diff --git a/.Rbuildignore b/.Rbuildignore index cfc2fc83c..e05151613 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -22,3 +22,4 @@ ^dsDanger_6.3.4.tar.gz$ ^\.circleci$ ^\.circleci/config\.yml$ +^\.github$ diff --git a/.github/.gitignore b/.github/.gitignore new file mode 100644 index 000000000..2d19fc766 --- /dev/null +++ b/.github/.gitignore @@ -0,0 +1 @@ +*.html diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml new file mode 100644 index 000000000..bfc9f4db3 --- /dev/null +++ b/.github/workflows/pkgdown.yaml @@ -0,0 +1,49 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help +on: + push: + branches: [main, master] + pull_request: + release: + types: [published] + workflow_dispatch: + +name: pkgdown.yaml + +permissions: read-all + +jobs: + pkgdown: + runs-on: ubuntu-latest + # Only restrict concurrency for non-PR jobs + concurrency: + group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }} + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + permissions: + contents: write + steps: + - uses: actions/checkout@v4 + + - uses: r-lib/actions/setup-pandoc@v2 + + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::pkgdown, local::. + needs: website + + - name: Build site + run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) + shell: Rscript {0} + + - name: Deploy to GitHub pages 🚀 + if: github.event_name != 'pull_request' + uses: JamesIves/github-pages-deploy-action@v4.5.0 + with: + clean: false + branch: gh-pages + folder: docs diff --git a/DESCRIPTION b/DESCRIPTION index 5188babe5..cc110b7f7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,11 +1,11 @@ Package: dsBaseClient -Title: DataSHIELD Client Functions +Title: 'DataSHIELD' Client Side Base Functions Version: 6.3.4 -Description: Base DataSHIELD functions for the client side. DataSHIELD is a software package which allows - you to do non-disclosive federated analysis on sensitive data. DataSHIELD analytic functions have +Description: Base 'DataSHIELD' functions for the client side. 'DataSHIELD' is a software package which allows + you to do non-disclosive federated analysis on sensitive data. 'DataSHIELD' analytic functions have been designed to only share non disclosive summary statistics, with built in automated output checking based on statistical disclosure control. With data sites setting the threshold values for - the automated output checks. + the automated output checks. For more details, see 'citation("dsBaseClient")'. Authors@R: c(person(given = "Paul", family = "Burton", role = c("aut"), @@ -77,6 +77,7 @@ Imports: Suggests: lme4, httr, + spelling, tibble, testthat, e1071, @@ -86,3 +87,4 @@ Suggests: DSLite RoxygenNote: 7.3.3 Encoding: UTF-8 +Language: en-GB diff --git a/R/ds.asNumeric.R b/R/ds.asNumeric.R index 7b4da435e..3e2b445fa 100644 --- a/R/ds.asNumeric.R +++ b/R/ds.asNumeric.R @@ -5,7 +5,7 @@ #' @details This function is based on the native R function \code{as.numeric}. #' However, it behaves differently with some specific classes of variables. For example, if the input #' object is of class factor, it first converts its values into characters and then convert those to -#' numerics. This behavior is important for the case where the input object is of class factor having +#' numerics. This behaviour is important for the case where the input object is of class factor having #' numbers as levels. In that case, the native R #' \code{as.numeric} function returns the underlying level codes and not the values as numbers. #' For example \code{as.numeric} in R converts the factor vector: \cr diff --git a/R/ds.corTest.R b/R/ds.corTest.R index 38fffceb9..3c9e42a81 100644 --- a/R/ds.corTest.R +++ b/R/ds.corTest.R @@ -10,7 +10,7 @@ #' used for the test. One of "pearson", "kendall", or "spearman", can be abbreviated. #' Default is set to "pearson". #' @param exact a logical indicating whether an exact p-value should be computed. Used for -#' Kendall's tau and Spearman's rho. See ‘Details’ of R stats function \code{cor.test} for +#' Kendall's tau and Spearman's rho. See \emph{Details} of R stats function \code{cor.test} for #' the meaning of NULL (the default). #' @param conf.level confidence level for the returned confidence interval. Currently #' only used for the Pearson product moment correlation coefficient if there are at least diff --git a/R/ds.dataFrameSubset.R b/R/ds.dataFrameSubset.R index 46878520b..1c5ff6a00 100644 --- a/R/ds.dataFrameSubset.R +++ b/R/ds.dataFrameSubset.R @@ -12,7 +12,7 @@ #' #' Server functions called: \code{dataFrameSubsetDS1} and \code{dataFrameSubsetDS2} #' -#' @param df.name a character string providing the name of the data frame to be subseted. +#' @param df.name a character string providing the name of the data frame to be subset. #' @param V1.name A character string specifying the name of the vector #' to which the Boolean operator is to be applied to define the subset. #' For more information see details. diff --git a/R/ds.dmtC2S.R b/R/ds.dmtC2S.R index 1f91efbfe..ee2e4be67 100644 --- a/R/ds.dmtC2S.R +++ b/R/ds.dmtC2S.R @@ -29,7 +29,7 @@ #' wish to change the connections you wish to use by default the call #' datashield.connections_default('opals.a') will set 'default.connections' #' to be 'opals.a' and so in the absence of specific instructions to the contrary -#' (e.g. by specifiying a particular dataset to be used via the +#' (e.g. by specifying a particular dataset to be used via the #' argument) all subsequent function calls will be to the datasets held in opals.a. #' If the argument is specified, it should be set without #' inverted commas: e.g. datasources=opals.a or datasources=default.connections. diff --git a/R/ds.elspline.R b/R/ds.elspline.R index c4a2bbdd8..01ddca05b 100644 --- a/R/ds.elspline.R +++ b/R/ds.elspline.R @@ -13,7 +13,7 @@ #' @param x the name of the input numeric variable #' @param n integer greater than 2, knots are computed such that they cut n equally-spaced #' intervals along the range of x -#' @param marginal logical, how to parametrize the spline, see Details +#' @param marginal logical, how to parametrise the spline, see Details #' @param names character, vector of names for constructed variables #' @param newobj a character string that provides the name for the output #' variable that is stored on the data servers. Default \code{elspline.newobj}. diff --git a/R/ds.forestplot.R b/R/ds.forestplot.R index 3b4873875..60227913c 100644 --- a/R/ds.forestplot.R +++ b/R/ds.forestplot.R @@ -1,10 +1,10 @@ #' @title Forestplot for SLMA models -#' @description Draws a foresplot of the coefficients for Study-Level Meta-Analysis performed with +#' @description Draws a forestplot of the coefficients for Study-Level Meta-Analysis performed with #' DataSHIELD #' -#' @param mod \code{list} List outputed by any of the SLMA models of DataSHIELD (\code{ds.glmerSLMA}, +#' @param mod \code{list} List outputted by any of the SLMA models of DataSHIELD (\code{ds.glmerSLMA}, #' \code{ds.glmSLMA}, \code{ds.lmerSLMA}) -#' @param variable \code{character} (default \code{NULL}) Variable to meta-analyze and visualize, by setting this +#' @param variable \code{character} (default \code{NULL}) Variable to meta-analyse and visualise, by setting this #' argument to \code{NULL} (default) the first independent variable will be used. #' @param method \code{character} (Default \code{"ML"}) Method to estimate the between study variance. #' See details from \code{?meta::metagen} for the different options. diff --git a/R/ds.glmPredict.R b/R/ds.glmPredict.R index ff0d7647e..96dfc792c 100644 --- a/R/ds.glmPredict.R +++ b/R/ds.glmPredict.R @@ -91,7 +91,7 @@ #' wish to change the connections you wish to use by default the call #' datashield.connections_default('opals.a') will set 'default.connections' #' to be 'opals.a' and so in the absence of specific instructions to the contrary -#' (e.g. by specifiying a particular dataset to be used via the +#' (e.g. by specifying a particular dataset to be used via the #' argument) all subsequent function calls will be to the datasets held in opals.a. #' If the argument is specified, it should be set without #' inverted commas: e.g. datasources=opals.a or datasources=default.connections. @@ -116,7 +116,7 @@ #' the name - if one was specified - of the dataframe being used as the basis for predictions, #' the output.type specified ('link', 'response' or 'terms'), the value of the #' dispersion parameter if one had been specified and the residual scale parameter (which is -#' multipled by sqrt(dispersion parameter) if one has been set). If output.type = 'terms', +#' multiplied by sqrt(dispersion parameter) if one has been set). If output.type = 'terms', #' the summary statistics for the fit and se.fit vectors are replaced by equivalent #' summary statistics for each column in fit and se.fit matrices which each have k columns #' if k terms are being summarised. diff --git a/R/ds.glmSLMA.R b/R/ds.glmSLMA.R index 7f3454bc0..9b46a6a40 100644 --- a/R/ds.glmSLMA.R +++ b/R/ds.glmSLMA.R @@ -263,7 +263,7 @@ #' them into their meta-analysis package of choice. #' @return \code{is.object.created} and \code{validity.check} are standard #' items returned by an assign function when the designated newobj appears to have -#' been successfuly created on the serverside at each study. This output is +#' been successfully created on the serverside at each study. This output is #' produced specifically by the assign function \code{glmSLMADS.assign} that writes #' out the glm object on the serverside #' @author Paul Burton, for DataSHIELD Development Team 07/07/20 diff --git a/R/ds.glmSummary.R b/R/ds.glmSummary.R index 38df81637..5629d937f 100644 --- a/R/ds.glmSummary.R +++ b/R/ds.glmSummary.R @@ -48,7 +48,7 @@ #' wish to change the connections you wish to use by default the call #' datashield.connections_default('opals.a') will set 'default.connections' #' to be 'opals.a' and so in the absence of specific instructions to the contrary -#' (e.g. by specifiying a particular dataset to be used via the +#' (e.g. by specifying a particular dataset to be used via the #' argument) all subsequent function calls will be to the datasets held in opals.a. #' If the argument is specified, it should be set without #' inverted commas: e.g. datasources=opals.a or datasources=default.connections. diff --git a/R/ds.igb_standards.R b/R/ds.igb_standards.R index fb7953f1e..89498a0ca 100644 --- a/R/ds.igb_standards.R +++ b/R/ds.igb_standards.R @@ -20,11 +20,20 @@ #' used: see \code{\link[DSI]{datashield.connections_default}}. #' @note For gestational ages between 24 and 33 weeks, the INTERGROWTH very early preterm #' standard is used. -#' @references International standards for newborn weight, length, and head circumference by -#' gestational age and sex: the Newborn Cross-Sectional Study of the INTERGROWTH-21st Project -#' Villar, José et al. The Lancet, Volume 384, Issue 9946, 857-868 -#' INTERGROWTH-21st very preterm size at birth reference charts. Lancet 2016 -#' doi.org/10.1016/S0140-6736(16) 00384-6. Villar, José et al. +#' @references +#' \itemize{ +#' \item Villar, J., Ismail, L.C., Victora, C.G., Ohuma, E.O., Bertino, E., +#' Altman, D.G., Lambert, A., Papageorghiou, A.T., Carvalho, M., Jaffer, Y.A., +#' Gravett, M.G., Purwar, M., Frederick, I.O., Noble, A.J., Pang, R., Barros, +#' F.C., Chumlea, C., Bhutta, Z.A., Kennedy, S.H., 2014. International +#' standards for newborn weight, length, and head circumference by gestational +#' age and sex: the Newborn Cross-Sectional Study of the INTERGROWTH-21st +#' Project. The Lancet 384, 857--868. https://doi.org/10.1016/S0140-6736(14)60932-6 +#' \item Villar, J., Giuliani, F., Fenton, T.R., Ohuma, E.O., Ismail, L.C., +#' Kennedy, S.H., 2016. INTERGROWTH-21st very preterm size at birth reference +#' charts. The Lancet 387, 844--845. https://doi.org/10.1016/S0140-6736(16)00384-6 +#' +#' } #' @return assigns the converted measurement as a new object on the server-side #' @author Demetris Avraam for DataSHIELD Development Team #' @export diff --git a/R/ds.ls.R b/R/ds.ls.R index 415c93f4d..2f65a3c8f 100644 --- a/R/ds.ls.R +++ b/R/ds.ls.R @@ -41,7 +41,7 @@ #' Server function called: \code{lsDS}. #' #' @param search.filter character string (potentially including \code{*} symbol) specifying the filter -#' for the object name that you want to find in the enviroment. For more information see \strong{Details}. +#' for the object name that you want to find in the environment. For more information see \strong{Details}. #' @param env.to.search an integer (e.g. in \code{2} or \code{2L} format) specifying the position #' in the search path of the environment to be explored. \code{1L} is the current active analytic #' environment on the server-side and is the default value of \code{env.to.search}. diff --git a/R/ds.lspline.R b/R/ds.lspline.R index 9aca23974..e044005cb 100644 --- a/R/ds.lspline.R +++ b/R/ds.lspline.R @@ -10,7 +10,7 @@ #' in slope as compared to the previous segment. #' @param x the name of the input numeric variable #' @param knots numeric vector of knot positions -#' @param marginal logical, how to parametrize the spline, see Details +#' @param marginal logical, how to parametrise the spline, see Details #' @param names character, vector of names for constructed variables #' @param newobj a character string that provides the name for the output #' variable that is stored on the data servers. Default \code{lspline.newobj}. diff --git a/R/ds.matrix.R b/R/ds.matrix.R index 6ee9bdfd5..b90356c59 100644 --- a/R/ds.matrix.R +++ b/R/ds.matrix.R @@ -27,7 +27,7 @@ #' #' @param mdata a character string specifying #' the name of a server-side scalar or vector. Also, a numeric value representing a -#' scalar specified from the client-side can be speficied. +#' scalar specified from the client-side can be specified #' Zeros, negative values and NAs are all allowed. #' For more information see \strong{Details}. #' @param from a character string specifying the source and nature of \code{mdata}. diff --git a/R/ds.matrixDiag.R b/R/ds.matrixDiag.R index f6edcbcd5..8c8ca877a 100644 --- a/R/ds.matrixDiag.R +++ b/R/ds.matrixDiag.R @@ -37,7 +37,7 @@ #' Server function called: \code{matrixDiagDS} #' @param x1 a character string specifying #' the name of a server-side scalar or vector. Also, a numeric value or vector -#' specified from the client-side can be speficied. This argument depends +#' specified from the client-side can be specified. This argument depends #' on the value specified in \code{aim}. #' For more information see \strong{Details}. #' @param aim a character string specifying the behaviour of the function. diff --git a/R/ds.ns.R b/R/ds.ns.R index 9c961fcf1..e98643d4d 100644 --- a/R/ds.ns.R +++ b/R/ds.ns.R @@ -8,7 +8,7 @@ #' sequence of interior knots, and the natural boundary conditions. These enforce the constraint #' that the function is linear beyond the boundary knots, which can either be supplied or default #' to the extremes of the data. -#' A primary use is in modeling formula to directly specify a natural spline term in a model. +#' A primary use is in modelling formula to directly specify a natural spline term in a model. #' @param x the predictor variable. Missing values are allowed. #' @param df degrees of freedom. One can supply df rather than knots; ns() then chooses #' df - 1 - intercept knots at suitably chosen quantiles of x (which will ignore missing values). diff --git a/R/ds.qlspline.R b/R/ds.qlspline.R index 45a3e2d33..9839d9843 100644 --- a/R/ds.qlspline.R +++ b/R/ds.qlspline.R @@ -18,7 +18,7 @@ #' intervals along x or a vector of numbers in (0; 1) specifying the quantiles explicitly. #' @param na.rm logical, whether NA should be removed when calculating quantiles, passed #' to na.rm of quantile. Default set to TRUE -#' @param marginal logical, how to parametrize the spline, see Details +#' @param marginal logical, how to parametrise the spline, see Details #' @param names character, vector of names for constructed variables #' @param newobj a character string that provides the name for the output #' variable that is stored on the data servers. Default \code{qlspline.newobj}. diff --git a/R/ds.ranksSecure.R b/R/ds.ranksSecure.R index 5a3affcaf..1d9d98ed9 100644 --- a/R/ds.ranksSecure.R +++ b/R/ds.ranksSecure.R @@ -1,7 +1,7 @@ # ds.ranksSecure #' @title Secure ranking of a vector across all sources #' @description Securely generate the ranks of a numeric vector and estimate -#' true qlobal quantiles across all data sources simultaneously +#' true global quantiles across all data sources simultaneously #' @details ds.ranksSecure is a clientside function which calls a series of #' other clientside and serverside functions to securely generate the global #' ranks of a numeric vector "V2BR" (vector to be ranked) @@ -43,7 +43,7 @@ #' of the clusters of values that are being ranked such that some values are #' treated as being missing and the processing stops, then setting #' generate.quantiles to FALSE allows the generation of ranks to complete so -#' they can then be used for non-parameteric analysis, even if the key values +#' they can then be used for non-parametric analysis, even if the key values #' cannot be estimated. A real example of an unusual configuration was in a #' reasonably large dataset of survival times, where a substantial proportion #' of survival profiles were censored at precisely 10 years. This meant that diff --git a/R/ds.recodeValues.R b/R/ds.recodeValues.R index d44cc8570..184ccea2b 100644 --- a/R/ds.recodeValues.R +++ b/R/ds.recodeValues.R @@ -4,7 +4,7 @@ #' @details This function recodes individual values with new individual values. This can #' apply to numeric and character values, factor levels and NAs. One particular use of #' \code{ds.recodeValues} is to convert NAs to an explicit value. This value is specified -#' in the argument \code{missing}. If tthe user want to recode only missing values, then it +#' in the argument \code{missing}. If the user want to recode only missing values, then it #' should also specify an identical vector of values in both arguments \code{values2replace.vector} #' and \code{new.values.vector} (see Example 2 below). #' Server function called: \code{recodeValuesDS} diff --git a/R/ds.sample.R b/R/ds.sample.R index d2a08ab33..08c1b04c1 100644 --- a/R/ds.sample.R +++ b/R/ds.sample.R @@ -45,7 +45,7 @@ #' case with the default name 'newobj.sample) using ds.dataFrameSort with the #' 'sampling.order' vector as the sort key, the output object is rendered #' equivalent to PRWa but with the rows randomly permuted (so the column reflecting -#' the vector 'sample.order' now runs from 1:length of obejct, while the +#' the vector 'sample.order' now runs from 1:length of object, while the #' column reflecting 'ID.seq' denoting the original order is now randomly ordered. #' If you need to return to the original order you can simply us ds.dataFrameSort #' again using the column reflecting 'ID.seq' as the sort key: diff --git a/R/ds.scatterPlot.R b/R/ds.scatterPlot.R index 827b32722..6c2c78058 100644 --- a/R/ds.scatterPlot.R +++ b/R/ds.scatterPlot.R @@ -6,7 +6,7 @@ #' permitted in DataSHIELD, this function allows the user to plot non-disclosive scatter plots. #' #' If the argument \code{method} is set to \code{'deterministic'}, the server-side function searches -#' for the \code{k-1} nearest neighbors of each single data point and calculates the centroid +#' for the \code{k-1} nearest neighbours of each single data point and calculates the centroid #' of such \code{k} points. #' The proximity is defined by the minimum Euclidean distances of z-score transformed data. #' @@ -52,7 +52,7 @@ #' This argument can be set as \code{'deteministic'} or \code{'probabilistic'}. #' Default \code{'deteministic'}. #' For more information see \strong{Details}. -#' @param k the number of the nearest neighbors for which their centroid is calculated. +#' @param k the number of the nearest neighbours for which their centroid is calculated. #' Default 3. #' For more information see \strong{Details}. #' @param noise the percentage of the initial variance that is used as the variance of the embedded diff --git a/R/ds.sqrt.R b/R/ds.sqrt.R index 9193dbbc7..e78011def 100644 --- a/R/ds.sqrt.R +++ b/R/ds.sqrt.R @@ -59,7 +59,7 @@ #' # and get their square roots #' ds.make(toAssign='rep((1:10)^2, times=10)', newobj='squares.vector', datasources=connections) #' ds.sqrt(x='squares.vector', newobj='sqrt.vector', datasources=connections) -#' # check the behavior of that operation by comparing the tables of squares.vector and sqrt.vector + # check the behaviour of that operation by comparing the tables of squares.vector and sqrt.vector #' ds.table(rvar='squares.vector')$output.list$TABLE_rvar.by.study_counts #' ds.table(rvar='sqrt.vector')$output.list$TABLE_rvar.by.study_counts #' diff --git a/R/ds.subset.R b/R/ds.subset.R index 40bd6ce05..03b2e7344 100644 --- a/R/ds.subset.R +++ b/R/ds.subset.R @@ -1,10 +1,10 @@ #' #' @title Generates a valid subset of a table or a vector #' @description 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). #' @details (1) If the input data is a table the user specifies the rows and/or columns to include in the subset; the columns can be -#' refered to by their names. Table subsetting can also be done using the name of a variable and a threshold (see example 3). +#' referred to by their names. Table subsetting can also be done using the name of a variable and a threshold (see example 3). #' (2) If the input data is a vector and the parameters 'rows', 'logical' and 'threshold' are all provided the last two are ignored #' (i.e. 