standardStats: standardStats

In JATSdecoder: A Metadata and Text Extraction and Manipulation Tool Set

standardStats

Description

Extracts and restructures statistical standard results like Z, t, Cohen's d, F, eta^2, r, R^2, chi^2, BF_10, Q, U, H, OR, RR, beta values into a matrix. Performs a recomputation of two- and one-sided p-values if possible. This function is implemented in get.stats which returns the results of allStats and standardStats. Besides only plain textual input, get.stats enables direct processing of different file formats (NISO-JATS coded XML, DOCX, HTML) without text preprocessing.

Usage

standardStats(
  x,
  stats.mode = "all",
  recalculate.p = TRUE,
  alternative = "undirected",
  checkP = FALSE,
  alpha = 0.05,
  criticalDif = 0.02,
  estimateZ = FALSE,
  T2t = FALSE,
  R2r = FALSE,
  select = NULL,
  rm.na.col = TRUE,
  warnings = TRUE
)

Arguments

x	result vector by allStats or chracter vector with a statistical test result per cell, e.g. c("t(12)=1.2, p>.05","chi2(2)=12.7, p<.05")
stats.mode	Select subset of standard stats. One of: c("all", "checkable", "computable", "uncomputable").
recalculate.p	Logical. If TRUE recalculates p values (for 2 sided test) if possible.
alternative	Character. Select test sidedness for recomputation of p-values from t-, r- and beta-values. One of c("undirected", "directed"). If "directed" is specified, p-values for directed null-hypothesis are added to the table but still require a manual inspection on consistency of the direction.
checkP	Logical. If TRUE observed and recalculated p-values are checked for consistency.
alpha	Numeric. Defines the alpha level to be used for error assignment.
criticalDif	Numeric. Sets the absolute maximum difference in reported and recalculated p-values for error detection.
estimateZ	Logical. If TRUE detected beta-/d-values are divided by the reported standard error "SE" to estimate Z-values ("Zest") for observed beta/d and computation of p-values. Further, t-values that are reported without degrees of freedom will be treated as an estimate for Z. Note: This is only valid, if Gauss-Marcov assumptions are met and a sufficiently large sample size is used. If a Z- or t-value with degrees of freedom is detected in a report of a beta-/d-coefficient with SE, no estimation of Z will be performed, although set to TRUE.
T2t	Logical. If TRUE capital letter T is treated as t-statistic.
R2r	Logical. If TRUE capital letter R is treated as correlation.
select	Select specific standard statistics only (e.g.: c("t", "F", "Chi2")).
rm.na.col	Logical. If TRUE removes all columns with only NA.
warnings	Logical. If FALSE warning messages are omitted.

Value

Matrix with recognized statistical standard results and recalculated p-values. Empty, if no result is detected.

Source

A minimal web application that extracts statistical results from single documents with get.stats is hosted at: https://www.get-stats.app/

Statistical results extracted with get.stats can be analyzed and used to identify articles stored in the PubMed Central library at: https://www.scianalyzer.com/.

References

Böschen (2021). "Evaluation of JATSdecoder as an automated text extraction tool for statistical results in scientific reports.” Scientific Reports. doi: 10.1038/s41598-021-98782-3.

See Also

study.character for extracting multiple study characteristics at once.

get.stats for extracting statistical results from textual input and different file formats.

Examples

x<-c("t(38.8)<=>1.96, p<=>.002","F(2,39)<=>4, p<=>.05",
"U(2)=200, p>.25","Z=2.1, F(20.8,22.6)=200, p<.005, 
BF(01)>4","chi=3.2, r(34)=-.7, p<.01, R2=76%.")
standardStats(x)

JATSdecoder documentation built on April 9, 2026, 9:08 a.m.