Merge branch 'main' into thierry

DESCRIPTION

 Package: eolpop
 Title: A demographic tool to quantify the impact of fatalities
-Version: 1.1
-Authors@R: 
+Version: 1.5
+Authors: 
     person(given = "Thierry",
            family = "Chambert",
            role = c("aut", "cre"),

inst/FR_EolPop_ANSI/runApp.R

+rm(list = ls(all.names = TRUE))
+setwd( paste0(getwd(),"/inst/FR_eolpop_ANSI/") )
+#setwd("../FR_eolpop_ANSI/")
+getwd()
+
+source("ui.R")
+source("server.R")
+
+shinyApp(ui = ui, server = server)
+

inst/FR_EolPop_UTF8/data_sf.csv

+Species;Species_fr;Species_en;classes_age;survie;fecondite
+Accipiter gentilis;Autour des palombes;Northern Goshawk;A0;0.55;0
+Accipiter gentilis;Autour des palombes;Northern Goshawk;A1;0.65;0.09
+Accipiter gentilis;Autour des palombes;Northern Goshawk;A2;0.78;0.54
+Accipiter nisus;Epervier d'europe ;Eurasian Sparrowhawk;A0;0.4;0
+Accipiter nisus;Epervier d'europe ;Eurasian Sparrowhawk;A1;0.62p;0.9
+Accipiter nisus;Epervier d'europe ;Eurasian Sparrowhawk;A2;0.64;1.23
+Aegypius monachus;Vautour moine;Cinereous Vulture;A0;0.84;0
+Aegypius monachus;Vautour moine;Cinereous Vulture;A1;0.86;0
+Aegypius monachus;Vautour moine;Cinereous Vulture;A2;0.86;0
+Aegypius monachus;Vautour moine;Cinereous Vulture;A3;0.86;0.27
+Aegypius monachus;Vautour moine;Cinereous Vulture;A4;0.86;0.27
+Aegypius monachus;Vautour moine;Cinereous Vulture;A5;0.95;0.28
+Alauda arvensis;Alouette des champs;Eurasian Skylark;A0;0.3;0
+Alauda arvensis;Alouette des champs;Eurasian Skylark;A1;0.66;1.43
+Alectoris rufa;Perdrix rouge;Red-legged partridge;A0;0.17;0
+Alectoris rufa;Perdrix rouge;Red-legged partridge;A1;0.45;2.19p
+Apus Apus;Martinet noir;Common Swift;A0;0.5p;0
+Apus Apus;Martinet noir;Common Swift;A1;0.75p;0.4p
+Apus Apus;Martinet noir;Common Swift;A2;0.77p;0.4p
+Apus Apus;Martinet noir;Common Swift;A3;0.79;0.81
+Aquila chrysaetos;Aigle royal;Golden Eagle;A0;0.71;0
+Aquila chrysaetos;Aigle royal;Golden Eagle;A1;0.85;0
+Aquila chrysaetos;Aigle royal;Golden Eagle;A2;0.85;0
+Aquila chrysaetos;Aigle royal;Golden Eagle;A3;0.85;0.12p
+Aquila chrysaetos;Aigle royal;Golden Eagle;A4;0.87;0.12p
+Aquila chrysaetos;Aigle royal;Golden Eagle;A5;0.9;0.24
+Aquila fasciata;Aigle de Bonelli;Bonelli's Eagle;A0;0.55;0
+Aquila fasciata;Aigle de Bonelli;Bonelli's Eagle;A1;0.62;0
+Aquila fasciata;Aigle de Bonelli;Bonelli's Eagle;A2;0.62;0.19
+Aquila fasciata;Aigle de Bonelli;Bonelli's Eagle;A3;0.84;0.49
