README.md
In iffylaw/PIC: Permafrost Index Computing
PIC (Permafrost Indices Computing)
0. Introduction
Figure 1. Map of the data location over QTP.
At present, there are dozens of different indices are used to evaluate the characteristics and dynamics of permafrost presence or absence, including:
- thawing/freezing degree-days of air and ground surface (DDTa/DDTs/DDFa/DDFs)
- seasonal thawing/freezing n factor (nt/nf)
- MAAT (mean annual air temperature)
- MAGT (mean annual ground temperature)
- MAGST (mean annual ground surface temperature)
- TTOP (the temperature at the top of permafrost)
- ALT (active layer thickness)
- maximum freeze depth (FD)
Figure 2. The Structure Diagram of PIC
Table 1. Most important user functions in the PIC.
| R function | Description and reference | Unit | Equation |
|-----------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------|------------|
| Temperature-related indices |
| Freezing_index | Freezing degree-days for air and ground | ℃ | (4,6) |
| Thawing_index | Thawing degree-days for air and ground | ℃ | (3,5) |
| MAAT | Mean annual air temperature | ℃ | (7) |
| MAGST | Mean annual ground surface temperature (5 cm) | ℃ | (8) |
| MAGT | Mean annual ground temperature (at 15 m) | ℃ | (10) |
| NT | Thawing n-factor | | (11) |
| NF | Freezing n-factor | | (12) |
| Surface_Offset | The difference between the MAGST and MAAT | ℃ | |
| Thermal_Offset | The difference between the TTOP and MAGST | ℃ | |
| Vegetation_Offset | The second term (Surface_Offset) is negative, and represents the reduction in MAGST due to vegetation effects in summer (vegetation offset) | ℃ | |
| Nival_Offset | The first term (Surface_Offset) on the right-hand-side is positive, and represents the elevation of MAGST over MAAT due to the insulating effect of winter snow cover (nival offset) | ℃ | |
| TTOP_Smith | The temperature at the top of the permafrost using Smith & Riseborough function | ℃ | (13) |
| TTOP_Kudryavtsev | The temperature at the top of the permafrost using Kudryavtsev function | ℃ | (14) |
| Depth-related indices |
| Freeze_depth_Stefan | Maximum freezing depth using Stefan function | m | (20) |
| Thaw_depth_Stefan | Active layer thickness using Stefan function | m | (16) |
| ALT_Kudryavtsev | Active layer thickness (ALT) or maximum thawing depth using Kudryavtsev function | m | (19) |
| Region |
| Spatial_Pic | Spatial changes with MAAT, DDTa, DDFa and ALT | m | (3,4,7,16) |
| Toolkit |
| Com_Indices_QTP | Computing all indices for all stations of the QTP | | |
| Outlier_Process | Process the abnormal value | | |
| VLH | Computing volumetric latent heat of fusion | J/m3 | (2) |
| Convert_4_ggplot | Convert the values of TTOP & ALT to one columns | | |
| Exist_Permafrost | To determine which stations exists permafrost by TTOP values | | |
| Statistic |
| Stat | Statistic functions with more 10 methods | | (21,22,23) |
| Spatial_Stat | Spatial statistic method, just for spatial trend | | (24) |
| Com_Stats_QTP | Computing the statistc values for one or both of these indices | | |
| Visualization |
| Plot_3M | Plot MAAT, MAGST, and MAGT for all stations or a station | | |
| Plot_TTOP_ALT | Plot TTOP and ALT for all stations or a station | | |
| ggplot_Pic | Plot multiple indices all stations or a station using ggplot2 | | |
| Map_Pic | Plot multiple indices all stations or a station using ggmap | | |
| Netcdf_Multiplot | Region visualization of NetCDF with multiple plots | | |
| Netcdf_Animation | Region animation of NetCDF | | |
1. Statistics
The stat function contains all statistical methods for station calculation. A spatial trend can also be computed using the Spatial_Stat function after the regional calculation.
Table 2. ALT Statistic values
| | Pishan | Hetian | Minfeng | Mangya | Yutian | Lenghu | Tuole | Yeniugou | Zhangye | Qilian | Shandan | Yongchang | Dacaidan | Delingha | Gangcha | Menyuan | Nuomuhong | Dulan | Qiabuqia | Xining | Wudaoliang | Xinghai | Shiquanhe | Gaize | Bange | Anduo | Pulan | Shenzha | Dangxiong | Lazi | Rikeze | Nimu | Lasa | Jiangzi | Cuona | Longzi | Pali | Zaduo | Yushu | Maduo | Qingshuihe | Shiqu | Changdou | Dege | Ganzi | Seda | Daofou | Maerkang | Xinlong | Zuogong | Kangding | Deqin |
|-----------|----------|----------|----------|--------|----------|---------|---------|----------|----------|---------|---------|-----------|----------|----------|---------|---------|-----------|---------|----------|----------|------------|---------|-----------|---------|--------|--------|---------|---------|-----------|---------|---------|----------|---------|---------|---------|---------|---------|--------|---------|--------|------------|--------|----------|---------|---------|--------|----------|----------|---------|---------|----------|---------|
| intercept | 1.84 | 1.63 | 1.73 | 4.99 | 1.30 | 2.21 | -0.55 | -1.43 | 1.96 | 3.40 | 4.85 | 2.57 | -0.33 | 2.84 | -1.41 | 0.21 | 1.72 | 2.67 | 3.48 | 1.98 | -0.10 | 1.72 | 5.77 | 3.49 | 0.03 | -0.82 | 2.75 | -0.87 | 3.70 | 2.94 | 2.19 | 1.34 | 0.57 | 2.15 | 4.02 | 2.72 | -0.99 | 0.11 | 2.68 | 0.15 | 0.40 | 0.42 | 0.68 | 4.16 | 1.52 | 1.04 | 1.84 | 0.40 | 1.68 | 3.64 | 1.75 | 2.36 |
| slope | -0.37 | -0.42 | -0.40 | -1.57 | -0.27 | -0.47 | 0.69 | 0.97 | -0.48 | -0.94 | -1.31 | -0.73 | 0.55 | -0.74 | 1.06 | 0.35 | -0.38 | -0.77 | -1.19 | -0.46 | 0.59 | -0.41 | -2.03 | -0.95 | 0.43 | 1.09 | -0.86 | 0.94 | -1.23 | -0.97 | -0.78 | -0.28 | -0.15 | -0.84 | -1.42 | -0.87 | 1.23 | 0.36 | -0.82 | 0.32 | 0.30 | 0.32 | -0.11 | -1.43 | -0.45 | 0.08 | -0.54 | -0.07 | -0.49 | -1.23 | -0.57 | -0.91 |
