Commit 30e65747 authored by Kunstler Georges's avatar Kunstler Georges
Browse files

process output ecocode TP

parent 571346b9
......@@ -327,7 +327,7 @@ fun.generate.pred.param.kikj.dat <- function(list.sd, Tf.low,
'sumTnTfBn.abs' = abs(seq.Tf-Tf.low)*
mean.sumBn/sd_sumTnTfBn.abs)
}
if(MAT.MAP.TF){
df$MAT <- rep(1,nrow(df))
df$MAP <- rep(1,nrow(df))
......@@ -649,7 +649,8 @@ new.data.rho <- fun.generate.pred.param.rho.dat( list.sd = list.res$list.sd,
seq.sumBn = list.var[[2]],
MAT.MAP.TF = MAT.MAP.TF,
intra.TF = intra.TF)
pred.res.rho <- easyPredCI.stabl(list.res, type = 'rho.intra', new.data.rho, alpha)
pred.res.rho <- easyPredCI.stabl(list.res, type = 'rho.intra',
new.data.rho, alpha)
pred.res.rho$Tf <- seq(from = list.var[[1]][['ql.o']],
to = list.var[[1]][['qh.o']],
length.out = 100) - list.var[[1]][['ql.o']]
......@@ -664,7 +665,8 @@ new.data.GiGj <- fun.generate.pred.param.kikj.dat( list.sd = list.res$list.sd,
seq.sumBn = list.var[[2]],
MAT.MAP.TF = MAT.MAP.TF,
intra.TF = intra.TF)
pred.res.GiGj <- easyPredCI.stabl(list.res, type = 'GiGj.intra', new.data.GiGj, alpha)
pred.res.GiGj <- easyPredCI.stabl(list.res, type = 'GiGj.intra',
new.data.GiGj, alpha)
pred.res.GiGj$Tf <- seq(from = list.var[[1]][['ql.o']],
to = list.var[[1]][['qh.o']],
length.out = 100) - list.var[[1]][['ql.o']]
......@@ -681,7 +683,8 @@ new.data.rho <- fun.generate.pred.param.dat(list.sd = list.res$list.sd,
Tf.high = list.var[[1]][['qh']],
seq.sumBn = list.var[[2]],
MAT.MAP.TF = MAT.MAP.TF)
pred.res.rho <- easyPredCI.param(list.res, type = 'alphal', new.data.rho, alpha)
pred.res.rho <- easyPredCI.param(list.res, type = 'alphal',
new.data.rho, alpha)
pred.res.rho$Tf <- seq(from = list.var[[1]][['ql.o']],
to = list.var[[1]][['qh.o']],
length.out = 100) - list.var[[1]][['ql.o']]
......@@ -713,7 +716,8 @@ new.data.kikj <- fun.generate.pred.param.kikj.dat( list.sd = list.res$list.sd,
seq.sumBn = list.var[[2]],
MAT.MAP.TF = MAT.MAP.TF,
intra.TF = intra.TF)
pred.res.kikj <- easyPredCI.stabl(list.res, type = 'kikj', new.data.kikj, alpha)
pred.res.kikj <- easyPredCI.stabl(list.res, type = 'kikj',
new.data.kikj, alpha)
pred.res.kikj$Tf <- seq(from = list.var[[1]][['ql.o']],
to = list.var[[1]][['qh.o']],
length.out = 100) - list.var[[1]][['ql.o']]
......
......@@ -192,7 +192,8 @@ load.data.for.lmer <- function(trait, data.type,
data.type,'rds',
sep = '.')))
df <- df[sample.vec, ]
print(paste('sub-sampled by',var.sample., 'by loading sample.vec'))
print(paste('sub-sampled by',var.sample.,
'by loading sample.vec', nrow(df)))
}
}
}
......
id,citation 1,"Kooyman, R.M. and Westoby, M. (2009) Costs of height gain in rainforest saplings: main stem scaling, functional traits and strategy variation across 75 species. Annals of Botany 104: 987-993." 2,"Kooyman, R.M., Rossetto, M., Allen, C. and Cornwell, W. (2012) Australian tropical and sub-tropical rainforest: phylogeny, functional biogeography and environmental gradients. Biotropica 44: 668-679." 3,"Condit, R. (1998). Tropical forest census plots. Springer, Berlin, Germany." 4,"Condit, R., Engelbrecht, B.M.J., Pino, D., Perez, R., Turner, B.L., (2013). Species distributions in response to individual soil nutrients and seasonal drought across a community of tropical trees. Proceedings of the National Academy of Sciences 110: 5064-5068." 5,"Yakushima Forest Environment Conservation Center, Ishihara, M.I., Suzuki, S.N., Nakamura, M., Enoki, T., Fujiwara, A., Hiura, T., Homma, K., Hoshino, D., Hoshizaki, K., Ida, H., Ishida, K., Itoh, A., Kaneko, T., Kubota, K., Kuraji, K., Kuramoto, S., Makita, A., Masaki, T., Namikawa, K., Niiyama, K., Noguchi, M., Nomiya, H., Ohkubo, T., Saito, S., Sakai, T., Sakimoto, M., Sakio, H., Shibano, H., Sugita, H., Suzuki, M., Takashima, A., Tanaka, N., Tashiro, N., Tokuchi, N., Yoshida, T., Yoshida, Y., (2011). Forest stand structure, composition, and dynamics in 34 sites over Japan. Ecological Research 26: 1007-1008. " 6,"Thompson, J., N. Brokaw, J. K. Zimmerman, R. B. Waide, E. M. Everham III, D. J. Lodge, C. M. Taylor, D. GarciaMontiel, and M. Fluet. (2002). Land use history, environment, and tree composition in a tropical forest. Ecological Applications 12: 1344-1363." 7,"Ouadraogo, D.-Y., Mortier, F., Gourlet-Fleury, S., Freycon, V., and Picard, N. (2013). Slow-growing species cope best with drought: evidence from long-term measurements in a tropical semi-deciduous moist forest of Central Africa. Journal of Ecology 101: 1459-1470." 8,"Gourlet-Fleury, S., V. Rossi, M. Rejou-Mechain, V. Freycon, A. Fayolle, L. Saint-Andr_, G. Cornu, J. Gerard, J. M. Sarrailh, and O. Flores. (2011). Environmental Filtering of Dense-Wooded Species Controls above-Ground Biomass Stored in African Moist Forests. Journal of Ecology 99: 981-90." 9,"Lasky, J.R., Sun, I., Su, S.-H., Chen, Z.-S., and Keitt, T.H. (2013). Trait-mediated effects of environmental filtering on tree community dynamics. Journal of Ecology 101: 722-733." 10,"Herault, B., Bachelot, B., Poorter, L., Rossi, V., Bongers, F., Chave, J., Paine, C.E., Wagner, F., and Baraloto, C. (2011). Functional traits shape ontogenetic growth trajectories of rain forest tree species. Journal of Ecology 99: 1431-1440." 11,"Herault, B., Ouallet, J., Blanc, L., Wagner, F., and Baraloto, C. (2010). Growth responses of neotropical trees to logging gaps. Journal of Applied Ecology 47: 821-831." 