+Aquila fasciata;Aigle de Bonelli;Bonelli's Eagle;A4;0.9;0.49
+Asio flammeus;Hibou des marais;short-eared Owl;A0;0.39p;0
+Asio flammeus;Hibou des marais;short-eared Owl;A1;0.58p;1.4p
+Bubo bubo;Grand Duc d'Europe;Eurasian eagle-owl;A0;0.56p;0
+Bubo bubo;Grand Duc d'Europe;Eurasian eagle-owl;A1;0.83p;0.3p
+Bubo bubo;Grand Duc d'Europe;Eurasian eagle-owl;A2;0.85p;0.59
+Burhinus oedicnemus;Oedicnème criard;Eurasian Stone curlew;A0;0.61;0
+Burhinus oedicnemus;Oedicnème criard;Eurasian Stone curlew;A1;0.81p;0
+Burhinus oedicnemus;Oedicnème criard;Eurasian Stone curlew;A2;0.84;0.33
+Buteo buteo;Buse variable;Common Buzzard;A0;0.61;0
+Buteo buteo;Buse variable;Common Buzzard;A1;0.86;0.25
+Buteo buteo;Buse variable;Common Buzzard;A2;0.89;0.25
+Buteo buteo;Buse variable;Common Buzzard;A3;0.85;0.78
+Carduelis cannabina;Linotte mélodieuse;Eurasian Linnet;A0;0.34;0
+Carduelis cannabina;Linotte mélodieuse;Eurasian Linnet;A1;0.41;1.29
+Carduelis carduelis;Chardonneret élégant;European Goldfinch;A0;0.4;0
+Carduelis carduelis;Chardonneret élégant;European Goldfinch;A1;0.45;1.19
+Carduelis chloris;Verdier d'Europe;European Greenfinch;A0;0.38;0
+Carduelis chloris;Verdier d'Europe;European Greenfinch;A1;0.47;1.1
+Ciconia ciconia;Cigogne blanche;White Stork;A0;0.49;0
+Ciconia ciconia;Cigogne blanche;White Stork;A1;0.7;0
+Ciconia ciconia;Cigogne blanche;White Stork;A2;0.7;1.25
+Ciconia ciconia;Cigogne blanche;White Stork;A3;0.69p;1.21p
+Ciconia ciconia;Cigogne blanche;White Stork;A4;0.73;1.18
+Ciconia nigra;Cigogne noire;Black Stork;A0;0.54p;0
+Ciconia nigra;Cigogne noire;Black Stork;A1;0.79p;0
+Ciconia nigra;Cigogne noire;Black Stork;A2;0.82p;0.55p
+Ciconia nigra;Cigogne noire;Black Stork;A3;0.84p;1.1
+Circus aeruginosus;Busard des roseaux;Western Marsh-harrier;A0;0.47p;0
+Circus aeruginosus;Busard des roseaux;Western Marsh-harrier;A1;0.7p;0.54p
+Circus aeruginosus;Busard des roseaux;Western Marsh-harrier;A2;0.72;1.08
+Circus cyaneus;Busard Saint-Martin;Hen Harrier;A0;0.34;0
+Circus cyaneus;Busard Saint-Martin;Hen Harrier;A1;0.56;0.49p
+Circus cyaneus;Busard Saint-Martin;Hen Harrier;A2;0.82;0.99
+Circus pygargus;Busard cendrée;Montagu's Harrier;A0;0.5;0
+Circus pygargus;Busard cendrée;Montagu's Harrier;A1;0.69p;0.49p
+Circus pygargus;Busard cendrée;Montagu's Harrier;A2;0.71;0.97
+Coturnix coturnix;Caille des blés;Common Quail;A0;0.2p;0
+Coturnix coturnix;Caille des blés;Common Quail;A1;0.29;2.28
+Delichon urbica;Hirondelle de fenêtre;Common House Martin;A0;0.24;0
