Leeyabot reboot

.github/ISSUE_TEMPLATE/new_release_checklist.md

@@ -0,0 +1,22 @@
+---
+name: Release
+about: Checklist! 
+---
+
+Since the dev branch only includes materials that have been peer-reviewed at least once this PR review process should be relatively smooth should. That being said, before merging this branch into main and the new release is created several things must be completed first. 
+
+* Open a PR into main branch, it should be titled with the new release number 
+* Let Leeyabot generate a report detailing how the Hector output has changed! 
+* Add text to the PR documenting the major model changes. The PR is going to serve as an important record 
+* Pass automated checks
+* Change the version number in the DESCRIPTION file 
+* Update the NEWS.md, are links additional materials necessary? Does the release need a new naming file? 
+* Check to make sure the internal package data is up to date (fxntable, inputstable, unitstable)
+
+After merging PR 
+
+* Create the release via zenodo 
+* Add the zenodo links to README / NEWS & push directly to main 
+* Create new dev branch & update the DESCRIPTION version number to support the pkgdown documentation for the developmental branch!
+* Add archived outputstreams to release assets!
+

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: hector
 Title: The Hector Simple Climate Model
-Version: 3.2.0
+Version: 3.2.0.9000
 Authors@R: c(person("Kalyn", "Dorheim", 
  email = "kalyn.dorheim@pnnl.gov",
  role = c("aut", "cre"),

NEWS.md

@@ -1,5 +1,7 @@
 # hector 3.2.0 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10698028.svg)](https://doi.org/10.5281/zenodo.10698028)
+
+* Fully documented in Dorheim, K., Gering, S., Gieseke, R., Hartin, C., Pressburger, L., Shiklomanov, A. N., Smith, S. J., Tebaldi, C., Woodard, D. L., and Bond-Lamberty, B.: Hector V3.2.0: functionality and performance of a reduced-complexity climate model, Geosci. Model Dev., 17, 4855–4869, https://doi.org/10.5194/gmd-17-4855-2024, 2024.
 * Correct aerosol forcing coefficients based on Zelinka et al. (2023)
 * Enable permafrost module and recalibrate model's default parameterization
 

