htsr-package

knitr::opts_chunk$set(
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HydroSciences Laboratory (IRD, CNRS, Univ. Montpellier), France

v1.1.4 - April 17, 2022

Content

Origin

Brief history

IRD and previously ORSTOM have developed quite early (in the 70ties) data bases for storing hydrological and meteorological time-series. During the 80ties the managing tools use home-made codes (Hydrom and Pluviom), which were in the late 90ties adapted with commercial applications like Microsoft Access or Oracle and more recently for web interface.

With the development of open access platforms and applications, in the one hand, and the need of more flexibility, in the other hand, it appears useful to build a set of functions able to manage hydro-meteo time-series independently of the operating system and of proprietary tools.

The htsr package was developed on the basis of the public domain data base management system Sqlite and on the hydro-meteo time-series data base application Hydraccess.

It works on Linux, Windows or MacOS platforms, with the free programming language R and the interface RStudio preliminary installed.

Hydraccess

Hydraccess was developed at IRD (https://www.ird.fr) by Philippe Vauchel. It is based on several tools provided by Microsoft Office (R) including Microsoft Access. It can be obtained from https://hybam.obs-mip.fr/fr/hydraccess-2/

Hydracces is available in French, English, Spanish, Portuguese and Russian.

Sqlite data base

Sqlite is an embedded data base on the public domain (https://en.wikipedia.org/wiki/SQLite). It is self-contained, and serverless, without preliminary configuration. It can be installed using the instructions given by https://sqlite.org/download.html. It can be used directly through many dedicated applications available for a large set of operating systems.

Principle

The Sqlite data base is organized with the same tables and fields as the Hydraccess structure, except that the table names are changed for practical reasons. A correspondence of these names in given in appendix.

In Hydraccess, two families or time-series coexist: "hydro data" (Type_Station = H) and "weather data" (Type_Station = M). The first one includes the main tables Cotes/WL, Debits/DI and Qualite/QU; the second one includes Pluies/PR and Meteo/WE. Other tables regarding discharge measurements or calibration are also affected to the "hydro data" family.

This distinction does not exist anymore in the Sqlite data base processes. That means that one should verify if no stations have the same name in the one and the other family. If it is the case the name must be changed before converting a Hydraccess data base in a Sqlite data base.

A time-series is always attached to a station, which describes its location and managing infos, and to a sensor, which is attached to the data type and to the used device. Both are indexed with a main id.

In Hydraccess:

In brief, that means that a time-series record must have 4 objects:

Practically it associates the two tables "station" and "sensor" with one of the five following: "water level", "discharge", "weather", "precipitation" or "quality".

The other associated tables can be used for intermediary calculations, like the computation of the discharge from the water level, or for more detailed information.

Dependencies

The following packages and their own dependencies are needed to apply the htsr package.

System library

User library

Special case of RODBC

Because Hydraccess is only configured for Microsoft Windows, the associated data bases work only on this platform. That means that the operation, which consists to convert a Hydraccess data base into a Sqlite data base must be done in this environment. The RODBC package is associated to the htsr package, but it can be only used in the Windows platform through the function d_convert_hydraccess. In particular, this function does not work on Linux.

Because a Hydraccess data base is proprietary depending, a preliminary configuration of the MS-Windows platform must be done:

File formats

Sqlite data base

Time-series

> tstab
   Date                Value Station Sensor
   <dttm>              <dbl> <fct>   <fct> 
 1 2015-10-03 12:00:00  2.17 CKS2500 IQ  

