git clone git@github.com:TheoreticalEcosystemEcology/STModel-Data.git
cd STModel-Data
Rscript install_dependencies.r
Note for mac users: this may fail if pg_config is not in your path. If so, you need to install psql first. This is easiest with macports:
sudo port install postgresql93
sudo ln -s /opt/local/lib/postgresql93/bin/* /opt/local/bin
Rscript install_dependencies.r
make -j all
If you want to get the data and you are not at UQAR or connected by wired, please follow this procedure:
- Modify
con_quicc_db.rto:
require("RPostgreSQL")
dbname <- "db_quicc_for"
dbhost <- "127.0.0.1"
dbport <- 55432
-
Open the VPN tunnel:
- Open the web page: https://eduvpn.uqar.ca.
- Login with your UQAR account (e.g. viss0001 is my username)
- Click on the icon «BD PostgreSQL SRBD04».
- The tunnel to the QUICCFOR DB is open.
-
Run
make -j all
Get only tree data: make treeData
Get only climatic data: make climData
Get only plot info data: make plotInfoData
Get only STM past-climate grid input (1970-2000): make STMClimate_grid Use to run STM on the past-climate
Get only SDM past-climate grid input (1970-2000): make SDMClimate_grid Used to project SDM
Retrieve shapefile of the study area (Lakes and boundaries): make SHP_area
The reshape script comes in two parts, the first, reshape/reshapeStates.r computes the
states, and the second, reshape/reshapeTransitions.r computes transitions between
states. In general, use the makefile, either with make -j all or make -j reshape to
run the scripts (which will use default options). The most important option, setting the
threshold basal area for the R state, can be changed by editing the variable at the
beginning of the makefile. To see other options and change them, run the scripts using
Rscript. Start with:
Rscript reshape/reshapeStates.r --help
Rscript reshape/reshapeTransitions.r --help
to get information on the options. There is an additional script,
reshape/reshapeClimTest.r, that does some testing. See its help for more information.
Finally, note that the file reshape/tmpStateData_r$N.rdata, where $N is the cutoff
for the R state, is a temporary file that should not be used. The correct output file,
assuming default options, is out_files/transitions_r$N.rdata.
Defaults:
- threshold basal area for determining the R state: 1 (change in makefile or with -r option)
- climate variables for transitions: annual mean temperature, annual precipitation
- output file: transitions_r1.rdata, where the number will be the r threshold
A rough outline of what the script does:
- Read coarse data from the treeData.csv, plotInfoData.csv, and climData.csv files produced by the sql queries.
- Collapse the tree data into a single state for each year sampled in each plot, using species lists specified in the script.
- Merge the collapsed data with the plotInfoData (to get lat/long)
- Merge this with the climate data into stateData. This is a dataframe with one row for each unique plot-year combination. This will output warnings if there are missing records in the climate or state data; do not ignore these warnings!
- Output some basic summary statistics on the states
- reshapes the sample data into a transition data frame, containing columns for the measurement years, the states, and the mean of the 2 climate variables
- drop all rows from both the transition and state objects containing a U state
- scale the climate variables in the transition data frame
- print the transition table to the console
- save the state and the transition objects, and the transformation for the climate variables, into a single .rdata file
| Column | Description |
|---|---|
| plot_id | Unique id of the plot |
| longitude | longitude of the plot (degree decimal) |
| latitude | latitude of the plot (degree decimal) |
| srid | Spatial Reference System Identifier. All plots have a srid code corresponding to the datum: WGS84 (see here). |
| Column | Description |
|---|---|
| plot_id | Unique id of the plot |
| year_measured | year of the measurement |
| id_spe | Species code, details are available in ./stm_code_species.csv file |
| basal area | basal area of the species in m²/ha |