12,"IFN. (2011). Les resultats issus des campagnes d'inventaire 2006, 2007, 2008, 2009, 2010 et 2011. Inventaire Forestier National, Nogent-sur-Vernisson, FR." 13,http://inventaire-forestier.ign.fr/spip/spip.php?rubrique153 14,"Villaescusa, R. & Diaz, R. (1998) Segundo Inventario Forestal Nacional (1986-1996), Ministerio de Medio Ambiente, ICONA, Madrid." 15,"Villanueva, J.A. (2004) Tercer Inventario Forestal Nacional (1997-2007). Comunidad de Madrid. Ministerio de Medio Ambiente, Madrid." 16,http://www.magrama.gob.es/es/desarrollo-rural/temas/politica-forestal/inventario-cartografia/inventario-forestal-nacional/default.aspx 17,http://www.lfi.ch/index-en.php 18,"Fridman, J., and Stahl, G. (2001). A three-step approach for modelling tree mortality in Swedish forests. Scandinavian Journal of Forest Research 16: 455-466." 19,http://www.fia.fs.fed.us/tools-data/ 20,"Wiser, S.K., Bellingham, P.J. & Burrows, L.E. (2001) Managing biodiversity information: development of New Zealand's National Vegetation Survey databank. New Zealand Journal of Ecology, 25: 1-17." 21,https://nvs.landcareresearch.co.nz/ 23,"Swenson, N.G., J.C. Stegen, S.J. Davies, D.L. Erickson, J. Forero-Montana, A.H. Hurlbert, W.J. Kress, J. Thompson, M. Uriarte, S.J. Wright and J.K. Zimmerman. (2012). Temporal turnover in the composition of tropical tree communities: functional determinism and phylogenetic stochasticity. Ecology 93: 490-499." 24,"Baraloto, C, P.C.E. Timothy, L. Poorter, J. Beauchene, D. Bonal, AM Domenach, B. H_rault, S. Patio, JC Roggy, and Jerome Chave. (2010). Decoupled Leaf and Stem Economics in Rain Forest Trees. Ecology Letters 13: 1338-47." 25,"Wright, S.J., Kitajima, K., Kraft, N.J.B., Reich, P.B., Wright, I.J., Bunker, D.E., Condit, R., Dalling, J.W., Davies, S.J., Daz, S., Engelbrecht, B.M.J., Harms, K.E., Hubbell, S.P., Marks, C.O., Ruiz-Jaen, M.C., Salvador, C.M. & Zanne, A.E. (2010) Functional traits and the growth-mortality trade-off in tropical trees. Ecology 91: 3664-3674." 26,"Brandli, U.-B. (Red.) 2010: Schweizerisches Landesforstinventar. Ergebnisse der dritten Erhebung 2004-2006. Birmensdorf, Eidgenossische Forschungsanstalt fur Wald, Schnee und Landschaft WSL. Bern, Bundesamt fur Umwelt, BAFU. 312 S."
\ No newline at end of file
id,citation 1,"Kooyman, R.M. and Westoby, M. (2009) Costs of height gain in rainforest saplings: main stem scaling, functional traits and strategy variation across 75 species. Annals of Botany 104: 987-993." 2,"Kooyman, R.M., Rossetto, M., Allen, C. and Cornwell, W. (2012) Australian tropical and sub-tropical rainforest: phylogeny, functional biogeography and environmental gradients. Biotropica 44: 668-679." 3,"Condit, R. (1998). Tropical forest census plots. Springer, Berlin, Germany." 4,"Condit, R., Engelbrecht, B.M.J., Pino, D., Perez, R., Turner, B.L., (2013). Species distributions in response to individual soil nutrients and seasonal drought across a community of tropical trees. Proceedings of the National Academy of Sciences 110: 5064-5068." 5,"Yakushima Forest Environment Conservation Center, Ishihara, M.I., Suzuki, S.N., Nakamura, M., Enoki, T., Fujiwara, A., Hiura, T., Homma, K., Hoshino, D., Hoshizaki, K., Ida, H., Ishida, K., Itoh, A., Kaneko, T., Kubota, K., Kuraji, K., Kuramoto, S., Makita, A., Masaki, T., Namikawa, K., Niiyama, K., Noguchi, M., Nomiya, H., Ohkubo, T., Saito, S., Sakai, T., Sakimoto, M., Sakio, H., Shibano, H., Sugita, H., Suzuki, M., Takashima, A., Tanaka, N., Tashiro, N., Tokuchi, N., Yoshida, T., Yoshida, Y., (2011). Forest stand structure, composition, and dynamics in 34 sites over Japan. Ecological Research 26: 1007-1008. " 6,"Thompson, J., N. Brokaw, J. K. Zimmerman, R. B. Waide, E. M. Everham III, D. J. Lodge, C. M. Taylor, D. GarciaMontiel, and M. Fluet. (2002). Land use history, environment, and tree composition in a tropical forest. Ecological Applications 12: 1344-1363." 7,"Ouadraogo, D.-Y., Mortier, F., Gourlet-Fleury, S., Freycon, V., and Picard, N. (2013). Slow-growing species cope best with drought: evidence from long-term measurements in a tropical semi-deciduous moist forest of Central Africa. Journal of Ecology 101: 1459-1470." 8,"Gourlet-Fleury, S., V. Rossi, M. Rejou-Mechain, V. Freycon, A. Fayolle, L. Saint-Andr_, G. Cornu, J. Gerard, J. M. Sarrailh, and O. Flores. (2011). Environmental Filtering of Dense-Wooded Species Controls above-Ground Biomass Stored in African Moist Forests. Journal of Ecology 99: 981-90." 9,"Lasky, J.R., Sun, I., Su, S.-H., Chen, Z.-S., and Keitt, T.H. (2013). Trait-mediated effects of environmental filtering on tree community dynamics. Journal of Ecology 101: 722-733." 10,"Herault, B., Bachelot, B., Poorter, L., Rossi, V., Bongers, F., Chave, J., Paine, C.E., Wagner, F., and Baraloto, C. (2011). Functional traits shape ontogenetic growth trajectories of rain forest tree species. Journal of Ecology 99: 1431-1440." 11,"Herault, B., Ouallet, J., Blanc, L., Wagner, F., and Baraloto, C. (2010). Growth responses of neotropical trees to logging gaps. Journal of Applied Ecology 47: 821-831." 12,"IFN. (2011). Les resultats issus des campagnes d'inventaire 2006, 2007, 2008, 2009, 2010 et 2011. Inventaire Forestier National, Nogent-sur-Vernisson, FR." 13,http://inventaire-forestier.ign.fr/spip/spip.php?rubrique153 14,"Villaescusa, R. & Diaz, R. (1998) Segundo Inventario Forestal Nacional (1986-1996), Ministerio de Medio Ambiente, ICONA, Madrid." 