11library(DBI )
2+ # library(tidyverse)
23
3- library(tictoc )
4- library(tidyverse )
5-
6- # rm(list = ls())
7- connection_sql = TRUE
8-
9-
10- # connection to the data base
11- if (connection_sql )
12- # conn_eurodiad <- dbConnect(RPostgres::Postgres(), dbname = 'eurodiad',
13- # host = 'citerne.bordeaux.irstea.priv',
14- # port = 5432,
15- # user = 'patrick.lambert',
16- # password = rstudioapi::askForPassword("Database password"))
17- conn_eurodiad <- connect()
4+ pkgload :: load_all(here :: here()) # simulate installation and give access to objects in the package
5+ # session <- shiny::MockShinySession$new() #new.env()
6+ # connect(session)
7+ # con <- get_con(session)
8+ # connection to the data base
9+ conn_eurodiad <- connect()
1810
1911# data upload ----
2012
2113# ---------------------------------------------------------------------- #
2214# # Catchment features ----
23- if (connection_sql ) {
24- data_catchment <- dbGetQuery(conn_eurodiad , " SELECT basin_id, basin_name, country, surface_area_drainage_basin as surface_area, ccm_area FROM diadesatlas.basin b
25- INNER JOIN diadesatlas.basin_outlet bo USING (basin_id);" ) %> %
15+ data_catchment <- dbGetQuery(conn_eurodiad ,
16+ " SELECT
17+ basin_id,
18+ basin_name,
19+ country,
20+ surface_area_drainage_basin as surface_area,
21+ ccm_area
22+ FROM
23+ diadesatlas.basin b
24+ INNER JOIN
25+ diadesatlas.basin_outlet bo
26+ USING (basin_id);" ) %> %
2627 tibble()
27-
28-
29- # write_rds(data_catchment, './data_input/data_catchment.rds')
30- } else {
31- data_catchment <- read_rds(' ./data_input/data_catchment.rds'
32- }
28+
3329# ---------------------------------------------------------------------- #
3430# # Distances between catchment ----
35- if ( connection_sql ) {
36- outlet_distance = dbGetQuery( conn_eurodiad , " SELECT
31+ outlet_distance = dbGetQuery( conn_eurodiad ,
32+ " SELECT
3733 b.basin_name AS departure,
3834 od.departure AS departure_id,
3935 b2.basin_name AS arrival,
@@ -48,37 +44,54 @@ INNER JOIN diadesatlas.basin b2 ON
4844ORDER BY departure, distance ;" ) %> %
4945 tibble()
5046
51- # write_rds(outlet_distance, "./data_input/outletDistance.rds")
52- } else {
53- outlet_distance <- read_rds( " ./data_input/outletDistance.rds"
54- }
5547
5648# ---------------------------------------------------------------------- #
5749# HyDiaD parameters ----
58- if (connection_sql ) {
59- hydiad_parameter <- dbGetQuery(conn_eurodiad , "
60- SELECT s.latin_name, s.local_name AS \" Lname\" , h.* FROM diadesatlas.hydiadparameter h
61- INNER JOIN diadesatlas.species s USING (species_id);" ) %> %
50+ hydiad_parameter <-
51+ dbGetQuery(conn_eurodiad ,
52+ " SELECT
53+ s.latin_name,
54+ s.local_name AS \" Lname\" ,
55+ h.*
56+ FROM
57+ diadesatlas.hydiadparameter h
58+ INNER JOIN
59+ diadesatlas.species s
60+ USING (species_id);" ) %> %
6261 tibble()
63-
64- # hydiad_parameter %>% write_rds("./data_input/HyDiaDParameter.rds")
6562
66- } else {
67- hydiad_parameter <- read_rds(" ./data_input/HyDiaDParameter.rds"
68- }
6963
7064
7165# ---------------------------------------------------------------------- #
7266# # HSI abd Nmax ----
73- if (connection_sql ) {
74- # a query to load HSI for only 8.5 scenario (which do not change between simulations)
75- query = " SELECT s.latin_name, basin_id, basin_name, country, surface_area_drainage_basin as surface_area, year, climatic_scenario, climatic_model_code, hsi FROM diadesatlas.hybrid_model_result hmr
76- INNER JOIN diadesatlas.species s USING (species_id)
77- INNER JOIN diadesatlas.basin b USING (basin_id)
78- INNER JOIN diadesatlas.climatic_model cm USING (climatic_model_id)
79- WHERE year > 0 AND climatic_scenario = 'rcp85'"
80-
81- data_hsi_nmax <- dbGetQuery(conn_eurodiad , query ) %> %
67+ # a query to load HSI for only 8.5 scenario (which do not change between simulations)
68+ query =
69+ " SELECT
70+ s.latin_name,
71+ basin_id,
72+ basin_name,
73+ country,
74+ surface_area_drainage_basin as surface_area,
75+ year,
76+ climatic_scenario,
