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Using the LGT3State program [ 26], we generated 1000 bootstrap distributions under the gene loss only model.
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Repeat this procedure many times to create the bootstrap distribution of correlation under the null hypothesis.
In addition, under the circumstances that the bootstrap distributions are potentially biased and skewed, the relationship between the bootstrap standard error and the BCa interval is not quite straightforward; therefore, we reported both the bootstrap standard error and the BCa interval as the complementary information to evaluate the accuracy of RV estimates.
We then reran the timing analyses and used the standard deviation of the bootstrap distribution to estimate the error in our estimate of the discrimination time.
If we now apply the LRT in the usual manner, the bootstrap distribution of the test statistic represents its distribution under the alternative.
To obtain the bootstrap distribution, the pairwise agreement measures were calculated for each of the 1000 bootstrap resamples.
The bootstrap distribution of the estimated quantiles can be described by a lognormal distribution.
For each of the 1000 bootstrap replicates, we calculated the difference between the 100th quantile of the W bootstrap distribution and the 0th quantile of the non-W-specific bootstrap distribution.
The SDs of the bootstrap distributions will provide estimates of SE.
This is according to a pairs bootstrap distribution approximation of the posterior, using a Pólya urn scheme.
The bootstrap approach is based on the assumption that the bootstrap distribution is similar to the sample distribution.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com