15,"Villanueva, J.A. (2004) Tercer Inventario Forestal Nacional (1997-2007). Comunidad de Madrid. Ministerio de Medio Ambiente, Madrid." 16,http://www.magrama.gob.es/es/desarrollo-rural/temas/politica-forestal/inventario-cartografia/inventario-forestal-nacional/default.aspx 17,http://www.lfi.ch/index-en.php 18,"Fridman, J., and Stahl, G. (2001). A three-step approach for modelling tree mortality in Swedish forests. Scandinavian Journal of Forest Research 16: 455-466." 19,http://www.fia.fs.fed.us/tools-data/ 20,"Wiser, S.K., Bellingham, P.J. & Burrows, L.E. (2001) Managing biodiversity information: development of New Zealand's National Vegetation Survey databank. New Zealand Journal of Ecology, 25: 1-17." 21,https://nvs.landcareresearch.co.nz/ 23,"Swenson, N.G., J.C. Stegen, S.J. Davies, D.L. Erickson, J. Forero-Montana, A.H. Hurlbert, W.J. Kress, J. Thompson, M. Uriarte, S.J. Wright and J.K. Zimmerman. (2012). Temporal turnover in the composition of tropical tree communities: functional determinism and phylogenetic stochasticity. Ecology 93: 490-499." 24,"Baraloto, C, P.C.E. Timothy, L. Poorter, J. Beauchene, D. Bonal, AM Domenach, B. Herault, S. Patido, JC Roggy, and Jerome Chave. (2010). Decoupled Leaf and Stem Economics in Rain Forest Trees. Ecology Letters 13: 1338-47." 25,"Wright, S.J., Kitajima, K., Kraft, N.J.B., Reich, P.B., Wright, I.J., Bunker, D.E., Condit, R., Dalling, J.W., Davies, S.J., Daz, S., Engelbrecht, B.M.J., Harms, K.E., Hubbell, S.P., Marks, C.O., Ruiz-Jaen, M.C., Salvador, C.M. & Zanne, A.E. (2010) Functional traits and the growth-mortality trade-off in tropical trees. Ecology 91: 3664-3674." 26,"Brandli, U.-B. (Red.) 2010: Schweizerisches Landesforstinventar. Ergebnisse der dritten Erhebung 2004-2006. Birmensdorf, Eidgenossische Forschungsanstalt fur Wald, Schnee und Landschaft WSL. Bern, Bundesamt fur Umwelt, BAFU. 312 S."
\ No newline at end of file
......
Data set name,Country,Data type,Plot size,Diameter at breast height threshold,Number of plots,Traits,Source trait data,References,Contact of person in charge of data formatting,Comments Panama,Panama,LPP,1 to 50 ha,1 cm,42,"Wood density, SLA, and Maximum height",local,"3,4,25","Plot data: R. Condit (conditr@gmail.com), Traits data: J. Wright (wrightj@si.edu)",The data used include both the 50 ha plot of BCI and the network of 1 ha plots from Condit et al. (2013). The two first census of BCI plot were excluded. Japan,Japan,LPP,0.35 to 1.05 ha,2.39 cm,16,"Wood density, SLA, and Maximum height",local,5,"Plot data: M. I. Ishihara (moni1000f_networkcenter@fsc.hokudai.ac.jp), Traits data: Y Onoda (yusuke.onoda@gmail.com)", Luquillo,Puerto Rico,LPP,16 ha,1 cm,1,"Wood density, SLA, and Maximum height",local,"6, 23","Plot data: J. Thompson (jiom@ceh.ac.uk) and J. Zimmerman (esskz@ites.upr.edu), Traits data: N. Swenson (swensonn@msu.edu )", M'Baiki,Central African Republic,LPP,4 ha,10 cm,10,Wood density and SLA,local,"7,8",G. Vieilledent (ghislain.vieilledent@cirad.fr), Fushan,Taiwan,LPP,25 ha,1 cm,1,Wood density and SLA,local,9,I-F. Sun (ifsun@mail.ndhu.edu.tw), Paracou,French Guiana,LPP,6.25 ha,10 cm,15,Wood density and SLA,local,"10,11,24","Plot data: B. Herault (bruno.herault@cirad.fr), Traits data: C. Baraloto (Chris.Baraloto@ecofog.gf)", France,France,NFI,0.017 to 0.07 ha,7.5 cm,41503,"Wood density, SLA, and Maximum height",TRY,"12,13",G. Kunstler (georges.kunstler@gmail.com),"The French NFI is based on temporary plot, but 5 years tree radial growth is estimated with short core. All trees with dbh > 7.5 cm, > 22.5 cm and > 37.5 cm were measured within a radius of 6 m, 9 m and 15 m, respectively. Plots are distributed over forest ecosystems on a 1-km 2 cell grid" Spain,Spain,NFI,0.0078 to 0.19 ha,7.5 cm,49855,"Wood density, SLA, and Maximum height",TRY,"14,15,16",M. Zavala (madezavala@gmail.com),"Each SFI plot included four concentric circular sub-plots of 5, 10, 15 and 25-m radius. In these sub-plots, adult trees were sampled when diameter at breast height (d.b.h.) was 7.5-12.4 cm, 12.5-22.4 cm, 22.5-42.5 cm and >= 42.5 cm, respectively." Swiss,Switzerland,NFI,0.02 to 0.05 ha,12 cm,2665,"Wood density, SLA, and Maximum height",TRY,"17,26",M. Hanewinkel & N. E. Zimmermann (niklaus.zimmermann@wsl.ch),"All trees with dbh > 12 cm and > 36 cm were measured within a radius of 7.98 m and 12.62 m, respectively." Sweden,Sweden,NFI,0.0019 to 0.0314 ha,5 cm,22904,"Wood density, SLA, and Maximum height",TRY,18,G. Stahl (Goran.Stahl@slu.se),"All trees with dbh > 10 cm, were measured on circular plots of 10 m radius." US,USA,NFI,0.0014 to 0.017 ha,2.54 cm,97434,"Wood density, SLA, and Maximum height",TRY,19,M. Vanderwel (Mark.Vanderwel@uregina.ca),FIA data are made up of cluster of 4 subplots of size 0.017 ha for tree dbh > 1.72 cm and nested in each subplot sapling plots of 0.0014 ha for trees dbh > 2.54 cm. The data of the four subplot were lumped together. Canada,Canada,NFI,0.02 to 0.18 ha,2 cm,15019,"Wood density, SLA, and Maximum height",TRY,,J. Caspersen (john.caspersen@utoronto.ca),The protocol is variable between Provinces. A large proportion of data is from the Quebec province and the plot are 10 m in radius in this Province. NZ,New Zealand,NFI,0.04 ha,3 cm,1415,"Wood density, SLA, and Maximum height",local,"20,21",D. Laughlin (d.laughlin@waikato.ac.nz),Plots are 20 x 20 m. NSW,Australia,NFI,0.075 to 0.36 ha,10 cm,30,"Wood density, and Maximum height",local,"1,2",R. M. Kooyman (robert@ecodingo.com.au),Permanents plots established by the NSW Department of State Forests or by RMK
