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Estimate temporal population variation (version 0.0.2)
Input Stoc count file, shaped and filtered with the 'preprocess population data' and 'filter species' tools.
Input species tabular file, with 5 columns (species ID, species name, species scientific name, specialization status).

STOC Estimate species population variation

What it does

Compute and plot trends of species population, using a glm model of formula : abundance ~ site + year. Testing the effect of site and year on abundance with quasipoisson distribution.


Input description

A first mandatory tabular file with species count shaped and filtered with the STOCs 'Preprocess population data' ans 'Filter species' tools.

A second optional "species details file" containing indicator status of species (Column with TRUE or FALSE), including the species name or ID (one used in the species count data). If you are not analyzing the default STOC data, you need one file of this kind.

Example dataset

"espece"  "nom"                       "nomscientific"               "indicateur"     "specialisation"
"ACCGEN"  "Autour des palombes"       "Accipiter gentilis"          FALSE            ""
"ACCNIS"  "Epervier d'Europe"         "Accipiter nisus"             FALSE            ""
"ACRARU"  "Rousserolle turdoïde"      "Acrocephalus arundinaceus"   FALSE            ""
"ACRMEL"  "Lusciniole à moustaches"   "Acrocephalus melanopogon"    FALSE            ""
"ACRPAL"  "Phragmite aquatique"       "Acrocephalus paludicola"     FALSE            ""
"ACRRIS"  "Rousserolle verderolle"    "Acrocephalus palustris"      FALSE            ""
"ACRSCH"  "Phragmite des joncs"       "Acrocephalus schoenobaenus"  FALSE            ""
"ACRSCI"  "Rousserolle effarvatte"    "Acrocephalus scirpaceus"     FALSE            ""
"ACTHYP"  "Chevalier guignette"       "Actitis hypoleucos"          FALSE            ""
"AEGCAU"  "Mésange à longue queue"    "Aegithalos caudatus"         FALSE            ""
"AEGFUN"  "Chouette de Tengmalm"      "Aegolius funereus"           FALSE            ""
"AIXGAL"  "Canard mandarin"           "Aix galericulata"            FALSE            ""
"AIXSPO"  "Canard carolin"            "Aix sponsa"                  FALSE            ""
"ALAARV"  "Alouette des champs"       "Alauda arvensis"             TRUE             "milieux agricoles"

Output

For each species present in the data, a plot of populations trend is created and stocked in a common data collection.

Two tabular files are created, they describe global tendencies and yearly variations.


Source

UnPublished script available at http://www.vigienature.fr/sites/vigienature/files/atoms/files/analysestoceps_0.zip the first version written by Romain Lorrilliere