Other Checks Things to Update

[wilsonsj100]

@zoeread

• NAs for TEROS in wetland plots are because there are only two at each depth here so we should find a way to remove those - fixed this and another issue that MSM UP logger was 432 in Metadata when should be 403.
• TMP redox is not broken up by plot yet - (ZR) I can't break this up by plot because that information don't come in with the Redox data, I'm not sure how to fix that. We might need redox metadata like we have for the other data types?
• TMP Teros is plotting weird things all the scales are 0-4000 which doesn't make sense for temp so we should investigate
• TMP Sapflow is also odd - we got to figure this out - Is this referring to the one tree in Control that has crazy high sapflow?

just thoughts for future

[wilsonsj100]

TEMPEST Redox metadata: https://docs.google.com/spreadsheets/d/1v8ufNiYdj-0TKaCFkOWgBkzcZMVxjEZp/edit?gid=209781919#gid=209781919

TEMPEST SF metadata source: https://docs.google.com/spreadsheets/d/1JejdfQ8Z7gbAJKg7PfZlwtEAGXFi0bNJ/edit?gid=209781919#gid=209781919

TMP:

• sap flow: randomize colors, put legend below
• Sap flow NAs: where are the NAs? It seems like we have a port with no associated tree ID can we check and see if it is actually a missing tree or if we shouldn't have anything in that port? If we shouldn't have anything in that port, let's remove it. A quick check would be is there any real data in a NA labeled line - maybe add a quick if else ; if Tree = NA, and there is data 0 - 1 in that column, print a warning. If not, remove.
• add logger IDs or a sensor number (might need legend below)
• same thing with the NAs
• add sonde ids so we can tell if it is a 200 or a 600 (for the WL, Temp, Salinity)
• change to having faceted by plot
• remove geom_line from the AQ plots if they have it
• if we do % transmission by the sonde-id rather than just by the plot (this is what is causing the 200%)
• Redox once it is mapped we can split by plot (C, F, S)
• Sonde file can be removed

CB Synoptic:

• sapflow looks great (only thing would be potentially adding the TR/UP in the legend
• Teros: add the port/address to the end of the ID and use as the plot color ID so we know which one is which
• Sonde: we don't need plot: Battery_v, TSS_mgL, Wiper current, wiper position, pH_mV, ODO_local, ODO_sat, FDOM_RFU, Conductivity, Turbidity_Raw

[zoeread]

TEMPEST Redox metadata: https://docs.google.com/spreadsheets/d/1v8ufNiYdj-0TKaCFkOWgBkzcZMVxjEZp/edit?gid=209781919#gid=209781919

TEMPEST SF metadata source: https://docs.google.com/spreadsheets/d/1JejdfQ8Z7gbAJKg7PfZlwtEAGXFi0bNJ/edit?gid=209781919#gid=209781919

TMP:

• sap flow: randomize colors, put legend below Did this, though it's still hard to tell what's what. I found that the very high SF tree is Tree C12 (1328) at TEMPEST.
• Sap flow NAs: where are the NAs? It seems like we have a port with no associated tree ID can we check and see if it is actually a missing tree or if we shouldn't have anything in that port? If we shouldn't have anything in that port, let's remove it. A quick check would be is there any real data in a NA labeled line - maybe add a quick if else ; if Tree = NA, and there is data 0 - 1 in that column, print a warning. If not, remove. It looks like the value for these NA Trees are either NA or 0. I added a line to remove NA Trees if the mean of their values is 0, otherwise to not filter the dataframe, and print "A sapflow sensor is not correctly matched with its tree ID"
• add logger IDs or a sensor number (might need legend below) I added the ID's in but there are so many now, I'm worried it's less useful than just having the depths

• same thing with the NAs some of the NA depths have zeroes as values, which is a possible value. They don't have a match in the metadata though, so I'm not sure if they're real values
• add sonde ids so we can tell if it is a 200 or a 600 (for the WL, Temp, Salinity) Done
• change to having faceted by plot Done
• remove geom_line from the AQ plots if they have it Done
• if we do % transmission by the sonde-id rather than just by the plot (this is what is causing the 200%) Done
• Redox once it is mapped we can split by plot (C, F, S) I read in the redox metadata but then realized there is no way for me to map this onto the redox data without the Plot and/or Logger information, which is not read in with the redox data. This is because the redox data has a totally different naming scheme than the rest of the sensor data (ex. "TEMPEST_REDOX_control_Redox15" vs "PNNL_33_sapflow" and "PNNL_23_Terosdata". The function in the code for pulling in data uses the Logger number in the data title to match it to the Plot, so that function would need to be changed to account for Redox, unless it's possible to rename these files so they match the rest of the naming scheme.
• Sonde file can be removed Left this part in so the code can also be used for CB

CB Synoptic:

• sapflow looks great (only thing would be potentially adding the TR/UP in the legend Done
• Teros: add the port/address to the end of the ID and use as the plot color ID so we know which one is which DONE
• Sonde: we don't need plot: Battery_v, TSS_mgL, Wiper current, wiper position, pH_mV, ODO_local, ODO_sat, FDOM_RFU, Conductivity, Turbidity_Raw Removed these from the plot. Is MSM the only location with a sonde? It also pulls in GWI but there is no data. Also, the pressure will go from about -7 to about -2 and back within 15 minutes. I'm not sure why.

[wilsonsj100]

For the logger and depth let's just not do that... it is too much. We might be able to set some bounds that are typical like if the temperature is over 30 C then write out which sensor it is and which logger it is on for the TEROs what do you think?

[wilsonsj100]

The TMP Redox thing is annoying... it would be nice if they followed the same scheme. I think we could probably find a way aroudn this, but I will need a minute to think about it. Changing the naming scheme at the loggernet scale would be good but would require changes to the pipeline.

[wilsonsj100]

For the Buoy data, yes we only have buoy data from MSM. I think the table is just turned on for GWI for some reason, but we will never have data from there. I am not sure why the pressure does that, but really the pressure is not very informative because it is a floating buoy so we don't use the pressure data to determine depth

[wilsonsj100]

I probably missed things - sorry if I did feel free to ping me again here. I will try to reread and check a little later as well.

[zoeread]

For the logger and depth let's just not do that... it is too much. We might be able to set some bounds that are typical like if the temperature is over 30 C then write out which sensor it is and which logger it is on for the TEROs what do you think?

That makes sense, I added code to write out the TEROS sensor info if the temperature is above 30 C.

[zoeread]

The TMP Redox thing is annoying... it would be nice if they followed the same scheme. I think we could probably find a way aroudn this, but I will need a minute to think about it. Changing the naming scheme at the loggernet scale would be good but would require changes to the pipeline.

I figured out how to change the function that reads in the files so that it correctly identifies the plot for redox! Now we can separate by plot for TEMPEST.