| r | -0.55 | -0.28 | -0.53 | -0.68 | -0.23 | -0.35 | 0.73 | 0.80 | -0.47 | -0.49 | -0.67 | -0.56 | 0.09 | -0.62 | 0.65 | 0.07 | -0.33 | -0.64 | -0.60 | -0.47 | 0.78 | -0.32 | -0.61 | -0.62 | 0.60 | 0.55 | -0.52 | 0.14 | -0.38 | -0.79 | -0.50 | -0.52 | -0.32 | -0.60 | -0.33 | -0.58 | 0.20 | 0.08 | -0.52 | 0.82 | 0.37 | 0.26 | -0.42 | -0.68 | -0.44 | 0.07 | -0.38 | -0.23 | -0.45 | -0.66 | -0.31 | -0.81 |
| rr | 0.30 | 0.08 | 0.28 | 0.46 | 0.05 | 0.13 | 0.54 | 0.65 | 0.22 | 0.24 | 0.44 | 0.31 | 0.01 | 0.38 | 0.42 | 0.00 | 0.11 | 0.41 | 0.36 | 0.22 | 0.61 | 0.10 | 0.37 | 0.39 | 0.36 | 0.30 | 0.27 | 0.02 | 0.14 | 0.62 | 0.25 | 0.27 | 0.10 | 0.36 | 0.11 | 0.34 | 0.04 | 0.01 | 0.27 | 0.67 | 0.14 | 0.07 | 0.18 | 0.46 | 0.19 | 0.00 | 0.14 | 0.05 | 0.21 | 0.44 | 0.09 | 0.66 |
| rmse | 4.03 | 3.05 | 3.32 | 1.52 | 3.46 | 2.84 | 1.24 | 1.53 | 2.40 | 1.35 | 2.55 | 2.19 | 1.52 | 2.26 | 1.26 | 1.39 | 2.30 | 1.86 | 1.60 | 2.58 | 0.60 | 1.47 | 1.27 | 1.98 | 1.14 | 0.66 | 2.12 | 1.07 | 1.65 | 2.46 | 2.04 | 3.85 | 2.69 | 1.72 | 1.21 | 2.30 | 0.67 | 1.16 | 1.82 | 0.74 | 0.56 | 0.80 | 3.07 | 2.18 | 2.35 | 0.83 | 2.57 | 3.60 | 2.58 | 2.07 | 2.37 | 2.17 |
| nrmse | 0.94 | 0.92 | 0.91 | 0.62 | 0.92 | 0.83 | 0.55 | 0.56 | 0.82 | 0.55 | 0.80 | 0.79 | 0.58 | 0.77 | 0.50 | 0.56 | 0.79 | 0.73 | 0.69 | 0.83 | 0.50 | 0.65 | 0.55 | 0.70 | 0.56 | 0.38 | 0.81 | 0.46 | 0.68 | 0.89 | 0.86 | 0.95 | 0.95 | 0.81 | 0.55 | 0.86 | 0.47 | 0.59 | 0.74 | 0.56 | 0.41 | 0.44 | 0.91 | 0.84 | 0.88 | 0.41 | 0.89 | 0.96 | 0.90 | 0.80 | 0.90 | 0.91 |
| sd_s | 0.09 | 0.08 | 0.08 | 0.18 | 0.07 | 0.08 | 0.11 | 0.13 | 0.06 | 0.07 | 0.08 | 0.06 | 0.11 | 0.08 | 0.10 | 0.11 | 0.08 | 0.07 | 0.08 | 0.05 | 0.09 | 0.08 | 0.11 | 0.12 | 0.12 | 0.08 | 0.08 | 0.08 | 0.08 | 0.09 | 0.06 | 0.09 | 0.10 | 0.06 | 0.08 | 0.07 | 0.04 | 0.09 | 0.10 | 0.08 | 0.09 | 0.09 | 0.09 | 0.07 | 0.08 | 0.08 | 0.07 | 0.08 | 0.07 | 0.07 | 0.06 | 0.13 |
| sd_k | 0.06 | 0.06 | 0.06 | 0.26 | 0.05 | 0.06 | 0.08 | 0.13 | 0.07 | 0.12 | 0.12 | 0.07 | 0.11 | 0.09 | 0.11 | 0.09 | 0.08 | 0.12 | 0.13 | 0.05 | 0.06 | 0.06 | 0.26 | 0.13 | 0.08 | 0.10 | 0.14 | 0.16 | 0.17 | 0.07 | 0.07 | 0.04 | 0.03 | 0.08 | 0.21 | 0.08 | 0.05 | 0.07 | 0.12 | 0.03 | 0.05 | 0.07 | 0.06 | 0.09 | 0.08 | 0.08 | 0.08 | 0.03 | 0.07 | 0.09 | 0.08 | 0.10 |
| mef | -1674.98 | -1209.29 | -1496.06 | -43.24 | -1952.95 | -684.35 | -122.00 | -74.20 | -1287.34 | -299.68 | -915.51 | -1227.18 | -177.31 | -651.32 | -87.25 | -143.32 | -739.12 | -648.08 | -334.96 | -2066.05 | -21.22 | -303.76 | -119.38 | -234.87 | -45.55 | -57.28 | -557.76 | -90.17 | -461.12 | -714.20 | -951.79 | -1814.19 | -613.21 | -749.58 | -188.69 | -829.40 | -113.58 | -84.98 | -271.57 | -41.15 | -17.23 | -45.91 | -1066.25 | -718.82 | -555.50 | -62.87 | -1346.71 | -1453.86 | -887.90 | -741.26 | -919.01 | -262.24 |
| nae | -0.94 | -0.92 | -0.92 | -0.58 | -0.92 | -0.83 | -0.56 | -0.55 | -0.81 | -0.55 | -0.80 | -0.80 | -0.58 | -0.77 | -0.50 | -0.57 | -0.79 | -0.73 | -0.69 | -0.83 | -0.48 | -0.65 | -0.53 | -0.70 | -0.55 | -0.39 | -0.81 | -0.45 | -0.68 | -0.90 | -0.86 | -0.95 | -0.95 | -0.82 | -0.55 | -0.86 | -0.47 | -0.58 | -0.74 | -0.56 | -0.41 | -0.44 | -0.91 | -0.83 | -0.88 | -0.41 | -0.89 | -0.96 | -0.90 | -0.80 | -0.90 | -0.92 |
| vr | 0.37 | 0.61 | 0.45 | 2.06 | 0.54 | 0.53 | 0.57 | 1.08 | 1.34 | 2.79 | 2.19 | 1.17 | 1.16 | 1.25 | 1.29 | 0.72 | 0.93 | 2.73 | 2.66 | 1.05 | 0.44 | 0.51 | 5.19 | 1.19 | 0.42 | 1.41 | 3.06 | 3.56 | 4.90 | 0.67 | 1.30 | 0.16 | 0.10 | 1.70 | 6.19 | 1.16 | 1.46 | 0.64 | 1.32 | 0.15 | 0.27 | 0.66 | 0.48 | 1.58 | 0.93 | 0.97 | 1.47 | 0.16 | 1.01 | 1.62 | 1.97 | 0.66 |
| pbias | 84.66 | 80.60 | 84.64 | 36.85 | 80.30 | 41.34 | 48.72 | 29.22 | 71.16 | 46.25 | 69.99 | 73.13 | 48.28 | 68.28 | 25.55 | 50.99 | 71.51 | 65.80 | 60.21 | 71.99 | 24.80 | 56.97 | 48.67 | 62.20 | 26.86 | 33.69 | 65.07 | 24.11 | 66.30 | 78.26 | 77.76 | 89.16 | 83.87 | 69.81 | 49.16 | 70.24 | 23.08 | 28.34 | 63.17 | 25.54 | 18.96 | 26.39 | 76.16 | 61.32 | 58.43 | 22.97 | 77.74 | 62.23 | 50.46 | 72.68 | 45.96 | 79.51 |
| nse | 0.10 | 0.12 | 0.08 | 0.31 | 0.13 | 0.50 | 0.14 | 0.47 | 0.12 | 0.15 | 0.12 | 0.09 | 0.18 | 0.11 | 0.48 | 0.11 | 0.10 | 0.09 | 0.12 | 0.13 | 0.48 | 0.13 | 0.04 | 0.11 | 0.51 | 0.15 | 0.19 | 0.45 | 0.01 | 0.13 | 0.09 | 0.06 | 0.12 | 0.14 | 0.09 | 0.18 | 0.50 | 0.51 | 0.14 | 0.54 | 0.54 | 0.40 | 0.16 | 0.26 | 0.34 | 0.43 | 0.13 | 0.35 | 0.44 | 0.09 | 0.49 | 0.14 |
| rsr | 0.95 | 0.94 | 0.96 | 0.83 | 0.93 | 0.71 | 0.93 | 0.73 | 0.94 | 0.92 | 0.94 | 0.96 | 0.91 | 0.94 | 0.72 | 0.94 | 0.95 | 0.95 | 0.94 | 0.93 | 0.72 | 0.93 | 0.98 | 0.94 | 0.70 | 0.92 | 0.90 | 0.74 | 1.00 | 0.93 | 0.95 | 0.97 | 0.94 | 0.93 | 0.95 | 0.91 | 0.71 | 0.70 | 0.93 | 0.68 | 0.68 | 0.78 | 0.92 | 0.86 | 0.81 | 0.75 | 0.93 | 0.80 | 0.75 | 0.95 | 0.71 | 0.93 |
| d | 0.03 | 0.04 | 0.03 | 0.14 | 0.03 | 0.04 | 0.11 | 0.13 | 0.04 | 0.07 | 0.04 | 0.04 | 0.08 | 0.05 | 0.12 | 0.10 | 0.05 | 0.05 | 0.07 | 0.03 | 0.21 | 0.07 | 0.10 | 0.08 | 0.11 | 0.15 | 0.05 | 0.10 | 0.07 | 0.05 | 0.04 | 0.03 | 0.05 | 0.05 | 0.08 | 0.04 | 0.08 | 0.10 | 0.07 | 0.16 | 0.20 | 0.15 | 0.04 | 0.04 | 0.05 | 0.12 | 0.04 | 0.03 | 0.04 | 0.05 | 0.04 | 0.08 |
2. Visualization
Station visualization can be produced by Plot_TTOP_ALT and Plot_3M. The Plot_TTOP_ALT function plots two TTOP or two ALT indices in a figure for all stations or stations with permafrost. VarName has the “TTOP” and “ALT” options, whereas SID has the “permafrost” and “all” options. The Plot_3M function draws the MAAT, MAGST, and MAGT indices. The two functions only plot these stations where permafrost exists when SID = “permafrost.”
Figure 3. TTOP visualization
Figure 4. MAAT animation
Figure 5. ALT animation
Figure 6. Spatial trend of MAAT, DDTa, DDFa and ALT.
Figure 7. Region visualization of ALT.
3. Examples
Several examples of the PIC application were presented here.