'rows' has precedence over the other two parameters then). #' IMPORTANT NOTE: If the requested subset is not valid (i.e. contains less than the allowed number of observations) all the values are diff --git a/R/ds.subsetByClass.R b/R/ds.subsetByClass.R index 5c6f92bb1..b3b14ec27 100644 --- a/R/ds.subsetByClass.R +++ b/R/ds.subsetByClass.R @@ -107,7 +107,7 @@ ds.subsetByClass <- function(x=NULL, subsets="subClasses", variables=NULL, datas } # call the server side function that does the job - # get the indices of the columns refered to by their names in the arguments + # get the indices of the columns referred to by their names in the arguments if(is.null(variables)){ cally <- paste0("subsetByClassDS('", x, "')") }else{ diff --git a/R/ds.table1D.R b/R/ds.table1D.R index 07df60eb3..8a13afdc7 100644 --- a/R/ds.table1D.R +++ b/R/ds.table1D.R @@ -10,10 +10,10 @@ #' count. This way it is possible the know the total count and combine total counts across data sources but it #' is not possible to identify the cell(s) that had the small counts which render the table invalid. #' @param x a character, the name of a numerical vector with discrete values - usually a factor. -#' @param type a character which represent the type of table to ouput: pooled table or one table for each +#' @param type a character which represent the type of table to output: pooled table or one table for each #' data source. If \code{type} is set to 'combine', a pooled 1-dimensional table is returned; if If \code{type} #' is set to 'split' a 1-dimensional table is returned for each data source. -#' @param warningMessage a boolean, if set to TRUE (deafult) a warning is displayed if any returned table is invalid. Warning +#' @param warningMessage a boolean, if set to TRUE (default) a warning is displayed if any returned table is invalid. Warning #' messages are suppressed if this parameter is set to FALSE. However the analyst can still view 'validity' information #' which are stored in the output object 'validity' - see the list of output objects. #' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the diff --git a/R/ds.table2D.R b/R/ds.table2D.R index 301a89936..0dee00abd 100644 --- a/R/ds.table2D.R +++ b/R/ds.table2D.R @@ -10,11 +10,11 @@ #' identify the cell(s) that had the small counts which render the table invalid. #' @param x a character, the name of a numerical vector with discrete values - usually a factor. #' @param y a character, the name of a numerical vector with discrete values - usually a factor. -#' @param type a character which represent the type of table to ouput: pooled table or one table for each +#' @param type a character which represent the type of table to output: pooled table or one table for each #' data source or both. If \code{type} is set to 'combine', a pooled 2-dimensional table is returned; If \code{type} #' is set to 'split' a 2-dimensional table is returned for each data source. If \code{type} is set to 'both' (default) #' a pooled 2-dimensional table plus a 2-dimensional table for each data source are returned. -#' @param warningMessage a boolean, if set to TRUE (deafult) a warning is displayed if any returned table is invalid. Warning +#' @param warningMessage a boolean, if set to TRUE (default) a warning is displayed if any returned table is invalid. Warning #' messages are suppressed if this parameter is set to FALSE. However the analyst can still view 'validity' information #' which are stored in the output object 'validity' - see the list of output objects. #' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the diff --git a/R/ds.unique.R b/R/ds.unique.R index 327585bd2..8f2717054 100644 --- a/R/ds.unique.R +++ b/R/ds.unique.R @@ -4,7 +4,7 @@ #' @details Will create a vector or list which has no duplicate values. #' #' Server function called: \code{uniqueDS} -#' @param x.name a character string providing the name of the varable, in the server, to perform \code{unique} upon +#' @param x.name a character string providing the name of the variable, in the server, to perform \code{unique} upon #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. Default \code{unique.newobj}. #' @param datasources a list of \code{\link[DSI]{DSConnection-class}} diff --git a/R/ds.vectorCalc.R b/R/ds.vectorCalc.R index f019c7bca..f8918aab4 100644 --- a/R/ds.vectorCalc.R +++ b/R/ds.vectorCalc.R @@ -3,10 +3,10 @@ #' @description Carries out a row-wise operation on two or more vector. The function calls no #' server side function; it uses the R operation symbols built in DataSHIELD. #' @details In DataSHIELD it is possible to perform an operation on vectors by just using the relevant -#' R symbols (e.g. '+' for addtion, '*' for multiplication, '-' for substraction and '/' for division). +#' R symbols (e.g. '+' for addition, '*' for multiplication, '-' for subtraction and '/' for division). #' This might however be inconvenient if the number of vectors to include in the operation is large. #' This function takes the names of two or more vectors and performs the desired operation which could be -#' an addition, a multiplication, a substraction or a division. If one or more vectors have a missing value +#' an addition, a multiplication, a subtraction or a division. If one or more vectors have a missing value #' at any one entry (i.e. observation), the operation returns a missing value ('NA') for that entry; the output #' vectors has, hence the same length as the input vectors. #' @param x a vector of characters, the names of the vectors to include in the operation. diff --git a/R/glmChecks.R b/R/glmChecks.R index c720fa45f..6dcfe2ee7 100644 --- a/R/glmChecks.R +++ b/R/glmChecks.R @@ -1,14 +1,14 @@ #' #' @title Checks if the elements in the glm model have the right characteristics #' @description This is an internal function required by the client function \code{ds.glm} -#' to verify all the variables and ensure the process does not halt inadvertanly. +#' to verify all the variables and ensure the process does not halt inadvertently #' @details the variables are checked to ensure they are defined, not empty (i.e. are not missing -#' at complete) and evantually (if 'offset' or 'weights') are of 'numeric' with non negative value +#' at complete) and eventually (if 'offset' or 'weights') are of 'numeric' with non negative value #' (if 'weights'). #' @param formula a character, a regression formula given as a string character #' @param data a character, the name of an optional data frame containing the variables in #' in the \code{formula}. -#' @param offset null or a numreric vector that can be used to specify an a priori known component to be +#' @param offset null or a numeric vector that can be used to specify an a priori known component to be #' included in the linear predictor during fitting. #' @param weights a character, the name of an optional vector of 'prior weights' to be used in the fitting #' process. Should be NULL or a numeric vector. diff --git a/R/logical2int.R b/R/logical2int.R index b2a6d20bb..575960c41 100644 --- a/R/logical2int.R +++ b/R/logical2int.R @@ -1,7 +1,7 @@ #' #' @title Turns a logical operator into an integer #' @description This is an internal function. -#' @details This function is called to turn a logical oprator given as a +#' @details This function is called to turn a logical operator given as a #' character into an integer: '>' is turned into 1, '>=' into 2, '<' into 3, #' '<=' into 4, '==' into 5 and '!=' into 6. #' @param obj a character, the logical parameter to turn into an integer diff --git a/R/meanByClassHelper0a.R b/R/meanByClassHelper0a.R index 21c6e90ca..c1c51c9b6 100644 --- a/R/meanByClassHelper0a.R +++ b/R/meanByClassHelper0a.R @@ -7,7 +7,7 @@ #' @param b a character, the name of a factor vector. #' @param type a character which represents the type of analysis to carry out. If \code{type} is set to #' 'combine', a pooled table of results is generated. If \code{type} is set to 'split', a table of results -#' is genrated for each study. +#' is generated for each study. #' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the #' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @return a table or a list of tables that hold the length of the numeric variable and its mean diff --git a/R/meanByClassHelper0b.R b/R/meanByClassHelper0b.R index 1419d53f2..89c1c17d6 100644 --- a/R/meanByClassHelper0b.R +++ b/R/meanByClassHelper0b.R @@ -2,13 +2,13 @@ #' @title Runs the computation if variables are within a table structure #' @description This is an internal function. #' @details This function is called by the function 'ds.meanByClass' to produce the final tables -#' if the user soecify a table structure. +#' if the user specify a table structure. #' @param x a character, the name of the dataset to get the subsets from. #' @param outvar a character vector, the names of the continuous variables #' @param covar a character vector, the names of up to 3 categorical variables #' @param type a character which represents the type of analysis to carry out. If \code{type} is set to #' 'combine', a pooled table of results is generated. If \code{type} is set to 'split', a table of results -#' is genrated for each study. +#' is generated for each study. #' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the #' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @return a table or a list of tables that hold the length of the numeric variable(s) and their mean diff --git a/R/meanByClassHelper2.R b/R/meanByClassHelper2.R index 9fac9125a..55dca1c33 100644 --- a/R/meanByClassHelper2.R +++ b/R/meanByClassHelper2.R @@ -2,12 +2,12 @@ #' @title Generates a table for pooled results #' @description This is an internal function. #' @details This function is called by the function 'ds.meanByClass' to produce the final table -#' if the user sets the parmater 'type' to combine (the default behaviour of 'ds.meanByClass'). +#' if the user sets the parameter 'type' to combine (the default behaviour of 'ds.meanByClass'). #' @param dtsources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the #' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @param tablenames a character vector, the name of the subset tables #' @param variables a character vector, the names of the continuous variables to computes a mean for. -#' @param invalidrecorder a list, holds informations about invalid subsets in each study. +#' @param invalidrecorder a list, holds information about invalid subsets in each study. #' @keywords internal #' @return a matrix, a table which contains the length, mean and standard deviation of each of the #' specified 'variables' in each subset table. diff --git a/R/meanByClassHelper3.R b/R/meanByClassHelper3.R index 61e61d1f8..4c834b78a 100644 --- a/R/meanByClassHelper3.R +++ b/R/meanByClassHelper3.R @@ -2,12 +2,12 @@ #' @title Generates results tables for each study separately #' @description This is an internal function. #' @details This function is called by the function 'ds.meanByClass' to produce the final tables -#' if the user sets the parmater 'type' to 'split'. +#' if the user sets the parameter 'type' to 'split'. #' @param dtsources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the #' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @param tablenames a character vector, the name of the subset tables #' @param variables a character vector, the names of the continuous variables to computes a mean for. -#' @param invalidrecorder a list, holds informations about invalid subsets in each study +#' @param invalidrecorder a list, holds information about invalid subsets in each study #' @keywords internal #' @return a list which one results table for each study. #' @author Gaye, A. @@ -19,7 +19,7 @@ meanByClassHelper3 <- function(dtsources, tablenames, variables, invalidrecorder finalist <- vector('list', length(dtsources)) for(s in 1:length(dtsources)){ - # now get the mean and SD for the continuous variables in each of tthe subset tables + # now get the mean and SD for the continuous variables in each of the subset tables finaltable <- matrix(numeric(0), ncol=numtables) finalrows <- c() for(z in 1:length(variables)){ diff --git a/README.md b/README.md index 173f08245..5c94ffc1c 100644 --- a/README.md +++ b/README.md @@ -1,14 +1,38 @@ -dsBaseClient -============ +## dsBaseClient: 'DataSHIELD' Client Side Base Functions -DataSHIELD client side base R library. +[![License](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.html) +[![](https://www.r-pkg.org/badges/version/dsBaseClient?color=black)](https://cran.r-project.org/package=dsBaseClient) +[![R build +status](https://github.com/datashield/dsBaseClient/workflows/R-CMD-check/badge.svg)](https://github.com/datashield/dsBaseClient/actions) +[![Codecov test coverage](https://codecov.io/gh/datashield/dsBaseClient/graph/badge.svg)](https://app.codecov.io/gh/datashield/dsBaseClient) -[![License](https://img.shields.io/badge/license-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.html) +## Installation -About -===== +You can install the released version of dsBaseClient from +[CRAN](https://cran.r-project.org/package=dsBaseClient) with: -DataSHIELD is a software package which allows you to do non-disclosive federated analysis on sensitive data. Our website (https://www.datashield.org) has in depth descriptions of what it is, how it works and how to install it. A key point to highlight is that DataSHIELD has a client-server infrastructure, so the dsBase package (https://github.com/datashield/dsBase) needs to be used in conjuction with the dsBaseClient package (https://github.com/datashield/dsBaseClient) - trying to use one without the other makes no sense. +``` r +install.packages("dsBaseClient") +``` + +And the development version from +[GitHub](https://github.com/datashield/dsBaseClient/) with: + + +``` r +install.packages("remotes") +remotes::install_github("datashield/dsBaseClient", "") + +# Install v6.3.4 with the following +remotes::install_github("datashield/dsBaseClient", "6.3.4") +``` + +For a full list of development branches, checkout https://github.com/datashield/dsBaseClient/branches + + +## About + +DataSHIELD is a software package which allows you to do non-disclosive federated analysis on sensitive data. Our website (https://www.datashield.org) has in depth descriptions of what it is, how it works and how to install it. A key point to highlight is that DataSHIELD has a client-server infrastructure, so the dsBase package (https://github.com/datashield/dsBase) needs to be used in conjunction with the dsBaseClient package (https://github.com/datashield/dsBaseClient) - trying to use one without the other makes no sense. Detailed instructions on how to install DataSHIELD are at https://www.datashield.org/wiki. @@ -21,3 +45,31 @@ The code here is organised as: | obiba CRAN | Where you probably should install DataSHIELD from. | | releases | Stable releases. | | master branch | Mostly in sync with the latest release, changes rarely. | + +## References + +[1] Burton P, Wilson R, Butters O, Ryser-Welch P, Westerberg A, Abarrategui L, Villegas-Diaz R, + Avraam D, Marcon Y, Bishop T, Gaye A, Escribà Montagut X, Wheater S (2025). + _dsBaseClient: 'DataSHIELD' Client Side Base Functions_. R package version 6.3.4. + +[2] Gaye A, Marcon Y, Isaeva J, LaFlamme P, Turner A, Jones E, Minion J, Boyd A, Newby C, Nuotio + M, Wilson R, Butters O, Murtagh B, Demir I, Doiron D, Giepmans L, Wallace S, Budin-Ljøsne I, + Oliver Schmidt C, Boffetta P, Boniol M, Bota M, Carter K, deKlerk N, Dibben C, Francis R, + Hiekkalinna T, Hveem K, Kvaløy K, Millar S, Perry I, Peters A, Phillips C, Popham F, Raab G, + Reischl E, Sheehan N, Waldenberger M, Perola M, van den Heuvel E, Macleod J, Knoppers B, + Stolk R, Fortier I, Harris J, Woffenbuttel B, Murtagh M, Ferretti V, Burton P (2014). + “DataSHIELD: taking the analysis to the data, not the data to the analysis.” _International + Journal of Epidemiology_, *43*(6), 1929-1944. . + +[3] Wilson R, W. Butters O, Avraam D, Baker J, Tedds J, Turner A, Murtagh M, R. Burton P (2017). + “DataSHIELD – New Directions and Dimensions.” _Data Science Journal_, *16*(21), 1-21. + . + +[4] Avraam D, Wilson R, Aguirre Chan N, Banerjee S, Bishop T, Butters O, Cadman T, Cederkvist L, + Duijts L, Escribà Montagut X, Garner H, Gonçalves G, González J, Haakma S, Hartlev M, + Hasenauer J, Huth M, Hyde E, Jaddoe V, Marcon Y, Mayrhofer M, Molnar-Gabor F, Morgan A, + Murtagh M, Nestor M, Nybo Andersen A, Parker S, Pinot de Moira A, Schwarz F, + Strandberg-Larsen K, Swertz M, Welten M, Wheater S, Burton P (2024). “DataSHIELD: + mitigating disclosure risk in a multi-site federated analysis platform.” _Bioinformatics + Advances_, *5*(1), 1-21. . + diff --git a/_pkgdown.yml b/_pkgdown.yml index 4c98f6e56..f46c2ebc7 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,3 +1,4 @@ template: + lang: en-GB params: bootswatch: simplex diff --git a/docs/404.html b/docs/404.html index fbf56f72d..761ee0b96 100644 --- a/docs/404.html +++ b/docs/404.html @@ -1,5 +1,5 @@ - + diff --git a/docs/LICENSE.html b/docs/LICENSE.html index 40494c29d..b495f5487 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -1,5 +1,5 @@ -NA • dsBaseClientNA • dsBaseClient diff --git a/docs/authors.html b/docs/authors.html index 6afd8ac43..123fdbbeb 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -1,5 +1,5 @@ -Authors and Citation • dsBaseClientAuthors and Citation • dsBaseClient @@ -105,15 +105,62 @@