\ No newline at end of file
Data set name,Country,Data type,Plot size,Diameter at breast height threshold,Number of plots,Traits,Source trait data,Evidences of disturbances and succession dynamics,References,Contact of person in charge of data formatting,Comments Panama,Panama,LPP,1 to 50 ha,1 cm,42,"Wood density, SLA, and Maximum height",local,"""Gap disturbances are common in the large 50ha BCI plot [see @Young-1991; @Hubbell-1999; @Lobo-2014]. Hubbell et al.[@Hubbell-1999] estimated that less than 30% of the plot experienced no disturbance over a 13-year period.""","3,4,25","Plot data: R. Condit (conditr@gmail.com), Traits data: J. Wright (wrightj@si.edu)",The data used include both the 50 ha plot of BCI and the network of 1 ha plots from Condit et al. (2013). The two first census of BCI plot were excluded. Japan,Japan,LPP,0.35 to 1.05 ha,2.39 cm,16,"Wood density, SLA, and Maximum height",local,"""The network of plot comprise 50% of old growth forest, 17% of old secondary forest and 33% of young secondary forest.""",5,"Plot data: M. I. Ishihara (moni1000f_networkcenter@fsc.hokudai.ac.jp), Traits data: Y Onoda (yusuke.onoda@gmail.com)", Luquillo,Puerto Rico,LPP,16 ha,1 cm,1,"Wood density, SLA, and Maximum height",local,"""The plot has been struck by hurricanes in 1989 and in 1998[@Uriarte-2009]. In addition, two-third of the plot is a secondary forest on land previously used for agriculture and logging[Uriarte-2009].""","6, 23","Plot data: J. Thompson (jiom@ceh.ac.uk) and J. Zimmerman (esskz@ites.upr.edu), Traits data: N. Swenson (swensonn@msu.edu )", M'Baiki,Central African Republic,LPP,4 ha,10 cm,10,Wood density and SLA,local,"""The plot network was established with three levels of harvesting and one control [@Ouedraogo-2013].""","7,8",G. Vieilledent (ghislain.vieilledent@cirad.fr), Fushan,Taiwan,LPP,25 ha,1 cm,1,Wood density and SLA,local,"""Fushan experienced several Typhoon disturbances in 1994 with tree fall events, the main effect was trees defoliation[@Lin-2011].""",9,I-F. Sun (ifsun@mail.ndhu.edu.tw), Paracou,French Guiana,LPP,6.25 ha,10 cm,15,Wood density and SLA,local,"""The plot network was established with three levels of harvesting and one control (Herault et al. 2010).""","10,11,24","Plot data: B. Herault (bruno.herault@cirad.fr), Traits data: C. Baraloto (Chris.Baraloto@ecofog.gf)", France,France,NFI,0.017 to 0.07 ha,7.5 cm,41503,"Wood density, SLA, and Maximum height",TRY,"""French forests monitored by the French National Forest Inventory experience several types of natural disturbances (such as wind, forest fire, and bark beetles) and harvesting. The age structure reconstructed by Vilen et al.[@Vilen-2012] shows that young forests represents a significant percentage of the forested area (see age distribution below).""","12,13",G. Kunstler (georges.kunstler@gmail.com),"The French NFI is based on temporary plot, but 5 years tree radial growth is estimated with short core. All trees with dbh > 7.5 cm, > 22.5 cm and > 37.5 cm were measured within a radius of 6 m, 9 m and 15 m, respectively. Plots are distributed over forest ecosystems on a 1-km 2 cell grid" Spain,Spain,NFI,0.0078 to 0.19 ha,7.5 cm,49855,"Wood density, SLA, and Maximum height",TRY,"""Spanish forests monitored by the Spanish National Forest Inventory experience several types of natural disturbances (such as wind, forest fire, and bark beetles) and harvesting. No data are available on the age structure of the plots.""","14,15,16",M. Zavala (madezavala@gmail.com),"Each SFI plot included four concentric circular sub-plots of 5, 10, 15 and 25-m radius. In these sub-plots, adult trees were sampled when diameter at breast height (d.b.h.) was 7.5-12.4 cm, 12.5-22.4 cm, 22.5-42.5 cm and >= 42.5 cm, respectively." Swiss,Switzerland,NFI,0.02 to 0.05 ha,12 cm,2665,"Wood density, SLA, and Maximum height",TRY,"""Swiss forests monitored by the Swiss National Forest Inventory experience several types of natural disturbances (such as wind, forest fire, and bark beetles) and harvesting. The age structure reconstructed by Vilen et al.[@Vilen-2012] shows that young forests represents a significant percentage of the forested area (see age distribution below).""","17,26",M. Hanewinkel & N. E. Zimmermann (niklaus.zimmermann@wsl.ch),"All trees with dbh > 12 cm and > 36 cm were measured within a radius of 7.98 m and 12.62 m, respectively." Sweden,Sweden,NFI,0.0019 to 0.0314 ha,5 cm,22904,"Wood density, SLA, and Maximum height",TRY,"""Swedish forests monitored by the Swedish National Forest Inventory experience several types of natural disturbances (such as wind, forest fire, and bark beetles) and harvesting. The age structure reconstructed by Vilen et al.[@Vilen-2012] shows that young forests represents a significant percentage of the forested area (see age distribution below).""",18,G. Stahl (Goran.Stahl@slu.se),"All trees with dbh > 10 cm, were measured on circular plots of 10 m radius." US,USA,NFI,0.0014 to 0.017 ha,2.54 cm,97434,"Wood density, SLA, and Maximum height",TRY,"""US forests monitored by the FIA experience several types of natural disturbances (such as wind, forest fire, and bark beetles) and harvesting. The age structure reconstructed by Pan et al.