+Delichon urbica;Hirondelle de fenêtre;Common House Martin;A1;0.39;1.43
+Elanus caeruleus;Elanion Blanc;Black-winged Kite;A0;0.47p;0
+Elanus caeruleus;Elanion Blanc;Black-winged Kite;A1;0.7p;0.88
+Emberiza calandra;Bruant proyer;Corn bunting;A0;0.37p;0
+Emberiza calandra;Bruant proyer;Corn bunting;A1;0.54p;1.18p
+Emberiza citrinella;Bruant jaune;Yellowhammer;A0;0.56;0
+Emberiza citrinella;Bruant jaune;Yellowhammer;A1;0.54;1.21
+Erithacus rubecula;Rouge-gorge familier;European Robin;A0;0.3p;0
+Erithacus rubecula;Rouge-gorge familier;European Robin;A1;0.44p;1.41p
+Falco naumanni;Faucon crecerellette;Lesser Kestrel;A0;0.45;0
+Falco naumanni;Faucon crecerellette;Lesser Kestrel;A1;0.7;0.53p
+Falco naumanni;Faucon crecerellette;Lesser Kestrel;A2;0.71;1.06
+Falco peregrinus;Faucon pèlerin;Peregrine Falcon;A0;0.42;0
+Falco peregrinus;Faucon pèlerin;Peregrine Falcon;A1;0.79p;0.44p
+Falco peregrinus;Faucon pèlerin;Peregrine Falcon;A2;0.81;0.88
+Falco tinnunculus;Faucon crecerelle;Common Kestrel;A0;0.33;0
+Falco tinnunculus;Faucon crecerelle;Common Kestrel;A1;0.67p;0.7p
+Falco tinnunculus;Faucon crecerelle;Common Kestrel;A2;0.69;1.41
+Ficedula hypoleuca;Gobemouche noir;European Pied Flycatcher;A0;0.28;0
+Ficedula hypoleuca;Gobemouche noir;European Pied Flycatcher;A1;0.48;0.83p
+Ficedula hypoleuca;Gobemouche noir;European Pied Flycatcher;A2;0.42;1.67
+Grus grus;Grue cendrée;Common Crane;A0;0.49;0
+Grus grus;Grue cendrée;Common Crane;A1;0.81;0
+Grus grus;Grue cendrée;Common Crane;A2;0.81;0
+Grus grus;Grue cendrée;Common Crane;A3;0.81;0
+Grus grus;Grue cendrée;Common Crane;A4;0.9;0.62
+Gypaetus barbatus;Gypaète barbu;Bearded vulture;A0;0.77;0
+Gypaetus barbatus;Gypaète barbu;Bearded vulture;A1;0.81;0
+Gypaetus barbatus;Gypaète barbu;Bearded vulture;A2;0.81;0
+Gypaetus barbatus;Gypaète barbu;Bearded vulture;A3;0.81;0
+Gypaetus barbatus;Gypaète barbu;Bearded vulture;A4;0.9;0
+Gypaetus barbatus;Gypaète barbu;Bearded vulture;A5;0.93;0
+Gypaetus barbatus;Gypaète barbu;Bearded vulture;A6;0.94;0.24
+Gyps fulvus;Vautour fauve;Eurasian Griffon;A0;0.86;0
+Gyps fulvus;Vautour fauve;Eurasian Griffon;A1;0.86;0
+Gyps fulvus;Vautour fauve;Eurasian Griffon;A2;0.89;0
+Gyps fulvus;Vautour fauve;Eurasian Griffon;A3;0.92p;0.2p
+Gyps fulvus;Vautour fauve;Eurasian Griffon;A4;0.98;0.41
+Haliaeetus albicilla;Pygargue à queue blanche;White-tailed Eagle;A0;0.82;0
+Haliaeetus albicilla;Pygargue à queue blanche;White-tailed Eagle;A1;0.82;0
