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Phylogenetic analyses were done using the neighbor-joining algorithm in the program PAUP 4.0b10 [ 89], and 1000 subsets were generated for Bootstrapping resampling of the data.
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Error bars are one standard deviation, estimated from bootstrap resampling of the stratigraphic ranges of species with 1000 iterations.
Bootstrap resampling of the data set revealed that estimates of variability and power were associated with considerable uncertainty.
Errors for the extinction and origination rates are represented by one standard deviation determined in each direction of a bootstrap resampling of the stratigraphic ranges of species based on 1000 iterations.
Stress orientation uncertainty was estimated using 2000 bootstrap resampling of the entire data (Hardebeck and Michael, 2006).
Bootstrap resampling of the NJ and P trees (1,000 and 100 replicates, respectively) was performed to provide statistical confidence to the topologies inferred.
Parametric bootstrap resampling of the reference matrix yielded a 95% confidence interval range for λ of 0.990 to 1.012 with an average of 1.0008.
This result is also robust to the underlying sampling variance of the diversity estimates, because bootstrap resampling of the individual bases in the sequence data also demonstrates a significant correlation (median rs = −0.61; 95% CI: −0.87, −0.17).
A customized routine for bootstrap resampling of the sequence data was compiled using Absoft Pro Fortran 8.0 (Rochester Hills, MI). Individual bases in the sequence data were sampled with replacement, and the Spearman Rank Correlation (rs) was obtained from the standardized diversities (divided by FP) of the three northern samples (HI, IR, SB) against chromosomal position.
§SD, standard deviation based on bootstrap resampling of the null distribution of observed epidemic patterns.
Standard errors and 95% confidence intervals were derived by bootstrap resampling of the data 1000 times.
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