[@Pan-2011] shows that young forests represents a significant percentage of the forested area (see age distribution below).""",19,M. Vanderwel (Mark.Vanderwel@uregina.ca),FIA data are made up of cluster of 4 subplots of size 0.017 ha for tree dbh > 1.72 cm and nested in each subplot sapling plots of 0.0014 ha for trees dbh > 2.54 cm. The data of the four subplot were lumped together. Canada,Canada,NFI,0.02 to 0.18 ha,2 cm,15019,"Wood density, SLA, and Maximum height",TRY,"""Canadian forests monitored by the regional forest monitoring programs experience several types of natural disturbances (such as wind, forest fire, and bark beetles) and harvesting. The age structure reconstructed by Pan et al.[@Pan-2011] shows that young forests represents a significant percentage of the forested area (see age distribution below).""",,J. Caspersen (john.caspersen@utoronto.ca),The protocol is variable between Provinces. A large proportion of data is from the Quebec province and the plot are 10 m in radius in this Province. NZ,New Zealand,NFI,0.04 ha,3 cm,1415,"Wood density, SLA, and Maximum height",local,"""New Zealand forests are experiencing disturbance by earthquake, landslide, storm and volcanic eruptions. According to Holdaway et al.[@Holdaway-2014] having been disturbed during their measurement interval.""","20,21",D. Laughlin (d.laughlin@waikato.ac.nz),Plots are 20 x 20 m. NSW,Australia,NFI,0.075 to 0.36 ha,10 cm,30,"Wood density, and Maximum height",local,The plot network was initially established in the 60s with different level of selection harvesting[@Kariuki-2006].,"1,2",R. M. Kooyman (robert@ecodingo.com.au),Permanents plots established by the NSW Department of State Forests or by RMK
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......
......@@ -20,6 +20,11 @@ and $N_i$ is the number of species in the local neighbourhood of the tree $i$.
Two main data type were used: national forest inventories data -- NFI, large permanent plots data -- LPP.
```
## Warning: package 'plyr' was built under R version 3.1.3
```
### Panama
- Data set name: Panama
......@@ -29,12 +34,13 @@ Two main data type were used: national forest inventories data -- NFI, large per
- Number of plots: 42
- Traits: Wood density, SLA, and Maximum height
- Source trait data: local
- Evidences of disturbances and succession dynamics: "Gap disturbances are common in the large 50ha BCI plot [see @Young-1991; @Hubbell-1999; @Lobo-2014]. Hubbell et al.[@Hubbell-1999] estimated that less than 30% of the plot experienced no disturbance over a 13-year period."
- Contact of person in charge of data formatting: Plot data: R. Condit (conditr@gmail.com), Traits data: J. Wright (wrightj@si.edu)
- Comments: The data used include both the 50 ha plot of BCI and the network of 1 ha plots from Condit et al. (2013). The two first census of BCI plot were excluded.
- References:
- Condit, R. (1998). Tropical forest census plots. Springer, Berlin, Germany.
- Condit, R., Engelbrecht, B.M.J., Pino, D., Perez, R., Turner, B.L., (2013). Species distributions in response to individual soil nutrients and seasonal drought across a community of tropical trees. Proceedings of the National Academy of Sciences 110: 5064-5068.
- Wright, S.J., Kitajima, K., Kraft, N.J.B., Reich, P.B., Wright, I.J., Bunker, D.E., Condit, R., Dalling, J.W., Davies, S.J., DŐaz, S., Engelbrecht, B.M.J., Harms, K.E., Hubbell, S.P., Marks, C.O., Ruiz-Jaen, M.C., Salvador, C.M. & Zanne, A.E. (2010) Functional traits and the growth-mortality trade-off in tropical trees. Ecology 91: 3664-3674.
- Wright, S.J., Kitajima, K., Kraft, N.J.B., Reich, P.B., Wright, I.J., Bunker, D.E., Condit, R., Dalling, J.W., Davies, S.J., DÍaz, S., Engelbrecht, B.M.J., Harms, K.E., Hubbell, S.P., Marks, C.O., Ruiz-Jaen, M.C., Salvador, C.M. & Zanne, A.E. (2010) Functional traits and the growth-mortality trade-off in tropical trees. Ecology 91: 3664-3674.
### Japan
......@@ -46,6 +52,7 @@ Two main data type were used: national forest inventories data -- NFI, large per
- Number of plots: 16
- Traits: Wood density, SLA, and Maximum height
- Source trait data: local
- Evidences of disturbances and succession dynamics: "The network of plot comprise 50% of old growth forest, 17% of old secondary forest and 33% of young secondary forest."
- Contact of person in charge of data formatting: Plot data: M. I. Ishihara (moni1000f_networkcenter@fsc.hokudai.ac.jp), Traits data: Y Onoda (yusuke.onoda@gmail.com)
- Comments:
- References:
......@@ -61,6 +68,7 @@ Two main data type were used: national forest inventories data -- NFI, large per
- Number of plots: 1
- Traits: Wood density, SLA, and Maximum height
- Source trait data: local
- Evidences of disturbances and succession dynamics: "The plot has been struck by hurricanes in 1989 and in 1998[@Uriarte-2009]. In addition, two-third of the plot is a secondary forest on land previously used for agriculture and logging[Uriarte-2009]."
- Contact of person in charge of data formatting: Plot data: J. Thompson (jiom@ceh.ac.uk) and J. Zimmerman (esskz@ites.upr.edu), Traits data: N. Swenson (swensonn@msu.edu )
- Comments:
- References:
......@@ -77,6 +85,7 @@ Two main data type were used: national forest inventories data -- NFI, large per
- Number of plots: 10
- Traits: Wood density and SLA
- Source trait data: local
- Evidences of disturbances and succession dynamics: "The plot network was established with three levels of harvesting and one control [@Ouedraogo-2013]."