#
# The example is designed to help users better use the PIC package
# Author: Lihui Luo (E-mail: luolh@lzb.ac.cn)
# Cold and Arid Regions Environmental and Engineering Research Institute,
# Chinese Academy of Sciences
# updated: 06/08/2018
#
##########################################################################################
# Compute temperature/depth-related indices using daily weather observations
##########################################################################################
# Thawing_index: DDTa
Thawing_index(Year=1980, TempName="Temperature", data=QTP_ATM, SID=52908)
Thawing_index(Year=1980:2010, TempName="Temperature", data=QTP_ATM, SID=52908)
# Thawing_index: DDTs
Thawing_index(Year=1980, TempName="GT", data=QTP_ATM, SID=52908)
Thawing_index(Year=1980:2010, TempName="GT", data=QTP_ATM, SID=52908)
# Freezing_index: DDFa
Freezing_index(Year=1980, TempName="Temperature", data=QTP_ATM, SID=52908)
Freezing_index(Year=1980:2010, TempName="Temperature", data=QTP_ATM, SID=52908)
# Freezing_index: DDFs
Freezing_index(Year=1980, TempName="GT", data=QTP_ATM, SID=52908)
Freezing_index(Year=1980:2010, TempName="GT", data=QTP_ATM, SID=52908)
# MAAT
MAAT(Year=1980, TempName="Temperature", data=QTP_ATM, SID=52908)
MAAT(Year=1980:2010, TempName="Temperature", data=QTP_ATM, SID=52908)
# NT
NT(Year=1980, AirTempName="Temperature", GroundTempName="GT", data=QTP_ATM, SID=52908)
NT(Year=1980:2010, AirTempName="Temperature", GroundTempName="GT", data=QTP_ATM, SID=52908)
# NF
NF(Year=1980, AirTempName="Temperature", GroundTempName="GT", data=QTP_ATM, SID=52908)
NF(Year=1980:2010, AirTempName="Temperature", GroundTempName="GT", data=QTP_ATM, SID=52908)
# MAGST
MAGST(Year=1980, AirTempName="Temperature", GroundTempName="GT", data=QTP_ATM, SID=52908)
MAGST(Year=1980:2010, AirTempName="Temperature", GroundTempName="GT", data=QTP_ATM, SID=52908)
# Temp_Amp_Daily
Temp_Ampl_Daily(Year=1980, MinTempName="GT_0_MIN", MaxTempName="GT_0_MAX", data=QTP_ATM, SID=52908)
Temp_Ampl_Daily(Year=1980:2010, MinTempName="Tmin", MaxTempName="GT_0_MAX", data=QTP_ATM, SID=52908)
# Temp_Amp_Manual
Temp_Ampl_Annual(Year=1980, MinTempName="GT_0_MIN", MaxTempName="GT_0_MAX", data=QTP_ATM, SID=52908)
Temp_Ampl_Annual(Year=1980:2010, MinTempName="GT_0_MIN", MaxTempName="GT_0_MAX", data=QTP_ATM, SID=52908)
# SoilTemp_Diff_Depths:soil temperature at 15 m
SoilTemp_Diff_Depths(Year=1980, depth=15, time=3600*12, AirTempName="Temperature", MinTempName="Tmin", MaxTempName="Tmax", data=QTP_ATM, SID=52908)
SoilTemp_Diff_Depths(Year=1980:2010, depth=15, time=3600*12, AirTempName="Temperature", MinTempName="Tmin", MaxTempName="Tmax", data=QTP_ATM, SID=52908)
# MAGT
MAGT(Year=1980, AirTempName="Temperature", MinTempName="Tmin", MaxTempName="Tmax", data=QTP_ATM, SID=52908)
MAGT(Year=1980:2010, AirTempName="Temperature", MinTempName="Tmin", MaxTempName="Tmax", data=QTP_ATM, SID=52908)
#Vegetation_Offset
Vegetation_Offset(Year=1980, AirTempName="Temperature", GroundTempName="GT", data=QTP_ATM, SID=52908)
Vegetation_Offset(Year=1980:2010, AirTempName="Temperature", GroundTempName="GT", data=QTP_ATM, SID=52908)
# Surface_Offset
Surface_Offset(Year=1980, AirTempName="Temperature", GroundTempName="GT", data=QTP_ATM, SID=52908)
Surface_Offset(Year=1980:2010, AirTempName="Temperature", GroundTempName="GT", data=QTP_ATM, SID=52908
# Thermal_Offset
Thermal_Offset(Year=1980, AirTempName="Temperature", GroundTempName="GT", data=QTP_ATM, SID=52908)
Thermal_Offset(Year=1980:2010, AirTempName="Temperature", GroundTempName="GT", data=QTP_ATM, SID=52908)
# Nival_Offset
Nival_Offset(Year=1980, AirTempName="Temperature", GroundTempName="GT", data=QTP_ATM, SID=52908)
Nival_Offset(Year=1980:2010, AirTempName="Temperature", GroundTempName="GT", data=QTP_ATM, SID=52908)
# TTOP_Smith
TTOP_Smith(Year=1980, AirTempName="Temperature", GroundTempName="GT", data=QTP_ATM, SID=52908)
TTOP_Smith(Year=1980:2010, AirTempName="Temperature", GroundTempName="GT", data=QTP_ATM, SID=52908)
# TTOP_Kudryavtsev
TTOP_Kudryavtsev(Year=1980, AirTempName="Temperature", GroundTempName="GT", MinGTName="GT_0_MIN", MaxGTName="GT_0_MAX", data=QTP_ATM, SID=52908)
TTOP_Kudryavtsev(Year=1980:2010, AirTempName="Temperature", GroundTempName="GT", MinGTName="GT_0_MIN", MaxGTName="GT_0_MAX", data=QTP_ATM, SID=52908)
# Thaw_depth_Stefan
Thaw_depth_Stefan(Year=1980, AirTempName="Temperature", data=QTP_ATM, SID=52908)
Thaw_depth_Stefan(Year=1980:2010, AirTempName="Temperature", data=QTP_ATM, SID=52908)
# Freeze_depth_Stefan is for seasonal frozen soil
Freeze_depth_Stefan(Year=1980, AirTempName="Temperature", data=QTP_ATM, SID=56444)
Freeze_depth_Stefan(Year=1980:2010, AirTempName="Temperature", data=QTP_ATM, SID=56444)
# ALT_Kudryavtsev
ALT_Kudryavtsev(Year=1980, AirTempName="Temperature", GroundTempName="GT", MinGTName="GT_0_MIN", MaxGTName="GT_0_MAX", data=QTP_ATM, SID=52908)
ALT_Kudryavtsev(Year=1980:2010, AirTempName="Temperature", GroundTempName="GT", MinGTName="GT_0_MIN", MaxGTName="GT_0_MAX", data=QTP_ATM, SID=52908)
##########################################################################################
# compute and save the temperature/depth-related indices
##########################################################################################
MAAT_QTP <- Com_Indices_QTP(VarName = "MAAT")
MAGST_QTP <- Com_Indices_QTP(VarName = "MAGST")
MAGT_QTP <- Com_Indices_QTP(VarName = "MAGT")
NT_QTP <- Com_Indices_QTP(VarName = "NT")
NF_QTP <- Com_Indices_QTP(VarName = "NF")
DDTa_QTP <- Com_Indices_QTP(VarName = "Thawing_index_air")
DDTs_QTP <- Com_Indices_QTP(VarName = "Thawing_index_ground")
DDFa_QTP <- Com_Indices_QTP(VarName = "Freezing_index_air")
DDFs_QTP <- Com_Indices_QTP(VarName = "Freezing_index_ground")
VO_QTP <- Com_Indices_QTP(VarName = "Vegetation_Offset")
SO_QTP <- Com_Indices_QTP(VarName = "Surface_Offset")
TO_QTP <- Com_Indices_QTP(VarName = "Thermal_Offset")
NO_QTP <- Com_Indices_QTP(VarName = "Nival_Offset")
TTOP_S_QTP <- Com_Indices_QTP(VarName = "TTOP_Smith")
TTOP_K_QTP <- Com_Indices_QTP(VarName = "TTOP_Kudryavtsev")
ALT_S_QTP <- Com_Indices_QTP(VarName = "Thaw_depth_Stefan")
FD_S_QTP <- Com_Indices_QTP(VarName = "Freeze_depth_Stefan")
ALT_K_QTP <- Com_Indices_QTP(VarName = "ALT_Kudryavtsev")
##########################################################################################
# process the outlier values
##########################################################################################
stations <- length(Station_Info$SID)
MAAT_QTP <- Outlier_Process(MAAT_QTP[,1:stations])
MAGST_QTP <- Outlier_Process(MAGST_QTP[,1:stations])
MAGT_QTP <- Outlier_Process(MAGT_QTP[,1:stations])
NT_QTP <- Outlier_Process(NT_QTP[,1:stations])
NF_QTP <- Outlier_Process(NF_QTP[,1:stations])