+Haliaeetus albicilla;Pygargue à queue blanche;White-tailed Eagle;A2;0.86;0
+Haliaeetus albicilla;Pygargue à queue blanche;White-tailed Eagle;A3;0.95;0
+Haliaeetus albicilla;Pygargue à queue blanche;White-tailed Eagle;A4;0.8p;0.26p
+Haliaeetus albicilla;Pygargue à queue blanche;White-tailed Eagle;A5;0.85;0.52
+Lanius collurio;Pie-grièche écorcheur;Red-backed Shrike;A0;0.34p;0
+Lanius collurio;Pie-grièche écorcheur;Red-backed Shrike;A1;0.5;1.21p
+Lanius excubitor;Pie-grièche grise ;Grey shrike;A0;0.45p;0
+Lanius excubitor;Pie-grièche grise ;Grey shrike;A1;0.66;1.26
+Lanius meridionalis;Pie-grièche méridionale;Iberian grey shrike;A0;0.38p;0
+Lanius meridionalis;Pie-grièche méridionale;Iberian grey shrike;A1;0.56p;0.75
+Lanius minor;Pie-grièche à poitrine rose;Lesser grey shrike;A0;0.37p;0
+Lanius minor;Pie-grièche à poitrine rose;Lesser grey shrike;A1;0.54p;2.39
+Lanius senator;Pie-grièche à tête rousse;Woodchat shrike;A0;0.34p;0
+Lanius senator;Pie-grièche à tête rousse;Woodchat shrike;A1;0.51p;1.29p
+Larus argentatus;Goéland argenté;European Herring Gull;A0;0.73;0
+Larus argentatus;Goéland argenté;European Herring Gull;A1;0.85;0
+Larus argentatus;Goéland argenté;European Herring Gull;A2;0.82;0
+Larus argentatus;Goéland argenté;European Herring Gull;A3;0.82;0
+Larus argentatus;Goéland argenté;European Herring Gull;A4;0.89;0.58
+Larus ridibundus;Mouette rieuse;Black-headed Gull;A0;0.56;0
+Larus ridibundus;Mouette rieuse;Black-headed Gull;A1;0.8;0.4p
+Larus ridibundus;Mouette rieuse;Black-headed Gull;A2;0.85;0.79
+Lullula arborea;Alouette lulu;Wood Lark;A0;0.21;0
+Lullula arborea;Alouette lulu;Wood Lark;A1;0.61;2.18
+Milvus migrans;Milan noir;Black Kite;A0;0.5p;0
+Milvus migrans;Milan noir;Black Kite;A1;0.74p;0.22p
+Milvus migrans;Milan noir;Black Kite;A2;0.76;0.44
+Milvus milvus;Milan royal;Red Kite;A0;0.61;0
+Milvus milvus;Milan royal;Red Kite;A1;0.77;0.32p
+Milvus milvus;Milan royal;Red Kite;A2;0.85;0.65
+Neophron percnopterus;Vautour percnoptère;Egyptian Vulture;A0;0.81;0
+Neophron percnopterus;Vautour percnoptère;Egyptian Vulture;A1;0.81;0
+Neophron percnopterus;Vautour percnoptère;Egyptian Vulture;A2;0.83;0
+Neophron percnopterus;Vautour percnoptère;Egyptian Vulture;A3;0.83;0.17p
+Neophron percnopterus;Vautour percnoptère;Egyptian Vulture;A4;0.74;0.17p
+Neophron percnopterus;Vautour percnoptère;Egyptian Vulture;A5;0.81;0.34
+Pandion haliaetus;Balbuzard pêcheur;Osprey;A0;0.46;0
