Updates accompanying manuscript revisions. Introduce different model …

…versions handling species that are not associated to agriculturally influenced habitats differently

Other/Agricultural_species.txt

@@ -0,0 +1,276 @@
+Adscita alpina
+Adscita dujardini
+Adscita geryon
+Adscita statices
+Aglais io
+Aglais urticae
+Agriades glandon
+Agriades orbitulus
+Anthocharis cardamines
+Aphantopus hyperantus
+Aporia crataegi
+Araschnia levana
+Aricia agestis
+Aricia artaxerxes
+Aricia nicias
+Boloria dia
+Boloria euphrosyne
+Boloria napaea
+Boloria pales
+Boloria selene
+Boloria titania
+Brenthis daphne
+Brenthis ino
+Brintesia circe
+Cacyreus marshalli
+Callophrys rubi
+Carcharodus alceae
+Carterocephalus palaemon
+Chazara briseis
+Coenonympha arcania
+Coenonympha darwiniana
+Coenonympha gardetta
+Coenonympha glycerion
+Coenonympha pamphilus
+Coenonympha tullia
+Colias alfacariensis
+Colias crocea
+Colias hyale
+Colias palaeno
+Colias phicomone
+Cupido alcetas
+Cupido argiades
+Cupido minimus
+Cupido osiris
+Cyaniris semiargus
+Erebia aethiops
+Erebia albergana
+Erebia arvernensis
+Erebia bubastis
+Erebia epiphron
+Erebia eriphyle
+Erebia euryale
+Erebia flavofasciata
+Erebia manto
+Erebia medusa
+Erebia melampus
+Erebia mnestra
+Erebia oeme
+Erebia pandrose
+Erebia pharte
+Erebia pronoe
+Erebia sudetica
+Erebia triarius
+Erebia tyndarus
+Erynnis tages
+Euchloe simplonia
+Eumedonia eumedon
+Euphydryas aurinia
+Euphydryas cynthia
+Fabriciana adippe
+Fabriciana niobe
+Glaucopsyche alexis
+Hamearis lucina
+Hesperia comma
+Heteropterus morpheus
+Hipparchia fagi
+Hipparchia genava
+Hipparchia semele
+Hipparchia statilinus
+Hyponephele lycaon
+Iolana iolas
+Iphiclides podalirius
+Issoria lathonia
+Jordanita globulariae
+Jordanita notata
+Jordanita subsolana
+Kretania trappi
+Lampides boeticus
+Lasiommata maera
+Lasiommata megera
+Lasiommata petropolitana
+Leptidea juvernica
+Leptidea sinapis
+Lycaena alciphron
+Lycaena dispar
+Lycaena helle
+Lycaena hippothoe
+Lycaena phlaeas
+Lycaena tityrus
+Lycaena virgaureae
+Lysandra bellargus
+Lysandra coridon
+Maniola jurtina
+Melanargia galathea
+Melitaea asteria
+Melitaea athalia aggr
+Melitaea aurelia
+Melitaea cinxia
+Melitaea deione
+Melitaea diamina
+Melitaea didyma
+Melitaea parthenoides
+Melitaea phoebe
+Melitaea varia
+Minois dryas
+Muschampia floccifera
+Muschampia lavatherae
+Ochlodes sylvanus
+Oeneis glacialis
+Papilio machaon
+Parnassius apollo
+Parnassius mnemosyne
+Phengaris alcon
+Phengaris arion
+Phengaris nausithous
+Phengaris teleius
+Pieris brassicae
+Pieris bryoniae
+Pieris mannii
+Pieris napi
+Pieris rapae
+Plebejus argus
+Plebejus argyrognomon
+Plebejus idas
+Polyommatus amandus
+Polyommatus damon
+Polyommatus daphnis
+Polyommatus dorylas
+Polyommatus eros
+Polyommatus escheri
+Polyommatus icarus
+Polyommatus thersites
+Pontia callidice
+Pontia edusa
+Pseudophilotes baton
+Pyrgus accreta
+Pyrgus alveus
+Pyrgus andromedae
+Pyrgus armoricanus
