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"methodological difficulty" is a correct and usable phrase in written English.
It is typically used when discussing research or scientific processes, to describe a challenge or obstacle related to the methodology being used. Example: "The results of the study were inconclusive due to a methodological difficulty in accurately measuring the participants' behavior."
Exact(28)
To avoid such a methodological difficulty, the proposed models still use slacks for those outputs.
It should be noted that social psychological work of the sort we have been describing is not without methodological difficulty.
EM allows us to fit the model in the presence of censored data, a methodological difficulty common to experiments involving speedup learning.
We used the latest developments in the application of the magnetic resonance geophysical method to confront the methodological difficulty of quantifying groundwater storage.
While this is also not without methodological difficulty, it goes some way towards addressing the problem of "ivory tower" subject pools.
When estimating the effects of a new connection in terms of FDIs, one major methodological difficulty is that other unobserved factors may account for the changes, rather than the existence of the new route.
Similar(32)
But, Dr. Lee said, studies lending support to the idea tended to be limited by methodological difficulties.
The paper discusses methodological difficulties.
The study protocol contains some methodological difficulties.
Methodological difficulties in this type of study are also discussed in the paper.
One of the methodological difficulties experienced in microcredit impact assessment studies include the fungibility of loans.
More suggestions(15)
methodological challenge
methodological hurdle
methodological obstacle
methodological dilemma
systematic difficulty
approach difficulty
process difficulty
ways difficulty
methodologies difficulty
methodological constraints
methodological issues
means difficulty
way difficulty
methodological challenges
procedural difficulty
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com