Citation

Burton P, Wilson R, Butters O, Ryser-Welch P, Westerberg A, Abarrategui L, Villegas-Diaz R, Avraam D, Avraam D, Marcon Y, Bishop T, Gaye A, EscribĂ -Montagut X, Wheater S (2025). -dsBaseClient: DataSHIELD Client Functions. +dsBaseClient: 'DataSHIELD' Client Side Base Functions. R package version 6.3.4. 

@Manual{,
-  title = {dsBaseClient: DataSHIELD Client Functions},
+  title = {dsBaseClient: 'DataSHIELD' Client Side 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 Demetris Avraam and Yannick Marcon and Tom Bishop and Amadou Gaye and Xavier EscribĂ -Montagut and Stuart Wheater},
   year = {2025},
   note = {R package version 6.3.4},
 }
+

Gaye A, Marcon Y, Isaeva J, LaFlamme P, Turner A, Jones E, Minion J, Boyd A, Newby C, Nuotio M, Wilson R, Butters O, Murtagh B, Demir I, Doiron D, Giepmans L, Wallace S, Budin-Ljøsne I, Schmidt C, Boffetta P, Boniol M, Bota M, Carter K, deKlerk N, Dibben C, Francis R, Hiekkalinna T, Hveem K, Kvaløy K, Millar S, Perry I, Peters A, Phillips C, Popham F, Raab G, Reischl E, Sheehan N, Waldenberger M, Perola M, van den Heuvel E, Macleod J, Knoppers B, Stolk R, Fortier I, Harris J, Woffenbuttel B, Murtagh M, Ferretti V, Burton P (2014). +“DataSHIELD: taking the analysis to the data, not the data to the analysis.” +International Journal of Epidemiology, 43(6), 1929–1944. +doi:10.1093/ije/dyu188. +

+ 
@Article{,
+  title = {{DataSHIELD: taking the analysis to the data, not the data to the analysis}},
+  author = {Amadou Gaye and Yannick Marcon and Julia Isaeva and Philippe {LaFlamme} and Andrew Turner and Elinor M Jones and Joel Minion and Andrew W Boyd and Christopher J Newby and Marja-Liisa Nuotio and Rebecca Wilson and Oliver Butters and Barnaby Murtagh and Ipek Demir and Dany Doiron and Lisette Giepmans and Susan E Wallace and Isabelle Budin-Lj{\o}sne and Carsten O. Schmidt and Paolo Boffetta and Mathieu Boniol and Maria Bota and Kim W Carter and Nick {deKlerk} and Chris Dibben and Richard W Francis and Tero Hiekkalinna and Kristian Hveem and Kirsti Kval{\o}y and Sean Millar and Ivan J Perry and Annette Peters and Catherine M Phillips and Frank Popham and Gillian Raab and Eva Reischl and Nuala Sheehan and Melanie Waldenberger and Markus Perola and Edwin {{van den Heuvel}} and John Macleod and Bartha M Knoppers and Ronald P Stolk and Isabel Fortier and Jennifer R Harris and Bruce H R Woffenbuttel and Madeleine J Murtagh and Vincent Ferretti and Paul R Burton},
+  journal = {International Journal of Epidemiology},
+  year = {2014},
+  volume = {43},
+  number = {6},
+  pages = {1929--1944},
+  doi = {10.1093/ije/dyu188},
+}
+

Wilson R, Butters O, Avraam D, Baker J, Tedds J, Turner A, Murtagh M, Burton P (2017). +“DataSHIELD – New Directions and Dimensions.” +Data Science Journal, 16(21), 1–21. +doi:10.5334/dsj-2017-021. +

+ 
@Article{,
+  title = {{DataSHIELD – New Directions and Dimensions}},
+  author = {Rebecca C. Wilson and Oliver W. Butters and Demetris Avraam and James Baker and Jonathan A. Tedds and Andrew Turner and Madeleine Murtagh and Paul R. Burton},
+  journal = {Data Science Journal},
+  year = {2017},
+  volume = {16},
+  number = {21},
+  pages = {1--21},
+  doi = {10.5334/dsj-2017-021},
+}
+

Avraam D, Wilson R, Aguirre Chan N, Banerjee S, Bishop T, Butters O, Cadman T, Cederkvist L, Duijts L, Escribà Montagut X, Garner H, Gonçalves G, González J, Haakma S, Hartlev M, Hasenauer J, Huth M, Hyde E, Jaddoe V, Marcon Y, Mayrhofer M, Molnar-Gabor F, Morgan A, Murtagh M, Nestor M, Nybo Andersen A, Parker S, Pinot de Moira A, Schwarz F, Strandberg-Larsen K, Swertz M, Welten M, Wheater S, Burton P (2024). +“DataSHIELD: mitigating disclosure risk in a multi-site federated analysis platform.” +Bioinformatics Advances, 5(1), 1–21. +doi:10.1093/bioadv/vbaf046. +

+ 
@Article{,
+  title = {{DataSHIELD: mitigating disclosure risk in a multi-site federated analysis platform}},
+  author = {Demetris Avraam and Rebecca C Wilson and Noemi {{Aguirre Chan}} and Soumya Banerjee and Tom R P Bishop and Olly Butters and Tim Cadman and Luise Cederkvist and Liesbeth Duijts and Xavier {{Escrib{\a`a} Montagut}} and Hugh Garner and Gon{\c c}alo {Gon{\c c}alves} and Juan R Gonz{\a'a}lez and Sido Haakma and Mette Hartlev and Jan Hasenauer and Manuel Huth and Eleanor Hyde and Vincent W V Jaddoe and Yannick Marcon and Michaela Th Mayrhofer and Fruzsina Molnar-Gabor and Andrei Scott Morgan and Madeleine Murtagh and Marc Nestor and Anne-Marie {{Nybo Andersen}} and Simon Parker and Angela {{Pinot de Moira}} and Florian Schwarz and Katrine Strandberg-Larsen and Morris A Swertz and Marieke Welten and Stuart Wheater and Paul R Burton},
+  journal = {Bioinformatics Advances},
+  year = {2024},
+  volume = {5},
+  number = {1},
+  pages = {1--21},
+  doi = {10.1093/bioadv/vbaf046},
+  editor = {Thomas Lengauer},
+  publisher = {Oxford University Press (OUP)},
+}
diff --git a/docs/index.html b/docs/index.html index 8b8ee557d..9e70df5c5 100644 --- a/docs/index.html +++ b/docs/index.html @@ -1,18 +1,18 @@ - + -DataSHIELD Client Functions • dsBaseClient +DataSHIELD Client Side Base Functions • dsBaseClient - - + +

+
+install.packages("remotes")
+remotes::install_github("datashield/dsBaseClient", "<BRANCH>")
+
+# Install v6.3.4 with the following
+remotes::install_github("datashield/dsBaseClient", "6.3.4")
+

For a full list of development branches, checkout https://github.com/datashield/dsBaseClient/branches

+ +
+

About +

+

DataSHIELD is a software package which allows you to do non-disclosive federated analysis on sensitive data. Our website (https://www.datashield.org) has in depth descriptions of what it is, how it works and how to install it. A key point to highlight is that DataSHIELD has a client-server infrastructure, so the dsBase package (https://github.com/datashield/dsBase) needs to be used in conjunction with the dsBaseClient package (https://github.com/datashield/dsBaseClient) - trying to use one without the other makes no sense.

Detailed instructions on how to install DataSHIELD are at https://www.datashield.org/wiki.

Discussion and help with using DataSHIELD can be obtained from The DataSHIELD Forum https://datashield.discourse.group/

The code here is organised as:

@@ -74,25 +88,33 @@

About - + Location What is it? - + obiba CRAN Where you probably should install DataSHIELD from. - + releases Stable releases. - + master branch Mostly in sync with the latest release, changes rarely. +

+
+

References +

+

[1] Burton P, Wilson R, Butters O, Ryser-Welch P, Westerberg A, Abarrategui L, Villegas-Diaz R, Avraam D, Marcon Y, Bishop T, Gaye A, Escribà Montagut X, Wheater S (2025). dsBaseClient: ‘DataSHIELD’ Client Side Base Functions. R package version 6.3.4.

+

[2] Gaye A, Marcon Y, Isaeva J, LaFlamme P, Turner A, Jones E, Minion J, Boyd A, Newby C, Nuotio M, Wilson R, Butters O, Murtagh B, Demir I, Doiron D, Giepmans L, Wallace S, Budin-Ljøsne I, Oliver Schmidt C, Boffetta P, Boniol M, Bota M, Carter K, deKlerk N, Dibben C, Francis R, Hiekkalinna T, Hveem K, Kvaløy K, Millar S, Perry I, Peters A, Phillips C, Popham F, Raab G, Reischl E, Sheehan N, Waldenberger M, Perola M, van den Heuvel E, Macleod J, Knoppers B, Stolk R, Fortier I, Harris J, Woffenbuttel B, Murtagh M, Ferretti V, Burton P (2014). “DataSHIELD: taking the analysis to the data, not the data to the analysis.” International Journal of Epidemiology, 43(6), 1929-1944. https://doi.org/10.1093/ije/dyu188.

+

[3] Wilson R, W. Butters O, Avraam D, Baker J, Tedds J, Turner A, Murtagh M, R. Burton P (2017). “DataSHIELD – New Directions and Dimensions.” Data Science Journal, 16(21), 1-21. https://doi.org/10.5334/dsj-2017-021.

+

[4] Avraam D, Wilson R, Aguirre Chan N, Banerjee S, Bishop T, Butters O, Cadman T, Cederkvist L, Duijts L, Escribà Montagut X, Garner H, Gonçalves G, González J, Haakma S, Hartlev M, Hasenauer J, Huth M, Hyde E, Jaddoe V, Marcon Y, Mayrhofer M, Molnar-Gabor F, Morgan A, Murtagh M, Nestor M, Nybo Andersen A, Parker S, Pinot de Moira A, Schwarz F, Strandberg-Larsen K, Swertz M, Welten M, Wheater S, Burton P (2024). “DataSHIELD: mitigating disclosure risk in a multi-site federated analysis platform.” Bioinformatics Advances, 5(1), 1-21. https://doi.org/10.1093/bioadv/vbaf046.