+Pyrgus cacaliae
+Pyrgus carlinae
+Pyrgus carthami
+Pyrgus malvae
+Pyrgus malvoides
+Pyrgus onopordi
+Pyrgus serratulae
+Pyrgus warrenensis
+Pyronia tithonus
+Rhagades pruni
+Satyrium acaciae
+Satyrium spini
+Satyrus ferula
+Scolitantides orion
+Speyeria aglaja
+Spialia sertorius
+Thymelicus acteon
+Thymelicus lineola
+Thymelicus sylvestris
+Vanessa atalanta
+Vanessa cardui
+Zygaena carniolica
+Zygaena ephialtes
+Zygaena exulans
+Zygaena fausta
+Zygaena filipendulae
+Zygaena lonicerae
+Zygaena loti
+Zygaena minos
+Zygaena purpuralis
+Zygaena romeo
+Zygaena transalpina
+Zygaena trifolii
+Zygaena viciae
+Aeropedellus variegatus
+Aiolopus strepens
+Aiolopus thalassinus
+Anacridium aegyptium
+Anonconotus alpinus
+Antaxius pedestris
+Arcyptera fusca
+Barbitistes obtusus
+Bohemanella frigida
+Calliptamus barbarus
+Calliptamus italicus
+Calliptamus siciliae
+Chorthippus albomarginatus
+Chorthippus apricarius
+Chorthippus biguttulus
+Chorthippus brunneus
+Chorthippus dorsatus
+Chorthippus eisentrauti
+Chorthippus mollis
+Chorthippus montanus
+Chorthippus parallelus
+Chorthippus vagans
+Chrysochraon dispar
+Conocephalus dorsalis
+Conocephalus fuscus
+Decticus verrucivorus
+Ephippiger ephippiger
+Ephippiger terrestris
+Ephippiger vicheti
+Euchorthippus declivus
+Eumodicogryllus bordigalensis
+Eupholidoptera chabrieri
+Euthystira brachyptera
+Gomphocerippus rufus
+Gomphocerus sibiricus
+Gryllomorpha dalmatina
+Gryllotalpa gryllotalpa
+Gryllus campestris
+Leptophyes albovittata
+Leptophyes laticauda
+Leptophyes punctatissima
+Locusta migratoria
+Mecostethus parapleurus
+Metrioptera bicolor
+Metrioptera brachyptera
+Metrioptera fedtschenkoi
+Metrioptera roeselii
+Metrioptera saussuriana
+Miramella alpina
+Miramella formosanta
+Myrmeleotettix maculatus
+Nemobius sylvestris
+Odontopodisma decipiens
+Oecanthus pellucens
+Oedaleus decorus
+Oedipoda caerulescens
+Oedipoda germanica
+Omocestus haemorrhoidalis
+Omocestus rufipes
+Omocestus viridulus
+Pachytrachis striolatus
+Pezotettix giornae
+Phaneroptera falcata
+Phaneroptera nana
+Pholidoptera aptera
+Pholidoptera fallax
+Pholidoptera griseoaptera
+Pholidoptera littoralis
+Platycleis albopunctata
+Podisma pedestris
+Podismopsis keisti
+Polysarcus denticauda
+Psophus stridulus
+Pteronemobius heydenii
+Ruspolia nitidula
+Saga pedo
+Sphingonotus caerulans
+Stauroderus scalaris
+Stenobothrus lineatus
+Stenobothrus nigromaculatus
+Stenobothrus rubicundulus
+Stenobothrus stigmaticus
+Stethophyma grossum
+Tetrix bipunctata
+Tetrix ceperoi
+Tetrix subulata
+Tetrix tenuicornis
+Tetrix undulata
+Tettigonia cantans
+Tettigonia caudata
+Tettigonia viridissima
+Uvarovitettix depressus
+Yersinella raymondii

README.md

@@ -6,26 +6,30 @@ The following R code files are included in the folder *R_Code*:
 
 -   **R_Main_analyses.R**: Main file containing all the relevant analyses reported in the study. Relies on processed data originating from analyses based on code in other files.
 
