diff --git a/DESCRIPTION b/DESCRIPTION index b628768..643caac 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: metaboMisc Title: Miscellaneous Functions for Metabolomics Analyses -Version: 0.5.7 +Version: 0.5.8 Authors@R: person("Jasen", "Finch", email = "jsf9@aber.ac.uk", role = c("aut", "cre")) Description: Miscellaneous helper functions for metabolomics analyses that do not yet have a permanent home. URL: https://jasenfinch.github.io/metaboMisc diff --git a/NAMESPACE b/NAMESPACE index 637c14e..0804971 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -83,6 +83,7 @@ importFrom(profilePro,processingParameters) importFrom(profilePro,technique) importFrom(purrr,map) importFrom(purrr,map_chr) +importFrom(purrr,map_df) importFrom(readr,write_csv) importFrom(stats,IQR) importFrom(stats,quantile) diff --git a/NEWS.md b/NEWS.md index a4098f8..afb4bb1 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +# metabMisc 0.5.8 + +* Numbers of characters in strings are now limited by `sanitiseTable()`. + # metaboMisc 0.5.7 * Removed `aberHRML/metaboData` from the Remotes field in the DESCRIPTION to ensure that the CRAN version of metaboData is installed. diff --git a/R/sanitise.R b/R/sanitise.R index 1351a1d..dda734f 100644 --- a/R/sanitise.R +++ b/R/sanitise.R @@ -1,15 +1,17 @@ #' Sanitise a data table -#' @description Sanitise a data table by restricting the number of rows and rounding numeric columns. +#' @description Sanitise a data table by restricting the number of rows or characters and rounding numeric columns. #' @param x A tibble or data.frame containing the data to be sanitised #' @param maxRows Maximum number of rows with which to restrict the table #' @param sigFig Significant figures with which to round numeric columns +#' @param maxCharacters Maximum number of characters allowed in a string before it is truncated #' @examples #' sanitiseTable(iris,maxRows = 10,sigFig = 1) #' @importFrom dplyr mutate_if +#' @importFrom purrr map_df #' @export -sanitiseTable <- function(x,maxRows = 5000,sigFig = 3){ +sanitiseTable <- function(x,maxRows = 5000,sigFig = 3,maxCharacters = 100){ x <- mutate_if(x,is.numeric,signif,digits = sigFig) if (nrow(x) > maxRows){ @@ -17,5 +19,18 @@ sanitiseTable <- function(x,maxRows = 5000,sigFig = 3){ x <- x[seq_len(maxRows),] } + a <- map_df(x,~{ + if (typeof(.x) == 'character'){ + limit_characters <- .x %>% + nchar() %>% + {. > maxCharacters} + + .x[limit_characters] <- str_sub(.x[limit_characters],1,maxCharacters) %>% + str_c(.,'...') + } + + return(.x) + }) + return(x) } diff --git a/_pkgdown.yml b/_pkgdown.yml index 146a9c3..3ed8d62 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1 +1 @@ -url: https://jasenfinch.github.io/metaboMisc/ \ No newline at end of file +url: https://jasenfinch.github.io/metaboMisc/ diff --git a/docs/404.html b/docs/404.html index e24e55f..688cbb6 100644 --- a/docs/404.html +++ b/docs/404.html @@ -71,7 +71,7 @@
diff --git a/docs/authors.html b/docs/authors.html index d46507d..e766a83 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -71,7 +71,7 @@ diff --git a/docs/index.html b/docs/index.html index f85b484..24b1da3 100644 --- a/docs/index.html +++ b/docs/index.html @@ -31,7 +31,7 @@ diff --git a/docs/news/index.html b/docs/news/index.html index 235ee42..ac75df0 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -71,7 +71,7 @@ @@ -114,6 +114,13 @@NEWS.md
+ sanitiseTable()
.Improved documentation and added examples.
Added unit testing infrastructure.
Added detectPretreatmentParameters
and detectModellingParameters
methods.
The magrittr
pipe (%>%
) is now re-exported.
The magrittr
pipe (%>%
) is now re-exported.
Analysis of Variance (ANOVA) is used to detect differences in total ion count (TIC) averages between batches/blocks.
