Articles

1. Choquet R., A.-M. Reboulet, R. Pradel, O. Gimenez J.-D. Lebreton. (2004). M-SURGE: new software specifically designed for multistate capture-recapture models. Animal Biodiversity and Conservation 27(1): 207-215.

1. L. Rouan, S. Cubaynes, C. Duchamp, C. Miquel, A.-M. Reboulet, O. Gimenez, J.-D. Lebreton, R. Choquet et R. Pradel (In press). Modèles de mélange en Capture-Recapture. Proceeding for JES 2008, Marseille.

.

________________________ with LIBRARIES 7.17 ________________________________

1) FIRST DOWNLOAD THE LIBRARIES V7.17 NEEDED BY E-SURGE V1.9,

M-SURGE V1.8.1 and U-CARE V 2.3.2.

----------------------------------------- STEP 1 ------------------------------------------

Download the librairies V 7.17
needed by E-SURGE V 1.9.0 and U-CARE V 2.3.2

available also from the MATLAB libraries site

                                       ------------------------------------------ STEP 2 ------------------------------------------

Download E-SURGE V 1.9.0 / M-SURGE V 1.8.5 / U-CARE V 2.3.2

________________________ with LIBRARIES 7.2 ________________________________

1) FIRST DOWNLOAD THE LIBRARIES V7.2 NEEDED BY E-SURGE V1.4,

M-SURGE V1.8.1 and U-CARE V 2.2.5.

LIBRARIES Version Matlab 7.2 (Windows XP, Vista).

2) DOWNLOAD E-SURGE V1.4.4, M-SURGE V1.8.1 and U-CARE V 2.2.5.

___________________________ with LIBRARIES 7.5 _____________________________

1) FIRST DOWNLOAD THE LIBRARIES V2007b NEEDED BY E-SURGE V1.4, M-SURGE V1.8.4 and U-CARE V 2.3.

LIBRARIES Version Matlab 7.5 (Windows Vista).

2) DOWNLOAD E-SURGE V1.4.4, M-SURGE V1.8.4 and U-CARE V 2.3.

___________________________ with LIBRARIES 7.9 _____________________________

1) FIRST DOWNLOAD THE LIBRARIES NEEDED BY E-SURGE V1.4, M-SURGE V1.8.4 and U-CARE V 2.3.

LIBRARIES Version Matlab 7.9

2) DOWNLOAD E-SURGE V1.4.4, M-SURGE V1.8.4 and U-CARE V 2.3.

 ___________________________ with LIBRARIES 9.0_____________________________

 Download the libraries V 9 needed by E-SURGE V 2.1.4, V2.2.0 and U-CARE V 2.3.4

                                             available also from the MATLAB libraries site

                                       ------------------------------------------ STEP 2 ------------------------------------------

                                      Download  versions E-SURGE V 2.1.4 or 2.2.0 and U-CARE V 2.3.4

An old software:

SODA for Stop Over Duration Analysis.

A software for Estimation of stopover duration by bootstrapping.

To execute SODA V1.1.1, first download the zip file M-SURGE Version 1.4.2 and unzip

this file in a directory of your choice. Then copy the executable SODA Version 1.1.1

(Windows) in the same directory

Chargé de Recherche CNRS

CEFE/CNRS
Campus du CNRS
1919, route de Mende
34293 Montpellier cedex 5

tél :  +33 4 67 61 32 87
fax:  +33 4 67 41 06 16

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Problématique et thèmes de recherche 