+Pandion haliaetus;Balbuzard pêcheur;Osprey;A1;0.82;0
+Pandion haliaetus;Balbuzard pêcheur;Osprey;A2;0.82;0.36p
+Pandion haliaetus;Balbuzard pêcheur;Osprey;A3;0.79;0.71
+Passer domesticus;Moineau domestique;House sparrow;A0;0.3;0
+Passer domesticus;Moineau domestique;House sparrow;A1;0.56;2.55
+Passer montanus;Moineau friquet;Eurasian tree sparrow;A0;0.49;0
+Passer montanus;Moineau friquet;Eurasian tree sparrow;A1;0.43;1.35
+Perdix perdix;Perdrix grise;Grey partridge;A0;0.22;0
+Perdix perdix;Perdrix grise;Grey partridge;A1;0.38;2.23
+Pernis apivorus;Bondrée apivore;European Honey-buzzard;A0;0.63;0
+Pernis apivorus;Bondrée apivore;European Honey-buzzard;A1;0.84;0
+Pernis apivorus;Bondrée apivore;European Honey-buzzard;A2;0.87;0.22p
+Pernis apivorus;Bondrée apivore;European Honey-buzzard;A3;0.81;0.22p
+Pernis apivorus;Bondrée apivore;European Honey-buzzard;A4;0.81;0.44
+Phylloscopus collybita;Pouillot véloce;Chiffchaff;A0;0.24;0
+Phylloscopus collybita;Pouillot véloce;Chiffchaff;A1;0.42;1.36p
+Pluvialis apricaria;Pluvier doré;Eurasian Golden Plover;A0;0.63;0
+Pluvialis apricaria;Pluvier doré;Eurasian Golden Plover;A1;0.82;0.21p
+Pluvialis apricaria;Pluvier doré;Eurasian Golden Plover;A2;0.7;0.42
+Regulus ignicapillus;Roitelet triple-bandeau;Common Firecrest;A0;0.17p;0
+Regulus ignicapillus;Roitelet triple-bandeau;Common Firecrest;A1;0.25p;2.07p
+Regulus regulus;Roitelet huppé;Goldcrest;A0;0.15p;0
+Regulus regulus;Roitelet huppé;Goldcrest;A1;0.23;2.08p
+Sterna hirundo;Sterne pierregarin;Common Tern;A0;0.59;0
+Sterna hirundo;Sterne pierregarin;Common Tern;A1;0.7;0
+Sterna hirundo;Sterne pierregarin;Common Tern;A2;0.63;0.29
+Sterna hirundo;Sterne pierregarin;Common Tern;A3;0.67;0.39p
+Sterna hirundo;Sterne pierregarin;Common Tern;A4;0.88;0.49
+Sturnus vulgaris;Etourneau sansonnet;Common Starling;A0;0.39;0
+Sturnus vulgaris;Etourneau sansonnet;Common Starling;A1;0.51;0.81
+Tetrax tetrax;Outarde canepetière;Little bustard;A0;0.25;0
+Tetrax tetrax;Outarde canepetière;Little bustard;A1;0.74;0.34
+Turdus merula;Merle noir;Eurasian Blackbird;A0;0.4;0
+Turdus merula;Merle noir;Eurasian Blackbird;A1;0.57;0.65
+Turdus philomelos;Grive musicienne;Song Thrush;A0;0.44;0
+Turdus philomelos;Grive musicienne;Song Thrush;A1;0.57;0.81
+Vanellus vanellus;Vanneau huppé;Northern Lapwing;A0;0.58;0
+Vanellus vanellus;Vanneau huppé;Northern Lapwing;A1;0.7p;0.22p
+Vanellus vanellus;Vanneau huppé;Northern Lapwing;A2;0.72;0.43

