L1_designtable

This script

Produces diagnostics tables and plots about the design table

Initializing

Design table “metadata//design_table.csv” and has 2425 rows, 3940 after expansion.

HTML outfile is “L1_designtable.html”.

Design table summary

Research name distribution

Code

# Drop rows without research names
dt_ex_rn <- dt_ex[!is.na(dt_ex$research_name),]

overall <- with(dt_ex_rn, table(Site, Plot))
knitr::kable(overall)

	C	F	OW	S	SWAMP	TR	UP	W	WTE
CRC	0	0	24	0	0	54	54	89	0
GCW	0	0	0	0	0	46	0	46	0
GWI	0	0	0	0	0	50	50	89	0
MSM	0	0	26	0	0	54	54	89	0
OWC	0	0	24	0	0	90	30	89	60
PTR	0	0	18	0	0	54	43	89	0
SWH	0	0	0	0	54	74	39	89	0
TMP	237	247	0	237	0	0	0	0	0

Code

overall_df <- as.data.frame(overall)
overall_df$Freq[overall_df$Freq == 0] <- NA_integer_
library(ggplot2)
theme_set(theme_bw())
ggplot(overall_df, aes(Site, Plot, size = Freq)) + 
    geom_point(na.rm = TRUE) + 
    ggtitle("research_name distribution by site and plot")

Loggernet variables to research name mapping

Code

# Make a 'clean' variable column
# Remove the (1), (2), etc.
dt_ex$lv_clean <- gsub("\\([0-9,]*\\)", "", dt_ex$loggernet_variable)
# Remove the A or B or C at end after number
dt_ex$lv_clean <- gsub("[ABC]$", "", dt_ex$lv_clean)
dt_ex$lv_clean <- gsub("Volt[ABC]_Avg", "Volt_Avg", dt_ex$lv_clean)

dt_ex$tb_clean <- gsub("[ABC]$", "", dt_ex$Table)
dt_ex$tb_clean <- tolower(dt_ex$tb_clean)
dt_ex$lv_clean <- with(dt_ex, paste(tb_clean, lv_clean, sep = "."))
mappings <- aggregate(lv_clean ~ research_name, data = dt_ex, FUN = function(x) paste(unique(x), sep = ","))
names(mappings)[2] <- "loggernet variable(s)"
knitr::kable(mappings)