+## Retrieve file paths and sample information for example data -files <- metaboData::filePaths('FIE-HRMS','BdistachyonEcotypes')[1:2] - -info <- metaboData::runinfo('FIE-HRMS','BdistachyonEcotypes')[1:2,] - -## Perform spectral binning -analysis <- binneR::binneRlyse(files, - info, - parameters = binneR::detectParameters(files)) -#> -#>#>-#> -#>#>#>#>#>#>#>#>#>#>#>#>#>#>#>-## Detect batch differences -batch_diff <- detectBatchDiff(analysis) -#>#>-## Display batch diffferences -batch_diff -#> NULL
## Retrieve file paths and sample information for example data +files <- metaboData::filePaths('FIE-HRMS','BdistachyonEcotypes')[1:2] + +info <- metaboData::runinfo('FIE-HRMS','BdistachyonEcotypes')[1:2,] + +## Perform spectral binning +analysis <- binneR::binneRlyse(files, + info, + parameters = binneR::detectParameters(files)) +#> +#> Attaching package: ‘purrr’ +#> The following object is masked from ‘package:metaboMisc’: +#> +#> reduce +#> binneR v2.6.2 Wed Nov 17 09:52:25 2021 +#> ________________________________________________________________________________ +#> Scans: 5:14 +#> ________________________________________________________________________________ +#> Reading raw data +#> Gathering bins +#> Removing single scan events +#> Averaging intensities across scans +#> Calculating bin metrics +#> Calculating accurate m/z +#> Building intensity matrix +#> Gathering file headers +#> +#> Completed! [2.6S] + +## Detect batch differences +batch_diff <- detectBatchDiff(analysis) +#> Batches with < 3 replicates removed: "3", "5" +#> Only 1 batch detected, skipping detection + +## Display batch diffferences +batch_diff +#> NULL +@@ -149,22 +149,37 @@
Samples with a total ion count (TIC) below 1.5 times the inter-quartile range are detected as miss injections.
+## Retrieve file paths and sample information for example data -files <- metaboData::filePaths('FIE-HRMS','BdistachyonEcotypes')[1:2] - -info <- metaboData::runinfo('FIE-HRMS','BdistachyonEcotypes')[1:2,] - -## Perform spectral binning -analysis <- binneR::binneRlyse(files, - info, - parameters = binneR::detectParameters(files)) -#>#>#>#>#>#>#>#>#>#>#>#>#>#>-## Detect miss injections -miss_injections <- detectMissInjections(analysis) - -## Display detected miss injections -miss_injections$missInjections -#> numeric(0)
## Retrieve file paths and sample information for example data +files <- metaboData::filePaths('FIE-HRMS','BdistachyonEcotypes')[1:2] + +info <- metaboData::runinfo('FIE-HRMS','BdistachyonEcotypes')[1:2,] + +## Perform spectral binning +analysis <- binneR::binneRlyse(files, + info, + parameters = binneR::detectParameters(files)) +#> binneR v2.6.2 Wed Nov 17 09:52:29 2021 +#> ________________________________________________________________________________ +#> Scans: 5:14 +#> ________________________________________________________________________________ +#> Reading raw data +#> Gathering bins +#> Removing single scan events +#> Averaging intensities across scans +#> Calculating bin metrics +#> Calculating accurate m/z +#> Building intensity matrix +#> Gathering file headers +#> +#> Completed! [1.9S] + +## Detect miss injections +miss_injections <- detectMissInjections(analysis) + +## Display detected miss injections +miss_injections$missInjections +#> numeric(0) +@@ -157,22 +157,37 @@
S4 object of class AnalysisParameters
+## Retrieve file paths and sample information for example data -files <- metaboData::filePaths('FIE-HRMS','BdistachyonEcotypes')[1:2] - -info <- metaboData::runinfo('FIE-HRMS','BdistachyonEcotypes')[1:2,] - -## Perform spectral binning -analysis <- binneR::binneRlyse(files, - info, - parameters = binneR::detectParameters(files)) -#>#>#>#>#>#>#>#>#>#>#>#>#>#>-## Detect modelling parameters -modelling_parameters <- detectModellingParameters(analysis) - -modelling_parameters -#> Parameters: -#>
