ForestFromCSV: ForestFromCSV
In arnhew99/Jasper: Jasper makes plots

ForestFromCSV

R Documentation

ForestFromCSV

Description

Plot a full-page Jasper figure containing a forest and associated extra columns, direct from an input CSV file. The R/Jasper code that renders the figure is also outputted. This may be edited by the user to include their own modifications.

Arguments

`file`	Path to input CSV file
`orient`	Page orientation, LANDSCAPE or PORTRAIT (default: PORTRAIT)
`filestem`	String to use as the filename, an appropriate extension is appended automatically (default: test)
`append_datetime`	(default: FALSE)
`type`	One of the valid SetPage file types (default: GUI)
`expandDataLoading`	Instead of using FormatForest, expand the details of how the ForestBasic object is being created (default: FALSE)
`StopIfCodeExists`	If the code from a previous run would be overwritten, then halt. Avoids accidental deletion of edits (default: TRUE)
`mainfont`	Font scaling applied to cex (default: 1)
`optimise.fontsize`	Automatically choose the largest font size such that the plot as a whole fits on the page (default: TRUE)
`auto.shrink.font`	If mainfont is too large, then automatically reduce it to the optimal (default: TRUE)
`optimise.line.spacing`	Select the top and bottom margins of the panel automatically such that a visually optimal line spacing is used. Useful for squashing forests with only a few rows (default: TRUE)
`line.spacing`	The target line spacing (default: 1.25)
`vertical.alignment`	Align the forest at the top, middle or bottom of the page (default: centre)
`LogScale`	X axis should be on the log scale (default: TRUE)
`ExponentiateDataOnPlot`	The contents of the data table should be exponentiated when plotted. For instance, if the data contains log RR but you want to plot RR (default: FALSE)
`DataLogged`	Deprecated; use ExponentiateDataOnPlot instead (default: NULL)
`EstimateCol`	Vector of CSV column names that provide point estimates (optional, overrides CSV column names) (default: NULL)
`StdErrCol`	Vector of CSV column names that provide point standard errors (optional, overrides CSV column names) (default: NULL)
`LCICol`	Vector of CSV column names that provide point lower confidence bounds (optional, overrides CSV column names) (default: NULL)
`UCICol`	Vector of CSV column names that provide point upper confidence bounds (optional, overrides CSV column names) (default: NULL)
`FormatPValue`	Instead of providing ColHeadings in the CSV file, provide a vector of CSV column names here to be formatted as P value (default: NULL)
`pvalue.use.lower.limit`	(default: FALSE)
`pvalue.lower.limit`	(default: 1e-100)
`pvalue.use.upper.limit`	(default: FALSE)
`pvalue.upper.limit`	(default: 0.01)
`ColHeadings`	Instead of providing ColHeadings in the CSV file, provide a vector of strings here, in the format "<CSV colname>=<print name>" (default: NULL)
`ColDecimalPlaces`	(default: NULL)
`plot.width`	Percentage of the page width to use for the drawing area of each forest. Applies to each forest. (default: 30)
`font`	Specify a font name to use on the whole page (default: NULL)
`forest.Range`	Deprecated, use forest.xlim (default: NULL)
`forest.xlim`	X axis limits for each forest. Use a list to give different limits for each forest (default: NULL)
`forest.xticks`	X axis ticks for each forest. Use a list to give different ticks for each forest (default: NULL)
`forest.hideticklabs`	(default: FALSE)
`forest.title`	Vector of titles to be placed centrally above each forest
`forest.titleY`	Y axis coordinate to align forest titles on (default: NULL)
`forest.title.axiscentred`	If TRUE, centre the title over the axis part only. If FALSE then centre over axis and estimate labels (default: FALSE)
`ylabels.offset`	(default: 0)
`lwd`	Line width (scaling) (default: 1)
`xlab`	X axis label
`mar`	Vector of margins, in order c(bottom, left, top, right) (default: c(7, 2, 7, 2))
`blank.labels.font`	Font style to use for labels that occur in blank rows of the forest. 1 is normal, 2 is bold, 3 is italic, 4 is bold italic. (default: 2)
`ValueLabels`	Add the ValueLabels column to the right of each forest (default: TRUE)
`ValueLabelsHeader`	Heading to be placed above the ValueLabels column
`ValueLabelsEffectSE`	(default: FALSE)
`ValueDigits`	Number of digits to print after the decimal point. Either, a single number used globally, or a vector of numbers, 1 per forest (default: NULL)
`ValueDigitsSE`	(default: NULL)
`HetTrendScale`	Font scaling applied to any heterogeneity or trend tests (default: 0.8)
`boxparm.stderr`	Provide the value of the smallest stderr to be used with computing the boxparm, instead of detecting it automatically. (default: NULL)
`boxparm.sharedstderr`	If TRUE, share box scaling information across all forests. If FALSE the scaling is determined on a per-forest basis. (default: TRUE)
`boxsizeoverride`	Disable scaling of boxes by inverse of variance (default: FALSE)
`boxTop`	(default: FALSE)
`blank.right.percent`	Percentage of the whole page to leave empty at the right. Useful for squashing figures into the top left (default: NULL)
`blank.left.percent`	(default: NULL)
`blank.bottom.percent`	Percentage of the whole page to leave empty at the bottom. (default: NULL)
`titlespace`	Proportion of the page to allocate to a title area at the top of the page (default: 0.1)
`footerspace`	Proportion of the page to allocate to a footer area at the bottom of the page (default: 0.1)
`footer.title`	Plot title to place at the bottom of the page above the standard footer. Supplying a vector of titles places each element on a new line (default: NULL)
`footer.title.cex`	Footer title scaling (default: NULL)
`mainTitle`	Main title to be added in the page title space (default: NULL)
`pointGroupsFactor`	(default: 0.9)
`additionalR`	Filename of further R code to be executed after the forest has been drawn but before the file closes. (default: NULL)
`suppress.date`	If TRUE, do not print the datetime or folder information at the bottom left of the page (default: FALSE)
`fixLabelsY`	(default: FALSE)
`attempt_adobe_kill`	(default: TRUE)