Gaps

> ze
# A tibble: 14 x 3
   date                valeur stacapt
   <dttm>               <dbl> <chr>  
 1 2015-10-03 17:00:00      1 _      
 2 2015-12-11 23:30:00      1 _ 
 ```

# Functions

6 categories of functions are provided by the htsr package, with, in addition, one short-cut
function. They are distinguished with a prefix character and listed below.

Infos on their uses are detailed in the on-line help or using in the console the command `?<FUNCTION_NAME>` or `help(<FUNCTION_NAME>)`.

## Short-cut function

* `fc(file)`, shortcut for file.choose(file), which is very frequently needed.

## Data base functions (prefix `d_` or `ds_`)

### Data base tools
* `d_backup(fsq)`, backups a htsr sqlite data base.

* `d_compact(bd.sqlite)`, compacts a htsr sqlite data base

* `d_create(fsq, cr_table = TRUE, bku = TRUE)`, creates a htsr sqlite data base

* `d_inventory(fsq, stalist = NA, form.out = NA)` or `ds_inventory(fsq)`, makes the inventory of a htsr sqlite data base. The second is a Shiny interface of `d_inventory`

* `d_sensor(fsq, op = "C", sta, sen, table = NA, name_fld = NA, value_fld = NA, bku = TRUE)`, or `ds_station(fsq)`, creates, modifies or removes a sensor. The second is a Shiny interface of 
`d_sensor`

* `d_station(fsq, op = "C", sta = NA, name_st = NA, name_fld = NA, value_fld = NA, bku = TRUE)`, or `ds_station(fsq)`, creates, modifies or removes a station. The second is a Shiny interface of 
`d_station`

* `d_table(fsq, table, op = "C", bku = TRUE)` creates or removes a table

### Data import/export

* `d_exp_discalib(fsq, sta, calib=TRUE, dism=TRUE)`, exports discharge measurements and calibrations from data base

* `d_exp_hts(fsq, sta, sen, rtime = FALSE, dstart, dend, rplot = FALSE)` or `ds_exp_hts(fsq)`, extract hts files from a sqlite data base. The second is a shiny interface of `d_exp_hts`

* `d_imp_hts(fsq, file, table, bku = TRUE)`, imports a hts file into a data base

* `d_rem_hts(fsq, table, sta, sen, start = NA, end = NA)`, removes a htsr record from a data base

* `d_wind(fsq, sta = NA, swd = NA, swv = NA)`, creates a wind table

### Conversion

* `d_convert_hydraccess(fsq, db.hydraccess)`,  converts a full Hydraccess database into a new htsr sqlite database. **NB:** Only works in Windows environment with a 32b R session.

* `d_convert_weewx(fsq, db.weewx, sta, name_st, tzo = "CET", bku = TRUE)`, converts a weewx data base (<http://weewx.com/>) into a htsr sqlite base


## File functions (prefix `f_`)

* `f_change_id(file, sta, sen, overwrite)`, changes station id or sensor id in a hts file.. Generates a file with the prefix `nw_`.

* `f_convert(file, form_start = "hts", form_end = "xlsx", ta = NA, sen = NA, output = NA, variable = NA)`, converts data-series file in another format: `hts`, `xls/xlsx`, `csv`) and viceversa.

* `f_csv_multivar(files, daily = TRUE, fileo = "fileo")`, build a multivariable table file in csv format.

* `f_properties(file, gaps = FALSE)` displays the properties of a hts time-series.

## Hydro-meteo time-series (prefix `h_` or `hs_`)

### Data manipulations

* `h_common(files)`, extracts 2 (or more) time-series on their common period. Generates a file with the prefix `co_`.

* `h_condition(files, condition)`, conditionally extracts a time-series regarding another one. Generates a file with the prefix `cd_`.

* `h_cumul(file, start = NA, end = NA)`, cumulates the values of a time-series. Generates a file with the prefix `cu_`.

* `h_nodata(file, threshold=NA, test="=", start=NA, end=NA)`, replaces values with NA conditionally or in a time interval. Generates a file with the prefix `na_`.

* `h_rbind(files, sensor, gap = TRUE)`, binds 2 time-series on consecutive periods

* `h_replace(file, old.val, new.val)`, replaces a value by another. Generates a file with the prefix `re_`.

* `h_rollav (file, ti = 7, position = c("central", "right"))`, computes a rolling average of a daily time-series. Generates a file with the prefix `ro_`.

* `h_substitute(files)`, substitutes the missing values in a series by existing values of another series. Generates a file with the prefix `su_`.

* `h_weightedsum(files, weights = NA, constant = 0)`, makes a weighted sum of time-series. Generates a file with the prefix `ws_`.

### Data critics

* `h_gaperr(file, nv = 1, itv0 = 43201, df)`, replaces errors with gaps in a time-series based on neighboring values. Generates a file with the prefix `eg_`.

* `h_gapfill(file, npdt)`, produces a simple gapfilling in a time-series. Generates a file with the prefix `gf_`.

* `h_gaprem_itv(file, itv0 = 43201)`, removes gaps in a time-series with a time interval threshold. Generates a file with the prefix `gr_`.

### Time treatments

* `hs_step(file)`, combines in a shiny environment both functions `h_timestep()` and `h_month()`  

* `h_timestep(file, tst, op = "M")`, computes infra-daily data with a fixed time step. Generates a file with the suffix `_xxxx`, where xxxx is the `tst` value.

* `h_month(file, op="M", ba=NA, rmna=FALSE, climedit=FALSE, caledit_j=FALSE, caledit_m=FALSE, gapfill=FALSE)`, makes monthly operations, based on a daily time-series.  Generates hts files with the suffixes `_C`, `_G` or `_M` and MS Excel files with the prefixes `ad_` and `cm_`.

* `h_restrict(file, start=NA, end=NA)`, restricts a series between 2 dates. Generates hts files with the suffixes `re_`.

* `h_season(file, monthstart)`, produces a seasonal selection. Generates a file with the prefix `sx_`, where x is 2, 3 or 4.


