Merge branch 'dev' of https://github.com/Big-Life-Lab/covid-19-wastew…

…ater into dev

README.md

@@ -28,6 +28,8 @@ See [license](LICENSE) for more information.
 
 **v1.1.0**
 
+Addresses issues: #59, #84, #90, #92, #93, #96, #97, #99, #102, #103, #104, #113, #114, #116.
+
 - **Variable name changes (breaking changes :bangbang:)**
 
   - `extractionVolMl`: Change from `sampleSizeL`. Description of the variable was also changed.
@@ -38,21 +40,27 @@ See [license](LICENSE) for more information.
   - `sampleStorageTempCDefault`: Change from `SampleStorageTempCDefault`.
   - `measureFractionAnalyzedDefault`: Change from `MeasureFractionAnalyzedDefault`.
 
-
 - **New variables**
 
 - Reporter
+
   - `organization`: Organization of reporter. Issue [#97](https://github.com/Big-Life-Lab/covid-19-wastewater/issues/97)
 
 - Sample
+
   - `reporterID`: Reporter ID. Currently, reporterID is `WWmeasure` table but reporter for samples can be different. Issue [#93](https://github.com/Big-Life-Lab/covid-19-wastewater/issues/93)
-  - `index`: Index number in case the sample was taken multiple times. Issue [#103](https://github.com/Big-Life-Lab/covid-19-wastewater/issues/103) 
-  - `InstrumentID`: Links with the Instrument table to describe the instrument used for sampling. Issue [#104](https://github.com/Big-Life-Lab/covid-19-wastewater/issues/104) 
+  - `index`: Index number in case the sample was taken multiple times. Issue [#103](https://github.com/Big-Life-Lab/covid-19-wastewater/issues/103)
+  - `InstrumentID`: Links with the Instrument table to describe the instrument used for sampling. Issue [#104](https://github.com/Big-Life-Lab/covid-19-wastewater/issues/104)
+
+- Site
+
+  - `publicHealthDepartment`: Public health department or region. The public health department or region where the site or institute is located. See also `healthRegion` if there is a separate regional health care delivery authority. Issue [#116](https://github.com/Big-Life-Lab/covid-19-wastewater/issues/116)
+  - `healthRegion`: Health planning region. The health planning authority where is site or insititute is located. See also `publicHealthDepartment`. Issue [#116](https://github.com/Big-Life-Lab/covid-19-wastewater/issues/116)
 
 - SiteMeasure
-  - `SampleID`: Makes sure that samples can easily be linked back to the site measurements, without the need for comparing dates. In case that multiple samples need to be linked to the same site measurement, create a comma separated list of sample IDs. 
-
+  - `SampleID`: Makes sure that samples can easily be linked back to the site measurements, without the need for comparing dates. In case that multiple samples need to be linked to the same site measurement, create a comma separated list of sample IDs.
 - **Deleted variable categories (breaking changes :bangbang:)**
+
   - `SiteMeasure` table, `aggregation` variable, all of the options that included normalization
     - `sdNr`,"Standard deviation, normalized",L'�cart type normalis�
     - `geoMnNr`,"Geometric mean, normalized",Moyenne g�om�trique normalis�e.
@@ -68,7 +76,7 @@ See [license](LICENSE) for more information.
 
   - Updated description of `WWMeasure` table, `unit` measure. These descriptions now reference gene or variant copies.
   - New `detected`: Gene copies or variant detected in the sampleGene or variant copies. Detected = 1. Gene or variant copiesNot detected = 0.
-  - New `porpVar`: Proportion of variant in sample.
+  - New `propVar`: Proportion of variant in sample.
   - `SiteMeasure` table, `type` variable
     - `wwBOD5c`, 5 day biochemical oxygen demand
     - `wwPtot`, Total phosphates
@@ -77,23 +85,22 @@ See [license](LICENSE) for more information.
 
     - `°C`, Degrees Celcius
     - `mm`, Millimeters
-    - `m3/h`, Cubic meters an hour
-    - `m3/d`, Cubic meters a day
+    - `m3/h`, Cubic meters per hour
+    - `m3/d`, Cubic meters per day
     - `mg/L`, Milligrams per liter
     - `pH`, pH units
     - `uS/cm`, Micro-siemens per centimeter
-
-
+
 - **Migrate .md files for tables**
-  
+
   - Variable and variable categories to CSV files. Please modify the appropriate CSV file for future updates. `metadata.md` is now automatically generated from the CSV files.
 
     - `Tables.csv`: list of tables.
     - `Variables.csv`: list of variables.
     - `VariableCategories`: list of categories for variables.
 
 - **Other**
-  - Missing values for the `value` field in the different tables should be reported using the following notation 'NA', and ideally follow with a note that explains why the value is missing. An example: Every day a daily average flow measurement is generated, yet because of fouling the instrument stopped functioning for one day which makes that this data is missing. 
+  - Missing values for the `value` field in the different tables should be reported using the following notation 'NA', and ideally follow with a note that explains why the value is missing. An example: Every day a daily average flow measurement is generated, yet because of fouling the instrument stopped functioning for one day which makes that this data is missing.
   - SQL template updated to reflect v1.1.0 (and also v1.0.0). These files are now automatically generated from the metadata tables (above). The SQL tables are in SQLite format.
   - Several small grammatical errors corrected in the English variable descriptions.
 

