Solved – Including time of day in a linear regression model

I think a partially linear modeling framework may be suitable for your problem. If you focus on one flower at the time, note that both the flower data and the air temperature data exhibit strong temporal cycles which peak roughly at the same time. So the simplest partially linear model you could consider for one flower would look like this:

FT_h = beta0 + beta1*AT_h + m(h) + epsilon_h,  

where FT_h is the flower temperature for the chosen flower at hour h, AT_h is the air temperature at hour h, m() is a smooth, unknown function meant to capture the temporal cycles you see in the temperature data and epsilon_h is an unknown error term. Here, h = 1, 2, 3, …, H is an index which counts how many hours you have represented in total in your flower data. In other words, this index counts your hours from the first to the last. If you have 9,000 hours represented in your data, for example, then H = 9,000. In this model, beta1 represents the hourly effect of air temperature on flower temperature, after controlling for temporal effects.

The model can be expanded by adding a linear effect for incident solar radiation (ISR):

FT_h = beta0 + beta1*AT_h + m(h) + beta2*ISR_h + epsilon_h.  

If you wanted to throw in wind direction as well, you could code this variable as taking the values North, South, East, West (or add variations like North-East, North-West, etc.) and include it in your model using dummy variables. For example, if you only code this variable as taking the values North, South, East or West, the flower-specific model could be expressed as:

FT_h = beta0 + beta1*AT_h + m(h) + beta2*ISR_h +        beta3*NorthDummy_h + beta3*EastDummy_h + beta4*WestDummy_h +               epsilon_h, 

where South is treated as the reference direction against which all others will be compared and NorthDummy_h is set to 1 if wind direction was North at hour h and 0 otherwise, EastDummy_h is set to 1 if wind direction was East at hour h and 0 otherwise and WestDummy_h is set to 1 if wind direction was West at hour h and 0 otherwise.

The challenging aspects of these models are:

1. The need to estimate the (unknown) degree of smoothness of the (unknown) temporal effect m() carefully, given that this is just a nuisance effect and the real interest is in estimating beta1;

2. The possibility that the error terms epsilon_h might be temporally correlated, which in turns can affect how item 1. above is addressed.

Many years ago, I conducted research on this very topic – see, for example – http://www.ghement.ca/217.pdf. However, I have not stayed current on the topic so it's possible there have been several advances on ways to handle item 1.

Intuitively, the temporal signal seen in the data is really strong while the air temperature signal is likely tiny by comparison. So you need to find the right balance when determining the degree of smoothness of the temporal effect, so as not to throw the baby with the bath water.

If you are interested in comparing effects of air temperature across flowers, you can expand the model even further. But I would start small to make sure I get a handle first on the simpler, flower-specific models.