Fix typos

R/asDataMatrixDS.R

@@ -3,7 +3,7 @@
 #' class for all columns in data.frames.
 #' @details This assign function is based on the native R function \code{data.matrix}
 #' If applied to a data.frame, the native R function \code{as.matrix}
-#' coverts all columns into character class. In contrast, if applied to
+#' converts all columns into character class. In contrast, if applied to
 #' a data.frame the native R function \code{data.matrix} converts
 #' the data.frame to a matrix but maintains all data columns in their
 #' original class

R/checkNegValueDS.R

@@ -1,7 +1,7 @@
 #'
 #' @title Checks if a numeric variable has negative values
 #' @description this function is only called by the client function \code{ds.glm}.
-#' @details if a user sets the parameter 'weights' on the client site function \code{ds.glm} this 
+#' @details if a user sets the parameter 'weights' on the client side function \code{ds.glm} this 
 #' server side function is called to verify that the 'weights' vector does not have negative values
 #' because no negative are allowed in weights.
 #' @param weights a numeric vector

R/densityGridDS.R

@@ -1,6 +1,6 @@
 #' 
 #' @title Generates a density grid with or without a priori defined limits
-#' @description Generates a density grid that can then be used for heatmap or countour plots.
+#' @description Generates a density grid that can then be used for heatmap or contour plots.
 #' @details Invalid cells (cells with count < to the set filter value for the minimum allowed
 #' counts in table cells) are turn to 0.
 #' @param xvect a numerical vector

R/dmtC2SDS.R

@@ -22,10 +22,10 @@
 #' @param ncols.transmit specifies the number of columns in the matrix to be created.
 #' Fixed by the clientside function as equal to the number of columns in
 #' the clientside DMT to be transferred.
-#' @param colnames.transmit a parser-transmissable vector specifying the name of each column
+#' @param colnames.transmit a parser-transmissible vector specifying the name of each column
 #' in the DMT being transferred from clientside to serverside.
 #' Generated automatically by clientside function from colnames of clientside DMT.
-#' @param colclass.transmit a parser-transmissable vector specifying the class of the
+#' @param colclass.transmit a parser-transmissible vector specifying the class of the
 #' vector representing each individual column in the DMT to be transferred.
 #' Generated automatically by clientside function. This allows the transmission of DMTs
 #' containing columns with different classes.If something is going to go wrong with

R/gamlssDS.R

@@ -1,5 +1,5 @@
 #'
-#' @title gamlssDS an aggregate function called by ds.galmss
+#' @title gamlssDS an aggregate function called by ds.gamlss
 #' @description This function calls the gamlssDS that is a wrapper function from 
 #' the gamlss R package. The function returns an object of class "gamlss", which 
 #' is a generalized additive model for location, scale and shape (GAMLSS). The 

R/glmerSLMADS.assign.R

@@ -5,7 +5,7 @@
 #' The analytic work engine is the glmer function in R which sits in the lme4 package.
 #' glmerSLMADS.assign fits a generalized linear mixed effects model (glme) - e.g. a logistic or
 #' Poisson regression model including both fixed and random effects - on data
-#' from each single data source and saves the regression outcomes on the serveside.
+#' from each single data source and saves the regression outcomes on the serverside.
 #' @param formula see help for ds.glmerSLMA
 #' @param offset see help for ds.glmerSLMA
 #' @param weights see help for ds.glmerSLMA

R/hetcorDS.R

@@ -1,7 +1,7 @@
 #' 
 #' @title Heterogeneous Correlation Matrix
 #' @description This function is based on the hetcor function from the R package \code{polycor}.
-#' @details Computes a heterogenous correlation matrix, consisting of Pearson product-moment
+#' @details Computes a heterogeneous correlation matrix, consisting of Pearson product-moment
 #' correlations between numeric variables, polyserial correlations between numeric and ordinal
 #' variables, and polychoric correlations between ordinal variables.
 #' @param data the name of a data frame consisting of factors, ordered factors, logical variables,