site/VariableCategory.csv

@@ -59,7 +59,7 @@ WWMeasure,unit,c,temperature in celsius,temp�ratures en degr�s Celsius
 WWMeasure,unit,bool,In cases where a boolean yes or no is required use bool,"Dans les cas o� un oui ou un non bool�en est requis, utilisez bool"
 WWMeasure,unit,other,Other measurement of viral copies or wastewater treatment plant parameter. Add description to UnitOther.,"Autre mesure de copies virales ou de qualit� des eaux us�es. Ajouter une description dans ""unitOther"""
 WWMeasure,aggregation,single,"This value is not an aggregate measurement in any way (ie. not a mean, median, max or any other) and can be a replicate value.","La valeur n'a subi aucune agr�gation (donc, la valeur n'est pas une moyenne, un maximum, etc.). La valeur peut �tre un r�plica."
-WWMeasure,aggregation,mean, Arithmetic mean,Moyenne arithm�tique.
+WWMeasure,aggregation,mean," Arithmetic mean",Moyenne arithm�tique.
 WWMeasure,aggregation,meanNr,"Arithmetic mean, normalized",Moyenne arithm�tique normalis�e.
 WWMeasure,aggregation,geoMn,Geometric mean,Moyenne g�om�trique.
 WWMeasure,aggregation,geoMnNr,"Geometric mean, normalized",Moyenne g�om�trique normalis�e.
@@ -96,7 +96,7 @@ Site,SampleTypeDefault,swrSed,Sediments obtained in sewer.,S�diments provenant
 Site,SampleTypeDefault,pstGrit,Raw wastewater after a treatment plant's headworks.,Eau us�e apr�s d�grillage et dessablage.
 Site,SampleTypeDefault,pSludge,Sludge produced by primary clarifiers.,Boue provenant d'un d�canteur primaire.
 Site,SampleTypeDefault,pEfflu,Effluent obtained after primary clarifiers.,Effluent obtenu apr�s un d�canteur primaire.
-Site,SampleTypeDefault,sSludge, Sludge produced by secondary clarifiers.,Boue provenant d'un d�canteur secondaire.
+Site,SampleTypeDefault,sSludge," Sludge produced by secondary clarifiers.",Boue provenant d'un d�canteur secondaire.
 Site,SampleTypeDefault,sEfflu,Effluent obtained after secondary clarifiers.,Effluent obtenu apr�s un d�canteur secondaire.
 Site,SampleTypeDefault,water,"Non-wastewater, coming from any kind of water body.",Eau non-us�e provenant de toute �tendue d'eau.
 Site,SampleTypeDefault,faeces,Fecal matter.,Mati�re f�cale.
@@ -140,7 +140,7 @@ AssayMethod,unit,gcGms,Gene copies per gram solids.,Copies de g�ne ou de varia
 AssayMethod,unit,gcL,Gene copies per liter.,Copies de g�ne ou de variant par litre.
 AssayMethod,unit,gcCrA,Gene copies per copy of crAssphage.,Copies de g�ne ou de variant par copie de CrAssphage
 AssayMethod,unit,other,Other measurement of viral copies. Add description to unitOther.,"Autre mesure de copies virales ou de qualit� des eaux us�es. Ajouter une description dans ""unitOther"""
-Instrument,type,online, An online sensor,Capteur en ligne.
+Instrument,type,online," An online sensor",Capteur en ligne.
 Instrument,type,lab,Offline laboratory analysis,Analyse en laboratoire.
 Instrument,type,hand,A handheld measurement analyzer.,Mesure � l'aide d'un capteur manuel.
 Instrument,type,atline,An atline analyzer with sampler.,Mesure � l'aide d'un �chantillonneur.
@@ -154,7 +154,7 @@ CovidPublicHealthData,type,posTest,Number of positive tests.,Nombre de tests pos
 CovidPublicHealthData,type,pPosRt,Percent positivity rate.,Pourcentage de positivit� des tests.
 CovidPublicHealthData,type,hospCen,Hospital census or the number of people admitted with covid-19.,Rencensement des patients admis � un h�pital avec la COVID-19.
 CovidPublicHealthData,type,hospAdm,Hospital admissions or patients newly admitted to hospital.,Nombre d'admissions ou nombre de patients admis � l'h�pital.
-CovidPublicHealthData,dateType,episode ,"Episode date is the earliest of onset, test or reported date.","Date estim�e � laquelle l'�pisode de maladie s'est d�clar�. Habituellement calcul� en se basant sur la date des premiers sympt�mes, la date de test ou la date de reportage. "
+CovidPublicHealthData,dateType,"episode ","Episode date is the earliest of onset, test or reported date.","Date estim�e � laquelle l'�pisode de maladie s'est d�clar�. Habituellement calcul� en se basant sur la date des premiers sympt�mes, la date de test ou la date de reportage. "
 CovidPublicHealthData,dateType,onset,"Earliest that symptoms were reported for this case. This data is often not known and reported. In lieu, episode is used.",Date � laquelle les premiers sympt�mes apparaissent. Cette donn�e est souvent inconnue. La date d'�pisode est alors commun�ment utilis�e.
 CovidPublicHealthData,dateType,report,"Date that the numbers were reported publicly. Typically, reported data and this measure is most commonly reported and used.",Date � laquelle la donn�e a �t� report�e � la sant� publique. Cette mesure est commun�ment utilis�e.
-CovidPublicHealthData,dateType,test,Date that the covid-19 test was performed.,Date � laquelle le test de COVID-19 a �t� effectu�.
+CovidPublicHealthData,dateType,test,Date that the covid-19 test was performed.,Date � laquelle le test de COVID-19 a �t� effectu�.