- Contact of person in charge of data formatting: G. Vieilledent (ghislain.vieilledent@cirad.fr)
- Comments:
- References:
......@@ -93,6 +102,7 @@ Two main data type were used: national forest inventories data -- NFI, large per
- Number of plots: 1
- Traits: Wood density and SLA
- Source trait data: local
- Evidences of disturbances and succession dynamics: "Fushan experienced several Typhoon disturbances in 1994 with tree fall events, the main effect was trees defoliation[@Lin-2011]."
- Contact of person in charge of data formatting: I-F. Sun (ifsun@mail.ndhu.edu.tw)
- Comments:
- References:
......@@ -108,12 +118,13 @@ Two main data type were used: national forest inventories data -- NFI, large per
- Number of plots: 15
- Traits: Wood density and SLA
- Source trait data: local
- Evidences of disturbances and succession dynamics: "The plot network was established with three levels of harvesting and one control (Herault et al. 2010)."
- Contact of person in charge of data formatting: Plot data: B. Herault (bruno.herault@cirad.fr), Traits data: C. Baraloto (Chris.Baraloto@ecofog.gf)
- Comments:
- References:
- Herault, B., Bachelot, B., Poorter, L., Rossi, V., Bongers, F., Chave, J., Paine, C.E., Wagner, F., and Baraloto, C. (2011). Functional traits shape ontogenetic growth trajectories of rain forest tree species. Journal of Ecology 99: 1431-1440.
- Herault, B., Ouallet, J., Blanc, L., Wagner, F., and Baraloto, C. (2010). Growth responses of neotropical trees to logging gaps. Journal of Applied Ecology 47: 821-831.
- Baraloto, C, P.C.E. Timothy, L. Poorter, J. Beauchene, D. Bonal, AM Domenach, B. H_rault, S. PatiĐo, JC Roggy, and Jerome Chave. (2010). Decoupled Leaf and Stem Economics in Rain Forest Trees. Ecology Letters 13: 1338-47.
- Baraloto, C, P.C.E. Timothy, L. Poorter, J. Beauchene, D. Bonal, AM Domenach, B. Herault, S. Patido, JC Roggy, and Jerome Chave. (2010). Decoupled Leaf and Stem Economics in Rain Forest Trees. Ecology Letters 13: 1338-47.
### France
......@@ -125,6 +136,7 @@ Two main data type were used: national forest inventories data -- NFI, large per
- Number of plots: 41503
- Traits: Wood density, SLA, and Maximum height
- Source trait data: TRY
- Evidences of disturbances and succession dynamics: "French forests monitored by the French National Forest Inventory experience several types of natural disturbances (such as wind, forest fire, and bark beetles) and harvesting. The age structure reconstructed by Vilen et al.[@Vilen-2012] shows that young forests represents a significant percentage of the forested area (see age distribution below)."
- Contact of person in charge of data formatting: G. Kunstler (georges.kunstler@gmail.com)
- Comments: The French NFI is based on temporary plot, but 5 years tree radial growth is estimated with short core. All trees with dbh > 7.5 cm, > 22.5 cm and > 37.5 cm were measured within a radius of 6 m, 9 m and 15 m, respectively. Plots are distributed over forest ecosystems on a 1-km 2 cell grid
- References:
......@@ -141,6 +153,7 @@ Two main data type were used: national forest inventories data -- NFI, large per
- Number of plots: 49855
- Traits: Wood density, SLA, and Maximum height
- Source trait data: TRY
- Evidences of disturbances and succession dynamics: "Spanish forests monitored by the Spanish National Forest Inventory experience several types of natural disturbances (such as wind, forest fire, and bark beetles) and harvesting. No data are available on the age structure of the plots."
- Contact of person in charge of data formatting: M. Zavala (madezavala@gmail.com)
- Comments: Each SFI plot included four concentric circular sub-plots of 5, 10, 15 and 25-m radius. In these sub-plots, adult trees were sampled when diameter at breast height (d.b.h.) was 7.5-12.4 cm, 12.5-22.4 cm, 22.5-42.5 cm and >= 42.5 cm, respectively.
- References:
......@@ -158,6 +171,7 @@ Two main data type were used: national forest inventories data -- NFI, large per
- Number of plots: 2665
- Traits: Wood density, SLA, and Maximum height
- Source trait data: TRY
- Evidences of disturbances and succession dynamics: "Swiss forests monitored by the Swiss National Forest Inventory experience several types of natural disturbances (such as wind, forest fire, and bark beetles) and harvesting. The age structure reconstructed by Vilen et al.[@Vilen-2012] shows that young forests represents a significant percentage of the forested area (see age distribution below)."
- Contact of person in charge of data formatting: M. Hanewinkel & N. E. Zimmermann (niklaus.zimmermann@wsl.ch)
- Comments: All trees with dbh > 12 cm and > 36 cm were measured within a radius of 7.98 m and 12.62 m, respectively.
- References:
......@@ -174,6 +188,7 @@ Two main data type were used: national forest inventories data -- NFI, large per
- Number of plots: 22904
- Traits: Wood density, SLA, and Maximum height
- Source trait data: TRY
- Evidences of disturbances and succession dynamics: "Swedish forests monitored by the Swedish National Forest Inventory experience several types of natural disturbances (such as wind, forest fire, and bark beetles) and harvesting. The age structure reconstructed by Vilen et al.[@Vilen-2012] shows that young forests represents a significant percentage of the forested area (see age distribution below)."
- Contact of person in charge of data formatting: G. Stahl (Goran.Stahl@slu.se)
- Comments: All trees with dbh > 10 cm, were measured on circular plots of 10 m radius.
- References:
......@@ -189,6 +204,7 @@ Two main data type were used: national forest inventories data -- NFI, large per
- Number of plots: 97434
- Traits: Wood density, SLA, and Maximum height
- Source trait data: TRY
- Evidences of disturbances and succession dynamics: "US forests monitored by the FIA experience several types of natural disturbances (such as wind, forest fire, and bark beetles) and harvesting. The age structure reconstructed by Pan et al.[@Pan-2011] shows that young forests represents a significant percentage of the forested area (see age distribution below)."
- Contact of person in charge of data formatting: M. Vanderwel (Mark.Vanderwel@uregina.ca)
- Comments: FIA data are made up of cluster of 4 subplots of size 0.017 ha for tree dbh > 1.72 cm and nested in each subplot sapling plots of 0.0014 ha for trees dbh > 2.54 cm. The data of the four subplot were lumped together.
- References:
......@@ -204,6 +220,7 @@ Two main data type were used: national forest inventories data -- NFI, large per
- Number of plots: 15019
- Traits: Wood density, SLA, and Maximum height
- Source trait data: TRY
- Evidences of disturbances and succession dynamics: "Canadian forests monitored by the regional forest monitoring programs experience several types of natural disturbances (such as wind, forest fire, and bark beetles) and harvesting. The age structure reconstructed by Pan et al.[@Pan-2011] shows that young forests represents a significant percentage of the forested area (see age distribution below)."
