I tested the effects of a chemical product on water parameters (ammonia, nitrite, nitrate, salinity, alkalinity, pH, dissolved oxygen and temperature). This product accelerate the conversion of ammonia to nitrite and to nitrate. The other water parameters varying according the ammonia concentrations.

For it, I have five treatments: one as control and four with different initial concentrations of ammonia.

I measured the water parameters at the time 0 (when I added the chemical product in the water), 24h, 72h and 96h hours after the addition of the chemical product. Each one of these times have four replicates.

I applied a PCA in the PAST considering the treatment and the time as groups. The first PCA axis showed differences along the time, while the second PCA axis showed differences among the treatments.

Now I want to test differences using a PERMANOVA whit two factors: a) treatment (an independent variable) and b) time (a dependent variable).

What R package I can use to test it? How I can inform these factor characteristics to the R into this analysis?

Thank you for the help!