## Retrieve file paths and sample information for example data +files <- metaboData::filePaths('FIE-HRMS','BdistachyonEcotypes')[1:2] + +info <- metaboData::runinfo('FIE-HRMS','BdistachyonEcotypes')[1:2,] + +## Perform spectral binning +analysis <- binneR::binneRlyse(files, + info, + parameters = binneR::detectParameters(files)) +#> binneR v2.6.2 Wed Nov 17 09:52:32 2021 +#> ________________________________________________________________________________ +#> Scans: 5:14 +#> ________________________________________________________________________________ +#> Reading raw data +#> Gathering bins +#> Removing single scan events +#> Averaging intensities across scans +#> Calculating bin metrics +#> Calculating accurate m/z +#> Building intensity matrix +#> Gathering file headers +#> +#> Completed! [1.9S] + +## Detect modelling parameters +modelling_parameters <- detectModellingParameters(analysis) + +modelling_parameters +#> Parameters: +#> +@@ -142,55 +142,71 @@
S4 object of class AnalysisParameters
+## Retreive example file paths and sample information -file_paths <- metaboData::filePaths('FIE-HRMS','BdistachyonEcotypes') %>% - .[61:63] - -sample_information <- metaboData::runinfo('FIE-HRMS','BdistachyonEcotypes') %>% - dplyr::filter(name == 'QC01' | name == 'QC02' | name == 'QC03') - -## Detect spectral binning parameters -bp <- binneR::detectParameters(file_paths) - -## Perform spectral binning -bd <- binneR::binneRlyse(file_paths,sample_information,bp) -#>#>#>#>#>#>#>#>#>#>#>#>#>#>-## Detect pre-treatment parameters -pp <- detectPretreatmentParameters(bd) -#>-pp -#> Parameters: -#> pre-treatment -#> QC -#> occupancyFilter -#> cls = class -#> QCidx = QC -#> occupancy = 2/3 -#> impute -#> cls = class -#> QCidx = QC -#> occupancy = 2/3 -#> parallel = variables -#> seed = 1234 -#> RSDfilter -#> cls = class -#> QCidx = QC -#> RSDthresh = 50 -#> removeQC -#> cls = class -#> QCidx = QC -#> occupancyFilter -#> maximum -#> cls = class -#> occupancy = 2/3 -#> impute -#> class -#> cls = class -#> occupancy = 2/3 -#> seed = 1234 -#> transform -#> TICnorm -#>
## Retreive example file paths and sample information +file_paths <- metaboData::filePaths('FIE-HRMS','BdistachyonEcotypes') %>% + .[61:63] + +sample_information <- metaboData::runinfo('FIE-HRMS','BdistachyonEcotypes') %>% + dplyr::filter(name == 'QC01' | name == 'QC02' | name == 'QC03') + +## Detect spectral binning parameters +bp <- binneR::detectParameters(file_paths) + +## Perform spectral binning +bd <- binneR::binneRlyse(file_paths,sample_information,bp) +#> binneR v2.6.2 Wed Nov 17 09:52:35 2021 +#> ________________________________________________________________________________ +#> Scans: 5:13 +#> ________________________________________________________________________________ +#> Reading raw data +#> Gathering bins +#> Removing single scan events +#> Averaging intensities across scans +#> Calculating bin metrics +#> Calculating accurate m/z +#> Building intensity matrix +#> Gathering file headers +#> +#> Completed! [2.7S] + +## Detect pre-treatment parameters +pp <- detectPretreatmentParameters(bd) +#> Only 1 batch detected, skipping detection + +pp +#> Parameters: +#> pre-treatment +#> QC +#> occupancyFilter +#> cls = class +#> QCidx = QC +#> occupancy = 2/3 +#> impute +#> cls = class +#> QCidx = QC +#> occupancy = 2/3 +#> parallel = variables +#> seed = 1234 +#> RSDfilter +#> cls = class +#> QCidx = QC +#> RSDthresh = 50 +#> removeQC +#> cls = class +#> QCidx = QC +#> occupancyFilter +#> maximum +#> cls = class +#> occupancy = 2/3 +#> impute +#> class +#> cls = class +#> occupancy = 2/3 +#> seed = 1234 +#> transform +#> TICnorm +#> +diff --git a/docs/reference/exportCSV.html b/docs/reference/exportCSV.html index a381af3..118d4f3 100644 --- a/docs/reference/exportCSV.html +++ b/docs/reference/exportCSV.html @@ -72,7 +72,7 @@ @@ -147,8 +147,9 @@
If the file path directory does not exist, the directory is created prior to export.