Les activités humaines ont été une source de création de nouveaux habitats (bords des routes, cultures abandonnées, sites pollués par l'industrie minière), qui ont permis l'expansion de nombreuses espèces et aussi la raréfaction et l'extinction d'autres. Ces milieux, généralement à forte hétérogénéité spatio-temporelle, entraînent des changements très rapides des pressions de sélection qui agissent sur les caractéristiques des populations d'espèces qui les occupent (cycle de vie, système de reproduction, adaptations écophysiologiques). Mes activités de recherche sont orientées vers l’étude d’espèces végétales colonisatrices de milieux perturbés par l’homme, principalement les sites miniers, avec comme but leur utilisation dans la restauration de ces milieux. En effet, certaines espèces végétales qui se développent sur des sites riches en métaux lourds sont susceptibles de tolérer des fortes concentrations de métaux dans le sol (Ni, Zn, Cd, etc.). Ces espèces végétales peuvent être utilisées pour la phytoremédiation de sites pollués. En particulier l’utilisation d’écotypes tolérants d’espèces végétales de la famille des Légumineuses ou des Graminées présentes sur les sites miniers, telles qu’Anthyllis vulneraria, Genista pilosa, Festuca arvernensis et Koeleria vallesiana font l’objet d’études en vue de leur utilisation pour revégétaliser les sites pollués. 

Liste de publications sélectionnées

Dechamps C.  Elvinger N. Meerts P.  Lefebvre C.  Escarré J. Colling G.  &  Noret N. (2011). Life history traits of the pseudometallophyte Thlaspi caerulescens in natural populations from Northern Europe. Plant Biology 13 (Suppl. 1) 125–135. pdf

Caño L., Escarré J., Vrieling K., Sans F.X. (2009). Palatability to a generalist herbivore, defence and growth of invasive and native Senecio species: testing the EICA hypothesis. Oecologia 159: 95-106. pdf

Garcia-Serrano H., Caño L., Escarré J., Fleck I., Sans F.X. (2009). Physiological comparison of alien Senecio inaequidens and S. pterophorus and native S. malacitanus: implications for invasion. Flora 204: 445–455. pdf

Vidal C., Chantreuil C., Berge O., Mauré L., Escarré J., Béna G., Brunel B., Cleyet-Marel J.-C. (2009). Mesorhizobium metallidurans sp. nov., a metalresistant symbiont of Anthyllis vulneraria growing on metallicolous soil in Languedoc, France. International Journal of Systematic and Evolutionary Microbiology 59: 850-855. pdf

Caño L., Escarré J., Fleck I., Blanco-Moreno J.M., Sans F.X. (2008). Increased fitness and plasticity of an invasive species in its introduced range: a study using Senecio pterophorus. Journal of Ecology 96: 468-476. pdf

Garcia-Serrano H., Escarré J., Caño L., Sans F.X. (2008). Comparing the effect of habitat on the magnitude of inbreeding depression in the Mediterranean native Senecio malacitanus and the alien S. inaequidens: consequences for invasive ability. Canadian Journal of Botany 86: 63-75. pdf

Dechamps C., Noret N., Mozek R., Escarré J., Lefèbvre C., Gruber W., Meerts P. (2008). Cost of adaptation to metalliferous environment for Thlaspi caerulescens: a field reciprocal transplantation approach. New Phytologist 177: 167-177. pdf

Caño L., Escarré J., Sans F.X. (2007). Factors affecting the invasion success of Senecio inaequidens and S. pterophorus in Mediterranean plant communities. Journal of Vegetation Science 18: 279-286. pdf

Noret N., Josens G., Escarré J., Lefèbvre C., Panichelli S., Meerts P. (2007). Development of Issoria lathonia (Lepidoptera: Nymphalidae) on zinc accumulating and non-accumulating Viola species  (Violaceae). Environmental Toxicology and Chemistry 26: 565-571. pdf

Noret N., Meerts P., Vanhaelen M., Dos Santos A., Escarré J. (2007). Do metal-rich plants deter herbivores? A field test of the defence hypothesis. Oecologia 152: 92-100. pdf

Frérot H., Lefèbvre C., Gruber W., Collin C., Dos Santos A., Escarré J. (2006). Specific interactions between local metallicolous plants improve the phytostabilization of mine soils. Plant and Soil 282: 53-65. pdf

Frérot H., Lefèbvre C., Petit C., Collin C., Dos Santos A., Escarré J. (2005). Zinc tolerance and hyperaccumulation in F1 and F2 offspring from intra and interecotype crosses of Thlaspi caerulescens. New Phytologist, 165(1): 111-119.pdf

