# Intervals in frequency panels

**URL:** <https://nextstrain.discourse.group/t/intervals-in-frequency-panels/465>\
**Category:** Uncategorized\
**Created:** [March 30, 2021, 11:47pm UTC](https://nextstrain.discourse.group/t/intervals-in-frequency-panels/465 "2021-03-30T23:47:39Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![andersonbrito](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/andersonbrito/32/72_2.png) [@andersonbrito](https://nextstrain.discourse.group/u/andersonbrito)\
**Post date:** [March 30, 2021, 11:47pm UTC](https://nextstrain.discourse.group/t/intervals-in-frequency-panels/465/1 "2021-03-30T23:47:39Z")

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Hi,

I’m trying to change the interval how frequencies are shown in the frequency panels, but by reading the [documentation](https://docs.nextstrain.org/projects/augur/en/stable/usage/cli/frequencies.html), I’m not sure what parameter does that. I tried editing `pivot_interval` and `narrow_bandwidth`, but nothing changed.

After updating augur, I tried to set `--pivot-interval-units` = weeks, but that led to this error message:

`augur: error: unrecognized arguments: --pivot-interval-units weeks`

Any suggestions?

Thank you,  
Anderson

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**Author:** ![jlhudd](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/jlhudd/32/583_2.png) [@jlhudd](https://nextstrain.discourse.group/u/jlhudd)\
**Post date:** [March 31, 2021, 4:41pm UTC](https://nextstrain.discourse.group/t/intervals-in-frequency-panels/465/2 "2021-03-31T16:41:41Z")

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You are on the right track, @andersonbrito! You’ll want to modify the `--pivot-interval` and/or `--pivot-interval-units` arguments for `augur frequencies` to change the spacing of frequency estimates. One way to get started would be to copy [the existing tip frequencies rule from the main Nextstrain ncov workflow](https://github.com/nextstrain/ncov/blob/75af68c081b440263777a269b769ba16a30068f4/workflow/snakemake_rules/main_workflow.smk#L1009-L1044).

If you are already using this rule in your workflow, you can override [the default frequencies parameters](https://github.com/nextstrain/ncov/blob/75af68c081b440263777a269b769ba16a30068f4/defaults/parameters.yaml#L81-L89) by defining your own values in your `builds.yaml` config file.

Since Augur does not recognize the `--pivot-interval-units` argument, my best guess is that the version of Augur is still too old somehow even after you updated. When you run `augur --version`, what version do you get?

Also, are you managing your Augur installation through a Conda environment outside of Snakemake or with Snakemake’s `--use-conda` flag? Or do you manage Augur with pip? (There are honestly too many ways to install Augur right now. 🙂 )

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**Author:** ![andersonbrito](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/andersonbrito/32/72_2.png) [@andersonbrito](https://nextstrain.discourse.group/u/andersonbrito)\
**Post date:** [March 31, 2021, 5:42pm UTC](https://nextstrain.discourse.group/t/intervals-in-frequency-panels/465/3 "2021-03-31T17:42:24Z")

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Hi @jlhudd,

My latest update led to `augur 10.2.0`. I updated augur inside conda, following [these instructions](https://docs.nextstrain.org/en/latest/guides/install/local-installation.html), using the command below.

```
# Update Nextstrain dependencies (mafft, etc.), Augur, and Nextstrain CLI.
conda update --all

```

It seems that is not the latest version, though. I see [here](https://pypi.org/project/nextstrain-augur/) that it is now on version `11.3.0`.

What would be the best way to update `augur`?

Best,

Anderson Brito

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**Author:** ![andersonbrito](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/andersonbrito/32/72_2.png) [@andersonbrito](https://nextstrain.discourse.group/u/andersonbrito)\
**Post date:** [March 31, 2021, 6:07pm UTC](https://nextstrain.discourse.group/t/intervals-in-frequency-panels/465/4 "2021-03-31T18:07:24Z")

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Hey,

I have now update `augur` using pip. It gave me `augur 11.3.0`, I made the edits you suggested above, and the frequency plot now shows weekly intervals.

Thank you for your help.

Cheers