print.copas {copas} | R Documentation |
Print and summary method for objects of class copas
.
## S3 method for class 'copas': print(x, ...) ## S3 method for class 'copas': summary(object, level=0.95, ...) ## S3 method for class 'summary.copas': print(x, digits = max(3, .Options$digits - 3), ...)
x |
An object of class copas or summary.copas . |
object |
An object of class copas . |
level |
The level used to calculate confidence intervals (between 0 and 1). |
digits |
Minimal number of significant digits, see
print.default . |
... |
other arguments to the function will be ignored (this option included only to conform with R standards) |
The summary.copas
function prints a summary of a Copas
analysis, performed using the function copas
. It complements
the graphical summary of the results, generated using
plot.copas
.
Specifically it prints a table where the:
first column corresponds to
the x-axis in plots 3 & 4 from plot.copas
;
second column corresponds to
the treatment effect displayed in plot 3 from plot.copas
;
third and fourth columns give the confidence intervals for this treatment effect,
fifth colum gives the p-value for an overall treatment effect,
sixth column gives
the p-value for residual publication bias (the y-axis of plot 4 from
plot.copas
(see help(plot.copas) under plot 4 for a further
explanation of this p-value))
seventh column gives an approximate estimate of the number of studies the model suggests remain unpublished if the probability of publishing the study with the largest SE is as in column 1.
Below this is displayed the results of the Copas analysis for the smallest degree of selection for which the p-value for evidence of residual selection bias exceeds 0.1. This is simply extracted from the corresponding row in the table above.
Lastly, the usual random effects estimate (based on the DerSimonianLaird method) and 95% confidence interval is printed.
The function print.copas
prints the summary information above
together with the following information:
Range of gamma0 values used (see help(copas)
);
Range of gamma1 values used (see help(copas)
);
Largest SE of all studies in meta-analysis;
Range of probability publishing trial with largest SE;
The next table gives details relating to the summary of the contour
plot. Specifically, it gives details from fitting a straight line
to each treatment-contour in the contour plot. Column 1 (headed
level) shows the treatment-contours; column 2 (nobs) shows the number
of observations used by the contour plot command within the
copas
function to plot this contour line; column 3
(adj.r.square) shows the adjusted r-square from fitting a straight
line to this contour; columns 4 & 5 show the slope and its standard
error from fitting a straight line to this contour.
A list is returned by the function summary.copas
with the
following elements:
slope |
Results for points on orthogonal line (a list with elements TE, seTE, lower, upper, z, p, level). |
publprob |
Vector of probabilities of publishing the smallest study. |
pval.rsb |
P-values for tests on presence of residual selection bias |
N.unpubl |
Approximate number of studies the model suggests remain unpublished |
adjust |
Result of Copas selection model adjusted for selection bias (a list with elements TE, seTE, lower, upper, z, p, level). |
pval.rsb.adj |
P-value for test on presence of residual selection
bias for adjusted effect given in adjust . |
N.unpubl.adj |
Approximate number of studies the model suggests
remain unpublished for adjusted effect given in adjust |
random |
Results for usual random effects model (a list with elements TE, seTE, lower, upper, z, p, level). |
sm |
A character string indicating underlying summary measure. |
ci.lab |
Label for confidence interval. |
James Carpenter James.Carpenter@lshtm.ac.uk, Guido Schwarzer sc@imbi.uni-freiburg.de
copas
, plot.copas
metabias
, metagen
# Load data # data(Fleiss93) # # Perform meta analysis, effect measure is odds ratio (OR) # meta1 <- metabin(event.e, n.e, event.c, n.c, data=Fleiss93, sm="OR") # # Perform Copas analysis # cop1 <- copas(meta1) summary(cop1, level=0.95)