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 09e6c01ec..97ec34a7e 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,5 +1,5 @@ -pandoc: 3.1.3 +pandoc: '3.4' pkgdown: 2.1.3 pkgdown_sha: ~ articles: {} -last_built: 2025-08-28T18:25Z +last_built: 2025-09-17T09:27Z diff --git a/docs/reference/checkClass.html b/docs/reference/checkClass.html index 3a79eb89f..db54dc45a 100644 --- a/docs/reference/checkClass.html +++ b/docs/reference/checkClass.html @@ -1,5 +1,5 @@ -Checks that an object has the same class in all studies — checkClass • dsBaseClientChecks that an object has the same class in all studies — checkClass • dsBaseClient diff --git a/docs/reference/colPercent.html b/docs/reference/colPercent.html index a9df171eb..f17b1a1fe 100644 --- a/docs/reference/colPercent.html +++ b/docs/reference/colPercent.html @@ -1,5 +1,5 @@ -Produces column percentages — colPercent • dsBaseClientProduces column percentages — colPercent • dsBaseClient diff --git a/docs/reference/computeWeightedMeans.html b/docs/reference/computeWeightedMeans.html index 08f278a5a..6aed4d331 100644 --- a/docs/reference/computeWeightedMeans.html +++ b/docs/reference/computeWeightedMeans.html @@ -1,5 +1,5 @@ -Compute Weighted Mean by Group — computeWeightedMeans • dsBaseClientCompute Weighted Mean by Group — computeWeightedMeans • dsBaseClientConverts a server-side R object into Boolean indicators — ds.Boole • dsBaseClientConverts a server-side R object into Boolean indicators — ds.Boole • dsBaseClientComputes the absolute values of a variable — ds.abs • dsBaseClientComputes the absolute values of a variable — ds.abs • dsBaseClientConverts a server-side R object into a character class — ds.asCharacter • dsBaseClientConverts a server-side R object into a character class — ds.asCharacter • dsBaseClientConverts a server-side R object into a matrix — ds.asDataMatrix • dsBaseClientConverts a server-side R object into a matrix — ds.asDataMatrix • dsBaseClientConverts a server-side numeric vector into a factor — ds.asFactor • dsBaseClientConverts a server-side numeric vector into a factor — ds.asFactor • dsBaseClient diff --git a/docs/reference/ds.asFactorSimple.html b/docs/reference/ds.asFactorSimple.html index b20c85d80..32283795b 100644 --- a/docs/reference/ds.asFactorSimple.html +++ b/docs/reference/ds.asFactorSimple.html @@ -1,5 +1,5 @@ -Converts a numeric vector into a factor — ds.asFactorSimple • dsBaseClientConverts a numeric vector into a factor — ds.asFactorSimple • dsBaseClientConverts a server-side R object into an integer class — ds.asInteger • dsBaseClientConverts a server-side R object into an integer class — ds.asInteger • dsBaseClientConverts a server-side R object into a list — ds.asList • dsBaseClientConverts a server-side R object into a list — ds.asList • dsBaseClientConverts a server-side R object into a logical class — ds.asLogical • dsBaseClientConverts a server-side R object into a logical class — ds.asLogical • dsBaseClientConverts a server-side R object into a matrix — ds.asMatrix • dsBaseClientConverts a server-side R object into a matrix — ds.asMatrix • dsBaseClientConverts a server-side R object into a numeric class — ds.asNumeric • dsBaseClientConverts a server-side R object into a numeric class — ds.asNumeric • dsBaseClientAssigns an R object to a name in the server-side — ds.assign • dsBaseClientAssigns an R object to a name in the server-side — ds.assign • dsBaseClient diff --git a/docs/reference/ds.auc.html b/docs/reference/ds.auc.html index f71e16cea..2c93a3083 100644 --- a/docs/reference/ds.auc.html +++ b/docs/reference/ds.auc.html @@ -1,5 +1,5 @@ -Calculates the Area under the curve (AUC) — ds.auc • dsBaseClientCalculates the Area under the curve (AUC) — ds.auc • dsBaseClientDraw boxplot — ds.boxPlot • dsBaseClientDraw boxplot — ds.boxPlot • dsBaseClientRenders boxplot — ds.boxPlotGG • dsBaseClientRenders boxplot — ds.boxPlotGG • dsBaseClientTake a data frame on the server side an arrange it to pass it to the boxplot function — ds.boxPlotGG_data_Treatment • dsBaseClientTake a data frame on the server side an arrange it to pass it to the boxplot function — ds.boxPlotGG_data_Treatment • dsBaseClient diff --git a/docs/reference/ds.boxPlotGG_data_Treatment_numeric.html b/docs/reference/ds.boxPlotGG_data_Treatment_numeric.html index 0faf70eb7..4e760a434 100644 --- a/docs/reference/ds.boxPlotGG_data_Treatment_numeric.html +++ b/docs/reference/ds.boxPlotGG_data_Treatment_numeric.html @@ -1,5 +1,5 @@ -Take a vector on the server side an arrange it to pass it to the boxplot function — ds.boxPlotGG_data_Treatment_numeric • dsBaseClientTake a vector on the server side an arrange it to pass it to the boxplot function — ds.boxPlotGG_data_Treatment_numeric • dsBaseClient diff --git a/docs/reference/ds.boxPlotGG_numeric.html b/docs/reference/ds.boxPlotGG_numeric.html index 9ddae53f5..a2f69f988 100644 --- a/docs/reference/ds.boxPlotGG_numeric.html +++ b/docs/reference/ds.boxPlotGG_numeric.html @@ -1,5 +1,5 @@ -Draw boxplot with information from a numeric vector — ds.boxPlotGG_numeric • dsBaseClientDraw boxplot with information from a numeric vector — ds.boxPlotGG_numeric • dsBaseClient diff --git a/docs/reference/ds.boxPlotGG_table.html b/docs/reference/ds.boxPlotGG_table.html index 12b1d1a49..46f7ed910 100644 --- a/docs/reference/ds.boxPlotGG_table.html +++ b/docs/reference/ds.boxPlotGG_table.html @@ -1,5 +1,5 @@ -Draw boxplot with information from a data frame — ds.boxPlotGG_table • dsBaseClientDraw boxplot with information from a data frame — ds.boxPlotGG_table • dsBaseClient diff --git a/docs/reference/ds.bp_standards.html b/docs/reference/ds.bp_standards.html index bfc145956..e3ab71fd8 100644 --- a/docs/reference/ds.bp_standards.html +++ b/docs/reference/ds.bp_standards.html @@ -1,5 +1,5 @@ -Calculates Blood pressure z-scores — ds.bp_standards • dsBaseClientCalculates Blood pressure z-scores — ds.bp_standards • dsBaseClientCombines values into a vector or list in the server-side — ds.c • dsBaseClientCombines values into a vector or list in the server-side — ds.c • dsBaseClient diff --git a/docs/reference/ds.cbind.html b/docs/reference/ds.cbind.html index 3c3033249..91ef0d49a 100644 --- a/docs/reference/ds.cbind.html +++ b/docs/reference/ds.cbind.html @@ -1,5 +1,5 @@ -Combines R objects by columns in the server-side — ds.cbind • dsBaseClientCombines R objects by columns in the server-side — ds.cbind • dsBaseClientChanges the reference level of a factor in the server-side — ds.changeRefGroup • dsBaseClientChanges the reference level of a factor in the server-side — ds.changeRefGroup • dsBaseClientClass of the R object in the server-side — ds.class • dsBaseClientClass of the R object in the server-side — ds.class • dsBaseClientProduces column names of the R object in the server-side — ds.colnames • dsBaseClientProduces column names of the R object in the server-side — ds.colnames • dsBaseClientIdentifies complete cases in server-side R objects — ds.completeCases • dsBaseClientIdentifies complete cases in server-side R objects — ds.completeCases • dsBaseClientGenerates a contour plot — ds.contourPlot • dsBaseClientGenerates a contour plot — ds.contourPlot • dsBaseClientCalculates the correlation of R objects in the server-side — ds.cor • dsBaseClientCalculates the correlation of R objects in the server-side — ds.cor • dsBaseClientTests for correlation between paired samples in the server-side — ds.corTest • dsBaseClientTests for correlation between paired samples in the server-side — ds.corTest • dsBaseClient @@ -75,7 +75,7 @@

Arguments

exact

a logical indicating whether an exact p-value should be computed. Used for -Kendall's tau and Spearman's rho. See ‘Details’ of R stats function cor.test for +Kendall's tau and Spearman's rho. See Details of R stats function cor.test for the meaning of NULL (the default).

diff --git a/docs/reference/ds.cov.html b/docs/reference/ds.cov.html index f2cf1fe95..3637997c7 100644 --- a/docs/reference/ds.cov.html +++ b/docs/reference/ds.cov.html @@ -1,5 +1,5 @@ -Calculates the covariance of R objects in the server-side — ds.cov • dsBaseClientCalculates the covariance of R objects in the server-side — ds.cov • dsBaseClientGenerates a data frame object in the server-side — ds.dataFrame • dsBaseClientGenerates a data frame object in the server-side — ds.dataFrame • dsBaseClientCreates missing values columns in the server-side — ds.dataFrameFill • dsBaseClientCreates missing values columns in the server-side — ds.dataFrameFill • dsBaseClient diff --git a/docs/reference/ds.dataFrameSort.html b/docs/reference/ds.dataFrameSort.html index 3b8717dc6..99e75c797 100644 --- a/docs/reference/ds.dataFrameSort.html +++ b/docs/reference/ds.dataFrameSort.html @@ -1,5 +1,5 @@ -Sorts data frames in the server-side — ds.dataFrameSort • dsBaseClientSorts data frames in the server-side — ds.dataFrameSort • dsBaseClient diff --git a/docs/reference/ds.dataFrameSubset.html b/docs/reference/ds.dataFrameSubset.html index 8176ff6ae..73448ea53 100644 --- a/docs/reference/ds.dataFrameSubset.html +++ b/docs/reference/ds.dataFrameSubset.html @@ -1,5 +1,5 @@ -Sub-sets data frames in the server-side — ds.dataFrameSubset • dsBaseClientSub-sets data frames in the server-side — ds.dataFrameSubset • dsBaseClient @@ -63,7 +63,7 @@

Arguments

df.name
-

a character string providing the name of the data frame to be subseted.

+

a character string providing the name of the data frame to be subset.

V1.name
diff --git a/docs/reference/ds.densityGrid.html b/docs/reference/ds.densityGrid.html index 976297973..4390d2b43 100644 --- a/docs/reference/ds.densityGrid.html +++ b/docs/reference/ds.densityGrid.html @@ -1,5 +1,5 @@ -Generates a density grid in the client-side — ds.densityGrid • dsBaseClientGenerates a density grid in the client-side — ds.densityGrid • dsBaseClientRetrieves the dimension of a server-side R object — ds.dim • dsBaseClientRetrieves the dimension of a server-side R object — ds.dim • dsBaseClientCopy a clientside data.frame, matrix or tibble to the serverside — ds.dmtC2S • dsBaseClientCopy a clientside data.frame, matrix or tibble to the serverside — ds.dmtC2S • dsBaseClientBasis for a piecewise linear spline with meaningful coefficients — ds.elspline • dsBaseClientBasis for a piecewise linear spline with meaningful coefficients — ds.elspline • dsBaseClientChecks if an object is defined on the server-side — ds.exists • dsBaseClientChecks if an object is defined on the server-side — ds.exists • dsBaseClientComputes the exponentials in the server-side — ds.exp • dsBaseClientComputes the exponentials in the server-side — ds.exp • dsBaseClientSecure ranking of a vector across all sources and use of these ranks to estimate global quantiles across all studies — ds.extractQuantiles • dsBaseClientSecure ranking of a vector across all sources and use of these ranks to estimate global quantiles across all studies — ds.extractQuantiles • dsBaseClientForestplot for SLMA models — ds.forestplot • dsBaseClientForestplot for SLMA models — ds.forestplot • dsBaseClientGeneralized Additive Models for Location Scale and Shape — ds.gamlss • dsBaseClient -Computes the WHO Growth Reference z-scores of anthropometric data — ds.getWGSR • dsBaseClientComputes the WHO Growth Reference z-scores of anthropometric data — ds.getWGSR • dsBaseClientFits Generalized Linear Model — ds.glm • dsBaseClientFits Generalized Linear Model — ds.glm • dsBaseClientApplies predict.glm() to a serverside glm object — ds.glmPredict • dsBaseClientApplies predict.glm() to a serverside glm object — ds.glmPredict • dsBaseClientFit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — ds.glmSLMA • dsBaseClientFit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA) — ds.glmSLMA • dsBaseClientSummarize a glm object on the serverside — ds.glmSummary • dsBaseClientSummarize a glm object on the serverside — ds.glmSummary • dsBaseClientFits Generalized Linear Mixed-Effect Models via Study-Level Meta-Analysis — ds.glmerSLMA • dsBaseClientFits Generalized Linear Mixed-Effect Models via Study-Level Meta-Analysis — ds.glmerSLMA • dsBaseClientGenerates a Heat Map plot — ds.heatmapPlot • dsBaseClientGenerates a Heat Map plot — ds.heatmapPlot • dsBaseClient diff --git a/docs/reference/ds.hetcor.html b/docs/reference/ds.hetcor.html index 2d17b5ccc..2373f7117 100644 --- a/docs/reference/ds.hetcor.html +++ b/docs/reference/ds.hetcor.html @@ -1,5 +1,5 @@ -Heterogeneous Correlation Matrix — ds.hetcor • dsBaseClientHeterogeneous Correlation Matrix — ds.hetcor • dsBaseClient diff --git a/docs/reference/ds.histogram.html b/docs/reference/ds.histogram.html index 4d62229a2..329bbf7aa 100644 --- a/docs/reference/ds.histogram.html +++ b/docs/reference/ds.histogram.html @@ -1,5 +1,5 @@ -Generates a histogram plot — ds.histogram • dsBaseClientGenerates a histogram plot — ds.histogram • dsBaseClient diff --git a/docs/reference/ds.igb_standards.html b/docs/reference/ds.igb_standards.html index 83a359844..1f04c7bbb 100644 --- a/docs/reference/ds.igb_standards.html +++ b/docs/reference/ds.igb_standards.html @@ -1,5 +1,5 @@ -Converts birth measurements to intergrowth z-scores/centiles — ds.igb_standards • dsBaseClientConverts birth measurements to intergrowth z-scores/centiles — ds.igb_standards • dsBaseClient @@ -116,12 +116,18 @@

Note

References

-

International standards for newborn weight, length, and head circumference by -gestational age and sex: the Newborn Cross-Sectional Study of the INTERGROWTH-21st Project -Villar, JosĂŠ et al. The Lancet, Volume 384, Issue 9946, 857-868 -INTERGROWTH-21st very preterm size at birth reference charts. Lancet 2016 -doi.org/10.1016/S0140-6736(16) 00384-6. Villar, JosĂŠ et al.