inst/FR_EolPop_UTF8/report.Rmd

+---
+title: "Rapport : analyse démographique (eolpop)"
+header-includes:
+- \usepackage{booktabs}
+output: pdf_document
+params:
+  intro: NA
+  analysis: NA
+  species: NA
+  def_pop_text: NA
+  vital_rates_mat: NA
+  
+  fatalities_unit: NA
+  fatalities_input_type: NA
+  fatalities_val1: NA
+  fatalities_val2: NA
+  
+  pop_size_unit: NA
+  pop_size_input_type: NA
+  pop_size_val1: NA
+  pop_size_val2: NA
+  
+  pop_growth_input_type: NA
+  pop_growth_val1: NA
+  pop_growth_val2: NA
+  
+  carrying_cap_unit: NA
+  carrying_cap_input_type: NA
+  carrying_cap_val1: NA
+  carrying_cap_val2: NA
+  
+  PDF_plot: NA
+  ECDF_plot: NA
+  impact_plot: NA
+  #trajectory_plot : NA
+  
+  time_horizon: NA
+  impact_table: NA
+  PrExt_table: NA 
+  
+  CI: NA
+  QT: NA
+  risk_A: NA
+  impact_QT_table: NA
+---
+
+### Date de création: `r strftime(Sys.Date(), "%d/%m/%Y")`
+
+### Type d'analyse réalisée : `r paste(params$analysis)`
+
+### Espèce analysée: `r paste(params$species)`  
+
+### Horizon temporel: `r paste(params$time_horizon)` ans    
+    
+***
+  
+## Contexte de l'étude
+`r paste(params$intro)`
+
+
+## Définition de la population impactée
+`r paste(params$def_pop_text)`
+
+
+***
+
+# Paramètres d'entrée utilisés
+
+## Mortalités annuelles
+*`r paste(params$fatalities_unit)`*  
+`r paste(params$fatalities_input_type)`  
+  
+**`r paste(params$fatalities_val1)` `r paste(params$fatalities_val2)`**
+
+
+
+## Taille de la population
+*`r paste(params$pop_size_unit)`*  
+`r paste(params$pop_size_input_type)`  
+  
+**`r paste(params$pop_size_val1)` `r paste(params$pop_size_val2)`**
+
+
+
+## Taux de croissance annuel
+`r paste(params$pop_growth_input_type)`  
+  
+**`r paste(params$pop_growth_val1)` `r paste(params$pop_growth_val2)`**
+
+
+
+## Capacité de charge
+*`r paste(params$carrying_cap_unit)`*  
+`r paste(params$carrying_cap_input_type)`  
+  
+**`r paste(params$carrying_cap_val1)` `r paste(params$carrying_cap_val2)`**
+
+
+## Paramètres démographiques
+```{r, echo=FALSE}
+kable(params$vital_rates_mat, align = "c", booktabs = TRUE)
+```  
+
+
+
+***
+
+
+# Résultats
+
+```{r, echo=FALSE}
+library(kableExtra)
+```
+
+## Impact global estimé au bout de `r params$time_horizon` ans
+```{r, echo=FALSE}
+kable(params$impact_table, align = "ccc", booktabs = TRUE)
+```  
+Note : Intervalle de confiance (IC) à `r params$CI`%  
+
+## Valeur de l'impact au quantile de `r params$QT`%
+(soit un risque de `r params$risk_A`% de sous-estimer l'impact)
+```{r, echo=FALSE}
+params$impact_QT_table
+```  
+
+## `r paste("Probabilité d'extinction à", params$time_horizon, "ans")`
+```{r, echo=FALSE}
+kable(params$PrExt_table, align = "c", booktabs = TRUE)
+```  
+
+
+
+## Graphique 1 : Densité de probabilité de l'impact relatif (à `r params$time_horizon` ans)
+```{r, echo=FALSE}
+params$PDF_plot
+```
+Note : La médiane et l'intervalle de confiance (IC à `r params$CI`%) sont montrés sur le graphe.  
+
+## Graphique 2 : Probabilité cumulée de l'impact relatif (à `r params$time_horizon` ans)
+```{r, echo=FALSE}
+params$ECDF_plot
+```
+Note : Quantile = `r params$QT`%,  
+soit un risque de `r params$risk_A`% de sous-estimer l'impact
+
+## Graphique 3 : Impact relatif au cours du temps
+```{r, echo=FALSE}
+params$impact_plot
+```
+Note : Intervalle de confiance (IC) à `r params$CI`%  

inst/ShinyApp/runApp.R → inst/FR_EolPop_UTF8/runApp.R

 rm(list = ls(all.names = TRUE))
-setwd( paste0(getwd(),"/inst/ShinyApp/") )
+#setwd( paste0(getwd(),"/inst/FR_eolpop/") )
+#setwd("../FR_eolpop/")
 getwd()
 
 source("ui.R")

