View source: R/ForestFromCSV.r
ForestFromCSV | R Documentation |
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.
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) |
Matt Arnold
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