+exportCSV(iris, "iris.csv") -#> [1] "iris.csv"
exportCSV(iris, "iris.csv") +#> [1] "iris.csv" +@@ -139,22 +139,37 @@
A tibble containing feature summaries
+## Retrieve file paths and sample information for example data -files <- metaboData::filePaths('FIE-HRMS','BdistachyonEcotypes')[1:2] - -info <- metaboData::runinfo('FIE-HRMS','BdistachyonEcotypes')[1:2,] - -## Perform spectral binning -analysis <- binneR::binneRlyse(files, - info, - parameters = binneR::detectParameters(files)) -#>#>#>#>#>#>#>#>#>#>#>#>#>#>-featureSummary(analysis) -#> # A tibble: 2 × 3 -#> Mode `Number of bins` `Missing Data (%)` -#> <chr> <int> <dbl> -#> 1 Negative 1188 6.48 -#> 2 Positive 1550 9.68
## Retrieve file paths and sample information for example data +files <- metaboData::filePaths('FIE-HRMS','BdistachyonEcotypes')[1:2] + +info <- metaboData::runinfo('FIE-HRMS','BdistachyonEcotypes')[1:2,] + +## Perform spectral binning +analysis <- binneR::binneRlyse(files, + info, + parameters = binneR::detectParameters(files)) +#> binneR v2.6.2 Wed Nov 17 09:52:39 2021 +#> ________________________________________________________________________________ +#> Scans: 5:14 +#> ________________________________________________________________________________ +#> Reading raw data +#> Gathering bins +#> Removing single scan events +#> Averaging intensities across scans +#> Calculating bin metrics +#> Calculating accurate m/z +#> Building intensity matrix +#> Gathering file headers +#> +#> Completed! [3.5S] + +featureSummary(analysis) +#> # A tibble: 2 × 3 +#> Mode `Number of bins` `Missing Data (%)` +#> <chr> <int> <dbl> +#> 1 Negative 1188 6.48 +#> 2 Positive 1550 9.68 +diff --git a/docs/reference/plotRSD-1.png b/docs/reference/plotRSD-1.png index 2fb9f21..ef02af5 100644 Binary files a/docs/reference/plotRSD-1.png and b/docs/reference/plotRSD-1.png differ diff --git a/docs/reference/plotRSD-2.png b/docs/reference/plotRSD-2.png index 1ec08ff..a0fbb88 100644 Binary files a/docs/reference/plotRSD-2.png and b/docs/reference/plotRSD-2.png differ diff --git a/docs/reference/plotRSD.html b/docs/reference/plotRSD.html index febf8b5..31e0627 100644 --- a/docs/reference/plotRSD.html +++ b/docs/reference/plotRSD.html @@ -72,7 +72,7 @@ @@ -144,20 +144,39 @@
A list of plots of RSD distributions
+## Retrieve file paths and sample information for example data -files <- metaboData::filePaths('FIE-HRMS','BdistachyonEcotypes')[1:2] - -info <- metaboData::runinfo('FIE-HRMS','BdistachyonEcotypes')[1:2,] - -## Perform spectral binning -analysis <- binneR::binneRlyse(files, - info, - parameters = binneR::detectParameters(files)) -#>#>#>#>#>#>#>#>#>#>#>#>#>#>-## Plot RSD distributions -plotRSD(analysis) -#> $n#> -#> $p#>
## Retrieve file paths and sample information for example data +files <- metaboData::filePaths('FIE-HRMS','BdistachyonEcotypes')[1:2] + +info <- metaboData::runinfo('FIE-HRMS','BdistachyonEcotypes')[1:2,] + +## Perform spectral binning +analysis <- binneR::binneRlyse(files, + info, + parameters = binneR::detectParameters(files)) +#> binneR v2.6.2 Wed Nov 17 09:52:44 2021 +#> ________________________________________________________________________________ +#> Scans: 5:14 +#> ________________________________________________________________________________ +#> Reading raw data +#> Gathering bins +#> Removing single scan events +#> Averaging intensities across scans +#> Calculating bin metrics +#> Calculating accurate m/z +#> Building intensity matrix +#> Gathering file headers +#> +#> Completed! [3S] + +## Plot RSD distributions +plotRSD(analysis) +#> $n + +#> +#> $p + +#> +@@ -150,66 +150,84 @@
S4 object of class Analysis