research_name	loggernet variable(s)
battery_voltage	checktable.BattV , sapflow.BattV_Avg , waterlevel600.BattV_Avg , terostable.BattV_Avg , climavue50_24hr.BattV_Min , exotable.Battery_v , waterlevel200.Aquatroll_ID, redox5.BattV
gw_act_cond	waterlevel600.Actual_Conductivity600, waterlevel200.Actual_Conductivity
gw_bar_pressure	waterlevel600.Barometric_Pressure600
gw_battery	waterlevel600.Battery_Int600
gw_density	waterlevel600.Water_Density600, waterlevel200.Water_Density
gw_depth	waterlevel600.Depth600, waterlevel200.Depth
gw_part_pressure	waterlevel600.RDO_part_Pressure600
gw_perc_sat	waterlevel600.RDO_perc_sat600
gw_ph	waterlevel600.pH600
gw_ph_mv	waterlevel600.pH_mV600
gw_ph_orp	waterlevel600.pH_ORP600
gw_pressure	waterlevel600.Pressure600, waterlevel200.Pressure
gw_rdo_conc	waterlevel600.RDO_concen600
gw_resistivity	waterlevel600.Resistivity600, waterlevel200.Resistivity
gw_salinity	waterlevel600.Salinity600, waterlevel200.Salinity
gw_spec_cond	waterlevel600.Specific_Conductivity600, waterlevel200.Specific_Conductivity
gw_tds	waterlevel600.TDS600, waterlevel200.TDS
gw_temperature	waterlevel600.Temperature600, waterlevel200.Temperature
gw_temperature_int	waterlevel600.Temperature_Int600
gw_voltage	waterlevel600.Voltage
gw_voltage_ext	waterlevel600.Voltage_Ext600
redox_10cm	redox5.RedoxRa, redox5.RedoxRb
redox_20cm	redox5.RedoxRa, redox5.RedoxRb
redox_35cm	redox5.RedoxRa, redox5.RedoxRb
redox_55cm	redox5.RedoxRa, redox5.RedoxRb
sapflow_3.5cm	sapflow.DiffVolt_Avg
sapflow_5cm	sapflow.DiffVolt_Avg
soil_EC_10cm	terostable.Teros
soil_EC_15cm	terosdata.Teros
soil_EC_30cm	terostable.Teros, terosdata.Teros
soil_EC_5cm	terosdata.Teros
soil_temp_10cm	terostable.Teros
soil_temp_15cm	terosdata.Teros
soil_temp_30cm	terostable.Teros, terosdata.Teros
soil_temp_5cm	terosdata.Teros
soil_vwc_10cm	terostable.Teros
soil_vwc_15cm	terosdata.Teros
soil_vwc_30cm	terostable.Teros, terosdata.Teros
soil_vwc_5cm	terosdata.Teros
solar_voltage	checktable.SolarV
sonde_cable	exotable.Cable_v
sonde_conductivity	exotable.Conductivity
sonde_depth	exotable.Depth_m
sonde_fdom	exotable.FDOM_QSU
sonde_fdom_rfu	exotable.FDOM_RFU
sonde_nlf_cond	exotable.NLF_conductivity
sonde_odo_local	exotable.ODO_local
sonde_odo_mgl	exotable.ODO_MgL
sonde_odo_sat	exotable.ODO_sat
sonde_orp	exotable.ORP_mv
sonde_ph	exotable.pH
sonde_ph_mv	exotable.pH_mv
sonde_pressure	exotable.Pressure_psia
sonde_salinity	exotable.Salinity_PPT
sonde_spcond	exotable.Specific_Conductivity_uScm
sonde_tds	exotable.TDS_mg_L
sonde_temp	exotable.Temp_
sonde_tss	exotable.TSS_MgL
sonde_turb_raw	exotable.Turbidity_Raw
sonde_turbidity	exotable.Turbidity_FNU
sonde_vpos	exotable.Vertical_Position_m
sonde_wipercur	exotable.Wiper_Current_ma
sonde_wiperpos	exotable.Wiper_Position_mv
wx_barpress15	climavue50_15min.BP_mbar , gcrew_met_15min.Barometric_Pressure_PB110B_Avg
wx_bpmax15	climavue50_15min.BP_mbar_Max
wx_bpmax24	climavue50_24hr.BP_mbar_Max
wx_bpmin15	climavue50_15min.BP_mbar_Min
wx_bpmin24	climavue50_24hr.BP_mbar_Min
wx_bptmn15	climavue50_15min.BP_mbar_TMn
wx_bptmn24	climavue50_24hr.BP_mbar_TMn
wx_bptmx15	climavue50_15min.BP_mbar_TMx
wx_bptmx24	climavue50_24hr.BP_mbar_TMx
wx_dist_min15	climavue50_15min.Dist_km_Min
wx_dist_tmn15	climavue50_15min.Dist_km_TMn
wx_gcrew_rain15	gcrew_met_15min.Rain_cm_Tot
wx_invalid_wind15	climavue50_15min.Invalid_Wind_Tot
wx_maxws_tmx15	climavue50_15min.MaxWS_ms_TMx
wx_maxws_tmx24	climavue50_24hr.MaxWS_ms_TMx
wx_maxws15	climavue50_15min.MaxWS_ms_Max, gcrew_met_15min.WS_ms_RM_Max
wx_maxws24	climavue50_24hr.MaxWS_ms_Max
wx_minws15	gcrew_met_15min.WS_ms_RM_Min
wx_par_den15	climavue50_15min.PAR_Den_C_Avg, gcrew_met_15min.PAR_Den_C_Avg
wx_par_den24	climavue50_24hr.PAR_Den_C_Avg
wx_par_tot15	climavue50_15min.PAR_Tot_C_Tot
wx_par_tot24	climavue50_24hr.PAR_Tot_C_Tot
wx_rain15	climavue50_15min.Rain_mm_Tot
wx_rain24	climavue50_24hr.Rain_mm_Tot
wx_rh15	climavue50_15min.RH , gcrew_met_15min.CleanRH
wx_rh24	climavue50_24hr.RH_Max
wx_rht15	climavue50_15min.RHT_C_Avg
wx_rht24	climavue50_24hr.RH_Min
wx_rhtmax24	climavue50_24hr.RHT_C_Max
wx_rhtmin24	climavue50_24hr.RHT_C_Min
wx_slr_fd15	climavue50_15min.SlrFD_W_Avg, gcrew_met_15min.SlrW_Avg
wx_slr_fd24	climavue50_24hr.SlrFD_W_Avg
wx_slr_tf15	climavue50_15min.SlrTF_MJ_Tot, gcrew_met_15min.SlrMJ_Tot
wx_slr_tf24	climavue50_24hr.SlrTF_MJ_Tot
wx_strikes15	climavue50_15min.Strikes_Tot
wx_svp15	gcrew_met_15min.SVP
wx_tempavg15	climavue50_15min.AirT_C_Avg, gcrew_met_15min.AirTC_Avg
wx_tempavg24	climavue50_24hr.AirT_C_Avg
wx_tempmax15	climavue50_15min.AirT_C_Max
wx_tempmax24	climavue50_24hr.AirT_C_Max
wx_tempmin15	climavue50_15min.AirT_C_Min
wx_tempmin24	climavue50_24hr.AirT_C_Min
wx_temptmn15	climavue50_15min.AirT_C_TMn
wx_temptmn24	climavue50_24hr.AirT_C_TMn
wx_temptmx15	climavue50_15min.AirT_C_TMx
wx_temptmx24	climavue50_24hr.AirT_C_TMx
wx_tilt_ns15	climavue50_15min.TiltNS_deg_Avg
wx_tilt_ns24	climavue50_24hr.TiltNS_deg_Max
wx_tilt_we15	climavue50_15min.TiltWE_deg_Avg
wx_tilt_we24	climavue50_24hr.TiltWE_deg_Max
wx_vappress15	climavue50_15min.VP_mbar_Avg
wx_vappress24	climavue50_24hr.VP_mbar_Avg
wx_vp15	gcrew_met_15min.VP
wx_winddir_sd115	climavue50_15min.WindDir_SD1_WVT
wx_winddir15	climavue50_15min.WindDir_D1_WVT, gcrew_met_15min.WindDir_RM_Avg
wx_winderrors24	climavue50_24hr.WS_ms_S_WVT
wx_windspeed15	climavue50_15min.WS_ms_S_WVT, gcrew_met_15min.WS_ms_RM_Avg

