Critical t values in R

The code you posted gives the critical value for a one-sided test (Hence the answer to you question is simply:

abs(qt(0.25, 40)) # 75% confidence, 1 sided (same as qt(0.75, 40))
abs(qt(0.01, 40)) # 99% confidence, 1 sided (same as qt(0.99, 40))

Note that the t-distribution is symmetric. For a 2-sided test (say with 99% confidence) you can use the critical value

abs(qt(0.01/2, 40)) # 99% confidence, 2 sided

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