DDTa_QTP <- Outlier_Process(DDTa_QTP[,1:stations])
DDTs_QTP <- Outlier_Process(DDTs_QTP[,1:stations])
DDFa_QTP <- Outlier_Process(DDFa_QTP[,1:stations])
DDFs_QTP <- Outlier_Process(DDFs_QTP[,1:stations])
VO_QTP <- Outlier_Process(VO_QTP[,1:stations])
SO_QTP <- Outlier_Process(SO_QTP[,1:stations])
TO_QTP <- Outlier_Process(TO_QTP[,1:stations])
NO_QTP <- Outlier_Process(NO_QTP[,1:stations])
TTOP_S_QTP <- Outlier_Process(TTOP_S_QTP[,1:stations])
TTOP_K_QTP <- Outlier_Process(TTOP_K_QTP[,1:stations])
ALT_S_QTP <- Outlier_Process(ALT_S_QTP[,1:stations])
FD_S_QTP <- Outlier_Process(FD_S_QTP[,1:stations])
ALT_K_QTP <- Outlier_Process(ALT_K_QTP[,1:stations])
##########################################################################################
# Save these indices to Rdata file
##########################################################################################
save(MAAT_QTP, file="I:/PIC/PIC/MAAT_QTP.Rdata")
save(MAGST_QTP, file="I:/PIC/PIC/MAGST_QTP.Rdata")
save(MAGT_QTP, file="I:/PIC/PIC/MAGT_QTP.Rdata")
save(NT_QTP, file="I:/PIC/PIC/NT_QTP.Rdata")
save(NF_QTP, file="I:/PIC/PIC/NF_QTP.Rdata")
save(DDTa_QTP, file="I:/PIC/PIC/DDTa_QTP.Rdata")
save(DDTs_QTP, file="I:/PIC/PIC/DDTs_QTP.Rdata")
save(DDFa_QTP, file="I:/PIC/PIC/DDFa_QTP.Rdata")
save(DDFs_QTP, file="I:/PIC/PIC/DDFs_QTP.Rdata")
save(VO_QTP, file="I:/PIC/PIC/VO_QTP.Rdata")
save(SO_QTP, file="I:/PIC/PIC/SO_QTP.Rdata")
save(TO_QTP, file="I:/PIC/PIC/TO_QTP.Rdata")
save(NO_QTP, file="I:/PIC/PIC/NO_QTP.Rdata")
save(TTOP_S_QTP, file="I:/PIC/PIC/TTOP_S_QTP.Rdata")
save(TTOP_K_QTP, file="I:/PIC/PIC/TTOP_K_QTP.Rdata")
save(ALT_S_QTP, file="I:/PIC/PIC/ALT_S_QTP.Rdata")
save(FD_S_QTP, file="I:/PIC/PIC/FD_S_QTP.Rdata")
save(ALT_K_QTP, file="I:/PIC/PIC/ALT_K_QTP.Rdata")
##########################################################################################
# to determine which stations may exist permafrost
##########################################################################################
Exist_Permafrost()
Exist_Permafrost(plot="yes")
##########################################################################################
# Statistic analysis of stations
##########################################################################################
# Single index
MAAT_QTP_Stat <- Com_Stats_QTP(ind1=MAAT_QTP)
MAGST_QTP_Stat <- Com_Stats_QTP(ind1=MAGST_QTP)
MAGT_QTP_Stat <- Com_Stats_QTP(ind1=MAGT_QTP)
NT_QTP_Stat <- Com_Stats_QTP(ind1=NT_QTP)
NF_QTP_Stat <- Com_Stats_QTP(ind1=NF_QTP)
DDTa_QTP_Stat <- Com_Stats_QTP(ind1=DDTa_QTP)
DDTs_QTP_Stat <- Com_Stats_QTP(ind1=DDTs_QTP)
DDFa_QTP_Stat <- Com_Stats_QTP(ind1=DDFa_QTP)
DDFs_QTP_Stat <- Com_Stats_QTP(ind1=DDFs_QTP)
VO_QTP_Stat <- Com_Stats_QTP(ind1=VO_QTP)
SO_QTP_Stat <- Com_Stats_QTP(ind1=SO_QTP)
TO_QTP_Stat <- Com_Stats_QTP(ind1=TO_QTP)
NO_QTP_Stat <- Com_Stats_QTP(ind1=NO_QTP)
TTOP_S_QTP_Stat <- Com_Stats_QTP(ind1=TTOP_S_QTP)
TTOP_K_QTP_Stat <- Com_Stats_QTP(ind1=TTOP_K_QTP)
ALT_S_QTP_Stat <- Com_Stats_QTP(ind1=ALT_S_QTP)
FD_S_QTP_Stat <- Com_Stats_QTP(ind1=FD_S_QTP)
ALT_K_QTP_Stat <- Com_Stats_QTP(ind1=ALT_K_QTP)
# Same two indices (TTOP & ALT)
TTOP_S_K_QTP_Stat <- Com_Stats_QTP(ind1=TTOP_S_QTP, ind2=TTOP_K_QTP)
ALT_S_K_QTP_Stat <- Com_Stats_QTP(ind1=ALT_S_QTP, ind2=ALT_K_QTP)
##########################################################################################
# Visualization of stations
##########################################################################################
# plot TTOP & ALT
Plot_TTOP_ALT(VarName="TTOP", SID="permafrost")
Plot_TTOP_ALT(VarName="TTOP", SID="all")
Plot_TTOP_ALT(VarName="ALT", SID="permafrost")
Plot_TTOP_ALT(VarName="ALT", SID="all")
# plot MAAT & MAGST & MAGT
Plot_3M(SID="permafrost")
Plot_3M(SID="all")
#-----------------------------------------------------------------------------------------
# ggplot2 MAAT & MAGST & MAGT
ggplot_pic(Type="3m", SID="all")
ggplot_Pic(Type="3m", SID="permafrost")
# ggplot2 n factor (nt & nf)
ggplot_Pic(Type="factor", SID="all")
ggplot_Pic(Type="factor", SID="permafrost")
# ggplot2 offset (Nival Offset & Surface Offset & Thermal Offset & Vegetation Offset)
ggplot_Pic(Type="offset", SID="all")
ggplot_Pic(Type="offset", SID="permafrost")
# ggplot2 Celsius degree-days (DDTa & DDTs & DDFa & DDFs)
ggplot_Pic(Type="cdd", SID="all")
ggplot_Pic(Type="cdd", SID="permafrost")
# ggplot2 TTOP using Smith & Riseborough, and Kudryavtsev function
ggplot_Pic(Type="ttop", SID="all")
ggplot_Pic(Type="ttop", SID="permafrost")
# ggplot2 ALT using Stefan & Kudryavtsev function
ggplot_Pic(Type="alt", SID="all")
ggplot_Pic(Type="alt", SID="permafrost")
# ggplot2 Freeze/Thaw Depth (ALT using Stefan & Kudryavtsev function)
ggplot_Pic(Type="depth", SID="all")
ggplot_Pic(Type="depth", SID="permafrost")
#-----------------------------------------------------------------------------------------
# ggmap: create a Gif animation
Map_Pic(VarName="MAAT")
Map_Pic(VarName="MAGST")
Map_Pic(VarName="MAGT")
Map_Pic(VarName="NF")
Map_Pic(VarName="NT")
Map_Pic(VarName="DDTa")
Map_Pic(VarName="DDTs")
Map_Pic(VarName="DDFa")
Map_Pic(VarName="DDFs")
Map_Pic(VarName="NO")
Map_Pic(VarName="SO")
Map_Pic(VarName="TO")
Map_Pic(VarName="VO")
Map_Pic(VarName="TTOP_S")
Map_Pic(VarName="TTOP_K")
Map_Pic(VarName="ALT_S")
Map_Pic(VarName="ALT_K")
#--------FD: Freeze Depth
Map_Pic(VarName="FD")
##########################################################################################
# Spatial PIC (MAAT & DDTa & DDFa & ALT & FD)
##########################################################################################
Spatial_Pic(NetCDFName="PIC_indices.nc", StartYear=1980, EndYear=2010)
# spatial visualization
Netcdf_Multiplot(NetCDFName = "PIC_indices.nc", VarName = "MAAT")
Netcdf_Multiplot(NetCDFName = "PIC_indices.nc", VarName = "DDTa")
Netcdf_Multiplot(NetCDFName = "PIC_indices.nc", VarName = "DDFa")
Netcdf_Multiplot(NetCDFName = "PIC_indices.nc", VarName = "ALT")
Netcdf_Multiplot(NetCDFName = "PIC_indices.nc", VarName = "FD")
# spatial animation
Netcdf_Animation(NetCDFName = "PIC_indices.nc", VarName = "MAAT")
Netcdf_Animation(NetCDFName = "PIC_indices.nc", VarName = "DDTa")
Netcdf_Animation(NetCDFName = "PIC_indices.nc", VarName = "DDFa")
Netcdf_Animation(NetCDFName = "PIC_indices.nc", VarName = "ALT")
Netcdf_Animation(NetCDFName = "PIC_indices.nc", VarName = "FD")
# spatial statistic
Spatial_Stat("PIC_indices.nc","MAAT")
Spatial_Stat("PIC_indices.nc","DDTa")
Spatial_Stat("PIC_indices.nc","DDFa")
Spatial_Stat("PIC_indices.nc","ALT")
Spatial_Stat("PIC_indices.nc","FD")
License
GNU-GPL 3.0
Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences
Please contact to Lihui Luo (E-mail: luolh@lzb.ac.cn)
updated: 06/08/2018
iffylaw/PIC documentation built on May 8, 2019, 9:26 a.m.