| Column | Description |
|---|---|
| plot_id | Unique id of the plot |
| year_measured | year of the measurement |
| mean_diurnal_range | Avg of monthly temperature ranges |
| isothermality | mean_diurnal_range ÷ temp_annual_range |
| temp_seasonality | Standard deviation of monthly-mean temperature estimates expressed as a percent of their mean |
| max_temp_warmest_period | Highest monthly maximum temperature |
| min_temp_coldest_period | Lowest monthly minimum temperature |
| temp_annual_range | max_temp_warmest_period – min_temp_coldest_period |
| mean_temperatre_wettest_quarter | Avg temperature during 3 wettest months |
| mean_temp_driest_quarter | Avg temperature during 3 driest months |
| mean_temp_warmest_quarter | Avg temperature during 3 warmest months |
| mean_temp_coldest_quarter | Avg temperature during 3 coldest months |
| annual_pp | Sum of monthly precipitation values |
| pp_wettest_period | Precipitation of the wettest month |
| pp_driest_period | Precipitation of the driest month |
| pp_seasonality | Standard deviation of the monthly precipitation estimates expressed as a percent of their mean |
| pp_wettest_quarter | Total precipitation of 3 wettest months |
| pp_driest_quarter | Total precipitation of 3 driest months |
| pp_warmest_quarter | Total precipitation of 3 warmest months |
| pp_coldest_quarter | Total precipitation of 3 coldest months |
| julian_day_number_start_growing_season | Julian day number at start of growing season |
| julian_day_number_at_end_growing_season | Julian day number at end of growing season |
| number_days_growing_season | Length of growing season (days) |
| total_pp_for_period_1 | Total precipitation 3 weeks prior to growing season |
| total_pp_for_period_3 | Total precipitation during the growing season |
| gdd_above_base_temp_for_period_3 | Degree days (above 5ºC) for growing season Variable |
| annual_mean_temp | Avg of mean monthly temperatures |
| annual_min_temp | Avg of min monthly temperatures |
| annual_max_temp | Avg of max monthly temperatures |
| mean_temp_for_period_3 | Average temperature during growing season |
| temp_range_for_period_3 | Highest maximum temperature minus lowest minimum temperature during growing |
Further details here
| Column | Description |
|---|---|
| x | x coordinate of the cell (longitude). i.e. x = 0 corresponds to min(longitude) |
| y | y coordinate of the cell (latitude). i.e. y = 0 corresponds to min(latitude) |
| year | year of the climate measurement. In the sql query, year column equal to 0 because the climate has been aggregated temporarily. |
| env1 | average of the mean temperature (°C) between 1970-2000. |
| env2 | average of the annual precipitation (meters) between 1970-2000. |
| Code | Species |
|---|---|
| 18032-ABI-BAL | Balsam fir |
| 18034-PIC-RUB | Red spruce |
| 19408-QUE-RUB | Red oak |
| 19462-FAG-GRA | American beech |
| 19466-ALN-NA | Saule |
| 19481-BET-ALL | Yellow birch |
| 19489-BET-PAP | White |
| 19511-OST-VIR | Ironwood |
| 21536-TIL-AME | Basswood |
| 22453-POP-BAL | Balsam poplar |
| 22463-POP-GRA | Large tooth |
| 24764-PRU-SER | Black cherry |
| 24799-PRU-PEN | Pin cherry |
| 25319-SOR-AME | American mountain-ash |
| 28728-ACE-RUB | Red maple |
| 28731-ACE-SAC | Sugar maple |
| 32931-FRA-AME | White ash |
| 32945-FRA-NIG | Black ash |
| 183295-PIC-GLA | White spruce |
| 183302-PIC-MAR | Black spruce |
| 183319-PIN-BAN | jack pine |
| 183412-LAR-LAR | Tamarack |
| 195773-POP-TRE | Trembling aspen |
| Code | Soil type |
|---|---|
| 0 | NODATA |
| 1 | Acrisols |
| 2 | Albeluvisols |
| 3 | Alisols |
| 4 | Andosols |
| 5 | Anthrosols |
| 6 | Arenosols |
| 7 | Calcisols |
| 8 | Cambisols |
| 9 | Chernozems |
| 10 | Cryosols |
| 11 | Durisols |
| 12 | Ferralsols |
| 13 | Fluvisols |
| 14 | Gleysols |
| 15 | Gypsisols |
| 16 | Histosols |
| 17 | Kastanozems |
| 18 | Leptosols |
| 19 | Lixisols |
| 20 | Luvisols |
| 21 | Nitisols |
| 22 | Phaeozems |
| 23 | Planosols |
| 24 | Plinthosols |
| 25 | Podzols |
| 27 | Regosols |
| 28 | Solonchaks |
| 29 | Solonetz |
| 30 | Stagnosols |
| 31 | Umbrisols |
| 32 | Vertisols |