- Contact of person in charge of data formatting: J. Caspersen (john.caspersen@utoronto.ca)
- Comments: The protocol is variable between Provinces. A large proportion of data is from the Quebec province and the plot are 10 m in radius in this Province.
- References:
......@@ -218,6 +235,7 @@ Two main data type were used: national forest inventories data -- NFI, large per
- Number of plots: 1415
- Traits: Wood density, SLA, and Maximum height
- Source trait data: local
- Evidences of disturbances and succession dynamics: "New Zealand forests are experiencing disturbance by earthquake, landslide, storm and volcanic eruptions. According to Holdaway et al.[@Holdaway-2014] having been disturbed during their measurement interval."
- Contact of person in charge of data formatting: D. Laughlin (d.laughlin@waikato.ac.nz)
- Comments: Plots are 20 x 20 m.
- References:
......@@ -234,6 +252,7 @@ Two main data type were used: national forest inventories data -- NFI, large per
- Number of plots: 30
- Traits: Wood density, and Maximum height
- Source trait data: local
- Evidences of disturbances and succession dynamics: The plot network was initially established in the 60s with different level of selection harvesting[@Kariuki-2006].
- Contact of person in charge of data formatting: R. M. Kooyman (robert@ecodingo.com.au)
- Comments: Permanents plots established by the NSW Department of State Forests or by RMK
- References:
......
......@@ -35,7 +35,8 @@ refs$citation <- iconv(refs$citation, "ISO_8859-2", "UTF-8")
replace_refs <- function(x){
ids <- as.numeric(unlist(strsplit(x,",")))
if(length(ids>0))
ret <- paste0("\n\t- ", refs$citation[match(ids, refs$id)], collapse="")
ret <- paste0("\n\t- ", refs$citation[match(ids, refs$id)],
collapse="")
else
ret <- ""
}
......
......@@ -466,6 +466,14 @@
Doi = {10.1146/annurev-ecolsys-110411-160411}
}
@book{Holdaway-2014,
title = {Annual carbon emissions associated with natural disturbance in {New} {Zealand}'s natural and planted forests.},
publisher = {Wellington: Ministry of Primary Industries},
author = {Holdaway, RJ and Mason, NWH and Easdale, T and Dymond, J and Betts, H and Wakelin, S and Moore, S},
year = {2014},
}
@Article{Hoof-2008,
Title = {Contrasting structure and function of pubescent and glabrous varieties of {Hawaiian \textit{{Metrosideros polymorpha}} (Myrtaceae)} at high elevation},
Author = {Hoof, Jennifer and Sack, Lawren and Webb, David T and Nilsen, Erik T},
......@@ -476,6 +484,16 @@
Volume = {40}
}
@article{Hubbell-1999,
title = {Light-gap disturbances, recruitment limitation, and tree diversity in {Neotropical} {Forest}},
volume = {283},
journal = {Science},
author = {Hubbell, S P and Foster, R B and O’brien, S T and Harms, K E and Condit, R and Weschler, B and Wright, S J and Lao, Loo De and S and O Brien, S T and Wechsler, B and Loo de Lao, S},
year = {1999},
pages = {554--557},
}
@Article{Ishihara-2011,
Title = {Forest stand structure, composition, and dynamics in 34 sites over Japan},
Author = {Ishihara, Masae I. and Suzuki, Satoshi N. and Nakamura, Masahiro and Enoki, Tsutomu and Fujiwara, Akio and Hiura, Tsutom and Homma, Kosuke and Hoshino, Daisuke and Hoshizaki, Kazuhiko and Ida, Hideyuki and Ishida, Ken and Itoh, Akira and Kaneko, Takayuki and Kubota, Kaname and Kuraji, Koichiro and Kuramoto, Shigeo and Makita, Akifumi and Masaki, Takashi and Namikawa, Kanji and Niiyama, Kaoru and Noguchi, Mahoko and Nomiya, Haruto and Ohkubo, Tatsuhiro and Saito, Satoshi and Sakai, Takeshi and Sakimoto, Michinori and Sakio, Hitoshi and Shibano, Hirofumi and Sugita, Hisashi and Suzuki, Mitsuo and Takashima, Atsushi and Tanaka, Nobuyuki and Tashiro, Naoaki and Tokuchi, Naoko and Yoshida, Toshiya and Yoshida, Yumiko},
......@@ -510,6 +528,16 @@
Volume = {15}
}
@article{Kariuki-2006,
title = {Diameter growth performance varies with species functional-group and habitat characteristics in subtropical rainforests},
volume = {225},
number = {1-3},
journal = {Forest Ecology and Management},
author = {Kariuki, Maina and Rolfe, Margaret and Smith, R.G.B. and Vanclay, J.K. and Kooyman, Robert M.},
year = {2006},
pages = {1--14},
}
@Book{Keddy-1989,
Title = {Competition},
Author = {Keddy, P. A.},
......@@ -654,6 +682,27 @@
Volume = {24}
}
@article{Lin-2011,
title = {Typhoon {Disturbance} and {Forest} {Dynamics}: {Lessons} from a {Northwest} {Pacific} {Subtropical} {Forest}},
volume = {14},
number = {1},
journal = {Ecosystems},
author = {Lin, Teng-Chiu and Hamburg, Steven P. and Lin, Kuo-Chuan and Wang, Lih-Jih and Chang, Chung-Te and Hsia, Yue-Joe and Vadeboncoeur, Matthew A. and Mabry McMullen, Cathy M. and Liu, Chiung-Pin},
year = {2011},
pages = {127--143},
}
@article{Lobo-2014,
title = {Spatial scale and sampling resolution affect measures of gap disturbance in a lowland tropical forest: implications for understanding forest regeneration and carbon storage},
volume = {281},
issn = {0962-8452, 1471-2954},
number = {1778},
journal = {Proceedings of the Royal Society B: Biological Sciences},
author = {Lobo, E. and Dalling, J. W.},
year = {2014},
pages = {20133218--20133218},
}
@Article{Lusk-2008,
Title = {Why are evergreen leaves so contrary about shade?},
Author = {Lusk, Christopher H and Reich, Peter B and Montgomery, Rebecca a and Ackerly, David D. and Cavender-Bares, Jeannine},