inst/FR_EolPop_UTF8/species_list.csv

+Species;Species_fr;Species_en;DistDispMoyKM
+Accipiter gentilis;Autour des palombes;Northern Goshawk;26
+Accipiter nisus;Epervier d'europe ;Eurasian Sparrowhawk;19.3
+Aegypius monachus;Vautour moine;Cinereous Vulture;25.4
+Alauda arvensis;Alouette des champs;Eurasian Skylark;15.7
+Alectoris rufa;Perdrix rouge;Red-legged partridge;0.9
+Apus Apus;Martinet noir;Common Swift;24
+Aquila chrysaetos;Aigle royal;Golden Eagle;35.7
+Aquila fasciata;Aigle de Bonelli;Bonelli's Eagle;37.1
+Asio flammeus;Hibou des marais;short-eared Owl;26.4
+Bubo bubo;Grand Duc d'Europe;Eurasian eagle-owl;26.4
+Burhinus oedicnemus;Oedicnème criard;Eurasian Stone curlew;24.5
+Buteo buteo;Buse variable;Common Buzzard;27.3
+Carduelis cannabina;Linotte mélodieuse;Eurasian Linnet;13
+Carduelis carduelis;Chardonneret élégant;European Goldfinch;14.2
+Carduelis chloris;Verdier d'Europe;European Greenfinch;11.1
+Ciconia ciconia;Cigogne blanche;White Stork;17.6
+Ciconia nigra;Cigogne noire;Black Stork;17.8
+Circus aeruginosus;Busard des roseaux;Western Marsh-harrier;40
+Circus cyaneus;Busard Saint-Martin;Hen Harrier;20.2
+Circus pygargus;Busard cendrée;Montagu's Harrier;32
+Coturnix coturnix;Caille des blés;Common Quail;12.5
+Delichon urbica;Hirondelle de fenêtre;Common House Martin;17.9
+Elanus caeruleus;Elanion Blanc;Black-winged Kite;38
+Emberiza calandra;Bruant proyer;Corn bunting;16.2
+Emberiza citrinella;Bruant jaune;Yellowhammer;15.4
+Erithacus rubecula;Rouge-gorge familier;European Robin;8.7
+Falco naumanni;Faucon crecerellette;Lesser Kestrel;19.7
+Falco peregrinus;Faucon pèlerin;Peregrine Falcon;21.9
+Falco tinnunculus;Faucon crecerelle;Common Kestrel;33.2
+Ficedula hypoleuca;Gobemouche noir;European Pied Flycatcher;15.1
+Grus grus;Grue cendrée;Common Crane;19.7
+Gypaetus barbatus;Gypaète barbu;Bearded vulture;63
+Gyps fulvus;Vautour fauve;Eurasian Griffon;32.2
+Haliaeetus albicilla;Pygargue à queue blanche;White-tailed Eagle;20.5
+Lanius collurio;Pie-grièche écorcheur;Red-backed Shrike;14.9
+Lanius excubitor;Pie-grièche grise ;Grey shrike;16.2
+Lanius meridionalis;Pie-grièche méridionale;Iberian grey shrike;16.2
+Lanius minor;Pie-grièche à poitrine rose;Lesser grey shrike;15.3
+Lanius senator;Pie-grièche à tête rousse;Woodchat shrike;15.1
+Larus argentatus;Goéland argenté;European Herring Gull;50.9
+Larus ridibundus;Mouette rieuse;Black-headed Gull;61.7
+Lullula arborea;Alouette lulu;Wood Lark;11.9
+Milvus migrans;Milan noir;Black Kite;32
+Milvus milvus;Milan royal;Red Kite;75
+Neophron percnopterus;Vautour percnoptère;Egyptian Vulture;22.8
+Pandion haliaetus;Balbuzard pêcheur;Osprey;43.6
+Passer domesticus;Moineau domestique;House sparrow;15.5
+Passer montanus;Moineau friquet;Eurasian tree sparrow;15
+Perdix perdix;Perdrix grise;Grey partridge;1.1
+Pernis apivorus;Bondrée apivore;European Honey-buzzard;23.5
+Phylloscopus collybita;Pouillot véloce;Chiffchaff;18.8
+Pluvialis apricaria;Pluvier doré;Eurasian Golden Plover;18.3
+Regulus ignicapillus;Roitelet triple-bandeau;Common Firecrest;7
+Regulus regulus;Roitelet huppé;Goldcrest;8.8
+Sterna hirundo;Sterne pierregarin;Common Tern;37.1
+Sturnus vulgaris;Etourneau sansonnet;Common Starling;12.3
+Tetrax tetrax;Outarde canepetière;Little bustard;23.5
+Turdus merula;Merle noir;Eurasian Blackbird;8.3
+Turdus philomelos;Grive musicienne;Song Thrush;13.2
+Vanellus vanellus;Vanneau huppé;Northern Lapwing;19.8