77+ climatic_model_code,
78+ hsi
79+ FROM
80+ diadesatlas.hybrid_model_result hmr
81+ INNER JOIN
82+ diadesatlas.species s
83+ USING (species_id)
84+ INNER JOIN
85+ diadesatlas.basin b
86+ USING (basin_id)
87+ INNER JOIN
88+ diadesatlas.climatic_model cm
89+ USING (climatic_model_id)
90+ WHERE
91+ year > 0
92+ AND climatic_scenario = 'rcp85'"
93+
94+ data_hsi_nmax <- dbGetQuery(conn_eurodiad , query ) %> %
8295 tibble() %> %
8396 # compute the maximum abundance (#) according to hsi,
8497 # maximal density (Dmax) , catchment area (ccm_area)
@@ -88,53 +101,75 @@ WHERE year > 0 AND climatic_scenario = 'rcp85'"
88101 mutate(Nmax = hsi * Dmax * surface_area ) %> %
89102 select(- c(surface_area , Dmax ))
90103
91- # write_rds(data_hsi_nmax, './data_input/data_hsi_Nmax.rds')
92-
93- rm(query )
94- } else {
95- data_hsi_nmax <- read_rds(' ./data_input/data_hsi_Nmax.rds'
96- }
104+ rm(query )
97105
98106
99107# No ccm_area for Bou_Regreg, Loukkos, Oum_er_Rbia, Sebou. use surface_area_drainage_basin
100108
101109# reference results
102- if (connection_sql ) {
103- reference_results <- dbGetQuery(conn_eurodiad ,
104- " SELECT s.latin_name, basin_id, basin_name, year, climatic_scenario, climatic_model_code, nit FROM diadesatlas.hybrid_model_result hmr
105- INNER JOIN diadesatlas.species s USING (species_id)
106- INNER JOIN diadesatlas.basin b USING (basin_id)
107- INNER JOIN diadesatlas.climatic_model cm USING (climatic_model_id)
108- WHERE year > 0 AND climatic_scenario = 'rcp85'
109- ORDER BY latin_name, basin_id, climatic_model_code" ) %> %
110+ reference_results <- dbGetQuery(conn_eurodiad ,
111+ " SELECT
112+ s.latin_name,
113+ basin_id,
114+ basin_name,
115+ year,
116+ climatic_scenario,
117+ climatic_model_code,
118+ nit
119+ FROM
120+ diadesatlas.hybrid_model_result hmr
121+ INNER JOIN
122+ diadesatlas.species s
123+ USING (species_id)
124+ INNER JOIN
125+ diadesatlas.basin b
126+ USING (basin_id)
127+ INNER JOIN
128+ diadesatlas.climatic_model cm
129+ USING (climatic_model_id)
130+ WHERE
131+ year > 0 AND
132+ climatic_scenario = 'rcp85'
133+ ORDER BY
134+ latin_name,
135+ basin_id,
136+ climatic_model_code" ) %> %
110137 tibble()
111138
112- # write_rds(reference_results, './data_input/referenceResults.rds')
113- } else {
114- reference_results <- read_rds(' ./data_input/referenceResults.rds'
115- }
116-
117-
118139# # initial abundance in catchments ----
119- if (connection_sql ) {
120- data_ni0 <- dbGetQuery(conn_eurodiad , " SELECT s.latin_name, basin_id, basin_name, surface_area_drainage_basin as surface_area, year, climatic_scenario, climatic_model_code, nit, hsi FROM diadesatlas.hybrid_model_result hmr
121- INNER JOIN diadesatlas.species s USING (species_id)
122- INNER JOIN diadesatlas.basin b USING (basin_id)
123- INNER JOIN diadesatlas.climatic_model cm USING (climatic_model_id)
124- WHERE climatic_scenario = 'rcp85'
125- AND year = 0
126- ORDER BY latin_name, basin_id, climatic_model_code" ) %> %
140+ data_ni0 <-
141+ dbGetQuery(conn_eurodiad ,
142+ " SELECT
143+ s.latin_name,
144+ basin_id,
145+ basin_name,
146+ surface_area_drainage_basin as surface_area,
147+ year,
148+ climatic_scenario,
149+ climatic_model_code,
150+ nit,
151+ hsi
152+ FROM
153+ diadesatlas.hybrid_model_result hmr
154+ INNER JOIN
155+ diadesatlas.species s
156+ USING (species_id)
157+ INNER JOIN
158+ diadesatlas.basin b
159+ USING (basin_id)
160+ INNER JOIN
161+ diadesatlas.climatic_model cm
162+ USING (climatic_model_id)
163+ WHERE
164+ climatic_scenario = 'rcp85'
165+ AND year = 0
166+ ORDER BY
167+ latin_name,
168+ basin_id,
169+ climatic_model_code" ) %> %
127170 tibble() %> %
128171 inner_join(hydiad_parameter %> %
129172 select(latin_name , Dmax ),
130173 by = ' latin_name' > %
131174 mutate(Nmax = hsi * Dmax * surface_area ) %> %
132175 select(- c(surface_area , Dmax ))
133-
134- # write_rds(data_ni0, './data_input/data_ni0.rds')
135- } else {
136- data_ni0 <- read_rds(' ./data_input/data_ni0.rds'
137- }
138-
139- #
140-
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