearchDS called by clientside function

Author

@@ -84,15 +84,15 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/DANGERpassPARSERDS.html b/docs/reference/DANGERpassPARSERDS.html index b127878..45913c3 100644 --- a/docs/reference/DANGERpassPARSERDS.html +++ b/docs/reference/DANGERpassPARSERDS.html @@ -1,11 +1,11 @@ -determines how a given R object or character string is managed by the DataSHIELD parser — DANGERpassPARSERDS • dsDangerdetermines how a given R object or character string is managed by the DataSHIELD parser — DANGERpassPARSERDS • dsDanger - +
@@ -31,13 +31,13 @@
- +
@@ -53,25 +53,25 @@

determines how a given R object or character string is managed by the DataSH

Arguments

-
transmit.object
+ + +
transmit.object

fully specified by equivalent clientside argument.

Value

- - -

information about whether the input object/string gets blocked or passed +

information about whether the input object/string gets blocked or passed by the parser. If it passes the parser, the object itself and a record of its class are passed back to the clientside.

Details

-

Serverside aggregate function DANGERpassPARSERDS called by clientside function -ds.DANGERpassPARSER which presents an R object or character string to the DataSHIELD R parser +

Serverside aggregate function DANGERpassPARSERDS called by clientside function +ds.DANGERpassPARSER which presents an R object or character string to the DataSHIELD R parser and determines whether it is passed or blocked by the parser. If it passes, it then explores what form it takes after it has traversed the parser. For further details -see help for ds.DANGERpassPARSER.

+see help for ds.DANGERpassPARSER.

Author

@@ -90,15 +90,15 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/DANGERplotDS.html b/docs/reference/DANGERplotDS.html index 00120fc..4fb351c 100644 --- a/docs/reference/DANGERplotDS.html +++ b/docs/reference/DANGERplotDS.html @@ -1,9 +1,9 @@ -DANGERplotDS — DANGERplotDS • dsDangerDANGERplotDS — DANGERplotDS • dsDanger - +
@@ -29,13 +29,13 @@
- +
@@ -49,22 +49,22 @@

DANGERplotDS

Arguments

-
x.name
+ + +
x.name

character string naming first object to be plotted on clientside from serverside to clientside

-
y.name
+
y.name

character string naming second object to be plotted on clientside

Value

- - -

DANGER function

+

DANGER function

Details

@@ -87,15 +87,15 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/DANGERprintDS.html b/docs/reference/DANGERprintDS.html index 64c4a4f..6f7ec95 100644 --- a/docs/reference/DANGERprintDS.html +++ b/docs/reference/DANGERprintDS.html @@ -1,9 +1,9 @@ -DANGERprintDS — DANGERprintDS • dsDangerDANGERprintDS — DANGERprintDS • dsDanger - +
@@ -29,13 +29,13 @@
- +
@@ -49,27 +49,27 @@

DANGERprintDS

Arguments

-
xName
+ + +
xName

character string naming first object to be printed on clientside from serverside to clientside

-
yName
+
yName

character string naming second object to be printed on clientside

-
zName
-

character string naming third object to be +

zName
+

character string naming third object to be printed on clientside

Value

- - -

DANGER function

+

DANGER function

Details

@@ -92,15 +92,15 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/DANGERsearchDS.html b/docs/reference/DANGERsearchDS.html index 043eb72..25e3d8a 100644 --- a/docs/reference/DANGERsearchDS.html +++ b/docs/reference/DANGERsearchDS.html @@ -1,10 +1,10 @@ -lists all environments on serverside — DANGERsearchDS • dsDangerlists all environments on serverside — DANGERsearchDS • dsDanger - +
@@ -30,13 +30,13 @@
- +
@@ -51,15 +51,13 @@

lists all environments on serverside

Value

- - -

a vector of character strings to the clientside giving the names of +

a vector of character strings to the clientside giving the names of each of the R environments on the serverside in order of their numeric "pos"

Details

-

Serverside aggregate function DANGERsearchDS called by clientside function -ds.DANGERsearch. No arguments need to be specified

+

Serverside aggregate function DANGERsearchDS called by clientside function +ds.DANGERsearch. No arguments need to be specified

Author

@@ -78,15 +76,15 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/DANGERseedEXTRACTDS.html b/docs/reference/DANGERseedEXTRACTDS.html index 05b4f76..c27e41b 100644 --- a/docs/reference/DANGERseedEXTRACTDS.html +++ b/docs/reference/DANGERseedEXTRACTDS.html @@ -1,9 +1,9 @@ -DANGERseedEXTRACT — DANGERseedEXTRACTDS • dsDangerDANGERseedEXTRACT — DANGERseedEXTRACTDS • dsDanger - +
@@ -29,13 +29,13 @@
- +
@@ -49,9 +49,7 @@

DANGERseedEXTRACT

Value

- - -

DANGER function

+

DANGER function

Details

@@ -74,15 +72,15 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/DANGERvarsEXTRACTDS.html b/docs/reference/DANGERvarsEXTRACTDS.html index 08d72bd..bd92cd5 100644 --- a/docs/reference/DANGERvarsEXTRACTDS.html +++ b/docs/reference/DANGERvarsEXTRACTDS.html @@ -1,9 +1,9 @@ -DANGERvarsEXTRACT — DANGERvarsEXTRACTDS • dsDangerDANGERvarsEXTRACT — DANGERvarsEXTRACTDS • dsDanger - +
@@ -29,13 +29,13 @@
- +
@@ -56,41 +56,41 @@