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
PIC (Permafrost Indices Computing)
0. Introduction
Figure 1. Map of the data location over QTP.
At present, there are dozens of different indices are used to evaluate the characteristics and dynamics of permafrost presence or absence, including:
- thawing/freezing degree-days of air and ground surface (DDTa/DDTs/DDFa/DDFs)
- seasonal thawing/freezing n factor (nt/nf)
- MAAT (mean annual air temperature)
- MAGT (mean annual ground temperature)
- MAGST (mean annual ground surface temperature)
- TTOP (the temperature at the top of permafrost)
- ALT (active layer thickness)
- maximum freeze depth (FD)
Figure 2. The Structure Diagram of PIC
Table 1. Most important user functions in the PIC.
| R function | Description and reference | Unit | Equation | |-----------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------|------------| | Temperature-related indices | | Freezing_index | Freezing degree-days for air and ground | ℃ | (4,6) | | Thawing_index | Thawing degree-days for air and ground | ℃ | (3,5) | | MAAT | Mean annual air temperature | ℃ | (7) | | MAGST | Mean annual ground surface temperature (5 cm) | ℃ | (8) | | MAGT | Mean annual ground temperature (at 15 m) | ℃ | (10) | | NT | Thawing n-factor | | (11) | | NF | Freezing n-factor | | (12) | | Surface_Offset | The difference between the MAGST and MAAT | ℃ | | | Thermal_Offset | The difference between the TTOP and MAGST | ℃ | | | Vegetation_Offset | The second term (Surface_Offset) is negative, and represents the reduction in MAGST due to vegetation effects in summer (vegetation offset) | ℃ | | | Nival_Offset | The first term (Surface_Offset) on the right-hand-side is positive, and represents the elevation of MAGST over MAAT due to the insulating effect of winter snow cover (nival offset) | ℃ | | | TTOP_Smith | The temperature at the top of the permafrost using Smith & Riseborough function | ℃ | (13) | | TTOP_Kudryavtsev | The temperature at the top of the permafrost using Kudryavtsev function | ℃ | (14) | | Depth-related indices | | Freeze_depth_Stefan | Maximum freezing depth using Stefan function | m | (20) | | Thaw_depth_Stefan | Active layer thickness using Stefan function | m | (16) | | ALT_Kudryavtsev | Active layer thickness (ALT) or maximum thawing depth using Kudryavtsev function | m | (19) | | Region | | Spatial_Pic | Spatial changes with MAAT, DDTa, DDFa and ALT | m | (3,4,7,16) | | Toolkit | | Com_Indices_QTP | Computing all indices for all stations of the QTP | | | | Outlier_Process | Process the abnormal value | | | | VLH | Computing volumetric latent heat of fusion | J/m3 | (2) | | Convert_4_ggplot | Convert the values of TTOP & ALT to one columns | | | | Exist_Permafrost | To determine which stations exists permafrost by TTOP values | | | | Statistic | | Stat | Statistic functions with more 10 methods | | (21,22,23) | | Spatial_Stat | Spatial statistic method, just for spatial trend | | (24) | | Com_Stats_QTP | Computing the statistc values for one or both of these indices | | | | Visualization | | Plot_3M | Plot MAAT, MAGST, and MAGT for all stations or a station | | | | Plot_TTOP_ALT | Plot TTOP and ALT for all stations or a station | | | | ggplot_Pic | Plot multiple indices all stations or a station using ggplot2 | | | | Map_Pic | Plot multiple indices all stations or a station using ggmap | | | | Netcdf_Multiplot | Region visualization of NetCDF with multiple plots | | | | Netcdf_Animation | Region animation of NetCDF | | |
1. Statistics
The stat function contains all statistical methods for station calculation. A spatial trend can also be computed using the Spatial_Stat function after the regional calculation.
Table 2. ALT Statistic values
| | Pishan | Hetian | Minfeng | Mangya | Yutian | Lenghu | Tuole | Yeniugou | Zhangye | Qilian | Shandan | Yongchang | Dacaidan | Delingha | Gangcha | Menyuan | Nuomuhong | Dulan | Qiabuqia | Xining | Wudaoliang | Xinghai | Shiquanhe | Gaize | Bange | Anduo | Pulan | Shenzha | Dangxiong | Lazi | Rikeze | Nimu | Lasa | Jiangzi | Cuona | Longzi | Pali | Zaduo | Yushu | Maduo | Qingshuihe | Shiqu | Changdou | Dege | Ganzi | Seda | Daofou | Maerkang | Xinlong | Zuogong | Kangding | Deqin | |-----------|----------|----------|----------|--------|----------|---------|---------|----------|----------|---------|---------|-----------|----------|----------|---------|---------|-----------|---------|----------|----------|------------|---------|-----------|---------|--------|--------|---------|---------|-----------|---------|---------|----------|---------|---------|---------|---------|---------|--------|---------|--------|------------|--------|----------|---------|---------|--------|----------|----------|---------|---------|----------|---------| | intercept | 1.84 | 1.63 | 1.73 | 4.99 | 1.30 | 2.21 | -0.55 | -1.43 | 1.96 | 3.40 | 4.85 | 2.57 | -0.33 | 2.84 | -1.41 | 0.21 | 1.72 | 2.67 | 3.48 | 1.98 | -0.10 | 1.72 | 5.77 | 3.49 | 0.03 | -0.82 | 2.75 | -0.87 | 3.70 | 2.94 | 2.19 | 1.34 | 0.57 | 2.15 | 4.02 | 2.72 | -0.99 | 0.11 | 2.68 | 0.15 | 0.40 | 0.42 | 0.68 | 4.16 | 1.52 | 1.04 | 1.84 | 0.40 | 1.68 | 3.64 | 1.75 | 2.36 | | slope | -0.37 | -0.42 | -0.40 | -1.57 | -0.27 | -0.47 | 0.69 | 0.97 | -0.48 | -0.94 | -1.31 | -0.73 | 0.55 | -0.74 | 1.06 | 0.35 | -0.38 | -0.77 | -1.19 | -0.46 | 0.59 | -0.41 | -2.03 | -0.95 | 0.43 | 1.09 | -0.86 | 0.94 | -1.23 | -0.97 | -0.78 | -0.28 | -0.15 | -0.84 | -1.42 | -0.87 | 1.23 | 0.36 | -0.82 | 0.32 | 0.30 | 0.32 | -0.11 | -1.43 | -0.45 | 0.08 | -0.54 | -0.07 | -0.49 | -1.23 | -0.57 | -0.91 | | r | -0.55 | -0.28 | -0.53 | -0.68 | -0.23 | -0.35 | 0.73 | 0.80 | -0.47 | -0.49 | -0.67 | -0.56 | 0.09 | -0.62 | 0.65 | 