### Hydro-meteo processes

* `h_stat_basic(file)`, gives basic statistics of a time-series

* `h_wl_di(fsq, sta, seni, seno, dstart = NA, dend = NA, dbo = TRUE)`, computes a discharge time-series from water levels data and calibration curves.

* `h_rainsnow(fpr, fta, ta0,ta1,sta=NA)`, shares the solid and liquid precipitations with a temperature criteria. Generates a file with the prefix `pr_`. Generates a file with the prefix `sn_`.

## Plot functions (prefix `p_` or `ps_`)

### General plots

* `ps_plothts(files)`, plots hts files. Shiny interface of `p_line` & `p_bar`

* Bar plotting

  + `p_bar(nbst = nbst, filei, serlab, title, type, rnorm, rtime, start, end, rfixy, y.down = NA, y.up = NA, pal)`

  + `p_bar_app(filename = NA, pset = TRUE, pfil = TRUE, rpal = 0,savefig = FALSE, width = 8, height = 6, fileo = "plot.png"`

* Line / point plotting

  + `p_line(nbst, filei, serlab, title, type, rnorm, rtime, start, end, rfixy, y.down, y.up, pal = pal, linet, rppt, pointt, linew, smooth)`

  + ` p_line_app (filename = NA, pset = TRUE, pfil = TRUE, rpal = 0, smooth = FALSE, savefig = FALSE, width = 8, height = 6, fileo = "plot.png")`

### Other plots

* `p_box_month(file, title = "Title", axeY = "Y-axis", savefig = FALSE, fileo = "plot.png", width = 8, height = 6)`, plots a boxplot of the 12 months of a time-series.

* `p_clim(p_clim <- function (files, type="line", hydro.month=1, title="Title", yaxis="Value", y.down=NA, y.up=NA, rpal=FALSE, pal=mapalette, legend.l=NA))`, plots climatologies in hydrological year.

* `p_discalib(fcalib, sen, plotcalib= TRUE, plotdism=TRUE, title="Title", savefig=FALSE, width= 8, height= 6, fout="plot.png", limx =FALSE, limy = FALSE, xinf=NA, xsup=NA, yinf=NA, ysup=NA)`, plots calibration curves water levels vs discharges.

* `p_gaps(nbf, title = "Inventory", BW = FALSE, margin = 0.1)`, plots of data inventory

* `p_hypso(file, abbrev, prop = FALSE, range=50, fact=5, title="Title", savefig=FALSE, width= 8,height= 6, fileo="plot.png")`, plots the hypsometry curve of one or more basins


* `p_scatter(files, intercept.zero = FALSE, remove.zero = FALSE, lg.axis = c(NA, NA),title = "Title")`, plots a scatter plot of 2 or more time-series

* `p_wind(data_wind, ws.int = 0.5, angle = 45, grid.line = 10, type = "default",  breaks = 5, offset = 5, paddle = FALSE)`, plots wind rose

## Weather functions (prefix `w_`)

* `w_atmp_alt (f_atmp, f_temp, alt0 = 0, alt)` computes atmospheric pressure, function of altitude.

* `w_etp (method = c("Turc", "Penman-Monteith", "Priestley-Taylor", "Makkink", "Heargraves-Samani"), freq = c("day", "month"), f_temp, f_relh = NA, f_radg = NA, f_radn = NA, f_atmp = NA, f_wvel = NA, f_tmin = NA, f_tmax = NA, lat = NA, alt = NA, albedo = NA, z = NA)`, computes the potential evapotranspiration with several methods. Generates a file with the prefix `xEtpyy_`, where x is J (daily) or M (monthly), and yy is Tu (Turc), PM (Penman-Monteith), PT (Priestley-Taylor), Ma (Makkink) or HS (Heargraves-Samani).

* `w_temp_alt (file , alt0 = 0, alt, grad = -0.0065)` computes temperature, function of altitude

## Miscellaneous functions (prefix `z_`)

* `z_coord(ncoord = NA, ccoord = NA, type)`, converts coordinate from numeric to character and reverse.

* `z_set (tz = FALSE, mapal = FALSE, confp = FALSE)`, edit settings for time zone and manual palette colors


# Development main references

## SQLite management

* SQLite, sql database engine, 2017, Tutorial Point, <https://www.tutorialspoint.com/sqlite/sqlite_pdf_version.htm>

* Ripley B., ODBC Connectivity, 2020. <https://CRAN.R-project.org/package=RODBC>

* <https://www.sqlite.org/index.html>

## R coding

* Chang W., 2013. R Graphics Cookbook. O'Reilly. 398p. ISBN 978-1-449-31695-2. Actualized on <https://r-graphics.org/>

* Wickham H., 2015. R Packages - Organize, test, document, and share your code. 
O'Reilly. 190p. ISBN 978-1-491-91059-7. Actualized version on <https://r-pkgs.org/>

* Wickham H. & Grolemund G., 2017. R for Data Science - Import, tidy, transform, 
visualize, and model data. O'Reilly. 494p. ISBN 978-1-491-91039-9. <https://r4ds.had.co.nz/>

* <https://www.tidyverse.org/>

# Appendix
## Correspondence of the data base tables between Hydraccess and Sqlite htsr
### Main tables

Designation Hydraccess Sqlite name


Discharge Debits DI
Precipitation Pluies PR
Quality Qualite QU
Sensors Capteurs SS
Station Station_Base ST
Weather Meteo WE
Water level Cotes WL


### Other tables

    Designation              Hydraccess       Sqlite name

       Basin                  Bassins             BA      
 Calibration Date            Etal_Dates           CD      
      Country                Zones_Pays           CO

Disch. measur. proceeding Jaugeages_Dep DP
Discharge measurement Jaugeages DM
Elevation zero Zero_NG EZ
Equipment Equipements EQ
Event Evenements EV
Large basis Bassins_Grands LB
Liquid flow calibration Etal_HQ LC
Manager Gestionnaires MG
Nature id Codes_Nature NC
Operating mode Modes_Opératoires OM
Origine id. Codes_Origine OC
Profile Profils_Data PF
Profile data Profils_Data PD
Propeller Helices PP
Quality id. Codes_Qualite QC
Region Regions RE
River Rivieres RV
Sensor comm. Capteurs_Comm SM
Sensor history Capteurs_HistApp SH
Settings Parametrage SE
Small basin Bassins_Petits SB
Solid flow calibration Etal_HK SC
Station equipment Stations_Equipment SQ
Station file Dossiers_Stations SF
Sub-zone Zone_Sous SZ
Temp_station2 Temp_Stations2 TS
Valve Vannes VA
Zone Zones ZO