Code

lv_to_rn <- aggregate(Site ~ lv_clean + research_name, data = dt_ex, FUN = function(x) length(unique(x)))

lv_to_site <- aggregate(research_name ~ Site + tb_clean + lv_clean, data = dt_ex, FUN = length)
for(tb in unique(lv_to_site$tb_clean)) {
    x <- lv_to_site[lv_to_site$tb_clean == tb,]
    p <- ggplot(x, aes(Site, lv_clean, size = research_name)) +
        geom_point(na.rm = TRUE) +
        ggtitle(tb)
    print(p)
}

Reproducibility

Code

sessionInfo()

R version 4.4.2 (2024-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.7.4

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ggplot2_3.5.1    testthat_3.2.1.1 readr_2.1.5      tidyr_1.3.1     
[5] lubridate_1.9.3 

loaded via a namespace (and not attached):
 [1] bit_4.0.5         gtable_0.3.5      jsonlite_1.8.8    crayon_1.5.2     
 [5] dplyr_1.1.4       compiler_4.4.2    brio_1.1.5        tidyselect_1.2.1 
 [9] parallel_4.4.2    scales_1.3.0      yaml_2.3.8        fastmap_1.2.0    
[13] R6_2.5.1          labeling_0.4.3    generics_0.1.3    knitr_1.46       
[17] htmlwidgets_1.6.4 tibble_3.2.1      desc_1.4.3        munsell_0.5.1    
[21] rprojroot_2.0.4   pillar_1.9.0      tzdb_0.4.0        rlang_1.1.3      
[25] utf8_1.2.4        xfun_0.44         bit64_4.0.5       pkgload_1.3.4    
[29] timechange_0.3.0  cli_3.6.2         withr_3.0.0       magrittr_2.0.3   
[33] grid_4.4.2        digest_0.6.35     vroom_1.6.5       rstudioapi_0.16.0
[37] hms_1.1.3         lifecycle_1.0.4   waldo_0.5.2       vctrs_0.6.5      
[41] evaluate_0.23     glue_1.7.0        farver_2.1.2      colorspace_2.1-0 
[45] fansi_1.0.6       rmarkdown_2.27    purrr_1.0.2       tools_4.4.2      
[49] pkgconfig_2.0.3   htmltools_0.5.8.1