diff --git a/book_source/03_topical_pages/02_pecan_standards.Rmd b/book_source/03_topical_pages/02_pecan_standards.Rmd index 819f8df8fd5..e0146f18b8d 100644 --- a/book_source/03_topical_pages/02_pecan_standards.Rmd +++ b/book_source/03_topical_pages/02_pecan_standards.Rmd @@ -30,9 +30,9 @@ General Note: dates in the database should be date-time (preferably with timezon ```{r, echo=FALSE,warning=FALSE,message=FALSE} names<-c("air_temperature", "air_temperature_max", "air_temperature_min", "air_pressure", "mole_fraction_of_carbon_dioxide_in_air", "moisture_content_of_soil_layer", "soil_temperature ", - "relative_humidity", "specific_humidity", "water_vapor_saturation_deficit","surface_downwelling_longwave_flux_in_air", + "relative_humidity", "specific_humidity", "water_vapor_saturation_deficit", "surface_downwelling_longwave_flux_in_air", "surface_downwelling_shortwave_flux_in_air", "surface_downwelling_photosynthetic_photon_flux_in_air", - "precipitation_flux", " ","wind_speed","eastward_wind", "northward_wind") + "precipitation_flux", " ", "wind_speed", "eastward_wind", "northward_wind") units <-c("K","K","K","Pa","mol/mol","kg m-2","K","%","1","Pa","W m-2","W m-2","mol m-2 s-1", "kg m-2 s-1", "degrees", "m/s", "m/s", "m/s") @@ -45,7 +45,7 @@ narr <- c("air","tmax","tmin","","","","","rhum","shum","","dlwrf","dswrf","","a ameriflux <- c("TA(C)","" ,"" , "PRESS (KPa)","CO2","","TS1(NOT DONE)", "RH","CALC(RH)","VPD(NOT DONE)","Rgl","Rg","PAR(NOT DONE)","PREC","WD","WS","CALC(WS+WD)","CALC(WS+WD)") -in_tab<-cbind(names,units,bety,isimip,cruncep,narr,ameriflux) +in_tab <- cbind(names, units, bety, isimip, cruncep, narr, ameriflux) colnames(in_tab)<- c("CF standard-name","units","BETY","Isimip","CRUNCEP","NARR", "Ameriflux") if (require("DT")){ datatable(in_tab, extensions = c('FixedColumns',"Buttons"), @@ -53,10 +53,10 @@ datatable(in_tab, extensions = c('FixedColumns',"Buttons"), dom = 'Bfrtip', scrollX = TRUE, fixedColumns = TRUE, - buttons = c('copy', 'csv', 'excel', 'pdf', 'print') - - ) + buttons = c('copy', 'csv', 'excel', 'pdf', 'print'), + escape = FALSE ) + ) } ``` @@ -66,8 +66,7 @@ datatable(in_tab, extensions = c('FixedColumns',"Buttons"), * standard_name is CF-convention standard names * units can be converted by udunits, so these can vary (e.g. the time denominator may change with time frequency of inputs) * soil moisture for the full column, rather than a layer, is soil_moisture_content -* A full list of PEcAn standard variable names, units and dimensions can be found here: https://github.com/PecanProject/pecan/blob/develop/base/utils/data/standard_vars.csv - +* The list of PEcAn standard variable names, units and dimensions are provided in a table in the [Output Standards]{#OutputStandards} section and maintained in the file: [base/utils/data/standard_vars.csv](https://github.com/PecanProject/pecan/blob/develop/base/utils/data/standard_vars.csv). For example, in the [MsTMIP-CRUNCEP](https://www.betydb.org/inputs/280) data, the variable `rain` should be `precipitation_rate`. We want to standardize the units as well as part of the `met2CF.` step. I believe we want to use the CF "canonical" units but retain the MsTMIP units any time CF is ambiguous about the units. @@ -78,15 +77,13 @@ The key is to process each type of met data (site, reanalysis, forecast, climate ##### Soil Data -Check out the [Soil Data] section on more into on creating a standard soil data file. +See the [Soil Data] section on more into on creating a standard soil data file. ##### Vegetation Data -Check Out the [Vegetation Data] section on more info on creating a standard vegetation data file - - +See the [Vegetation Data] section on more info on creating a standard vegetation data file -### Output Standards +### Output Standards {#OutputStandards} * created by `model2netcdf` functions * based on format used by [MsTMIP](http://nacp.ornl.gov/MsTMIP_variables.shtml)