-
+ +

  • Villar, J., Ismail, L.C., Victora, C.G., Ohuma, E.O., Bertino, E., + Altman, D.G., Lambert, A., Papageorghiou, A.T., Carvalho, M., Jaffer, Y.A., + Gravett, M.G., Purwar, M., Frederick, I.O., Noble, A.J., Pang, R., Barros, + F.C., Chumlea, C., Bhutta, Z.A., Kennedy, S.H., 2014. International + standards for newborn weight, length, and head circumference by gestational + age and sex: the Newborn Cross-Sectional Study of the INTERGROWTH-21st + Project. The Lancet 384, 857–868. https://doi.org/10.1016/S0140-6736(14)60932-6

    • +

  • Villar, J., Giuliani, F., Fenton, T.R., Ohuma, E.O., Ismail, L.C., + Kennedy, S.H., 2016. INTERGROWTH-21st very preterm size at birth reference + charts. The Lancet 387, 844–845. https://doi.org/10.1016/S0140-6736(16)00384-6

    • +

Author

Demetris Avraam for DataSHIELD Development Team

diff --git a/docs/reference/ds.isNA.html b/docs/reference/ds.isNA.html index 71f189225..7fa98292c 100644 --- a/docs/reference/ds.isNA.html +++ b/docs/reference/ds.isNA.html @@ -1,5 +1,5 @@ -Checks if a server-side vector is empty — ds.isNA • dsBaseClientChecks if a server-side vector is empty — ds.isNA • dsBaseClientChecks if a server-side object is valid — ds.isValid • dsBaseClientChecks if a server-side object is valid — ds.isValid • dsBaseClientCalculates the kurtosis of a numeric variable — ds.kurtosis • dsBaseClientCalculates the kurtosis of a numeric variable — ds.kurtosis • dsBaseClient diff --git a/docs/reference/ds.length.html b/docs/reference/ds.length.html index cef16b2b9..f71fef07e 100644 --- a/docs/reference/ds.length.html +++ b/docs/reference/ds.length.html @@ -1,5 +1,5 @@ -Gets the length of an object in the server-side — ds.length • dsBaseClientGets the length of an object in the server-side — ds.length • dsBaseClientProduces levels attributes of a server-side factor — ds.levels • dsBaseClientProduces levels attributes of a server-side factor — ds.levels • dsBaseClientRepresents follow-up in multiple states on multiple time scales — ds.lexis • dsBaseClientRepresents follow-up in multiple states on multiple time scales — ds.lexis • dsBaseClientConstructs a list of objects in the server-side — ds.list • dsBaseClientConstructs a list of objects in the server-side — ds.list • dsBaseClient diff --git a/docs/reference/ds.listClientsideFunctions.html b/docs/reference/ds.listClientsideFunctions.html index 42ae76a38..46871aa7d 100644 --- a/docs/reference/ds.listClientsideFunctions.html +++ b/docs/reference/ds.listClientsideFunctions.html @@ -1,5 +1,5 @@ -Lists client-side functions — ds.listClientsideFunctions • dsBaseClientLists client-side functions — ds.listClientsideFunctions • dsBaseClient diff --git a/docs/reference/ds.listDisclosureSettings.html b/docs/reference/ds.listDisclosureSettings.html index b8b8faf88..205f07cfa 100644 --- a/docs/reference/ds.listDisclosureSettings.html +++ b/docs/reference/ds.listDisclosureSettings.html @@ -1,5 +1,5 @@ -Lists disclosure settings — ds.listDisclosureSettings • dsBaseClientLists disclosure settings — ds.listDisclosureSettings • dsBaseClient diff --git a/docs/reference/ds.listOpals.html b/docs/reference/ds.listOpals.html index 2b1bf9da9..977c9afc3 100644 --- a/docs/reference/ds.listOpals.html +++ b/docs/reference/ds.listOpals.html @@ -1,5 +1,5 @@ -Lists all Opal objects in the analytic environment — ds.listOpals • dsBaseClientLists all Opal objects in the analytic environment — ds.listOpals • dsBaseClientLists server-side functions — ds.listServersideFunctions • dsBaseClientLists server-side functions — ds.listServersideFunctions • dsBaseClient diff --git a/docs/reference/ds.lmerSLMA.html b/docs/reference/ds.lmerSLMA.html index c684039aa..acc1a8257 100644 --- a/docs/reference/ds.lmerSLMA.html +++ b/docs/reference/ds.lmerSLMA.html @@ -1,5 +1,5 @@ -Fits Linear Mixed-Effect model via Study-Level Meta-Analysis — ds.lmerSLMA • dsBaseClientFits Linear Mixed-Effect model via Study-Level Meta-Analysis — ds.lmerSLMA • dsBaseClientComputes logarithms in the server-side — ds.log • dsBaseClientComputes logarithms in the server-side — ds.log • dsBaseClientPerforms direct call to a server-side aggregate function — ds.look • dsBaseClientPerforms direct call to a server-side aggregate function — ds.look • dsBaseClientlists all objects on a server-side environment — ds.ls • dsBaseClientlists all objects on a server-side environment — ds.ls • dsBaseClientBasis for a piecewise linear spline with meaningful coefficients — ds.lspline • dsBaseClientBasis for a piecewise linear spline with meaningful coefficients — ds.lspline • dsBaseClientCalculates a new object in the server-side — ds.make • dsBaseClientCalculates a new object in the server-side — ds.make • dsBaseClientCreates a matrix on the server-side — ds.matrix • dsBaseClientCreates a matrix on the server-side — ds.matrix • dsBaseClientCalculates de determinant of a matrix in the server-side — ds.matrixDet • dsBaseClientCalculates de determinant of a matrix in the server-side — ds.matrixDet • dsBaseClientReturns matrix determinant to the client-side — ds.matrixDet.report • dsBaseClientReturns matrix determinant to the client-side — ds.matrixDet.report • dsBaseClientCalculates matrix diagonals in the server-side — ds.matrixDiag • dsBaseClientCalculates matrix diagonals in the server-side — ds.matrixDiag • dsBaseClientSpecifies the dimnames of the server-side matrix — ds.matrixDimnames • dsBaseClientSpecifies the dimnames of the server-side matrix — ds.matrixDimnames • dsBaseClientInverts a server-side square matrix — ds.matrixInvert • dsBaseClientInverts a server-side square matrix — ds.matrixInvert • dsBaseClient diff --git a/docs/reference/ds.matrixMult.html b/docs/reference/ds.matrixMult.html index fd42b4e34..737b4cca5 100644 --- a/docs/reference/ds.matrixMult.html +++ b/docs/reference/ds.matrixMult.html @@ -1,5 +1,5 @@ -Calculates tow matrix multiplication in the server-side — ds.matrixMult • dsBaseClientCalculates tow matrix multiplication in the server-side — ds.matrixMult • dsBaseClientTransposes a server-side matrix — ds.matrixTranspose • dsBaseClientTransposes a server-side matrix — ds.matrixTranspose • dsBaseClient diff --git a/docs/reference/ds.mean.html b/docs/reference/ds.mean.html index 87e37e260..5bac04db2 100644 --- a/docs/reference/ds.mean.html +++ b/docs/reference/ds.mean.html @@ -1,5 +1,5 @@ -Computes server-side vector statistical mean — ds.mean • dsBaseClientComputes server-side vector statistical mean — ds.mean • dsBaseClientComputes the mean and standard deviation across categories — ds.meanByClass • dsBaseClientComputes the mean and standard deviation across categories — ds.meanByClass • dsBaseClientComputes the mean and standard deviation across groups defined by one factor — ds.meanSdGp • dsBaseClientComputes the mean and standard deviation across groups defined by one factor — ds.meanSdGp • dsBaseClientMerges two data frames in the server-side — ds.merge • dsBaseClientMerges two data frames in the server-side — ds.merge • dsBaseClientReturns server-side messages to the client-side — ds.message • dsBaseClientReturns server-side messages to the client-side — ds.message • dsBaseClientGets the metadata associated with a variable held on the server — ds.metadata • dsBaseClientGets the metadata associated with a variable held on the server — ds.metadata • dsBaseClientMultivariate Imputation by Chained Equations — ds.mice • dsBaseClientMultivariate Imputation by Chained Equations — ds.mice • dsBaseClientReturn the names of a list object — ds.names • dsBaseClientReturn the names of a list object — ds.names • dsBaseClient diff --git a/docs/reference/ds.ns.html b/docs/reference/ds.ns.html index fdcce4dce..1a30398fe 100644 --- a/docs/reference/ds.ns.html +++ b/docs/reference/ds.ns.html @@ -1,5 +1,5 @@ -Generate a Basis Matrix for Natural Cubic Splines — ds.ns • dsBaseClientGenerate a Basis Matrix for Natural Cubic Splines — ds.ns • dsBaseClientGets the number of missing values in a server-side vector — ds.numNA • dsBaseClientGets the number of missing values in a server-side vector — ds.numNA • dsBaseClientBasis for a piecewise linear spline with meaningful coefficients — ds.qlspline • dsBaseClientBasis for a piecewise linear spline with meaningful coefficients — ds.qlspline • dsBaseClientComputes the quantiles of a server-side variable — ds.quantileMean • dsBaseClientComputes the quantiles of a server-side variable — ds.quantileMean • dsBaseClientGenerates Binomial distribution in the server-side — ds.rBinom • dsBaseClientGenerates Binomial distribution in the server-side — ds.rBinom • dsBaseClientGenerates Normal distribution in the server-side — ds.rNorm • dsBaseClientGenerates Normal distribution in the server-side — ds.rNorm • dsBaseClientGenerates Poisson distribution in the server-side — ds.rPois • dsBaseClientGenerates Poisson distribution in the server-side — ds.rPois • dsBaseClientGenerates Uniform distribution in the server-side — ds.rUnif • dsBaseClientGenerates Uniform distribution in the server-side — ds.rUnif • dsBaseClientSecure ranking of a vector across all sources — ds.ranksSecure • dsBaseClientSecure ranking of a vector across all sources — ds.ranksSecure • dsBaseClient @@ -42,7 +42,7 @@

Secure ranking of a vector across all sources

Securely generate the ranks of a numeric vector and estimate -true qlobal quantiles across all data sources simultaneously

+true global quantiles across all data sources simultaneously

@@ -102,7 +102,7 @@

Arguments

of the clusters of values that are being ranked such that some values are treated as being missing and the processing stops, then setting generate.quantiles to FALSE allows the generation of ranks to complete so -they can then be used for non-parameteric analysis, even if the key values +they can then be used for non-parametric analysis, even if the key values cannot be estimated. A real example of an unusual configuration was in a reasonably large dataset of survival times, where a substantial proportion of survival profiles were censored at precisely 10 years. This meant that diff --git a/docs/reference/ds.rbind.html b/docs/reference/ds.rbind.html index 6e1637332..6a117c6da 100644 --- a/docs/reference/ds.rbind.html +++ b/docs/reference/ds.rbind.html @@ -1,5 +1,5 @@ -Combines R objects by rows in the server-side — ds.rbind • dsBaseClientCombines R objects by rows in the server-side — ds.rbind • dsBaseClientReshapes server-side grouped data — ds.reShape • dsBaseClientReshapes server-side grouped data — ds.reShape • dsBaseClientRecodes the levels of a server-side factor vector — ds.recodeLevels • dsBaseClientRecodes the levels of a server-side factor vector — ds.recodeLevels • dsBaseClient diff --git a/docs/reference/ds.recodeValues.html b/docs/reference/ds.recodeValues.html index 18321a5ba..ef260dde7 100644 --- a/docs/reference/ds.recodeValues.html +++ b/docs/reference/ds.recodeValues.html @@ -1,5 +1,5 @@ -Recodes server-side variable values — ds.recodeValues • dsBaseClientRecodes server-side variable values — ds.recodeValues • dsBaseClientCreates a repetitive sequence in the server-side — ds.rep • dsBaseClientCreates a repetitive sequence in the server-side — ds.rep • dsBaseClientReplaces the missing values in a server-side vector — ds.replaceNA • dsBaseClientReplaces the missing values in a server-side vector — ds.replaceNA • dsBaseClientDeletes server-side R objects — ds.rm • dsBaseClientDeletes server-side R objects — ds.rm • dsBaseClient diff --git a/docs/reference/ds.rowColCalc.html b/docs/reference/ds.rowColCalc.html index 8980645b0..bfbd73861 100644 --- a/docs/reference/ds.rowColCalc.html +++ b/docs/reference/ds.rowColCalc.html @@ -1,5 +1,5 @@ -Computes rows and columns sums and means in the server-side — ds.rowColCalc • dsBaseClientComputes rows and columns sums and means in the server-side — ds.rowColCalc • dsBaseClientPerforms random sampling and permuting of vectors, dataframes and matrices — ds.sample • dsBaseClientPerforms random sampling and permuting of vectors, dataframes and matrices — ds.sample • dsBaseClientGenerates non-disclosive scatter plots — ds.scatterPlot • dsBaseClientGenerates non-disclosive scatter plots — ds.scatterPlot • dsBaseClientGenerates a sequence in the server-side — ds.seq • dsBaseClientGenerates a sequence in the server-side — ds.seq • dsBaseClientCreates a default set of Opal objects called 'default.opals' — ds.setDefaultOpals • dsBaseClientCreates a default set of Opal objects called 'default.opals' — ds.setDefaultOpals • dsBaseClient diff --git a/docs/reference/ds.setSeed.html b/docs/reference/ds.setSeed.html index 509f0b2c9..eac16115c 100644 --- a/docs/reference/ds.setSeed.html +++ b/docs/reference/ds.setSeed.html @@ -1,5 +1,5 @@ -Server-side random number generation — ds.setSeed • dsBaseClientServer-side random number generation — ds.setSeed • dsBaseClient diff --git a/docs/reference/ds.skewness.html b/docs/reference/ds.skewness.html index c072b2fea..ad9e9fa11 100644 --- a/docs/reference/ds.skewness.html +++ b/docs/reference/ds.skewness.html @@ -1,5 +1,5 @@ -Calculates the skewness of a server-side numeric variable — ds.skewness • dsBaseClientCalculates the skewness of a server-side numeric variable — ds.skewness • dsBaseClientComputes the square root values of a variable — ds.sqrt • dsBaseClientComputes the square root values of a variable — ds.sqrt • dsBaseClientGenerates a valid subset of a table or a vector — ds.subset • dsBaseClientGenerates a valid subset of a table or a vector — ds.subset • dsBaseClient @@ -43,8 +43,8 @@

Generates a valid subset of a table or a vector

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).

@@ -107,7 +107,7 @@

Value

Details

(1) If the input data is a table the user specifies the rows and/or columns to include in the subset; the columns can be -refered to by their names. Table subsetting can also be done using the name of a variable and a threshold (see example 3). +referred to by their names. Table subsetting can also be done using the name of a variable and a threshold (see example 3). (2) If the input data is a vector and the parameters 'rows', 'logical' and 'threshold' are all provided the last two are ignored (i.e. 'rows' has precedence over the other two parameters then). IMPORTANT NOTE: If the requested subset is not valid (i.e. contains less than the allowed number of observations) all the values are diff --git a/docs/reference/ds.subsetByClass.html b/docs/reference/ds.subsetByClass.html index dc7a1f950..b401a1562 100644 --- a/docs/reference/ds.subsetByClass.html +++ b/docs/reference/ds.subsetByClass.html @@ -1,5 +1,5 @@ -Generates valid subset(s) of a data frame or a factor — ds.subsetByClass • dsBaseClientGenerates valid subset(s) of a data frame or a factor — ds.subsetByClass • dsBaseClientGenerates the summary of a server-side object — ds.summary • dsBaseClientGenerates the summary of a server-side object — ds.summary • dsBaseClient diff --git a/docs/reference/ds.table.html b/docs/reference/ds.table.html index 4be9831bd..bcd1b6127 100644 --- a/docs/reference/ds.table.html +++ b/docs/reference/ds.table.html @@ -1,5 +1,5 @@ -Generates 1-, 2-, and 3-dimensional contingency tables with option of assigning to serverside only and producing chi-squared statistics — ds.table • dsBaseClientGenerates 1-, 2-, and 3-dimensional contingency tables with option of assigning to serverside only and producing chi-squared statistics — ds.table • dsBaseClientGenerates 1-dimensional contingency tables — ds.table1D • dsBaseClientGenerates 1-dimensional contingency tables — ds.table1D • dsBaseClientGenerates 2-dimensional contingency tables — ds.table2D • dsBaseClientGenerates 2-dimensional contingency tables — ds.table2D • dsBaseClientApplies a Function Over a Ragged Array on the server-side — ds.tapply.assign • dsBaseClientApplies a Function Over a Ragged Array on the server-side — ds.tapply.assign • dsBaseClientApplies a Function Over a Server-Side Ragged Array — ds.tapply • dsBaseClientApplies a Function Over a Server-Side Ragged Array — ds.tapply • dsBaseClientChecks if an R object exists on the server-side — ds.testObjExists • dsBaseClientChecks if an R object exists on the server-side — ds.testObjExists • dsBaseClientFlattens Server-Side Lists — ds.unList • dsBaseClientFlattens Server-Side Lists — ds.unList • dsBaseClientPerform 'unique' on a variable on the server-side — ds.unique • dsBaseClientPerform 'unique' on a variable on the server-side — ds.unique • dsBaseClient @@ -52,7 +52,7 @@

Arguments

x.name
-

a character string providing the name of the varable, in the server, to perform unique upon

+

a character string providing the name of the variable, in the server, to perform unique upon

newobj
diff --git a/docs/reference/ds.var.html b/docs/reference/ds.var.html index 1e6f5fa0a..109a1e78e 100644 --- a/docs/reference/ds.var.html +++ b/docs/reference/ds.var.html @@ -1,5 +1,5 @@ -Computes server-side vector variance — ds.var • dsBaseClientComputes server-side vector variance — ds.var • dsBaseClient diff --git a/docs/reference/ds.vectorCalc.html b/docs/reference/ds.vectorCalc.html index 7448bba7c..385c3eca9 100644 --- a/docs/reference/ds.vectorCalc.html +++ b/docs/reference/ds.vectorCalc.html @@ -1,5 +1,5 @@ -Performs a mathematical operation on two or more vectors — ds.vectorCalc • dsBaseClientPerforms a mathematical operation on two or more vectors — ds.vectorCalc • dsBaseClientSplits character by '$' and returns the single characters — extract • dsBaseClientSplits character by '$' and returns the single characters — extract • dsBaseClient diff --git a/docs/reference/getPooledMean.html b/docs/reference/getPooledMean.html index 710cf1a8d..5f25fe1c9 100644 --- a/docs/reference/getPooledMean.html +++ b/docs/reference/getPooledMean.html @@ -1,5 +1,5 @@ -Gets a pooled statistical mean — getPooledMean • dsBaseClientGets a pooled statistical mean — getPooledMean • dsBaseClient diff --git a/docs/reference/getPooledVar.html b/docs/reference/getPooledVar.html index 773ef096f..b1136e230 100644 --- a/docs/reference/getPooledVar.html +++ b/docs/reference/getPooledVar.html @@ -1,5 +1,5 @@ -Gets a pooled variance — getPooledVar • dsBaseClientGets a pooled variance — getPooledVar • dsBaseClient diff --git a/docs/reference/glmChecks.html b/docs/reference/glmChecks.html index 45aa606cb..f2ea44350 100644 --- a/docs/reference/glmChecks.html +++ b/docs/reference/glmChecks.html @@ -1,6 +1,6 @@ -Checks if the elements in the glm model have the right characteristics — glmChecks • dsBaseClientChecks if the elements in the glm model have the right characteristics — glmChecks • dsBaseClient @@ -42,7 +42,7 @@

Checks if the elements in the glm model have the right characteristics

This is an internal function required by the client function ds.glm -to verify all the variables and ensure the process does not halt inadvertanly.