R/lexisDS2.R

@@ -3,7 +3,7 @@
 #' @description The second serverside function called by ds.lexis.
 #' @details This is the assign
 #' function which actually creates
-#' the expanded dataframe containing surival data for a piecewise exponential
+#' the expanded dataframe containing survival data for a piecewise exponential
 #' regression. lexisDS2 also
 #' carries out a series of disclosure checks and if the arguments or data fail any of
 #' those tests,

R/lmerSLMADS.assign.R

@@ -1,10 +1,10 @@
 #' @title Fitting linear mixed effect models - serverside function
-#' @description lmerSLMADS.assing is the same as lmerSLMADS2 which fits a linear
+#' @description lmerSLMADS.assign is the same as lmerSLMADS2 which fits a linear
 #' mixed effects model (lme) per study and saves the outcomes in each study
 #' @details lmerSLMADS.assign is a serverside function called by ds.lmerSLMA on the clientside.
 #' The analytic work engine is the lmer function in R which sits in the lme4 package.
 #' lmerSLMADS.assign fits a linear mixed effects model (lme) including both fixed and random
-#' effects - on data from each single data source and saves the regression outcomes on the serveside.
+#' effects - on data from each single data source and saves the regression outcomes on the serverside.
 #' @param formula see help for ds.lmerSLMA
 #' @param offset see help for ds.lmerSLMA
 #' @param weights see help for ds.lmerSLMA

R/meanDS.R

@@ -1,5 +1,5 @@
 #'
-#' @title Computes statistical mean of a vectores
+#' @title Computes statistical mean of a vector
 #' @description Calculates the mean value.
 #' @details if the length of input vector is less than the set filter
 #' a missing value is returned.

R/metadataDS.R

@@ -4,7 +4,7 @@
 #' @details The function returns the metadata, obtained from attributes function.
 #' @param x a string character, containing the name  of the specified variable
 #' @return a list containing the metadata. The elements of the list will depend
-#' on the meatadata available.
+#' on the metadata available.
 #' @author Stuart Wheater, for DataSHIELD Development Team
 #' @export
 #'

R/qlsplineDS.R

@@ -15,7 +15,7 @@
 #' probabilities directly (the vector is passed to argument probs of quantile).
 #' @param x the name of the input numeric variable
 #' @param q numeric, a single scalar greater or equal to 2 for a number of equal-frequency
-#' intervals along x or a vector of numbers in (0; 1) specifying the quantiles explicitely.
+#' 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

R/repDS.R

@@ -41,7 +41,7 @@
 #' help for <rep>" (see above). This parameter is usually fully defined by
 #' the argument <times> in the call to \code{ds.rep} that itself calls \code{repDS}.
 #' @param length.out.transmit This argument fixes the length of
-#' the output repetive sequence vector
+#' the output repetitive sequence vector
 #' For behaviour see help for \code{ds.rep} and "details from native R
 #' help for <rep>" (see above). This parameter is usually fully defined by
 #' the argument <length.out> in the call to \code{ds.rep} that itself calls \code{repDS}.

R/rmDS.R

@@ -9,7 +9,7 @@
 #' fail because the effect of the function is to delete the object and so
 #' it would be impossible to write it anywhere.
 #' @param x.names.transmit, the names of the objects to be deleted converted
-#' into transmissable form, a comma seperated list of character  string. The
+#' into transmissible form, a comma separated list of character string. The
 #' argument is specified via the <x.names> argument of ds.rm
 #' @return the specified object is deleted from the serverside. If this
 #' is successful the message "Object <x.names> successfully deleted" is returned

R/table1DDS.R

@@ -5,7 +5,7 @@
 #' @details It generates a 1-dimensional tables where valid (non-disclosive) 1-dimensional tables are defined 
 #' as data from sources where no table cells have counts between 1 and the set threshold. When the output table
 #' is invalid all cells but the total count are replaced by missing values. Only the total count is visible 
-#' on the table returned to the client site. A message is also returned with the 1-dimensional; the message 
+#' on the table returned to the client side. A message is also returned with the 1-dimensional; the message 
 #' says "invalid table - invalid counts present" if the table is invalid and 'valid table' otherwise.
 #' @param xvect a numerical vector with discrete values - usually a factor.
 #' @return a list which contains two elements: 'table', the 1-dimensional table and 'message' a message which

R/tableDS.R

@@ -6,15 +6,15 @@
 #' the table requested in the format specified by \code{ds.table}. For more
 #' information see help for \code{ds.table} in DataSHIELD and the \code{table} function
 #' in native R.
-#' @param rvar.transmit is a character string (in inverted commas) specifiying the
+#' @param rvar.transmit is a character string (in inverted commas) specifying the
 #' name of the variable defining the rows in all of the 2 dimensional
 #' tables that form the output. Fully specified by <rvar> argument in \code{ds.table}.
 #' For more information see help for \code{ds.table}
-#' @param cvar.transmit is a character string specifiying the
+#' @param cvar.transmit is a character string specifying the
 #' name of the variable defining the columns in all of the 2 dimensional
 #' tables that form the output. Fully specified by <cvar> argument in \code{ds.table}.
 #' For more information see help for \code{ds.table}
-#' @param stvar.transmit is a character string specifiying the
+#' @param stvar.transmit is a character string specifying the
 #' name of the variable that indexes the separate two dimensional
 #' tables in the output if the call specifies a 3 dimensional table.
 #' Fully specified by <stvar> argument in \code{ds.table}.

R/tableDS.assign.R

@@ -8,15 +8,15 @@
 #' as an object named by the <newobj> argument of \code{ds.table}. For more
 #' information see help for \code{ds.table} in DataSHIELD and the \code{table} function
 #' in native R.
-#' @param rvar.transmit is a character string (in inverted commas) specifiying the
+#' @param rvar.transmit is a character string (in inverted commas) specifying the
 #' name of the variable defining the rows in all of the 2 dimensional
 #' tables that form the output. Fully specified by <rvar> argument in \code{ds.table}.
 #' For more information see help for \code{ds.table}
-#' @param cvar.transmit is a character string specifiying the
+#' @param cvar.transmit is a character string specifying the
 #' name of the variable defining the columns in all of the 2 dimensional
 #' tables that form the output. Fully specified by <cvar> argument in \code{ds.table}.
 #' For more information see help for \code{ds.table}
-#' @param stvar.transmit is a character string specifiying the
+#' @param stvar.transmit is a character string specifying the
 #' name of the variable that indexes the separate two dimensional
 #' tables in the output if the call specifies a 3 dimensional table.
 #' Fully specified by <stvar> argument in \code{ds.table}.

R/tableDS2.R

@@ -13,15 +13,15 @@
 #' is nevertheless TRUE, the name for the serverside table object defaults
 #' to 'newObj'. Fully specified by <newobj> argument in \code{ds.table}.
 #' For more information see help for \code{ds.table}
-#' @param rvar.transmit is a character string (in inverted commas) specifiying the
+#' @param rvar.transmit is a character string (in inverted commas) specifying the
 #' name of the variable defining the rows in all of the 2 dimensional
 #' tables that form the output. Fully specified by <rvar> argument in \code{ds.table}.
 #' For more information see help for \code{ds.table}
-#' @param cvar.transmit is a character string specifiying the
+#' @param cvar.transmit is a character string specifying the
 #' name of the variable defining the columns in all of the 2 dimensional
 #' tables that form the output. Fully specified by <cvar> argument in \code{ds.table}.
 #' For more information see help for \code{ds.table}
-#' @param stvar.transmit is a character string specifiying the
+#' @param stvar.transmit is a character string specifying the
 #' name of the variable that indexes the separate two dimensional
 #' tables in the output if the call specifies a 3 dimensional table.
 #' Fully specified by <stvar> argument in \code{ds.table}.

README.md

@@ -32,7 +32,7 @@ For a full list of development branches, checkout https://github.com/datashield/
 
 ## 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 conjuction with the dsBaseClient package (https://github.com/datashield/dsBaseClient) - trying to use one without the other makes no sense.
+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://wiki.datashield.org/. The code here is organised as:
 
@@ -66,6 +66,6 @@ Detailed instructions on how to install DataSHIELD are at https://wiki.datashiel
   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, Morris AvSwertz, Welten M, Wheater S, Burton P (2024). “DataSHIELD:
+  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>.