--   **R_Climate_change.R**: Code used to compute climate change variables
+-   **R_Climate_change.R**: Code used to compute climate change variables.
 
--   **R_Land_use_change.R**: Code used to compute land-use change variables
+-   **R_Land_use_change.R**: Code used to compute land-use change variables.
 
--   **R_Temperature_niche.R**: Code used to compute species' temperature niches
+-   **R_Temperature_niche.R**: Code used to compute species' temperature niches.
 
--   **R_Proportion_Switzerland.R**: Code used to calculate species distribution proportions in Switzerland
+-   **R_Proportion_Switzerland.R**: Code used to calculate species distribution proportions in Switzerland.
 
 -   **R_Occupancy_detection_models.R**: Code used to prepare species records data and run occupancy-detection models. This code was run on a HPC cluster.
 
 -   **f_occ_det.R**: Helper function used to run occupancy-detection models in Stan.
 
 The following Stan code files are included in the folder *Stan_Code*:
 
--   **Stan_regression.stan**: Stan model code of the regression model fitted to species trends.
+-   **Stan_regression_full.stan**: Stan model code of the regression model fitted to species trends. Full model used for versions 2 and 3.
+
+-   **Stan_regression_restricted.stan**: Stan model code of the regression model fitted to species trends. Restricted model used for version 1 (parameter estimates for agricultural area and grassland-use intensity change only rely on species of agriculturally influenced habitats).
 
 -   **Stan_occ_det_cmdstan.stan**: Stan model code of the occupancy-detection models.
 
 The folder *Other* contains:
 
--   **Bash_start_HPC_cluster.sh**: example of the shell code used to run occupancy-detection models on the HPC cluster
+-   **Bash_start_HPC_cluster.sh**: example of the shell code used to run occupancy-detection models on the HPC cluster.
+
+-   **specieslist.txt**: List of all 390 study species and the insect groups they belong to.
 
--   **specieslist.txt**: List of all 390 study species and the insect groups they belong to
+-   **Agricultural_species.txt**: List of species (partly) bound to agriculturally influenced habitats.

R_Code/R_Climate_change.R

@@ -24,7 +24,7 @@ d_climate <- d_climate %>%
   mutate(date_dummy = paste(year, as.numeric(month), 1, sep = "-"),
          ndays = days_in_month(as.Date(date_dummy)))
 
-# bioclimatic regions
+# bioclimatic zones
 d_zone <- fread('Data/d_zone.csv')
 
 # records data

R_Code/R_Land_use_change.R

@@ -346,7 +346,7 @@ for (region_i in unique(d_AgrArea_reg$zone)){
            zone = region_i,
            var = "AgrArea_prop")
 
-  # AgrArea -------------------------------------------------------------------------.
+  # AgrArea --------------------------------------------------------------------.
   target_AgrArea <- d_AgrArea_reg %>% 
     filter(zone == region_i)
 
@@ -455,7 +455,7 @@ for (region_i in unique(d_AgrArea_reg$zone)){
 
   for (i in 1:(50/timestep)){
 
-    # AgrArea_prop ------------------------------------------------------------------.
+    # AgrArea_prop -------------------------------------------------------------.
 
     # change
     change_mean <- mean(pred_AgrArea_prop[, i * timestep + 1] - pred_AgrArea_prop[, (i-1) * timestep + 1])
@@ -488,7 +488,7 @@ for (region_i in unique(d_AgrArea_reg$zone)){
       bind_rows(d_as_gam_smry, .)
 
 
-    # IAR -------------------------------------------------------------------.
+    # IAR ----------------------------------------------------------------------.
 
     # change
     change_mean <- mean(pred_IAR[, i * timestep + 1] - pred_IAR[, (i-1) * timestep + 1])