0.07 | -0.33 | -0.64 | -0.60 | -0.47 | 0.78 | -0.32 | -0.61 | -0.62 | 0.60 | 0.55 | -0.52 | 0.14 | -0.38 | -0.79 | -0.50 | -0.52 | -0.32 | -0.60 | -0.33 | -0.58 | 0.20 | 0.08 | -0.52 | 0.82 | 0.37 | 0.26 | -0.42 | -0.68 | -0.44 | 0.07 | -0.38 | -0.23 | -0.45 | -0.66 | -0.31 | -0.81 | | rr | 0.30 | 0.08 | 0.28 | 0.46 | 0.05 | 0.13 | 0.54 | 0.65 | 0.22 | 0.24 | 0.44 | 0.31 | 0.01 | 0.38 | 0.42 | 0.00 | 0.11 | 0.41 | 0.36 | 0.22 | 0.61 | 0.10 | 0.37 | 0.39 | 0.36 | 0.30 | 0.27 | 0.02 | 0.14 | 0.62 | 0.25 | 0.27 | 0.10 | 0.36 | 0.11 | 0.34 | 0.04 | 0.01 | 0.27 | 0.67 | 0.14 | 0.07 | 0.18 | 0.46 | 0.19 | 0.00 | 0.14 | 0.05 | 0.21 | 0.44 | 0.09 | 0.66 | | rmse | 4.03 | 3.05 | 3.32 | 1.52 | 3.46 | 2.84 | 1.24 | 1.53 | 2.40 | 1.35 | 2.55 | 2.19 | 1.52 | 2.26 | 1.26 | 1.39 | 2.30 | 1.86 | 1.60 | 2.58 | 0.60 | 1.47 | 1.27 | 1.98 | 1.14 | 0.66 | 2.12 | 1.07 | 1.65 | 2.46 | 2.04 | 3.85 | 2.69 | 1.72 | 1.21 | 2.30 | 0.67 | 1.16 | 1.82 | 0.74 | 0.56 | 0.80 | 3.07 | 2.18 | 2.35 | 0.83 | 2.57 | 3.60 | 2.58 | 2.07 | 2.37 | 2.17 | | nrmse | 0.94 | 0.92 | 0.91 | 0.62 | 0.92 | 0.83 | 0.55 | 0.56 | 0.82 | 0.55 | 0.80 | 0.79 | 0.58 | 0.77 | 0.50 | 0.56 | 0.79 | 0.73 | 0.69 | 0.83 | 0.50 | 0.65 | 0.55 | 0.70 | 0.56 | 0.38 | 0.81 | 0.46 | 0.68 | 0.89 | 0.86 | 0.95 | 0.95 | 0.81 | 0.55 | 0.86 | 0.47 | 0.59 | 0.74 | 0.56 | 0.41 | 0.44 | 0.91 | 0.84 | 0.88 | 0.41 | 0.89 | 0.96 | 0.90 | 0.80 | 0.90 | 0.91 | | sd_s | 0.09 | 0.08 | 0.08 | 0.18 | 0.07 | 0.08 | 0.11 | 0.13 | 0.06 | 0.07 | 0.08 | 0.06 | 0.11 | 0.08 | 0.10 | 0.11 | 0.08 | 0.07 | 0.08 | 0.05 | 0.09 | 0.08 | 0.11 | 0.12 | 0.12 | 0.08 | 0.08 | 0.08 | 0.08 | 0.09 | 0.06 | 0.09 | 0.10 | 0.06 | 0.08 | 0.07 | 0.04 | 0.09 | 0.10 | 0.08 | 0.09 | 0.09 | 0.09 | 0.07 | 0.08 | 0.08 | 0.07 | 0.08 | 0.07 | 0.07 | 0.06 | 0.13 | | sd_k | 0.06 | 0.06 | 0.06 | 0.26 | 0.05 | 0.06 | 0.08 | 0.13 | 0.07 | 0.12 | 0.12 | 0.07 | 0.11 | 0.09 | 0.11 | 0.09 | 0.08 | 0.12 | 0.13 | 0.05 | 0.06 | 0.06 | 0.26 | 0.13 | 0.08 | 0.10 | 0.14 | 0.16 | 0.17 | 0.07 | 0.07 | 0.04 | 0.03 | 0.08 | 0.21 | 0.08 | 0.05 | 0.07 | 0.12 | 0.03 | 0.05 | 0.07 | 0.06 | 0.09 | 0.08 | 0.08 | 0.08 | 0.03 | 0.07 | 0.09 | 0.08 | 0.10 | | mef | -1674.98 | -1209.29 | -1496.06 | -43.24 | -1952.95 | -684.35 | -122.00 | -74.20 | -1287.34 | -299.68 | -915.51 | -1227.18 | -177.31 | -651.32 | -87.25 | -143.32 | -739.12 | -648.08 | -334.96 | -2066.05 | -21.22 | -303.76 | -119.38 | -234.87 | -45.55 | -57.28 | -557.76 | -90.17 | -461.12 | -714.20 | -951.79 | -1814.19 | -613.21 | -749.58 | -188.69 | -829.40 | -113.58 | -84.98 | -271.57 | -41.15 | -17.23 | -45.91 | -1066.25 | -718.82 | -555.50 | -62.87 | -1346.71 | -1453.86 | -887.90 | -741.26 | -919.01 | -262.24 | | nae | -0.94 | -0.92 | -0.92 | -0.58 | -0.92 | -0.83 | -0.56 | -0.55 | -0.81 | -0.55 | -0.80 | -0.80 | -0.58 | -0.77 | -0.50 | -0.57 | -0.79 | -0.73 | -0.69 | -0.83 | -0.48 | -0.65 | -0.53 | -0.70 | -0.55 | -0.39 | -0.81 | -0.45 | -0.68 | -0.90 | -0.86 | -0.95 | -0.95 | -0.82 | -0.55 | -0.86 | -0.47 | -0.58 | -0.74 | -0.56 | -0.41 | -0.44 | -0.91 | -0.83 | -0.88 | -0.41 | -0.89 | -0.96 | -0.90 | -0.80 | -0.90 | -0.92 | | vr | 0.37 | 0.61 | 0.45 | 2.06 | 0.54 | 0.53 | 0.57 | 1.08 | 1.34 | 2.79 | 2.19 | 1.17 | 1.16 | 1.25 | 1.29 | 0.72 | 0.93 | 2.73 | 2.66 | 1.05 | 0.44 | 0.51 | 5.19 | 1.19 | 0.42 | 1.41 | 3.06 | 3.56 | 4.90 | 0.67 | 1.30 | 0.16 | 0.10 | 1.70 | 6.19 | 1.16 | 1.46 | 0.64 | 1.32 | 0.15 | 0.27 | 0.66 | 0.48 | 1.58 | 0.93 | 0.97 | 1.47 | 0.16 | 1.01 | 1.62 | 1.97 | 0.66 | | pbias | 84.66 | 80.60 | 84.64 | 36.85 | 80.30 | 41.34 | 48.72 | 29.22 | 71.16 | 46.25 | 69.99 | 73.13 | 48.28 | 68.28 | 25.55 | 50.99 | 71.51 | 65.80 | 60.21 | 71.99 | 24.80 | 56.97 | 48.67 | 62.20 | 26.86 | 33.69 | 65.07 | 24.11 | 66.30 | 78.26 | 77.76 | 89.16 | 83.87 | 69.81 | 49.16 | 70.24 | 23.08 | 28.34 | 63.17 | 25.54 | 18.96 | 26.39 | 76.16 | 61.32 | 58.43 | 22.97 | 77.74 | 62.23 | 50.46 | 72.68 | 45.96 | 79.51 | | nse | 0.10 | 0.12 | 0.08 | 0.31 | 0.13 | 0.50 | 0.14 | 0.47 | 0.12 | 0.15 | 0.12 | 0.09 | 0.18 | 0.11 | 0.48 | 0.11 | 0.10 | 0.09 | 0.12 | 0.13 | 0.48 | 0.13 | 0.04 | 0.11 | 0.51 | 0.15 | 0.19 | 0.45 | 0.01 | 0.13 | 0.09 | 0.06 | 0.12 | 0.14 | 0.09 | 0.18 | 0.50 | 0.51 | 0.14 | 0.54 | 0.54 | 0.40 | 0.16 | 0.26 | 0.34 | 0.43 | 0.13 | 0.35 | 0.44 | 0.09 | 0.49 | 0.14 | | rsr | 0.95 | 0.94 | 0.96 | 0.83 | 0.93 | 0.71 | 0.93 | 0.73 | 0.94 | 0.92 | 0.94 | 0.96 | 0.91 | 0.94 | 0.72 | 0.94 | 0.95 | 0.95 | 0.94 | 0.93 | 0.72 | 0.93 | 0.98 | 0.94 | 0.70 | 0.92 | 0.90 | 0.74 | 1.00 | 0.93 | 0.95 | 0.97 | 0.94 | 0.93 | 0.95 | 0.91 | 0.71 | 0.70 | 0.93 | 0.68 | 0.68 | 0.78 | 0.92 | 0.86 | 0.81 | 0.75 | 0.93 | 0.80 | 0.75 | 0.95 | 0.71 | 0.93 | | d | 0.03 | 0.04 | 0.03 | 0.14 | 0.03 | 0.04 | 0.11 | 0.13 | 0.04 | 0.07 | 0.04 | 0.04 | 0.08 | 0.05 | 0.12 | 0.10 | 0.05 | 0.05 | 0.07 | 0.03 | 0.21 | 0.07 | 0.10 | 0.08 | 0.11 | 0.15 | 0.05 | 0.10 | 0.07 | 0.05 | 0.04 | 0.03 | 0.05 | 0.05 | 0.08 | 0.04 | 0.08 | 0.10 | 0.07 | 0.16 | 0.20 | 0.15 | 0.04 | 0.04 | 0.05 | 0.12 | 0.04 | 0.03 | 0.04 | 0.05 | 0.04 | 0.08 |
2. Visualization
Station visualization can be produced by Plot_TTOP_ALT and Plot_3M. The Plot_TTOP_ALT function plots two TTOP or two ALT indices in a figure for all stations or stations with permafrost. VarName has the “TTOP” and “ALT” options, whereas SID has the “permafrost” and “all” options. The Plot_3M function draws the MAAT, MAGST, and MAGT indices. The two functions only plot these stations where permafrost exists when SID = “permafrost.”
Figure 3. TTOP visualization
Figure 4. MAAT animation
Figure 5. ALT animation
Figure 6. Spatial trend of MAAT, DDTa, DDFa and ALT.
Figure 7. Region visualization of ALT.
3. Examples
Several examples of the PIC application were presented here.