DANGERvarsEXTRACT

Arguments

-
xName
+ + +
xName

character string naming first variable to be copied from serverside to clientside

-
yName
+
yName

character string naming second variable to be copied from serverside to clientside

-
zName
+
zName

character string naming third variable to be copied from serverside to clientside

-
uName
+
uName

character string naming fourth variable to be copied from serverside to clientside

-
vName
+
vName

character string naming fifth variable to be copied from serverside to clientside

-
wName
+
wName

character string naming sixth variable to be copied from serverside to clientside

Value

- - -

DANGER function

+

DANGER function

Details

@@ -113,15 +113,15 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/index.html b/docs/reference/index.html index 0c363d4..e380ccc 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,9 +1,9 @@ -Function reference • dsDangerPackage index • dsDanger - +
@@ -29,7 +29,7 @@
- +
@@ -48,13 +48,11 @@

All functions

DANGERdfEXTRACTDS()

-

DANGER function returning data.frame (df) from processing servers to -clientside - *** DEPRECATED DANGERdmtEXTRACTDS ***

+

DANGER function returning data.frame (df) from processing servers to clientside - *** DEPRECATED DANGERdmtEXTRACTDS ***

DANGERdmtEXTRACTDS()

-

DANGER function returning data.frame, Matrix or tibble (DMT) from -processing servers to clientside

+

DANGER function returning data.frame, Matrix or tibble (DMT) from processing servers to clientside

DANGERlistcodeDS()

@@ -96,15 +94,15 @@

All functions
-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 85a31d8..9a6c6eb 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -1,45 +1,17 @@ - - - - /404.html - - - /authors.html - - - /index.html - - - /reference/DANGERc2sMATDFDS.html - - - /reference/DANGERdfEXTRACTDS.html - - - /reference/DANGERdmtEXTRACTDS.html - - - /reference/DANGERlistcodeDS.html - - - /reference/DANGERpassPARSERDS.html - - - /reference/DANGERplotDS.html - - - /reference/DANGERprintDS.html - - - /reference/DANGERsearchDS.html - - - /reference/DANGERseedEXTRACTDS.html - - - /reference/DANGERvarsEXTRACTDS.html - - - /reference/index.html - + +/404.html +/authors.html +/index.html +/reference/DANGERc2sMATDFDS.html +/reference/DANGERdfEXTRACTDS.html +/reference/DANGERdmtEXTRACTDS.html +/reference/DANGERlistcodeDS.html +/reference/DANGERpassPARSERDS.html +/reference/DANGERplotDS.html +/reference/DANGERprintDS.html +/reference/DANGERsearchDS.html +/reference/DANGERseedEXTRACTDS.html +/reference/DANGERvarsEXTRACTDS.html +/reference/index.html + diff --git a/man/DANGERlistcodeDS.Rd b/man/DANGERlistcodeDS.Rd index 7881690..66ed3e4 100644 --- a/man/DANGERlistcodeDS.Rd +++ b/man/DANGERlistcodeDS.Rd @@ -18,7 +18,7 @@ a vector of character containing the code for the function, or a stop error mess list the code for a named fucntion in a named package } \details{ -Serverside aggregate function {DANGERsearchDS} called by clientside function +Serverside aggregate function \code{DANGERsearchDS} called by clientside function } \author{ Stuart Wheater, DataSHIELD Team. diff --git a/man/DANGERpassPARSERDS.Rd b/man/DANGERpassPARSERDS.Rd index bb83f1a..6f76399 100644 --- a/man/DANGERpassPARSERDS.Rd +++ b/man/DANGERpassPARSERDS.Rd @@ -20,11 +20,11 @@ and determines whether it is passed by the parser and, if so, what form it takes after it has traversed the parser. } \details{ -Serverside aggregate function {DANGERpassPARSERDS} called by clientside function -{ds.DANGERpassPARSER} which presents an R object or character string to the DataSHIELD R parser +Serverside aggregate function \code{DANGERpassPARSERDS} called by clientside function +\code{ds.DANGERpassPARSER} which presents an R object or character string to the DataSHIELD R parser and determines whether it is passed or blocked by the parser. If it passes, it then explores what form it takes after it has traversed the parser. For further details -see help for {ds.DANGERpassPARSER}. +see help for \code{ds.DANGERpassPARSER}. } \author{ Paul Burton (2020) diff --git a/man/DANGERsearchDS.Rd b/man/DANGERsearchDS.Rd index 6249548..e4cae14 100644 --- a/man/DANGERsearchDS.Rd +++ b/man/DANGERsearchDS.Rd @@ -15,8 +15,8 @@ creates a list of the names of all of the serverside environments } \details{ -Serverside aggregate function {DANGERsearchDS} called by clientside function -{ds.DANGERsearch}. No arguments need to be specified +Serverside aggregate function \code{DANGERsearchDS} called by clientside function +\code{ds.DANGERsearch}. No arguments need to be specified } \author{ Paul Burton 2020