Garcia Serrano H.,  Escarré J., Garnier E., Sans F.X. (2005). A comparative growth analysis between alien invader and native Senecio species with distinct distribution ranges. Ecoscience 12: 35-43.pdf

Noret N., Meerts P., Tolrà R., Poschenrieder C., Barceló J., Escarré J. (2005). Palatability of Thlaspi caerulescens for snails: influence of Zn and glucosinolates. New Phytologist, 165(3): 763-772.pdf

Sans F.X., Escarré J., Lepart J., Hopkins F. (2002). Positive vs. negative interactions in Picris hieracioides L., a mid-successional species of Mediterranean secondary succession. Plant Ecology, 162: 109-122.pdf

Escarré J., Lefèbvre C., Gruber W., Leblanc M., Lepart J., Rivière Y., Delay B. (2000). Zinc and Cadmium hyperaccumulation by Thlaspi caerulescens J. et C. Presl from metalliferous and non- metalliferous sites in the Mediterranean area : implications for phyto- remediation. New Phytologist, 145(3): 429-437. pdf

Lepart J., Escarré J. (1983). La succession végétale, mécanismes et modèles : analyse bibliographique. Bulletin d'Ecologie 14: 133-178.pdf

-----------------------------------
Readme E-SURGE 1.7.1 (10/06/2010):
-----------------------------------

E-SURGE Version 1.7.1
multiEvent SURvival Generalized Estimation
General Software for multievent capture-recapture models

-------------------------------------------------------------

R.Choquet,
CEFE UMR 5175,
CNRS, 1919 Route de Mende
34 293 Montpellier cedex 5, FRANCE
Cette adresse e-mail est protégée contre les robots spammeurs. Vous devez activer le JavaScript pour la visualiser.

-------------------------------------------------------------

To be cited as :

Choquet, R., Rouan, L., Pradel, R. (2009). Program E-SURGE: a software application for fitting Multievent models.  
Series: Environmental and Ecological Statistics , Vol. 3 Thomson, David L.; Cooch, Evan G.; Conroy, Michael J. (Eds.) p 845-865

Choquet, R. (2007). E-SURGE 1-0 user’s manual. CEFE, UMR 5175, CNRS, Montpellier, France.
( http://ftp.cefe.cnrs.fr/biom/Soft-CR/ ).

-------------------------------------------------------------
    INSTALLATION
-------------------------------------------------------------

Uses library Matlab Component Runtime 7.9 provided by the program "MCRInstaller_M_7_9.exe", see read_me_install.txt

ASSOCIATIONS (done automatically during installation for windows XP):
 E-SURGE results are saved in files with extension ".out" (e.g. "model1.out"). They can be accessed from E-SURGE
 provided an editor is associated to this extension. To activate this possibility, prior to running E-SURGE
 associate files with extension ".out" to an editor. This can be done simply by creating a text file named,
 say, tempo.out, and following the dialogue after having double-clicked on this file. Because of potential
 side effects we recommend you choose "Wordpad".

-------------------------------------------------------------------
Main new features in E-SURGE 1.7.1 (compared with E-SURGE 1.6.4):
-------------------------------------------------------------------

1) A non parametric Bootstrap option is available. Results are saved in
two files: a) in a text file 'Bootstrap.txt' and b) in a Matlab file
'Bootstrap.mat'

2) Two new families of models were added :
  a) HMM for models conditional to the first occasion (SOD)
  b) HMM for closed population models

3) Input/output files were improved. In particular, an extended Excel
format can be built from the current one.

4) The implementation and the interface for shortcuts were changed.
There is no more restriction for the choice of the name of the shortcut
except that the first character must be a letter. Furthermore, a
shortcut can be defined from another one.

5) A new format called the 'headed format' was defined. This format
is similar to the file format used in statistical software like R, SAS.
The notion of groups is extended to the notion of covariates
(quantitative or qualitative).

6) The automatic building of shortcuts is made from the information
given in the headed format.