```

Fields of the main tables

They correspond to French spelling, which is used in Hydraccess. The compulsory fields are marked with (!).

Stations_Base/ST

Ordre, Type_Station (!), Id_Station (!), Id_Secondaire, Id_Tertiaire, Type_Meteo, Nom, Pays, Zone, SousZone, GrandBassin, Bassin, PetitBassin, Riviere, Gestionnaire, Latitude, Longitude, Altitude, Superficie_bv, Mois_Debut_Hydro, Debut_Activite, Activite, Critere_OuiNon, Critere_Numerique, Critere_Texte, Nom_Observateur, Adresse, Teletransmission, Enregistreur, Fictive, Commentaire, Flag, District, Localite

Capteurs/SS

Type_Station (!), Id_Station (!), Capteur (!), Table (!), Nature, Description, Commentaire, Code_Limni, Principal, Fictif, Maj_Journaliers, Maj_Traduction, Acquisition_Auto, Operationnel, Liste_Inst, Liste_Jour, Liste_Mois, Agregation, Decalage_Temps, Mini, Maxi, Gradient_Maxi, Precision, Decimales, Pente

Cotes/WL, Debits/DI, Meteo/WE, Qualite/QU

Type_Station (!), Id_Station (!), Capteur (!), Table (!), Date (!), Valeur, Origine, Qualite

Pluies/PR

Type_Station (!), Id_Station (!), Capteur (!), Table (!), Date (!), Valeur, Origine, Qualite, Nature



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htsr documentation built on April 17, 2022, 9:05 a.m.