Data and codes of "Habitat fragmentation mediates the mechanisms underlying long-term climate-driven thermophilization in birds"

Description for DATA and CODE

This is the original data used in the ecological paper titled "Habitat fragmentation mediates the mechanisms underlying long-term climate-driven thermophilization in birds". There are a total of four Rscript files, four RData files, and 1 README txt file：

###################### DATA ###################

【Distribution_sti_islandpram.RData】includes 3 data frames:

• 1. distribution: presence-absence data for 60 species (rows) on 53 transects(columns) from 36 islands summarising over 10 years (from 2012 to 2021) in the thousand island lake in China;
• 2. sti: STI values ("sti") for 60 species ("sp");
• 3. islandpram: island area ("area", in hectare) and isolation ("DM", in meter) for 53 transects ("mark") on 36 islands ("island).

【Figure 3a.RData】includes 2 data frames:

• 1. cti.local: data for occurrence-based CTI ("CTI") on each transect ("mark) and island ("island) and in each year ("year"); including columns of mean/sd of posterior CTI.
• 2. cti.region: data for regional occurrence-based CTI ("CTI") in each year ("year"); including columns of mean/sd of posterior CTI.

【Figure 4ab & Figure 5ab.RData】includes 5 data frames:

• 1. psi.year: posterior mean "year" effect and 95% CrI in occupancy rate ("mean", "low", "high") for each species ("sp"); column "sig" means significant or not in "year" effect;
• 2. eps.year: posterior mean "year" effect and 95% CrI in extinction rate ("mean", "low", "high") for each species ("sp"); column "sig" means significant or not in "year" effect;
• 3. gam.year: posterior mean "year" effect and 95% CrI in colonization rate ("mean", "low", "high") for each species ("sp"); column "sig" means significant or not in "year" effect;
• 4. eps.increase: posterior estimated effect ("mean", "sd", "low", "high") of all predictors for cold species ("sp") that increase in extinction rate; column "sig.all" indicate significant effect or not in 80% or 95% CrI;
• 5. gam.increase: posterior estimated effect ("mean", "sd", "low", "high") of all predictors for warm species ("sp") that increase in colonization rate. "sig.all" indicate significant effect or not in 80% or 95% CrI.

【Figure 3b&4c.RData】includes 3 data frames:

• 1. cti.abun: abundance-weighted CTI ("cti") on each transect ("mark) and island ("island) and in each year ("year");
• 2. region.cti.abun: regional abundance-weighted CTI ("cti") in each year ("year") ;
• 3. abun.trend: temporal trend ("mean", "se" of year effect) for each species ("sp") and STI ("sti")

###################### CODE ###################

【Figure 3a.R】code for visualizing the temporal trend in occurrence-based CTI.

【Figure 4ab & Figure 5ab.R】code for analyzing and visualizing the relationship between STI and temporal trend in occupancy rate, the relationship between STI and temporal trends in colonization rate or extinction rate; as well as the code for visualizing the mediate effect of habitat fragmentation on two driving processes of thermophilizaiton.

【Figure 3b&4c.R】code for LMM to produce and visualize temporal trends in abundance-weighted CTI both on island level and regional level; as well as code for analyzing the relationship between STI and temporal trend in total abundance.

【MSOM.R】code for multi-species occupancy model