+#> -#>#>-#> -#>#>-#> -#>-## Retrieve file paths and sample information for example data -files <- metaboData::filePaths('FIE-HRMS','BdistachyonEcotypes')[1:2] - -info <- metaboData::runinfo('FIE-HRMS','BdistachyonEcotypes')[1:2,] - -## Detect spectral binning parameters -bp <- binneR::detectParameters(files) - -## Perform spectral binning -analysis <- binneR::binneRlyse(files, - info, - parameters = bp) -#>#>#>#>#>#>#>#>#>#>#>#>#>#>-## Declare pre-treatment parameters -pre_treatment_parameters <- analysisParameters('pre-treatment') -parameters(pre_treatment_parameters, - 'pre-treatment') <- preTreatmentParameters( - list( - occupancyFilter = 'maximum', - impute = 'all', - transform = 'TICnorm' - ) -) -changeParameter(pre_treatment_parameters,'parallel') <- 'no' - -## Perform pre-treatment -pre_treated_data <- preTreatModes(analysis, - pre_treatment_parameters) -#> -#> metabolyseR v0.14.3 Mon Sep 27 11:19:44 2021 -#> ________________________________________________________________________________ -#> Parameters: -#> pre-treatment -#> occupancyFilter -#> maximum -#> cls = class -#> occupancy = 2/3 -#> impute -#> all -#> occupancy = 2/3 -#> parallel = no -#> seed = 1234 -#> transform -#> TICnorm -#> -#> ________________________________________________________________________________ -#> -#> Negative mode… Negative mode ✓ [0.5S] -#> Positive mode… Positive mode ✓ [0.6S] -#> ________________________________________________________________________________ -#> -#> Complete! [1.2S] -#>
library(metabolyseR) +#> +#> Attaching package: ‘metabolyseR’ +#> The following object is masked from ‘package:stats’: +#> +#> anova +#> The following objects are masked from ‘package:base’: +#> +#> raw, split + +## Retrieve file paths and sample information for example data +files <- metaboData::filePaths('FIE-HRMS','BdistachyonEcotypes')[1:2] + +info <- metaboData::runinfo('FIE-HRMS','BdistachyonEcotypes')[1:2,] + +## Detect spectral binning parameters +bp <- binneR::detectParameters(files) + +## Perform spectral binning +analysis <- binneR::binneRlyse(files, + info, + parameters = bp) +#> binneR v2.6.2 Wed Nov 17 09:52:51 2021 +#> ________________________________________________________________________________ +#> Scans: 5:14 +#> ________________________________________________________________________________ +#> Reading raw data +#> Gathering bins +#> Removing single scan events +#> Averaging intensities across scans +#> Calculating bin metrics +#> Calculating accurate m/z +#> Building intensity matrix +#> Gathering file headers +#> +#> Completed! [2.5S] + +## Declare pre-treatment parameters +pre_treatment_parameters <- analysisParameters('pre-treatment') +parameters(pre_treatment_parameters, + 'pre-treatment') <- preTreatmentParameters( + list( + occupancyFilter = 'maximum', + impute = 'all', + transform = 'TICnorm' + ) +) +changeParameter(pre_treatment_parameters,'parallel') <- 'no' + +## Perform pre-treatment +pre_treated_data <- preTreatModes(analysis, + pre_treatment_parameters) +#> +#> metabolyseR v0.14.5 Wed Nov 17 09:52:53 2021 +#> ________________________________________________________________________________ +#> Parameters: +#> pre-treatment +#> occupancyFilter +#> maximum +#> cls = class +#> occupancy = 2/3 +#> impute +#> all +#> occupancy = 2/3 +#> parallel = no +#> seed = 1234 +#> transform +#> TICnorm +#> +#> ________________________________________________________________________________ +#> +#> Negative mode… Negative mode ✓ [1.1S] +#> Positive mode… Positive mode ✓ [0.9S] +#> ________________________________________________________________________________ +#> +#> Complete! [2.1S] +#> +@@ -157,43 +157,65 @@
Isotope and adduct features are filtered based on the maximum intensity peak for each molecular formulas.