+to verify all the variables and ensure the process does not halt inadvertently

@@ -63,7 +63,7 @@

Arguments

offset
-

null or a numreric vector that can be used to specify an a priori known component to be +

null or a numeric vector that can be used to specify an a priori known component to be included in the linear predictor during fitting.

@@ -84,7 +84,7 @@

Value

Details

the variables are checked to ensure they are defined, not empty (i.e. are not missing -at complete) and evantually (if 'offset' or 'weights') are of 'numeric' with non negative value +at complete) and eventually (if 'offset' or 'weights') are of 'numeric' with non negative value (if 'weights').

diff --git a/docs/reference/index.html b/docs/reference/index.html index 434e9559f..66ffc0598 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,5 +1,5 @@ -Package index • dsBaseClientPackage index • dsBaseClient diff --git a/docs/reference/isAssigned.html b/docs/reference/isAssigned.html index 647e2e011..8044eb8b6 100644 --- a/docs/reference/isAssigned.html +++ b/docs/reference/isAssigned.html @@ -1,5 +1,5 @@ -Checks an object has been generated on the server side — isAssigned • dsBaseClientChecks an object has been generated on the server side — isAssigned • dsBaseClient diff --git a/docs/reference/isDefined.html b/docs/reference/isDefined.html index 0ce3e931e..f2cbb94bb 100644 --- a/docs/reference/isDefined.html +++ b/docs/reference/isDefined.html @@ -1,5 +1,5 @@ -Checks if the objects are defined in all studies — isDefined • dsBaseClientChecks if the objects are defined in all studies — isDefined • dsBaseClient diff --git a/docs/reference/logical2int.html b/docs/reference/logical2int.html index 4cc21e0ac..34f4853fb 100644 --- a/docs/reference/logical2int.html +++ b/docs/reference/logical2int.html @@ -1,5 +1,5 @@ -Turns a logical operator into an integer — logical2int • dsBaseClientTurns a logical operator into an integer — logical2int • dsBaseClient @@ -61,7 +61,7 @@

Value

Details

-

This function is called to turn a logical oprator given as a +

This function is called to turn a logical operator given as a character into an integer: '>' is turned into 1, '>=' into 2, '<' into 3, '<=' into 4, '==' into 5 and '!=' into 6.

diff --git a/docs/reference/meanByClassHelper0a.html b/docs/reference/meanByClassHelper0a.html index 979937ec1..98dd1e0e7 100644 --- a/docs/reference/meanByClassHelper0a.html +++ b/docs/reference/meanByClassHelper0a.html @@ -1,5 +1,5 @@ -Computes the mean values of a numeric vector across a factor vector — meanByClassHelper0a • dsBaseClientComputes the mean values of a numeric vector across a factor vector — meanByClassHelper0a • dsBaseClient @@ -62,7 +62,7 @@

Arguments

type

a character which represents the type of analysis to carry out. If type is set to 'combine', a pooled table of results is generated. If type is set to 'split', a table of results -is genrated for each study.

+is generated for each study.

datasources
diff --git a/docs/reference/meanByClassHelper0b.html b/docs/reference/meanByClassHelper0b.html index 284939d1b..4e4fb247f 100644 --- a/docs/reference/meanByClassHelper0b.html +++ b/docs/reference/meanByClassHelper0b.html @@ -1,5 +1,5 @@ -Runs the computation if variables are within a table structure — meanByClassHelper0b • dsBaseClientRuns the computation if variables are within a table structure — meanByClassHelper0b • dsBaseClient @@ -66,7 +66,7 @@

Arguments

type

a character which represents the type of analysis to carry out. If type is set to 'combine', a pooled table of results is generated. If type is set to 'split', a table of results -is genrated for each study.

+is generated for each study.

datasources
@@ -82,7 +82,7 @@

Value

Details

This function is called by the function 'ds.meanByClass' to produce the final tables -if the user soecify a table structure.

+if the user specify a table structure.

Author

diff --git a/docs/reference/meanByClassHelper1.html b/docs/reference/meanByClassHelper1.html index 6384341b8..9df03a529 100644 --- a/docs/reference/meanByClassHelper1.html +++ b/docs/reference/meanByClassHelper1.html @@ -1,5 +1,5 @@ -Generates subset tables — meanByClassHelper1 • dsBaseClientGenerates subset tables — meanByClassHelper1 • dsBaseClient diff --git a/docs/reference/meanByClassHelper2.html b/docs/reference/meanByClassHelper2.html index deb75ea3a..5466cbedf 100644 --- a/docs/reference/meanByClassHelper2.html +++ b/docs/reference/meanByClassHelper2.html @@ -1,5 +1,5 @@ -Generates a table for pooled results — meanByClassHelper2 • dsBaseClientGenerates a table for pooled results — meanByClassHelper2 • dsBaseClient @@ -65,7 +65,7 @@

Arguments

invalidrecorder
-

a list, holds informations about invalid subsets in each study.

+

a list, holds information about invalid subsets in each study.

@@ -76,7 +76,7 @@

Value

Details

This function is called by the function 'ds.meanByClass' to produce the final table -if the user sets the parmater 'type' to combine (the default behaviour of 'ds.meanByClass').

+if the user sets the parameter 'type' to combine (the default behaviour of 'ds.meanByClass').

Author

diff --git a/docs/reference/meanByClassHelper3.html b/docs/reference/meanByClassHelper3.html index d3ca83eb2..d3bcf8f14 100644 --- a/docs/reference/meanByClassHelper3.html +++ b/docs/reference/meanByClassHelper3.html @@ -1,5 +1,5 @@ -Generates results tables for each study separately — meanByClassHelper3 • dsBaseClientGenerates results tables for each study separately — meanByClassHelper3 • dsBaseClient @@ -65,7 +65,7 @@

Arguments

invalidrecorder
-

a list, holds informations about invalid subsets in each study

+

a list, holds information about invalid subsets in each study

@@ -75,7 +75,7 @@

Value

Details

This function is called by the function 'ds.meanByClass' to produce the final tables -if the user sets the parmater 'type' to 'split'.

+if the user sets the parameter 'type' to 'split'.

