When using the R, frequently a series of commands is required to obtain the required output. To enter multiple commands sequentially can be rather tedious. Furthermore, if a mistake is made, you will need to start again!<\/p>\n\n\n\n
Generally, it is preferable to save the commands as a script file (a text file of sequential R commands) that can be opened in R. A new script file can be created in RStudio by selecting File -> New File -> R Script form the menu bar.<\/p>\n\n\n\n
A script can be opened by selecting File -> Open File and then manoeuvre to the file location.<\/p>\n\n\n\n
This page contains some useful scripts that are used in this book.<\/p>\n\n\n\n
To use a script, select the appropriate hyperlink below. This should open a new browser window that contains the script (code). Select ALL<\/strong> (Ctrl-A) the text and copy it to the clipboard (Ctrl-C).<\/p>\n\n\n\n Create a new script in R (File -> New File -> R Script) and paste (Ctrl-V) the contents of the clipboard into the script editor.<\/p>\n\n\n\n Save the file and give it an appropriate name in your preferred location.<\/p>\n\n\n\n To run the script<\/strong>; select all the text in the script editor (Ctrl-A), copy it to the clipboard (Ctrl-C), paste it into the console (Ctrl-V) and hit return.<\/p>\n\n\n\n Functions:<\/strong><\/p>\n\n\n\n Mode<\/a> (calculate the mode of a variable)<\/p>\n\n\n\n BAplot<\/a> (create Bland-Altman1<\/a><\/sup> plots)<\/p>\n\n\n\n ba_ggplot<\/a> (create Bland-Altman2<\/a><\/sup> plots with ggplot)<\/p>\n\n\n\n nhs_number_validation<\/a> (check if an NHS number is valid)<\/p>\n\n\n\n Dot Plot Data<\/a> Function for comparison of genetic sequences. Returns a matrix with the first sequence as rows and second sequence as columns. Adapted from seqinr package3<\/a><\/sup>.<\/p>\n\n\n\n KMatRisk<\/a> (create Kaplan-Meier survival curves with numbers at risk)<\/p>\n\n\n\n cool survival function<\/a><\/p>\n\n\n\n For this function<\/a>, the RcmdrPlugin.KMggplot2, survival and ggfortify packages4<\/a><\/sup>5<\/a><\/sup>6<\/a><\/sup> should be installed, but there is no need to load the packages with the library command.<\/em><\/p>\n\n\n\n Export2Office<\/a> (function by Tom Wenseleers that exports the active plot window directly to a Microsoft Powerpoint PPTX slide or a Microsoft Word DOCX file). The library ReporteRs7<\/a><\/sup> and it dependencies should be installed<\/a>.<\/p>\n\n\n\n Pairwise alignment of DNA<\/a> Please refer to a little book of R for bioinformatics 8<\/a><\/sup><\/p>\n\n\n\n Plots as PDF, JPG or TIF <\/a>(example on how to create pdf, jpg and tif files from plots created)<\/p>\n\n\n\n To create an SVG file, install the package svglite9<\/a><\/sup>. Open the library and create a new file for the plot in the default directory (called Rplots.svg):<\/p>\n\n\n\n Now populate this file with a plot and close the file:<\/p>\n\n\n\n Group dates by year <\/a>(example on how to group dates by year; use the data file dates.rda<\/a> with this example)<\/p>\n\n\n\n Create a survival curve from dates<\/a>; a data frame that contains the date of diagnosis and date of failure (example on how to convert dates to follow up time and how to create the censor variable; use survivaldates.rda<\/a> with this example).<\/p>\n\n\n\n Revalue of map values (factors) with the plyr package 10<\/a><\/sup> (for example month names from the first date of the month:<\/p>\n\n\n\n Convert incorrectly formatted data into appropriately declared variables that allow subsequent analysis.<\/strong><\/p>\n\n\n\n It is a common error to group variables incorrectly and create a separate variable (column) for each group. However, variables should be in columns and the group is a separate variable. An example is show here<\/a>.<\/p>\n\n\n\n Open an SPSS .sav file in R<\/strong><\/p>\n\n\n\n Method 1:<\/strong><\/p>\n\n\n\n This may give an error like: re-encoding from utf-8 Warning message: In read.spss(a1, reencode = “utf-8”, to.data.frame = TRUE) : Unrecognized record type 7, subtype 18 encountered in system file<\/em><\/p>\n\n\n\n Method 2:<\/strong><\/p>\n\n\n\n Solar Functions (Equation of Time<\/a>)<\/strong><\/p>\n\n\n\n convert_dd_dms<\/a><\/p>\n\n\n\n convert_dms_dd<\/a><\/p>\n\n\n\n equation_of_time<\/a><\/p>\n\n\n\n sun_declination<\/a><\/p>\n\n\n\n sun_rise_formula<\/a><\/p>\n\n\n\n Other functions<\/strong><\/p>\n\n\n\n R Objects and Operators<\/a><\/p>\n\n\n\n Common R Functions<\/a><\/p>\n\n\n\n Helpful R Functions in Packages<\/a><\/p>\n\n\n\ninstall.packages(\"ReporteRs\")<\/span><\/em>\ninstall.packages(\"ReporteRsjars\")<\/span><\/em><\/code><\/pre>\n\n\n\nlibrary(svglite)<\/span><\/em>\nsvglite()<\/span><\/em><\/code><\/pre>\n\n\n\nggplot() + <\/span><\/em>\ngeom_point(aes(x=c(1,2,3,4),y=c(4,3,2,1))) + <\/span><\/em>\ntheme_bw()<\/span><\/em>\ndev.off()<\/span><\/em><\/code><\/pre>\n\n\n\nlibrary(plyr)<\/em><\/span>\nmonth<-mapvalues(activity$ActivityMonth,from=c('01\/01\/2014','01\/02\/2014','01\/03\/2014','01\/04\/2014','01\/05\/2014','01\/06\/2014','01\/07\/2014','01\/08\/2014','01\/09\/2014','01\/10\/2014','01\/11\/2014','01\/12\/2014'),to=c('Jan','Feb','Mar','Apr','May','Jun','Jul','Aug','Sep','Oct','Nov','Dec'))<\/em><\/span><\/code><\/pre>\n\n\n\n\n
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