+#>#>-## Assign molecular formulas -p <- assignmentParameters('FIE') - -assignment <- assignMFs(peakData,p) -#>#>#>-#> -#> -#> -#> -#> -#> -#> -#> -#> -#> -#> -#>#>#>#>#>#>#>#>#>#>#>#>#>#>#>#>#> -#>-## Retrieve assigned data -assigned_data <- metabolyseR::analysisData( - assignedData(assignment), - tibble::tibble(sample = seq_len(nrow(peakData))) - ) - -reduced_data <- metaboMisc::reduce(assigned_data) - -reduced_data -#> -#> AnalysisData object containing: -#> -#> Samples: 60 -#> Features: 1 -#> Info: 1 -#>
library(MFassign) +#> Loading required package: ggraph +#> Loading required package: ggplot2 + +## Assign molecular formulas +p <- assignmentParameters('FIE') + +assignment <- assignMFs(peakData,p) +#> +#> MFassign v0.7.10 Wed Nov 17 09:52:56 2021 +#> ________________________________________________________________________________ +#> Assignment Parameters: +#> +#> Technique: FIE +#> Max M: 1000 +#> Max MF score: 5 +#> PPM threshold: 5 +#> Relationship limit: 0.001 +#> +#> Adducts: +#> n: [M-H]1-, [M+Cl]1-, [M+K-2H]1-, [M-2H]2-, [M+Cl37]1-, [2M-H]1- +#> p: [M+H]1+, [M+K]1+, [M+Na]1+, [M+K41]1+, [M+NH4]1+, [M+2H]2+, [2M+H]1+ +#> Isotopes: 13C, 18O, 13C2 +#> Transformations: M - [O] + [NH2], M - [OH] + [NH2], M + [H2], M - [H2] + [O], M - [H] + [CH3], M - [H] + [NH2], M - [H] + [OH], M + [H2O], M - [H3] + [H2O], M - [H] + [CHO2], M - [H] + [SO3], M - [H] + [PO3H2] +#> ________________________________________________________________________________ +#> No. m/z: 9 +#> Calculating correlations … +#> Calculating correlations ✓ [24 correlations] [0.1S] +#> Filtering correlations … +#> Filtering correlations ✓ [24 correlations] [0S] +#> Preparing correlations … +#> Preparing correlations ✓ [0S] +#> Calculating relationships … +#> Calculating relationships ✓ [12.4S] +#> Adduct & isotope assignment … +#> Adduct & isotope assignment ✓ [15.7S] +#> Transformation assignment iteration 1 … +#> Transformation assignment iteration 1 ✓ [0S] +#> ________________________________________________________________________________ +#> +#> Complete! [28.2S] + +## Retrieve assigned data +assigned_data <- metabolyseR::analysisData( + assignedData(assignment), + tibble::tibble(sample = seq_len(nrow(peakData))) + ) + +reduced_data <- metaboMisc::reduce(assigned_data) + +reduced_data +#> +#> AnalysisData object containing: +#> +#> Samples: 60 +#> Features: 1 +#> Info: 1 +#> +diff --git a/docs/reference/sanitiseTable.html b/docs/reference/sanitiseTable.html index 9029ab6..187209d 100644 --- a/docs/reference/sanitiseTable.html +++ b/docs/reference/sanitiseTable.html @@ -72,7 +72,7 @@ @@ -120,7 +120,7 @@
Sanitise a data table by restricting the number of rows and rounding numeric columns.
-sanitiseTable(x, maxRows = 5000, sigFig = 3)+
sanitiseTable(x, maxRows = 5000, sigFig = 3, maxCharacters = 100)
sigFig | Significant figures with which to round numeric columns |
+
---|---|
maxCharacters | +Maximum number of characters allowed in a string before it is truncated |
+
+sanitiseTable(iris,maxRows = 10,sigFig = 1) -#>#> Sepal.Length Sepal.Width Petal.Length Petal.Width Species -#> 1 5 4 1 0.2 setosa -#> 2 5 3 1 0.2 setosa -#> 3 5 3 1 0.2 setosa -#> 4 5 3 2 0.2 setosa -#> 5 5 4 1 0.2 setosa -#> 6 5 4 2 0.4 setosa -#> 7 5 3 1 0.3 setosa -#> 8 5 3 2 0.2 setosa -#> 9 4 3 1 0.2 setosa -#> 10 5 3 2 0.1 setosa
sanitiseTable(iris,maxRows = 10,sigFig = 1) +#> Number of rows in table restricted to 10. +#> Sepal.Length Sepal.Width Petal.Length Petal.Width Species +#> 1 5 4 1 0.2 setosa +#> 2 5 3 1 0.2 setosa +#> 3 5 3 1 0.2 setosa +#> 4 5 3 2 0.2 setosa +#> 5 5 4 1 0.2 setosa +#> 6 5 4 2 0.4 setosa +#> 7 5 3 1 0.3 setosa +#> 8 5 3 2 0.2 setosa +#> 9 4 3 1 0.2 setosa +#> 10 5 3 2 0.1 setosa +@@ -125,10 +125,10 @@
+if (FALSE) { -suitableParallelPlan() -} -
if (FALSE) { +suitableParallelPlan() +} +