Author

diff --git a/docs/reference/meanByClassHelper4.html b/docs/reference/meanByClassHelper4.html index 6899d2d08..2b8f40b7d 100644 --- a/docs/reference/meanByClassHelper4.html +++ b/docs/reference/meanByClassHelper4.html @@ -1,5 +1,5 @@ -Gets the subset tables out of the list (i.e. unlist) — meanByClassHelper4 • dsBaseClientGets the subset tables out of the list (i.e. unlist) — meanByClassHelper4 • dsBaseClient diff --git a/docs/reference/rowPercent.html b/docs/reference/rowPercent.html index 022065df9..df9685296 100644 --- a/docs/reference/rowPercent.html +++ b/docs/reference/rowPercent.html @@ -1,5 +1,5 @@ -Produces row percentages — rowPercent • dsBaseClientProduces row percentages — rowPercent • dsBaseClient diff --git a/docs/reference/subsetHelper.html b/docs/reference/subsetHelper.html index c992325c4..0a94aa1b3 100644 --- a/docs/reference/subsetHelper.html +++ b/docs/reference/subsetHelper.html @@ -1,5 +1,5 @@ -Ensures that the requested subset is not larger than the original object — subsetHelper • dsBaseClientEnsures that the requested subset is not larger than the original object — subsetHelper • dsBaseClient diff --git a/inst/CITATION b/inst/CITATION new file mode 100644 index 000000000..cf856ce67 --- /dev/null +++ b/inst/CITATION @@ -0,0 +1,134 @@ +bibentry("Manual", + other = unlist(citation(auto = meta), recursive = FALSE)) + +bibentry( + bibtype = "Article", + title = "{DataSHIELD: taking the analysis to the data, not the data to the analysis}", + author = c( + person("Amadou", "Gaye"), + person("Yannick", "Marcon"), + person("Julia", "Isaeva"), + person("Philippe", "{LaFlamme}"), + person("Andrew", "Turner"), + person("Elinor M", "Jones"), + person("Joel", "Minion"), + person("Andrew W", "Boyd"), + person("Christopher J", "Newby"), + person("Marja-Liisa", "Nuotio"), + person("Rebecca", "Wilson"), + person("Oliver", "Butters"), + person("Barnaby", "Murtagh"), + person("Ipek", "Demir"), + person("Dany", "Doiron"), + person("Lisette", "Giepmans"), + person("Susan E", "Wallace"), + person("Isabelle", "Budin-Lj{\\o}sne"), + person("Carsten O.", "Schmidt"), + person("Paolo", "Boffetta"), + person("Mathieu", "Boniol"), + person("Maria", "Bota"), + person("Kim W", "Carter"), + person("Nick", "{deKlerk}"), + person("Chris", "Dibben"), + person("Richard W", "Francis"), + person("Tero", "Hiekkalinna"), + person("Kristian", "Hveem"), + person("Kirsti", "Kval{\\o}y"), + person("Sean", "Millar"), + person("Ivan J", "Perry"), + person("Annette", "Peters"), + person("Catherine M", "Phillips"), + person("Frank", "Popham"), + person("Gillian", "Raab"), + person("Eva", "Reischl"), + person("Nuala", "Sheehan"), + person("Melanie", "Waldenberger"), + person("Markus", "Perola"), + person("Edwin", "{van den Heuvel}"), + person("John", "Macleod"), + person("Bartha M", "Knoppers"), + person("Ronald P", "Stolk"), + person("Isabel", "Fortier"), + person("Jennifer R", "Harris"), + person("Bruce H R", "Woffenbuttel"), + person("Madeleine J", "Murtagh"), + person("Vincent", "Ferretti"), + person("Paul R", "Burton") + ), + journal = "International Journal of Epidemiology", + year = "2014", + volume = "43", + number = "6", + pages = "1929--1944", + doi = "10.1093/ije/dyu188", +) + +bibentry( + bibtype = "Article", + title = "{DataSHIELD – New Directions and Dimensions}", + author = c( + person("Rebecca C.", "Wilson"), + person("Oliver W.", "Butters"), + person("Demetris", "Avraam"), + person("James", "Baker"), + person("Jonathan A.", "Tedds"), + person("Andrew", "Turner"), + person("Madeleine", "Murtagh"), + person("Paul R.", "Burton") + ), + journal = "Data Science Journal", + year = "2017", + volume = "16", + number = "21", + pages = "1--21", + doi = "10.5334/dsj-2017-021" +) + +bibentry( + bibtype = "Article", + title = "{DataSHIELD: mitigating disclosure risk in a multi-site federated analysis platform}", + author = c( + person("Demetris", "Avraam"), + person("Rebecca C", "Wilson"), + person("Noemi", "{Aguirre Chan}"), + person("Soumya", "Banerjee"), + person("Tom R P", "Bishop"), + person("Olly", "Butters"), + person("Tim", "Cadman"), + person("Luise", "Cederkvist"), + person("Liesbeth", "Duijts"), + person("Xavier", "{Escrib{\\a`a} Montagut}"), + person("Hugh", "Garner"), + person("Gon{\\c c}alo", "Gon{\\c c}alves"), + person("Juan R", "Gonz{\\a'a}lez"), + person("Sido", "Haakma"), + person("Mette", "Hartlev"), + person("Jan", "Hasenauer"), + person("Manuel", "Huth"), + person("Eleanor", "Hyde"), + person("Vincent W V", "Jaddoe"), + person("Yannick", "Marcon"), + person("Michaela Th", "Mayrhofer"), + person("Fruzsina", "Molnar-Gabor"), + person("Andrei Scott", "Morgan"), + person("Madeleine", "Murtagh"), + person("Marc", "Nestor"), + person("Anne-Marie", "{Nybo Andersen}"), + person("Simon", "Parker"), + person("Angela", "{Pinot de Moira}"), + person("Florian", "Schwarz"), + person("Katrine", "Strandberg-Larsen"), + person("Morris A", "Swertz"), + person("Marieke", "Welten"), + person("Stuart", "Wheater"), + person("Paul R", "Burton") + ), + journal = "Bioinformatics Advances", + year = "2024", + volume = "5", + number = "1", + pages = "1--21", + doi = "10.1093/bioadv/vbaf046", + editor = person("Thomas", "Lengauer"), + publisher = "Oxford University Press (OUP)" +) diff --git a/inst/WORDLIST b/inst/WORDLIST new file mode 100644 index 000000000..b51917533 --- /dev/null +++ b/inst/WORDLIST @@ -0,0 +1,307 @@ +Amongst +BMI +Banerjee +Bannert +Barros +Bertino +Bhutta +Bioinformatics +Boffetta +Boniol +Bota +Bucur +Budin +Cadman +Carvalho +Cederkvist +Chumlea +Clientside +Codecov +DMT +DSI +DV +DataSHIELD +DataSHIELD's +Demir +Diaz +Dibben +Doiron +Duijts +Escribà +Fenton +Ferretti +Forestplot +Fortier +GAMLSS +GLME +GLMEs +Gabor +Giepmans +González +Gonçalves +Gravett +HC +Haakma +Hartlev +Hasenauer +Heuvel +Hiekkalinna +Huth +Hveem +IDSEQ +INTERGROWTH +IRLS +Isaeva +Jaddoe +Jaffer +Knoppers +Kvaløy +LME +LMEs +LaFlamme +Ljøsne +MUAC +Macleod +Mayrhofer +Millar +Montagut +Murtagh +Newby +Nuotio +Nvalid +Nybo +Ohuma +PIRLS +PRWa +Papageorghiou +Perola +Pinot +Polychoric +Polyserial +Popham +Purwar +REstricted +Raab +Raphson +Reischl +Rigby +Roption +Ryser +SDS +SDs +SLMA +SSF +SURVTIME +Schwarz +Serverside +Sheehan +Stasinopoulos +Stolk +Strandberg +Swertz +TSF +Tedds +UID +VarCovMatrix +Victora +Villar +Villegas +Waldenberger +Welch +Welten +Woffenbuttel +Zbp +ag +aic +analyse +analysed +analysing +anonymised +anthropometric +asFactor +asFactorDS +asFactorSimple +asFactorSimpleDS +behaviour +bfa +bp +byrow +casewise +categorising +cbind +cbinded +centile +centiles +centre +characterised +chisq +clientside +cov +crit +cvar +cyc +dataFrameSort +dataframefill +datashield +datasource +datasources +de +deKlerk +defaultMethod +df +disclosive +discriminative +dmt +dmtC +docx +doi +ds +dsBase +eg +elspline +exponentials +extractQuantile +extractQuantiles +extractQuantilesDS +forestplot +gamlss +gamlssDS +gd +getOpals +ggplot +glim +glm +glmPredict +glmPredict's +glmPredictDS +glmSLMA +glmSLMADS +glmSummary +glmSummaryDS +glmer +glmerMod +glms +hbp +hca +hcircm +hetcor +heterogenous +hfa +https +ie +igb +imputationSet +intergrowth +iter +kendall +labelled +lencm +lfa +listOpals +listOpalsIreminds +lme +lmer +lmerMod +loess +lspline +maximises +meanByClass +metafor +mfa +miceDS +mids +modelled +modelling +na +namesDS +ncol +ncols +nearPD +neighbour +neighbours +newObj +newdata +newdataname +newobj +nfilter +nhlbi +nih +normalised +nrows +ns +obiba +optimisation +organised +panelaggregation +parametrise +patho +pb +pearson +ped +penalised +perc +poisson +polychoric +polyserial +pre +predictorMatrix +probs +pseudodata +pseudorandom +qlspline +quasipoisson +rBinom +rNorm +rPois +rUnif +ra +ranksSecure +ranksSecureDS +rbinded +recodeValues +recognise +recognised +releasers +resid +rvar +sampleDS +se +serverside +setDefaultOpals +setSeedDS +skinfold +skinfolds +sortkey +spearman +ssa +standardised +stringShort +studyside +studysideMessages +stvar +subClasses +subsetByClass +subsetObject +summarised +summarises +tapply +th +tibble +tol +tsa +unlist +useNA +vals +vectorcalc +visualise +visualised +wfa +wfh +wfl +wlr +wtkg +www +xlevels +xyz +zscore +zscores diff --git a/man/ds.asNumeric.Rd b/man/ds.asNumeric.Rd index a07204c18..9928942a5 100644 --- a/man/ds.asNumeric.Rd +++ b/man/ds.asNumeric.Rd @@ -32,7 +32,7 @@ This function is based on the native R function \code{as.numeric}. This function is based on the native R function \code{as.numeric}. However, it behaves differently with some specific classes of variables. For example, if the input object is of class factor, it first converts its values into characters and then convert those to -numerics. This behavior is important for the case where the input object is of class factor having +numerics. This behaviour is important for the case where the input object is of class factor having numbers as levels. In that case, the native R \code{as.numeric} function returns the underlying level codes and not the values as numbers. For example \code{as.numeric} in R converts the factor vector: \cr diff --git a/man/ds.corTest.Rd b/man/ds.corTest.Rd index fac90553f..6277df16a 100644 --- a/man/ds.corTest.Rd +++ b/man/ds.corTest.Rd @@ -24,7 +24,7 @@ used for the test. One of "pearson", "kendall", or "spearman", can be abbreviate Default is set to "pearson".} \item{exact}{a logical indicating whether an exact p-value should be computed. Used for -Kendall's tau and Spearman's rho. See ‘Details’ of R stats function \code{cor.test} for +Kendall's tau and Spearman's rho. See \emph{Details} of R stats function \code{cor.test} for the meaning of NULL (the default).} \item{conf.level}{confidence level for the returned confidence interval. Currently diff --git a/man/ds.dataFrameSubset.Rd b/man/ds.dataFrameSubset.Rd index 58b557fe5..4d2afc18d 100644 --- a/man/ds.dataFrameSubset.Rd +++ b/man/ds.dataFrameSubset.Rd @@ -18,7 +18,7 @@ ds.dataFrameSubset( ) } \arguments{ -\item{df.name}{a character string providing the name of the data frame to be subseted.} +\item{df.name}{a character string providing the name of the data frame to be subset.} \item{V1.name}{A character string specifying the name of the vector to which the Boolean operator is to be applied to define the subset. diff --git a/man/ds.dmtC2S.Rd b/man/ds.dmtC2S.Rd index 4453cf73a..51ef6a964 100644 --- a/man/ds.dmtC2S.Rd +++ b/man/ds.dmtC2S.Rd @@ -23,7 +23,7 @@ that will be the dataset used by default if no other dataset is specified. If yo wish to change the connections you wish to use by default the call datashield.connections_default('opals.a') will set 'default.connections' to be 'opals.a' and so in the absence of specific instructions to the contrary -(e.g. by specifiying a particular dataset to be used via the +(e.g. by specifying a particular dataset to be used via the argument) all subsequent function calls will be to the datasets held in opals.a. If the argument is specified, it should be set without inverted commas: e.g. datasources=opals.a or datasources=default.connections. diff --git a/man/ds.elspline.Rd b/man/ds.elspline.Rd index e6e32197a..d7f20819d 100644 --- a/man/ds.elspline.Rd +++ b/man/ds.elspline.Rd @@ -19,7 +19,7 @@ ds.elspline( \item{n}{integer greater than 2, knots are computed such that they cut n equally-spaced intervals along the range of x} -\item{marginal}{logical, how to parametrize the spline, see Details} +\item{marginal}{logical, how to parametrise the spline, see Details} \item{names}{character, vector of names for constructed variables} diff --git a/man/ds.forestplot.Rd b/man/ds.forestplot.Rd index 6ce3d54c6..408dc2d30 100644 --- a/man/ds.forestplot.Rd +++ b/man/ds.forestplot.Rd @@ -7,10 +7,10 @@ ds.forestplot(mod, variable = NULL, method = "ML", layout = "JAMA") } \arguments{ -\item{mod}{\code{list} List outputed by any of the SLMA models of DataSHIELD (\code{ds.glmerSLMA}, +\item{mod}{\code{list} List outputted by any of the SLMA models of DataSHIELD (\code{ds.glmerSLMA}, \code{ds.glmSLMA}, \code{ds.lmerSLMA})} -\item{variable}{\code{character} (default \code{NULL}) Variable to meta-analyze and visualize, by setting this +\item{variable}{\code{character} (default \code{NULL}) Variable to meta-analyse and visualise, by setting this argument to \code{NULL} (default) the first independent variable will be used.} \item{method}{\code{character} (Default \code{"ML"}) Method to estimate the between study variance. @@ -20,7 +20,7 @@ See details from \code{?meta::metagen} for the different options.} See details from \code{?meta::metagen} for the different options.} } \description{ -Draws a foresplot of the coefficients for Study-Level Meta-Analysis performed with +Draws a forestplot of the coefficients for Study-Level Meta-Analysis performed with DataSHIELD } \examples{ diff --git a/man/ds.glmPredict.Rd b/man/ds.glmPredict.Rd index e156e6c97..32e5c9f5d 100644 --- a/man/ds.glmPredict.Rd +++ b/man/ds.glmPredict.Rd @@ -87,7 +87,7 @@ that will be the dataset used by default if no other dataset is specified. If yo wish to change the connections you wish to use by default the call datashield.connections_default('opals.a') will set 'default.connections' to be 'opals.a' and so in the absence of specific instructions to the contrary -(e.g. by specifiying a particular dataset to be used via the +(e.g. by specifying a particular dataset to be used via the argument) all subsequent function calls will be to the datasets held in opals.a. If the argument is specified, it should be set without inverted commas: e.g. datasources=opals.a or datasources=default.connections. @@ -114,7 +114,7 @@ the output always includes: the name of the serverside glm object being predicte the name - if one was specified - of the dataframe being used as the basis for predictions, the output.type specified ('link', 'response' or 'terms'), the value of the dispersion parameter if one had been specified and the residual scale parameter (which is -multipled by sqrt(dispersion parameter) if one has been set). If output.type = 'terms', +multiplied by sqrt(dispersion parameter) if one has been set). If output.type = 'terms', the summary statistics for the fit and se.fit vectors are replaced by equivalent summary statistics for each column in fit and se.fit matrices which each have k columns if k terms are being summarised. diff --git a/man/ds.glmSLMA.Rd b/man/ds.glmSLMA.Rd index f0a9863d4..d4acff4cf 100644 --- a/man/ds.glmSLMA.Rd +++ b/man/ds.glmSLMA.Rd @@ -172,7 +172,7 @@ them into their meta-analysis package of choice. \code{is.object.created} and \code{validity.check} are standard items returned by an assign function when the designated newobj appears to have -been successfuly created on the serverside at each study. This output is +been successfully created on the serverside at each study. This output is produced specifically by the assign function \code{glmSLMADS.assign} that writes out the glm object on the serverside } diff --git a/man/ds.glmSummary.Rd b/man/ds.glmSummary.Rd index d7906d311..897dbae90 100644 --- a/man/ds.glmSummary.Rd +++ b/man/ds.glmSummary.Rd @@ -24,7 +24,7 @@ that will be the dataset used by default if no other dataset is specified. If yo wish to change the connections you wish to use by default the call datashield.connections_default('opals.a') will set 'default.connections' to be 'opals.a' and so in the absence of specific instructions to the contrary -(e.g. by specifiying a particular dataset to be used via the +(e.g. by specifying a particular dataset to be used via the argument) all subsequent function calls will be to the datasets held in opals.a. If the argument is specified, it should be set without inverted commas: e.g. datasources=opals.a or datasources=default.connections. diff --git a/man/ds.igb_standards.Rd b/man/ds.igb_standards.Rd index 499220a21..e9ab20f51 100644 --- a/man/ds.igb_standards.Rd +++ b/man/ds.igb_standards.Rd @@ -54,11 +54,19 @@ For gestational ages between 24 and 33 weeks, the INTERGROWTH very early preterm standard is used. } \references{ -International standards for newborn weight, length, and head circumference by -gestational age and sex: the Newborn Cross-Sectional Study of the INTERGROWTH-21st Project -Villar, José et al. The Lancet, Volume 384, Issue 9946, 857-868 -INTERGROWTH-21st very preterm size at birth reference charts. Lancet 2016 -doi.org/10.1016/S0140-6736(16) 00384-6. Villar, José et al. +\itemize{ + \item Villar, J., Ismail, L.C., Victora, C.G., Ohuma, E.O., Bertino, E., + Altman, D.G., Lambert, A., Papageorghiou, A.T., Carvalho, M., Jaffer, Y.A., + Gravett, M.G., Purwar, M., Frederick, I.O., Noble, A.J., Pang, R., Barros, + F.C., Chumlea, C., Bhutta, Z.A., Kennedy, S.H., 2014. International + standards for newborn weight, length, and head circumference by gestational + age and sex: the Newborn Cross-Sectional Study of the INTERGROWTH-21st + Project. The Lancet 384, 857--868. https://doi.org/10.1016/S0140-6736(14)60932-6 + \item Villar, J., Giuliani, F., Fenton, T.R., Ohuma, E.O., Ismail, L.C., + Kennedy, S.H., 2016. INTERGROWTH-21st very preterm size at birth reference + charts. The Lancet 387, 844--845. https://doi.org/10.1016/S0140-6736(16)00384-6 + +} } \author{ Demetris Avraam for DataSHIELD Development Team diff --git a/man/ds.ls.Rd b/man/ds.ls.Rd index e1b5d324e..207af8548 100644 --- a/man/ds.ls.Rd +++ b/man/ds.ls.Rd @@ -13,7 +13,7 @@ ds.ls( } \arguments{ \item{search.filter}{character string (potentially including \code{*} symbol) specifying the filter -for the object name that you want to find in the enviroment. For more information see \strong{Details}.} +for the object name that you want to find in the environment. For more information see \strong{Details}.} \item{env.to.search}{an integer (e.g. in \code{2} or \code{2L} format) specifying the position in the search path of the environment to be explored. \code{1L} is the current active analytic diff --git a/man/ds.lspline.Rd b/man/ds.lspline.Rd index 0cf8e5aae..c0189ce40 100644 --- a/man/ds.lspline.Rd +++ b/man/ds.lspline.Rd @@ -18,7 +18,7 @@ ds.lspline( \item{knots}{numeric vector of knot positions} -\item{marginal}{logical, how to parametrize the spline, see Details} +\item{marginal}{logical, how to parametrise the spline, see Details} \item{names}{character, vector of names for constructed variables} diff --git a/man/ds.matrix.Rd b/man/ds.matrix.Rd index b2928c3ed..d60a91832 100644 --- a/man/ds.matrix.Rd +++ b/man/ds.matrix.Rd @@ -18,7 +18,7 @@ ds.matrix( \arguments{ \item{mdata}{a character string specifying the name of a server-side scalar or vector. Also, a numeric value representing a -scalar specified from the client-side can be speficied. +scalar specified from the client-side can be specified Zeros, negative values and NAs are all allowed. For more information see \strong{Details}.} diff --git a/man/ds.matrixDiag.Rd b/man/ds.matrixDiag.Rd index 84fdba387..268e5148c 100644 --- a/man/ds.matrixDiag.Rd +++ b/man/ds.matrixDiag.Rd @@ -15,7 +15,7 @@ ds.matrixDiag( \arguments{ \item{x1}{a character string specifying the name of a server-side scalar or vector. Also, a numeric value or vector -specified from the client-side can be speficied. This argument depends +specified from the client-side can be specified. This argument depends on the value specified in \code{aim}. For more information see \strong{Details}.