......@@ -925,6 +974,17 @@
Volume = {20}
}
@article{Pan-2011,
title = {Age structure and disturbance legacy of {North} {American} forests},
volume = {8},
number = {3},
journal = {Biogeosciences},
author = {Pan, Y. and Chen, J. M. and Birdsey, R. and McCullough, K. and He, L. and Deng, F.},
year = {2011},
pages = {715--732},
}
@Article{Penuelas-2010a,
Title = {Higher allocation to low cost chemical defenses in invasive species of {Hawaii}},
Author = {Pe{\~n}uelas, Josep and Sardans, Jordi and Llusia, Joan and Owen, {SM} and Silva, J and Niinemets, {\"U}},
......@@ -1227,6 +1287,16 @@
Volume = {74}
}
@article{Uriarte-2009,
title = {Natural disturbance and human land use as determinants of tropical forest dynamics: results from a forest simulator},
volume = {79},
number = {3},
journal = {Ecological Monographs},
author = {Uriarte, María and Canham, C D and Thompson, Jill and Zimmerman, Jess K and Murphy, L and Sabat, Alberto M. and Fetcher, Ned and Haines, Bruce L.},
year = {2009},
pages = {423--443}
}
@Article{Uriarte-2010,
Title = {Trait similarity, shared ancestry and the structure of neighbourhood interactions in a subtropical wet forest: implications for community assembly.},
Author = {Uriarte, Mar{\'\i}a and Swenson, Nathan G and Chazdon, Robin L and Comita, L S and John Kress, W and Erickson, David and Forero-Monta{\~n}a, Jimena and Zimmerman, Jess K and Thompson, Jill},
......@@ -1234,9 +1304,16 @@
Year = {2010},
Pages = {1503--1514},
Volume = {13},
}
Doi = {10.1111/j.1461-0248.2010.01541.x},
Keywords = {13,1503,1514,2010,ecology letters,environmental filtering,genetic conservatism,luquillo forest dynamics plot,niche differentiation,phylo-,spatially explicit models,species interactions}
@article{Vilen-2012,
title = {Reconstructed forest age structure in {Europe} 1950–2010},
volume = {286},
journal = {Forest Ecology and Management},
author = {Vilén, T. and Gunia, K. and Verkerk, P.J. and Seidl, R. and Schelhaas, M.-J. and Lindner, M. and Bellassen, V.},
year = {2012},
pages = {203--218},
}
@Book{Villaescusa-1998,
......@@ -1355,6 +1432,17 @@
Volume = {91}
}
@article{Young-1991,
title = {Crown {Asymmetry}, {Treefalls}, and {Repeat} {Disturbance} of {Broad}-{Leaved} {Forest} {Gaps}},
volume = {72},
number = {4},
journal = {Ecology},
author = {Young, Truman P. and Hubbell, Stephen P.},
year = {1991},
pages = {1464-1471},
}
@Article{Zanne-2010,
Title = {Angiosperm wood structure: global patterns in vessel anatomy and their relation to wood density and potential conductivity},
Author = {Zanne, Amy E and Westoby, Mark and Falster, Daniel S and Ackerly, David D and Loarie, Scott R and Arnold, Sarah {EJ} and Coomes, David A},
......
......@@ -22,18 +22,12 @@ for trait in "'SLA'" "'Wood.density'" "'Max.height'" ; do
# ALL data
for i in `seq 1 3` ; do
Rscript -e "source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(c(model.files.lmer.Tf.1[$i]), run.lmer,$trait, sample.size = $samplesize, var.sample = 'sp.name');print('done')" &
for i in `seq 1 2` ; do
Rscript -e "source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.1[$i], run.lmer,$trait, sample.size =10, sample.vec.TF = TRUE) "
done
for i in `seq 1 3` ; do
Rscript -e "source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(c(model.files.lmer.Tf.2[$i]), run.lmer,$trait, sample.size = $samplesize, var.sample = 'sp.name');print('done')" &
done
done
for i in `seq 1 3` ; do
Rscript -e "source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(c(model.files.lmer.Tf.Multi[$i]), run.lmer,'Multi', data.type ='Multi', sample.size = $samplesize, var.sample = 'sp.name');print('done')" &
done
wait
......@@ -8,7 +8,7 @@ source("R/analysis/lmer.run.R")
format.all.output.lmer(file.name = "NA.wwf.results.nolog.all.rds",
list.file.name = 'list.lmer.out.all.NA.simple.ecocode.rds',
models = c(model.files.lmer.Tf.2),
models = c(model.files.lmer.Tf.2, model.files.lmer.Tf.4),
traits = c("SLA", "Wood.density", "Max.height"))
## format.all.output.lmer(file.name = "NA.wwf.results.nolog.all.rds",
......
......@@ -191,16 +191,26 @@ fun.plot.all.param(list.all.results.set, model = 'lmer.LOGLIN.ER.AD.Tf.MAT.MAP.r
MAT.MAP.TF = TRUE)
dev.off()
fun.plot.all.stabl(list.all.results.set, model = 'lmer.LOGLIN.ER.AD.Tf.r.set.species',
pdf('figs/stabl.set.pdf')
fun.plot.all.stabl(list.all.results.set,
model = 'lmer.LOGLIN.ER.AD.Tf.r.set.species',
MAT.MAP.TF = FALSE)
x11()
fun.plot.all.stabl(list.all.results.intra, model = 'lmer.LOGLIN.ER.AD.Tf.intra.r.set.species',
MAT.MAP.TF = FALSE, intra.TF = TRUE, data.type ='intra')
dev.off()
x11()
fun.plot.all.rho(list.all.results.set, model = 'lmer.LOGLIN.ER.AD.Tf.r.set.species',
MAT.MAP.TF = FALSE)
x11()
fun.plot.all.rho(list.all.results.intra, model = 'lmer.LOGLIN.ER.AD.Tf.intra.r.set.species',
pdf('figs/stabl.set.intra.pdf')
fun.plot.all.stabl(list.all.results.intra,
model = 'lmer.LOGLIN.ER.AD.Tf.intra.r.set.species',
MAT.MAP.TF = FALSE, intra.TF = TRUE, data.type ='intra')
dev.off()
pdf('figs/rho.set.pdf')
fun.plot.all.rho(list.all.results.set,
model = 'lmer.LOGLIN.ER.AD.Tf.r.set.species',
MAT.MAP.TF = FALSE)
dev.off()
pdf('figs/rho.set.intra.pdf')
fun.plot.all.rho(list.all.results.intra,
model = 'lmer.LOGLIN.ER.AD.Tf.intra.r.set.species',
MAT.MAP.TF = FALSE, intra.TF = TRUE, data.type ='intra')
dev.off()
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