#
# The example is designed to help users better use the PIC package
# Author: Lihui Luo (E-mail: luolh@lzb.ac.cn)
# Cold and Arid Regions Environmental and Engineering Research Institute,
# Chinese Academy of Sciences
# updated: 06/08/2018
#
##########################################################################################
# Compute temperature/depth-related indices using daily weather observations
##########################################################################################
# Thawing_index: DDTa
Thawing_index(Year=1980, TempName="Temperature", data=QTP_ATM, SID=52908)
Thawing_index(Year=1980:2010, TempName="Temperature", data=QTP_ATM, SID=52908)
# Thawing_index: DDTs
Thawing_index(Year=1980, TempName="GT", data=QTP_ATM, SID=52908)
Thawing_index(Year=1980:2010, TempName="GT", data=QTP_ATM, SID=52908)
# Freezing_index: DDFa
Freezing_index(Year=1980, TempName="Temperature", data=QTP_ATM, SID=52908)
Freezing_index(Year=1980:2010, TempName="Temperature", data=QTP_ATM, SID=52908)
# Freezing_index: DDFs
Freezing_index(Year=1980, TempName="GT", data=QTP_ATM, SID=52908)
Freezing_index(Year=1980:2010, TempName="GT", data=QTP_ATM, SID=52908)
# MAAT
MAAT(Year=1980, TempName="Temperature", data=QTP_ATM, SID=52908)
MAAT(Year=1980:2010, TempName="Temperature", data=QTP_ATM, SID=52908)
# NT
NT(Year=1980, AirTempName="Temperature", GroundTempName="GT", data=QTP_ATM, SID=52908)
NT(Year=1980:2010, AirTempName="Temperature", GroundTempName="GT", data=QTP_ATM, SID=52908)
# NF
NF(Year=1980, AirTempName="Temperature", GroundTempName="GT", data=QTP_ATM, SID=52908)
NF(Year=1980:2010, AirTempName="Temperature", GroundTempName="GT", data=QTP_ATM, SID=52908)
# MAGST
MAGST(Year=1980, AirTempName="Temperature", GroundTempName="GT", data=QTP_ATM, SID=52908)
MAGST(Year=1980:2010, AirTempName="Temperature", GroundTempName="GT", data=QTP_ATM, SID=52908)
# Temp_Amp_Daily
Temp_Ampl_Daily(Year=1980, MinTempName="GT_0_MIN", MaxTempName="GT_0_MAX", data=QTP_ATM, SID=52908)
Temp_Ampl_Daily(Year=1980:2010, MinTempName="Tmin", MaxTempName="GT_0_MAX", data=QTP_ATM, SID=52908)
# Temp_Amp_Manual
Temp_Ampl_Annual(Year=1980, MinTempName="GT_0_MIN", MaxTempName="GT_0_MAX", data=QTP_ATM, SID=52908)
Temp_Ampl_Annual(Year=1980:2010, MinTempName="GT_0_MIN", MaxTempName="GT_0_MAX", data=QTP_ATM, SID=52908)
# SoilTemp_Diff_Depths:soil temperature at 15 m
SoilTemp_Diff_Depths(Year=1980, depth=15, time=3600*12, AirTempName="Temperature", MinTempName="Tmin", MaxTempName="Tmax", data=QTP_ATM, SID=52908)
SoilTemp_Diff_Depths(Year=1980:2010, depth=15, time=3600*12, AirTempName="Temperature", MinTempName="Tmin", MaxTempName="Tmax", data=QTP_ATM, SID=52908)
# MAGT
MAGT(Year=1980, AirTempName="Temperature", MinTempName="Tmin", MaxTempName="Tmax", data=QTP_ATM, SID=52908)
MAGT(Year=1980:2010, AirTempName="Temperature", MinTempName="Tmin", MaxTempName="Tmax", data=QTP_ATM, SID=52908)
#Vegetation_Offset
Vegetation_Offset(Year=1980, AirTempName="Temperature", GroundTempName="GT", data=QTP_ATM, SID=52908)
Vegetation_Offset(Year=1980:2010, AirTempName="Temperature", GroundTempName="GT", data=QTP_ATM, SID=52908)
# Surface_Offset
Surface_Offset(Year=1980, AirTempName="Temperature", GroundTempName="GT", data=QTP_ATM, SID=52908)
Surface_Offset(Year=1980:2010, AirTempName="Temperature", GroundTempName="GT", data=QTP_ATM, SID=52908
# Thermal_Offset
Thermal_Offset(Year=1980, AirTempName="Temperature", GroundTempName="GT", data=QTP_ATM, SID=52908)
Thermal_Offset(Year=1980:2010, AirTempName="Temperature", GroundTempName="GT", data=QTP_ATM, SID=52908)
# Nival_Offset
Nival_Offset(Year=1980, AirTempName="Temperature", GroundTempName="GT", data=QTP_ATM, SID=52908)
Nival_Offset(Year=1980:2010, AirTempName="Temperature", GroundTempName="GT", data=QTP_ATM, SID=52908)
# TTOP_Smith
TTOP_Smith(Year=1980, AirTempName="Temperature", GroundTempName="GT", data=QTP_ATM, SID=52908)
TTOP_Smith(Year=1980:2010, AirTempName="Temperature", GroundTempName="GT", data=QTP_ATM, SID=52908)
# TTOP_Kudryavtsev
TTOP_Kudryavtsev(Year=1980, AirTempName="Temperature", GroundTempName="GT", MinGTName="GT_0_MIN", MaxGTName="GT_0_MAX", data=QTP_ATM, SID=52908)
TTOP_Kudryavtsev(Year=1980:2010, AirTempName="Temperature", GroundTempName="GT", MinGTName="GT_0_MIN", MaxGTName="GT_0_MAX", data=QTP_ATM, SID=52908)
# Thaw_depth_Stefan
Thaw_depth_Stefan(Year=1980, AirTempName="Temperature", data=QTP_ATM, SID=52908)
Thaw_depth_Stefan(Year=1980:2010, AirTempName="Temperature", data=QTP_ATM, SID=52908)
# Freeze_depth_Stefan is for seasonal frozen soil
Freeze_depth_Stefan(Year=1980, AirTempName="Temperature", data=QTP_ATM, SID=56444)
Freeze_depth_Stefan(Year=1980:2010, AirTempName="Temperature", data=QTP_ATM, SID=56444)
# ALT_Kudryavtsev
ALT_Kudryavtsev(Year=1980, AirTempName="Temperature", GroundTempName="GT", MinGTName="GT_0_MIN", MaxGTName="GT_0_MAX", data=QTP_ATM, SID=52908)
ALT_Kudryavtsev(Year=1980:2010, AirTempName="Temperature", GroundTempName="GT", MinGTName="GT_0_MIN", MaxGTName="GT_0_MAX", data=QTP_ATM, SID=52908)
##########################################################################################
# compute and save the temperature/depth-related indices
##########################################################################################
MAAT_QTP <- Com_Indices_QTP(VarName = "MAAT")
MAGST_QTP <- Com_Indices_QTP(VarName = "MAGST")
MAGT_QTP <- Com_Indices_QTP(VarName = "MAGT")
NT_QTP <- Com_Indices_QTP(VarName = "NT")
NF_QTP <- Com_Indices_QTP(VarName = "NF")
DDTa_QTP <- Com_Indices_QTP(VarName = "Thawing_index_air")
DDTs_QTP <- Com_Indices_QTP(VarName = "Thawing_index_ground")
DDFa_QTP <- Com_Indices_QTP(VarName = "Freezing_index_air")
DDFs_QTP <- Com_Indices_QTP(VarName = "Freezing_index_ground")
VO_QTP <- Com_Indices_QTP(VarName = "Vegetation_Offset")
SO_QTP <- Com_Indices_QTP(VarName = "Surface_Offset")
TO_QTP <- Com_Indices_QTP(VarName = "Thermal_Offset")
NO_QTP <- Com_Indices_QTP(VarName = "Nival_Offset")
TTOP_S_QTP <- Com_Indices_QTP(VarName = "TTOP_Smith")
TTOP_K_QTP <- Com_Indices_QTP(VarName = "TTOP_Kudryavtsev")
ALT_S_QTP <- Com_Indices_QTP(VarName = "Thaw_depth_Stefan")
FD_S_QTP <- Com_Indices_QTP(VarName = "Freeze_depth_Stefan")
ALT_K_QTP <- Com_Indices_QTP(VarName = "ALT_Kudryavtsev")
##########################################################################################
# process the outlier values
##########################################################################################
stations <- length(Station_Info$SID)
MAAT_QTP <- Outlier_Process(MAAT_QTP[,1:stations])
MAGST_QTP <- Outlier_Process(MAGST_QTP[,1:stations])
MAGT_QTP <- Outlier_Process(MAGT_QTP[,1:stations])
NT_QTP <- Outlier_Process(NT_QTP[,1:stations])
NF_QTP <- Outlier_Process(NF_QTP[,1:stations])
