You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
The documentation states that when argument pc.biplot = TRUE, this should scale the observations up by sqrt(n) and scale the variables scaled down by sqrt(n). However, looking at the source, only the observations are scaled, but not the variables:
if (pc.biplot) {
df.u <- df.u * nobs.factor
}
If this is to be inline with the documentation, I believe this should be:
However, I can see that df.v later gets scaled in a completely different way, regardless of whether pc.biplot = TRUE. Perhaps I'm missing something.
Scale - obs.scale and var.scale
The documentation also states the scale factor α allows the variances of the components to be apportioned between the row
points and column vectors by representing the approximation X as X = (U Λ^α) (Λ^(1−α) V^T).
The default value for the scale argument is 1 as expected. However, the default value for obs.scale = 1 - scale and var.scale = scale.
It looks like the two default values for obs.scale and var.scale should be swapped? At least that's how I would interpret it from the documentation.
The text was updated successfully, but these errors were encountered:
hphillips97
changed the title
Scaling issues with arguments: pc.biplot, obs.scale, var.scale
Scaling issues arguments: pc.biplot, obs.scale, var.scale
Jan 9, 2025
hphillips97
changed the title
Scaling issues arguments: pc.biplot, obs.scale, var.scale
Scaling arguments: pc.biplot, obs.scale, var.scale
Jan 9, 2025
Uh oh!
There was an error while loading. Please reload this page.
Variable arrows - pc.biplot
The documentation states that when argument pc.biplot = TRUE, this should scale the observations up by sqrt(n) and scale the variables scaled down by sqrt(n). However, looking at the source, only the observations are scaled, but not the variables:
If this is to be inline with the documentation, I believe this should be:
However, I can see that df.v later gets scaled in a completely different way, regardless of whether pc.biplot = TRUE. Perhaps I'm missing something.
Scale - obs.scale and var.scale
The documentation also states the scale factor α allows the variances of the components to be apportioned between the row
points and column vectors by representing the approximation X as X = (U Λ^α) (Λ^(1−α) V^T).
The default value for the scale argument is 1 as expected. However, the default value for obs.scale = 1 - scale and var.scale = scale.
It looks like the two default values for obs.scale and var.scale should be swapped? At least that's how I would interpret it from the documentation.
The text was updated successfully, but these errors were encountered: