This is an R Notebook to help visualize the results of your ocean sampling. Pretty cool huh?

Some directions: Execute chunks by clicking the Run button within the chunk or by placing your cursor inside it and pressing Cmd+Shift+Enter.

Add a new chunk by clicking the Insert Chunk button on the toolbar or by pressing Cmd+Option+I.

When you save the notebook, an HTML file containing the code and output will be saved alongside it (click the Preview button or press Cmd+Shift+K to preview the HTML file).

The preview shows you a rendered HTML copy of the contents of the editor. Consequently, unlike Knit, Preview does not run any R code chunks. Instead, the output of the chunk when it was last run in the editor is displayed.

Note that the echo = FALSE parameter was added to the code chunk to prevent printing of the R code that generated the plot.

Set up environment

Plot depth profile

#Answer Questions

Question 1. Are you able to detect any stratification based on the temperature or salinity profiles?

Answer= Yes, stratification can be detected by observing changes in temperature or salinity profiles. This can be observed with the depth profile on the graphs.

##Calculate Light Attenuation

Insert Caption Here.
Attenuation Coefficient
Kd_Licor 0.34
Kd_Secchi 0.96

#Answer Questions

Question 2. Does the light attenuation coefficient you calculated with the secchi depth match that of the Licor meter. Why do you think this is the case?

Answer= No, the light attenuation coefficient of the secchi depth and the Licor meter do not match. I would think that the secchi disk is based off of how the human visualizes the disk in the water and that could leave room for more error than the Licor meter. The Licro meter measures the PAR quantitatively.

Question 3. Do a little research. Does the light attenuation coefficient you calculated with the Licor meter seem reasonable for a coastal estuarine system? How do you think it might differ from that of the open ocean?

Answer= Yes, I think that the coefficent that I calulated for the Licor meter does seem resonable for the coastal estuarine system. This is becuase the 0.34 m-1 value I got falls within the typical estuarine range. This would vary from the open ocean since the ocean is a little clearer, the li-cor value are usually lower. Another reason could be becuase stuaries have a shallower photic zone. The light penetrated of teh deeper offshore of the ocean.

#Make Discrete Sample Table
Insert Caption Here.
Nitrate (mg/L) Nitrite (mg/L) Phosphate (mg/L) Salinity (ppt) Chl A Fluorescence (IVF)
Surface 0.3 0 0.01 13 575.9
Bottom 0.4 0 0.04 13 146.9

#Answer Questions

Question 4. Were there differences between the bottom and surface water pertaining to nutrient and chlorophyll a fluorescence? Why do you think these differences/similarities were observed? Why do you think there is a relationship between chlorophyll a fluorescence and nutrients concentrations?

Answer= Yes, there were differences between the bottom and surface water. The chl A Florescence of the surface of 575.9 and the bottom is 146.9. I think these differences could have occurred because the surface has high light and and nutrient depletion occurs on the surface of the water. At the bottom there is low light and nutrient accumulation. The realtionshio that seems to occur between chlorophyll a florescence and nutrient concentrations is that as nutrients increase the growth of phytoplanton increases. As the phytoplankton biomass increases, the chlorophyll a fluorescence increases. This is seen as a positive realationship between the two.