DDTa_QTP <- Outlier_Process(DDTa_QTP[,1:stations])
DDTs_QTP <- Outlier_Process(DDTs_QTP[,1:stations])
DDFa_QTP <- Outlier_Process(DDFa_QTP[,1:stations])
DDFs_QTP <- Outlier_Process(DDFs_QTP[,1:stations])
VO_QTP <- Outlier_Process(VO_QTP[,1:stations])
SO_QTP <- Outlier_Process(SO_QTP[,1:stations])
TO_QTP <- Outlier_Process(TO_QTP[,1:stations])
NO_QTP <- Outlier_Process(NO_QTP[,1:stations])
TTOP_S_QTP <- Outlier_Process(TTOP_S_QTP[,1:stations])
TTOP_K_QTP <- Outlier_Process(TTOP_K_QTP[,1:stations])
ALT_S_QTP <- Outlier_Process(ALT_S_QTP[,1:stations])
FD_S_QTP <- Outlier_Process(FD_S_QTP[,1:stations])
ALT_K_QTP <- Outlier_Process(ALT_K_QTP[,1:stations])
##########################################################################################
# Save these indices to Rdata file
##########################################################################################
save(MAAT_QTP, file="I:/PIC/PIC/MAAT_QTP.Rdata")
save(MAGST_QTP, file="I:/PIC/PIC/MAGST_QTP.Rdata")
save(MAGT_QTP, file="I:/PIC/PIC/MAGT_QTP.Rdata")
save(NT_QTP, file="I:/PIC/PIC/NT_QTP.Rdata")
save(NF_QTP, file="I:/PIC/PIC/NF_QTP.Rdata")
save(DDTa_QTP, file="I:/PIC/PIC/DDTa_QTP.Rdata")
save(DDTs_QTP, file="I:/PIC/PIC/DDTs_QTP.Rdata")
save(DDFa_QTP, file="I:/PIC/PIC/DDFa_QTP.Rdata")
save(DDFs_QTP, file="I:/PIC/PIC/DDFs_QTP.Rdata")
save(VO_QTP, file="I:/PIC/PIC/VO_QTP.Rdata")
save(SO_QTP, file="I:/PIC/PIC/SO_QTP.Rdata")
save(TO_QTP, file="I:/PIC/PIC/TO_QTP.Rdata")
save(NO_QTP, file="I:/PIC/PIC/NO_QTP.Rdata")
save(TTOP_S_QTP, file="I:/PIC/PIC/TTOP_S_QTP.Rdata")
save(TTOP_K_QTP, file="I:/PIC/PIC/TTOP_K_QTP.Rdata")
save(ALT_S_QTP, file="I:/PIC/PIC/ALT_S_QTP.Rdata")
save(FD_S_QTP, file="I:/PIC/PIC/FD_S_QTP.Rdata")
save(ALT_K_QTP, file="I:/PIC/PIC/ALT_K_QTP.Rdata")
##########################################################################################
# to determine which stations may exist permafrost
##########################################################################################
Exist_Permafrost()
Exist_Permafrost(plot="yes")
##########################################################################################
# Statistic analysis of stations
##########################################################################################
# Single index
MAAT_QTP_Stat <- Com_Stats_QTP(ind1=MAAT_QTP)
MAGST_QTP_Stat <- Com_Stats_QTP(ind1=MAGST_QTP)
MAGT_QTP_Stat <- Com_Stats_QTP(ind1=MAGT_QTP)
NT_QTP_Stat <- Com_Stats_QTP(ind1=NT_QTP)
NF_QTP_Stat <- Com_Stats_QTP(ind1=NF_QTP)
DDTa_QTP_Stat <- Com_Stats_QTP(ind1=DDTa_QTP)
DDTs_QTP_Stat <- Com_Stats_QTP(ind1=DDTs_QTP)
DDFa_QTP_Stat <- Com_Stats_QTP(ind1=DDFa_QTP)
DDFs_QTP_Stat <- Com_Stats_QTP(ind1=DDFs_QTP)
VO_QTP_Stat <- Com_Stats_QTP(ind1=VO_QTP)
SO_QTP_Stat <- Com_Stats_QTP(ind1=SO_QTP)
TO_QTP_Stat <- Com_Stats_QTP(ind1=TO_QTP)
NO_QTP_Stat <- Com_Stats_QTP(ind1=NO_QTP)
TTOP_S_QTP_Stat <- Com_Stats_QTP(ind1=TTOP_S_QTP)
TTOP_K_QTP_Stat <- Com_Stats_QTP(ind1=TTOP_K_QTP)
ALT_S_QTP_Stat <- Com_Stats_QTP(ind1=ALT_S_QTP)
FD_S_QTP_Stat <- Com_Stats_QTP(ind1=FD_S_QTP)
ALT_K_QTP_Stat <- Com_Stats_QTP(ind1=ALT_K_QTP)
# Same two indices (TTOP & ALT)
TTOP_S_K_QTP_Stat <- Com_Stats_QTP(ind1=TTOP_S_QTP, ind2=TTOP_K_QTP)
ALT_S_K_QTP_Stat <- Com_Stats_QTP(ind1=ALT_S_QTP, ind2=ALT_K_QTP)
##########################################################################################
# Visualization of stations
##########################################################################################
# plot TTOP & ALT
Plot_TTOP_ALT(VarName="TTOP", SID="permafrost")
Plot_TTOP_ALT(VarName="TTOP", SID="all")
Plot_TTOP_ALT(VarName="ALT", SID="permafrost")
Plot_TTOP_ALT(VarName="ALT", SID="all")
# plot MAAT & MAGST & MAGT
Plot_3M(SID="permafrost")
Plot_3M(SID="all")
#-----------------------------------------------------------------------------------------
# ggplot2 MAAT & MAGST & MAGT
ggplot_pic(Type="3m", SID="all")
ggplot_Pic(Type="3m", SID="permafrost")
# ggplot2 n factor (nt & nf)
ggplot_Pic(Type="factor", SID="all")
ggplot_Pic(Type="factor", SID="permafrost")
# ggplot2 offset (Nival Offset & Surface Offset & Thermal Offset & Vegetation Offset)
ggplot_Pic(Type="offset", SID="all")
ggplot_Pic(Type="offset", SID="permafrost")
# ggplot2 Celsius degree-days (DDTa & DDTs & DDFa & DDFs)
ggplot_Pic(Type="cdd", SID="all")
ggplot_Pic(Type="cdd", SID="permafrost")
# ggplot2 TTOP using Smith & Riseborough, and Kudryavtsev function
ggplot_Pic(Type="ttop", SID="all")
ggplot_Pic(Type="ttop", SID="permafrost")
# ggplot2 ALT using Stefan & Kudryavtsev function
ggplot_Pic(Type="alt", SID="all")
ggplot_Pic(Type="alt", SID="permafrost")
# ggplot2 Freeze/Thaw Depth (ALT using Stefan & Kudryavtsev function)
ggplot_Pic(Type="depth", SID="all")
ggplot_Pic(Type="depth", SID="permafrost")
#-----------------------------------------------------------------------------------------
# ggmap: create a Gif animation
Map_Pic(VarName="MAAT")
Map_Pic(VarName="MAGST")
Map_Pic(VarName="MAGT")
Map_Pic(VarName="NF")
Map_Pic(VarName="NT")
Map_Pic(VarName="DDTa")
Map_Pic(VarName="DDTs")
Map_Pic(VarName="DDFa")
Map_Pic(VarName="DDFs")
Map_Pic(VarName="NO")
Map_Pic(VarName="SO")
Map_Pic(VarName="TO")
Map_Pic(VarName="VO")
Map_Pic(VarName="TTOP_S")
Map_Pic(VarName="TTOP_K")
Map_Pic(VarName="ALT_S")
Map_Pic(VarName="ALT_K")
#--------FD: Freeze Depth
Map_Pic(VarName="FD")
##########################################################################################
# Spatial PIC (MAAT & DDTa & DDFa & ALT & FD)
##########################################################################################
Spatial_Pic(NetCDFName="PIC_indices.nc", StartYear=1980, EndYear=2010)
# spatial visualization
Netcdf_Multiplot(NetCDFName = "PIC_indices.nc", VarName = "MAAT")
Netcdf_Multiplot(NetCDFName = "PIC_indices.nc", VarName = "DDTa")
Netcdf_Multiplot(NetCDFName = "PIC_indices.nc", VarName = "DDFa")
Netcdf_Multiplot(NetCDFName = "PIC_indices.nc", VarName = "ALT")
Netcdf_Multiplot(NetCDFName = "PIC_indices.nc", VarName = "FD")
# spatial animation
Netcdf_Animation(NetCDFName = "PIC_indices.nc", VarName = "MAAT")
Netcdf_Animation(NetCDFName = "PIC_indices.nc", VarName = "DDTa")
Netcdf_Animation(NetCDFName = "PIC_indices.nc", VarName = "DDFa")
Netcdf_Animation(NetCDFName = "PIC_indices.nc", VarName = "ALT")
Netcdf_Animation(NetCDFName = "PIC_indices.nc", VarName = "FD")
# spatial statistic
Spatial_Stat("PIC_indices.nc","MAAT")
Spatial_Stat("PIC_indices.nc","DDTa")
Spatial_Stat("PIC_indices.nc","DDFa")
Spatial_Stat("PIC_indices.nc","ALT")
Spatial_Stat("PIC_indices.nc","FD")
License
GNU-GPL 3.0
Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences
Please contact to Lihui Luo (E-mail: luolh@lzb.ac.cn)
updated: 06/08/2018
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