} diff --git a/man/ds.ns.Rd b/man/ds.ns.Rd index 910511729..28ffaaa04 100644 --- a/man/ds.ns.Rd +++ b/man/ds.ns.Rd @@ -55,7 +55,7 @@ a basis matrix for representing the family of piecewise-cubic splines with the s sequence of interior knots, and the natural boundary conditions. These enforce the constraint that the function is linear beyond the boundary knots, which can either be supplied or default to the extremes of the data. -A primary use is in modeling formula to directly specify a natural spline term in a model. +A primary use is in modelling formula to directly specify a natural spline term in a model. } \author{ Demetris Avraam for DataSHIELD Development Team diff --git a/man/ds.qlspline.Rd b/man/ds.qlspline.Rd index 93460e65a..003f6b3ad 100644 --- a/man/ds.qlspline.Rd +++ b/man/ds.qlspline.Rd @@ -23,7 +23,7 @@ intervals along x or a vector of numbers in (0; 1) specifying the quantiles expl \item{na.rm}{logical, whether NA should be removed when calculating quantiles, passed to na.rm of quantile. Default set to TRUE} -\item{marginal}{logical, how to parametrize the spline, see Details} +\item{marginal}{logical, how to parametrise the spline, see Details} \item{names}{character, vector of names for constructed variables} diff --git a/man/ds.ranksSecure.Rd b/man/ds.ranksSecure.Rd index 3fd8ed8eb..294a754f7 100644 --- a/man/ds.ranksSecure.Rd +++ b/man/ds.ranksSecure.Rd @@ -51,7 +51,7 @@ is usually the setting to use. But, if there is some abnormal configuration of the clusters of values that are being ranked such that some values are treated as being missing and the processing stops, then setting generate.quantiles to FALSE allows the generation of ranks to complete so -they can then be used for non-parameteric analysis, even if the key values +they can then be used for non-parametric analysis, even if the key values cannot be estimated. A real example of an unusual configuration was in a reasonably large dataset of survival times, where a substantial proportion of survival profiles were censored at precisely 10 years. This meant that @@ -181,7 +181,7 @@ occurred. } \description{ Securely generate the ranks of a numeric vector and estimate -true qlobal quantiles across all data sources simultaneously +true global quantiles across all data sources simultaneously } \details{ ds.ranksSecure is a clientside function which calls a series of diff --git a/man/ds.recodeValues.Rd b/man/ds.recodeValues.Rd index 5ebe1f675..6b775bc9d 100644 --- a/man/ds.recodeValues.Rd +++ b/man/ds.recodeValues.Rd @@ -52,7 +52,7 @@ them to a matched set of alternative specified values. This function recodes individual values with new individual values. This can apply to numeric and character values, factor levels and NAs. One particular use of \code{ds.recodeValues} is to convert NAs to an explicit value. This value is specified -in the argument \code{missing}. If tthe user want to recode only missing values, then it +in the argument \code{missing}. If the user want to recode only missing values, then it should also specify an identical vector of values in both arguments \code{values2replace.vector} and \code{new.values.vector} (see Example 2 below). Server function called: \code{recodeValuesDS} diff --git a/man/ds.sample.Rd b/man/ds.sample.Rd index 776da329f..357882d5f 100644 --- a/man/ds.sample.Rd +++ b/man/ds.sample.Rd @@ -147,7 +147,7 @@ but they join the sample in random order. By sorting the output object (in this case with the default name 'newobj.sample) using ds.dataFrameSort with the 'sampling.order' vector as the sort key, the output object is rendered equivalent to PRWa but with the rows randomly permuted (so the column reflecting -the vector 'sample.order' now runs from 1:length of obejct, while the +the vector 'sample.order' now runs from 1:length of object, while the column reflecting 'ID.seq' denoting the original order is now randomly ordered. If you need to return to the original order you can simply us ds.dataFrameSort again using the column reflecting 'ID.seq' as the sort key: diff --git a/man/ds.scatterPlot.Rd b/man/ds.scatterPlot.Rd index bbcfa5b5d..798c08447 100644 --- a/man/ds.scatterPlot.Rd +++ b/man/ds.scatterPlot.Rd @@ -27,7 +27,7 @@ This argument can be set as \code{'deteministic'} or \code{'probabilistic'}. Default \code{'deteministic'}. For more information see \strong{Details}.} -\item{k}{the number of the nearest neighbors for which their centroid is calculated. +\item{k}{the number of the nearest neighbours for which their centroid is calculated. Default 3. For more information see \strong{Details}.} @@ -60,7 +60,7 @@ 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 \code{method} is set to \code{'deterministic'}, the server-side function searches -for the \code{k-1} nearest neighbors of each single data point and calculates the centroid +for the \code{k-1} nearest neighbours of each single data point and calculates the centroid of such \code{k} points. The proximity is defined by the minimum Euclidean distances of z-score transformed data. diff --git a/man/ds.sqrt.Rd b/man/ds.sqrt.Rd index b42ecaedb..638d26a5f 100644 --- a/man/ds.sqrt.Rd +++ b/man/ds.sqrt.Rd @@ -71,7 +71,6 @@ specified by the user through the argument \code{newobj}, otherwise is named by # and get their square roots ds.make(toAssign='rep((1:10)^2, times=10)', newobj='squares.vector', datasources=connections) ds.sqrt(x='squares.vector', newobj='sqrt.vector', datasources=connections) - # check the behavior of that operation by comparing the tables of squares.vector and sqrt.vector ds.table(rvar='squares.vector')$output.list$TABLE_rvar.by.study_counts ds.table(rvar='sqrt.vector')$output.list$TABLE_rvar.by.study_counts diff --git a/man/ds.subset.Rd b/man/ds.subset.Rd index 3db5e3b3a..2b2d91b99 100644 --- a/man/ds.subset.Rd +++ b/man/ds.subset.Rd @@ -41,12 +41,12 @@ no data are return to the user, the generated subset dataframe is stored on the } \description{ 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). } \details{ (1) If the input data is a table the user specifies the rows and/or columns to include in the subset; the columns can be -refered to by their names. Table subsetting can also be done using the name of a variable and a threshold (see example 3). +referred to by their names. Table subsetting can also be done using the name of a variable and a threshold (see example 3). (2) If the input data is a vector and the parameters 'rows', 'logical' and 'threshold' are all provided the last two are ignored (i.e. 'rows' has precedence over the other two parameters then). IMPORTANT NOTE: If the requested subset is not valid (i.e. contains less than the allowed number of observations) all the values are diff --git a/man/ds.table1D.Rd b/man/ds.table1D.Rd index d480b3bb1..b79ee21ee 100644 --- a/man/ds.table1D.Rd +++ b/man/ds.table1D.Rd @@ -14,11 +14,11 @@ ds.table1D( \arguments{ \item{x}{a character, the name of a numerical vector with discrete values - usually a factor.} -\item{type}{a character which represent the type of table to ouput: pooled table or one table for each +\item{type}{a character which represent the type of table to output: pooled table or one table for each data source. If \code{type} is set to 'combine', a pooled 1-dimensional table is returned; if If \code{type} is set to 'split' a 1-dimensional table is returned for each data source.} -\item{warningMessage}{a boolean, if set to TRUE (deafult) a warning is displayed if any returned table is invalid. Warning +\item{warningMessage}{a boolean, if set to TRUE (default) a warning is displayed if any returned table is invalid. Warning messages are suppressed if this parameter is set to FALSE. However the analyst can still view 'validity' information which are stored in the output object 'validity' - see the list of output objects.} diff --git a/man/ds.table2D.Rd b/man/ds.table2D.Rd index aec01d734..3d0e2a2c2 100644 --- a/man/ds.table2D.Rd +++ b/man/ds.table2D.Rd @@ -17,12 +17,12 @@ ds.table2D( \item{y}{a character, the name of a numerical vector with discrete values - usually a factor.} -\item{type}{a character which represent the type of table to ouput: pooled table or one table for each +\item{type}{a character which represent the type of table to output: pooled table or one table for each data source or both. If \code{type} is set to 'combine', a pooled 2-dimensional table is returned; If \code{type} is set to 'split' a 2-dimensional table is returned for each data source. If \code{type} is set to 'both' (default) a pooled 2-dimensional table plus a 2-dimensional table for each data source are returned.} -\item{warningMessage}{a boolean, if set to TRUE (deafult) a warning is displayed if any returned table is invalid. Warning +\item{warningMessage}{a boolean, if set to TRUE (default) a warning is displayed if any returned table is invalid. Warning messages are suppressed if this parameter is set to FALSE. However the analyst can still view 'validity' information which are stored in the output object 'validity' - see the list of output objects.} diff --git a/man/ds.unique.Rd b/man/ds.unique.Rd index 072510a43..61d6355bd 100644 --- a/man/ds.unique.Rd +++ b/man/ds.unique.Rd @@ -7,7 +7,7 @@ ds.unique(x.name = NULL, newobj = NULL, datasources = NULL) } \arguments{ -\item{x.name}{a character string providing the name of the varable, in the server, to perform \code{unique} upon} +\item{x.name}{a character string providing the name of the variable, in the server, to perform \code{unique} upon} \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default \code{unique.newobj}.} diff --git a/man/ds.vectorCalc.Rd b/man/ds.vectorCalc.Rd index 6c97d344e..87d7a5dd7 100644 --- a/man/ds.vectorCalc.Rd +++ b/man/ds.vectorCalc.Rd @@ -26,10 +26,10 @@ server side function; it uses the R operation symbols built in DataSHIELD. } \details{ In DataSHIELD it is possible to perform an operation on vectors by just using the relevant -R symbols (e.g. '+' for addtion, '*' for multiplication, '-' for substraction and '/' for division). +R symbols (e.g. '+' for addition, '*' for multiplication, '-' for subtraction and '/' for division). This might however be inconvenient if the number of vectors to include in the operation is large. This function takes the names of two or more vectors and performs the desired operation which could be -an addition, a multiplication, a substraction or a division. If one or more vectors have a missing value +an addition, a multiplication, a subtraction or a division. If one or more vectors have a missing value at any one entry (i.e. observation), the operation returns a missing value ('NA') for that entry; the output vectors has, hence the same length as the input vectors. } diff --git a/man/glmChecks.Rd b/man/glmChecks.Rd index af57ca542..ec482bed6 100644 --- a/man/glmChecks.Rd +++ b/man/glmChecks.Rd @@ -12,7 +12,7 @@ glmChecks(formula, data, offset, weights, datasources) \item{data}{a character, the name of an optional data frame containing the variables in in the \code{formula}.} -\item{offset}{null or a numreric vector that can be used to specify an a priori known component to be +\item{offset}{null or a numeric vector that can be used to specify an a priori known component to be included in the linear predictor during fitting.} \item{weights}{a character, the name of an optional vector of 'prior weights' to be used in the fitting @@ -26,11 +26,11 @@ an integer 0 if check was passed and 1 if failed } \description{ This is an internal function required by the client function \code{ds.glm} -to verify all the variables and ensure the process does not halt inadvertanly. +to verify all the variables and ensure the process does not halt inadvertently } \details{ the variables are checked to ensure they are defined, not empty (i.e. are not missing -at complete) and evantually (if 'offset' or 'weights') are of 'numeric' with non negative value +at complete) and eventually (if 'offset' or 'weights') are of 'numeric' with non negative value (if 'weights'). } \author{ diff --git a/man/logical2int.Rd b/man/logical2int.Rd index 2baf8ebe5..14517f63d 100644 --- a/man/logical2int.Rd +++ b/man/logical2int.Rd @@ -16,7 +16,7 @@ an integer This is an internal function. } \details{ -This function is called to turn a logical oprator given as a +This function is called to turn a logical operator given as a character into an integer: '>' is turned into 1, '>=' into 2, '<' into 3, '<=' into 4, '==' into 5 and '!=' into 6. } diff --git a/man/meanByClassHelper0a.Rd b/man/meanByClassHelper0a.Rd index 3880fa393..ec7fed67e 100644 --- a/man/meanByClassHelper0a.Rd +++ b/man/meanByClassHelper0a.Rd @@ -13,7 +13,7 @@ meanByClassHelper0a(a, b, type, datasources) \item{type}{a character which represents the type of analysis to carry out. If \code{type} is set to 'combine', a pooled table of results is generated. If \code{type} is set to 'split', a table of results -is genrated for each study.} +is generated for each study.} \item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} diff --git a/man/meanByClassHelper0b.Rd b/man/meanByClassHelper0b.Rd index fbaa90aed..56dd89d10 100644 --- a/man/meanByClassHelper0b.Rd +++ b/man/meanByClassHelper0b.Rd @@ -15,7 +15,7 @@ meanByClassHelper0b(x, outvar, covar, type, datasources) \item{type}{a character which represents the type of analysis to carry out. If \code{type} is set to 'combine', a pooled table of results is generated. If \code{type} is set to 'split', a table of results -is genrated for each study.} +is generated for each study.} \item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} @@ -29,7 +29,7 @@ This is an internal function. } \details{ This function is called by the function 'ds.meanByClass' to produce the final tables -if the user soecify a table structure. +if the user specify a table structure. } \author{ Gaye, A. diff --git a/man/meanByClassHelper2.Rd b/man/meanByClassHelper2.Rd index 38c98a934..27a763d74 100644 --- a/man/meanByClassHelper2.Rd +++ b/man/meanByClassHelper2.Rd @@ -14,7 +14,7 @@ the default set of connections will be used: see \link[DSI]{datashield.connectio \item{variables}{a character vector, the names of the continuous variables to computes a mean for.} -\item{invalidrecorder}{a list, holds informations about invalid subsets in each study.} +\item{invalidrecorder}{a list, holds information about invalid subsets in each study.} } \value{ a matrix, a table which contains the length, mean and standard deviation of each of the @@ -25,7 +25,7 @@ This is an internal function. } \details{ This function is called by the function 'ds.meanByClass' to produce the final table -if the user sets the parmater 'type' to combine (the default behaviour of 'ds.meanByClass'). +if the user sets the parameter 'type' to combine (the default behaviour of 'ds.meanByClass'). } \author{ Gaye, A. diff --git a/man/meanByClassHelper3.Rd b/man/meanByClassHelper3.Rd index e4fffdca7..ee80e814f 100644 --- a/man/meanByClassHelper3.Rd +++ b/man/meanByClassHelper3.Rd @@ -14,7 +14,7 @@ the default set of connections will be used: see \link[DSI]{datashield.connectio \item{variables}{a character vector, the names of the continuous variables to computes a mean for.} -\item{invalidrecorder}{a list, holds informations about invalid subsets in each study} +\item{invalidrecorder}{a list, holds information about invalid subsets in each study} } \value{ a list which one results table for each study. @@ -24,7 +24,7 @@ This is an internal function. } \details{ This function is called by the function 'ds.meanByClass' to produce the final tables -if the user sets the parmater 'type' to 'split'. +if the user sets the parameter 'type' to 'split'. } \author{ Gaye, A. diff --git a/tests/testthat/connection_to_datasets/login_details.R b/tests/testthat/connection_to_datasets/login_details.R index 95a001a5f..2ce4ca2de 100644 --- a/tests/testthat/connection_to_datasets/login_details.R +++ b/tests/testthat/connection_to_datasets/login_details.R @@ -4,7 +4,7 @@ source("connection_to_datasets/init_local_settings.R") init.ip.address() -# create blank enviroment of test data +# create blank environment of test data ds.test_env <- new.env() # this option helps DSI to find the connection objects by looking in the right environment diff --git a/tests/testthat/dstest_functions/ds_expect_variables.R b/tests/testthat/dstest_functions/ds_expect_variables.R index 54d051c43..abb504c78 100644 --- a/tests/testthat/dstest_functions/ds_expect_variables.R +++ b/tests/testthat/dstest_functions/ds_expect_variables.R @@ -13,9 +13,9 @@ # ds_expect_variables <- function(expected.variables) { - studies.current.varables <- ds.ls() + studies.current.variables <- ds.ls() - for (study.current.varables in studies.current.varables) { - expect_setequal(study.current.varables$objects.found, expected.variables) + for (study.current.variables in studies.current.variables) { + expect_setequal(study.current.variables$objects.found, expected.variables) } } diff --git a/tests/testthat/test-arg-ds.ls.R b/tests/testthat/test-arg-ds.ls.R index 9509a527f..f4405ee77 100644 --- a/tests/testthat/test-arg-ds.ls.R +++ b/tests/testthat/test-arg-ds.ls.R @@ -26,7 +26,7 @@ test_that("setup", { context("ds.ls::arg") test_that("containing escape sequence", { - res1 <- ds.ls(search.filter="_:A:_Enviroment") + res1 <- ds.ls(search.filter="_:A:_Environment") expect_length(res1, 1) expect_equal(res1, "Warning: Code replacing wildcard (i.e. '*') is '_:A:_' but this appears in your original search filter string - please respecify") @@ -36,7 +36,7 @@ test_that("containing escape sequence", { expect_length(res2, 1) expect_equal(res2, "Warning: Code replacing wildcard (i.e. '*') is '_:A:_' but this appears in your original search filter string - please respecify") - res3 <- ds.ls(search.filter="Enviroment_:A:_") + res3 <- ds.ls(search.filter="Environment_:A:_") expect_length(res3, 1) expect_equal(res3, "Warning: Code replacing wildcard (i.e. '*') is '_:A:_' but this appears in your original search filter string - please respecify") diff --git a/tests/testthat/test-smk-ds.subset.R b/tests/testthat/test-smk-ds.subset.R index cc19a71ae..4accdfe5e 100644 --- a/tests/testthat/test-smk-ds.subset.R +++ b/tests/testthat/test-smk-ds.subset.R @@ -34,7 +34,7 @@ test_that("subD_exists", { expect_true(res$sim3) }) -context("ds.subset::smk::generate a subset of the assigned table (by default the table is named 'D') with the first 50 observations and the two first columns refered to by their names") +context("ds.subset::smk::generate a subset of the assigned table (by default the table is named 'D') with the first 50 observations and the two first columns referred to by their names") ds.subset(subset='subD2', x='D', rows=c(1:50), cols = c('DIS_DIAB','PM_BMI_CONTINUOUS')) res <- ds.exists('subD2') test_that("subD2_exists", {