run_analysis.R

@@ -7,38 +7,40 @@ library(magrittr)
 library(eolpop)
 
 ## Inputs
-nsim = 3
+nsim = 100
 
-pop_size_mean = 12000
-pop_size_se = 0
-pop_size_type = "Ntotal"
+pop_size_mean = 126
+pop_size_se = 2
+pop_size_type = "Npair"
 
-carrying_capacity_mean = 50000
-carrying_capacity_se = 0
+carrying_capacity_mean = 718
+carrying_capacity_se = 185.8
 
-fatalities_mean = c(0, 1250) #c(0, 5, 3, 4, 2, 1, 4, 2, 2, 3)
-fatalities_se = c(0, 0) # c(0, rep(0.5,9))
+fatalities_mean = c(0, 1.5) #c(0, 5, 3, 4, 2, 1, 4, 2, 2, 3)
+fatalities_se = c(0, 0.194) # c(0, rep(0.5,9))
 length(fatalities_mean)
 
 # onset_year = c(2010, 2013, 2016) #, 2016, 2017, 2019, 2020, 2020, 2020, 2021) #rep(2010, 10)#
 
-survivals <- c(0.70, 0.83, 0.88, 0.90)
-fecundities <- c(0, 0, 0, 0.27)
+# Bruant Proyer
+survivals <- c(0.37, 0.54)
+fecundities <- c(0, 1.18)
 lambda( build_Leslie(s = survivals, f = fecundities) )
+(lambda( build_Leslie(s = survivals, f = fecundities) ) - 1)*100
+
+pop_growth_mean = 1
+pop_growth_se = 0.05
 
-#pop_growth_mean = 1.07932597
-#pop_growth_mean = 1.044
-pop_growth_mean = 1.044
-pop_growth_se = 0
 
 model_demo = NULL # M2_noDD_WithDemoStoch #M1_noDD_noDemoStoch #M4_WithDD_WithDemoStoch #M3_WithDD_noDemoStoch #
-time_horizon = 60
-coeff_var_environ = 0
+time_horizon = 20
+coeff_var_environ = sqrt(0.08)
 fatal_constant = "M"
 cumulated_impacts = FALSE
 
 # Pop size total
 N000 <- pop_vector(pop_size = pop_size_mean, pop_size_type = pop_size_type, s = survivals, f = fecundities)
+N000
 sum(N000)
 
 # Define K
@@ -46,8 +48,7 @@ K = pop_vector(pop_size = carrying_capacity_mean, pop_size_type = pop_size_type,
 K
 
 # Define theoretical rMAX for the species
-#rMAX_species <- rMAX_spp(surv = tail(survivals,1), afr = min(which(fecundities != 0)))
-rMAX_species <- 0.11
+rMAX_species <- rMAX_spp(surv = tail(survivals,1), afr = min(which(fecundities != 0)))
 rMAX_species
 
 ##  Avoid unrealistic scenarios
@@ -75,6 +76,8 @@ lambda( build_Leslie(s = s_calibrated, f = f_calibrated) )
 ##==============================================================================
 ##                         Analyses (simulations)                             ==
 ##==============================================================================
+set.seed(128)
+
 time <- system.time(
   run0 <- run_simul(nsim = nsim,
                     cumulated_impacts = cumulated_impacts,
@@ -109,6 +112,7 @@ time <- system.time(
 time
 
 
+
 out = list()
 out$run = run0
 dim(out$run$N)