------------------------------------------------------
Several bugs detected in E-SURGE 1.7.1 are now fixed:
------------------------------------------------------

1) Retrieve model works now for individual effects (fixed or random)

2) i+t(1)*xind(1)+t(2)*xind(2)+t(3)*xind(3) works now

3) The syntax "t.[t(1_3)*xind(1_3)]" equivalent to
"i+t(1)*xind(1)+t(2)*xind(2)+t(3)*xind(3)" works now

4) The option "Modify Model info" doesn't continue to delete output files.

-------------------------------------------------------------------
Main new features in E-SURGE 1.6.4 (compared with E-SURGE 1.6.2):
-------------------------------------------------------------------

1) Enable equality constraints between mathematical parameters of different type

2) Disable the reduced list of biological parameters is now allowed

3) i+t(1_3)*xind(1_3) works now (V1.6.5 21/04/10)

------------------------------------------------------
Several bugs detected in E-SURGE 1.6.2 are now fixed:
------------------------------------------------------

1) Output bugs were corrected

-------------------------------------------------------------------
Main new features in E-SURGE 1.6.2 (compared with E-SURGE 1.6.0):
-------------------------------------------------------------------

1) A new excel file results is available upon request on menu.

2) Additional informations are now available on the text file result.

3) A new data input format is proposed (Headed format). It extends
the old data formats Biomeco and Mark.

4) The keyword "nexte" has now only one level instead of A levels.
nexte(list) is no more supported.

5) Several improvements have been done on the graphical interface.

6) An option to standardized environmental covariates is available
in GEMACO

------------------------------------------------------
Several bugs detected in E-SURGE 1.6.0 are now fixed:
------------------------------------------------------

1) bug corrected in retrieve model when the number of occasions is bigger
than 26.  

2) E-SURGE can now deal with individuals covariates and retired individuals.

-------------------------------------------------------------------
Main new features in E-SURGE 1.6.0 (compared with E-SURGE 1.4.4):
-------------------------------------------------------------------

1) random effects for individual (i.i.d)

2) random effects for group (i.i.d)

3) Expected Maximisation (E.M) algorithm

4) Hybrid algorithm (E.M (20) + Quasi-Newton)

------------------------------------------------------
Several bugs detected in E-SURGE 1.4.4 are now fixed:
------------------------------------------------------

1) Bug detected and corrected in E-SURGE concerning multiple random (bug not present in 1.1.1)

2) Bug detected and corrected in E-SURGE concerning the identity link

3) Bug detected and corrected concerning the name of the model (name was sometimes cut in the 1.1.1)


-------------------------------------------------------------------
Main new features in E-SURGE 1.4.4 (compared with E-SURGE 1.1.1):
-------------------------------------------------------------------

1) Individual co-variates were added

2) Display data from E-SURGE is now possible

3) Excel output file can be disconnected

------------------------------------------------------
Several bugs detected in E-SURGE 1.4 are now fixed:
------------------------------------------------------

1) Bug detected and corrected in GEMACO concerning additive model (bug not present in 1.1.1)

2) Bug detected and corrected in GEMACO concerning non individual co-variates (bug not present in 1.1.1)

3) Bug detected and corrected in the save of pattern after retrieve model


4) Constraint matrix can now be saved and re-loaded.

-------------------------------------------------------------------
Main new features in E-SURGE 1.1.1 (compared with E-SURGE 1.0.6):
-------------------------------------------------------------------

1) The calculation of the analytical gradient is faster and decreases memory requirements.
Thus the estimation of the model rank is now very fast.

2) The exit from IVFV is also faster because the building of the reduced set of parameters was changed.

------------------------------------------------------
Several bugs detected in E-SURGE 1.0.6 are now fixed:
------------------------------------------------------

1) The definition of initial state probabilities as a product of several elementary matrices works now.
This was not working in the previous version.

2) A bug for the analytical gradient with unequal time intervals of multistate model was detected and corrected.

3) With multiple random initial values, the biological parameters are now correct.   
This was unreliable in the previous version.