README.Rmd

@@ -58,7 +58,8 @@ hector_tas_results$scenario <- ifelse(hector_tas_results$year <= 2016, "historic
 ggplot(hector_tas_results) +
  geom_line(aes(year, value, color = scenario), linewidth = 1) +
  theme_bw(base_size = 15) +
- labs(color = NULL, x = NULL, y = expression("Temperature Anomaly ("~degree~"C)")) +
+ theme(axis.title = element_text(size = 12))+
+ labs(color = NULL, x = NULL, y = expression("Temperature Anomaly Relative to 1750 ("~degree~"C)")) +
  scale_color_manual(values = SSP_COLORS)
 ```
 

inst/include/component_data.hpp

@@ -256,7 +256,7 @@
 // methane component
 #define D_CH4_CONC "CH4" CONCENTRATION_EXTENSION
 #define D_PREINDUSTRIAL_CH4 "M0"
-#define D_RF_CH4 "FCH4"
+#define D_RF_CH4 D_RF_PREFIX "CH4"
 #define D_EMISSIONS_CH4 "CH4_emissions"
 #define D_CONSTRAINT_CH4 "CH4_constrain"
 #define D_NATURAL_CH4 "CH4N"

inst/include/forcing_component.hpp

@@ -120,7 +120,7 @@ class ForcingComponent : public IModelComponent {
 
  // Aerosol parameters for aerosol-cloud interactions (RFaci) see equation
  // Equation 7.SM.1.2 of IPCC AR6
- double const aci_beta = 2.279759; // see Dorheim et al. in prep
+ double const aci_beta = 2.279759; // Dorheim et al. 2024
  double const s_BCOC = 111.05064063; // (Tg C yr-1) IPCC AR6 7.SM.1.3.1
  double const s_SO2 =
  (260.34644166 * 1000) *

inst/include/h_util.hpp

@@ -26,7 +26,7 @@
  * \brief The model version number to be included in logs and outputs.
  * \note Manually update the git tag to match this.
  */
-#define MODEL_VERSION "3.2.0"
+#define MODEL_VERSION "3.2.0.9000"
 
 #define OUTPUT_DIRECTORY "output/"
 

inst/input/hector_ssp119.ini

@@ -37,7 +37,7 @@ preind_interdeep_c=37100 ; intermediate and deep ocean C, IPCC AR6 Figure 5.12
 atmos_co2=590.33 ; initial atmospheric carbon pool Pg C of CO2 size used in spin up, consistent with C0
 C0=277.15 ; preindustrial CO2 from table 7.SM.1 IPCC AR6; CO2 radiative forcing is calibrated to this value
 npp_flux0=56.2 ; preindustrial net primary production, Pg C/yr from Ito et al. 2011
-;pf.npp_flux0=5.6 ; cf. Figure 3 in Chen et al. 2017 10.1088/1748-9326/aa8978 
+;pf.npp_flux0=5.6 ; cf. Figure 3 in Chen et al. 2017 10.1088/1748-9326/aa8978
 ;nonpf.npp_flux0=50.6
 
 veg_c=550 ; initial vegetation pool, Pg C
@@ -73,16 +73,16 @@ f_litterd=0.98 ; Fraction of litter flux to detritus (balance to soil)
 ;nonpf.f_litterd=0.98
 
 ; Anthropogenic contributions: emissions, direct air carbon capture and storage, and land use change, Pg C/yr
-ffi_emissions=csv:tables/ssp119_emiss-constraints_rf.csv 
+ffi_emissions=csv:tables/ssp119_emiss-constraints_rf.csv
 daccs_uptake=csv:tables/ssp119_emiss-constraints_rf.csv
 luc_emissions=csv:tables/ssp119_emiss-constraints_rf.csv
 luc_uptake=csv:tables/ssp119_emiss-constraints_rf.csv
 
 ; CO2 and temperature effects on the carbon cycle
-beta=0.53 ; CO2 fertilization factor (unitless), calibrated to historical observations see Dorheim et al. in prep for details
+beta=0.53 ; CO2 fertilization factor (unitless), calibrated to historical observations Dorheim et al. 2024 for details
 ;pf.beta=0.53
 ;nonpf.beta=0.53
-q10_rh=1.76 ; Heterotrophic respiration temperature sensitivity factor (unitless), calibrated to historical observations see Dorheim et al. in prep for details
+q10_rh=1.76 ; Heterotrophic respiration temperature sensitivity factor (unitless), calibrated to historical observations Dorheim et al. 2024 for details
 ;pf.q10_rh=1.76
 ;nonpf.q10_rh=1.76
 
@@ -165,10 +165,10 @@ baseyear=1750 ; when to start reporting; by definition, all F=0 in this year
 delta_co2=0.05 ; (unitless) forcing tropospheric adjustments for CO2 (7.3.2.1 of IPCC AR6)
 delta_ch4=-.14 ; (unitless) forcing tropospheric adjustments for CH4 (7.3.2.2 of IPCC AR6)
 delta_n2o=0.07 ; (unitless) forcing tropospheric adjustments for N2O (7.3.2.3 of IPCC AR6)
-rho_bc=0.06386286 ; (W yr m–2 C Tg–1) see Dorheim et al. in prep
-rho_oc=-0.006407143 ; (W yr m–2 C Tg–1) see Dorheim et al. in prep
-rho_so2=-7.469841e-06 ; (W yr m–2 S Gg-1) see Dorheim et al. in prep
-rho_nh3=-0.002146032 ; (W yr m–2 NH3Tg–1) see Dorheim et al. in prep
+rho_bc=0.06386286 ; (W yr m–2 C Tg–1) Dorheim et al. 2024
+rho_oc=-0.006407143 ; (W yr m–2 C Tg–1) Dorheim et al. 2024
+rho_so2=-7.469841e-06 ; (W yr m–2 S Gg-1) Dorheim et al. 2024
+rho_nh3=-0.002146032 ; (W yr m–2 NH3Tg–1) Dorheim et al. 2024
 
 ; Miscellaneous radiative forcings are by default zero, but can read in from a input table to
 ; represent additional forcings not modeled by Hector (e.g. solar, bc on snow, jet contrails)
@@ -178,7 +178,7 @@ RF_misc[1750]=0
 ;------------------------------------------------------------------------
 [temperature]
 S=3.0 ; equilibrium climate sensitivity for 2xCO2 degC (A.4.4 of IPCC AR6)
-diff=2.38 ; ocean heat diffusivity, cm2/s calibrated to historical observations see Dorheim et al. in prep for details
+diff=2.38 ; ocean heat diffusivity, cm2/s calibrated to historical observations Dorheim et al. 2024 for details
 alpha=1.0 ; uncertainty scaling factor for aerosol forcing
 volscl=1.0 ; uncertainty scaling factor for volcanic forcing
 qco2=3.75 ; 2×CO2 RF (7.3.2 of IPCC AR6)
@@ -232,7 +232,7 @@ delta_HFC32=0.0 ; tropospheric adjustments scalar unitless (7.3.2.4 IPCC AR6
 molarMass=52.0 ; grams
 HFC32_emissions=csv:tables/ssp119_emiss-constraints_rf.csv
 
-[HFC4310_halocarbon] 
+[HFC4310_halocarbon]
 ; This is equivalent to HFC-43-10mee
 tau=17.0 ; lifetime in years (Table 7.SM.7 IPPC AR6)
 rho_HFC4310=0.000357 ; radiative efficiencies W/m2/ppt (Table 7.SM.7 IPPC AR6)

inst/input/hector_ssp126.ini

@@ -79,10 +79,10 @@ luc_emissions=csv:tables/ssp126_emiss-constraints_rf.csv
 luc_uptake=csv:tables/ssp126_emiss-constraints_rf.csv
 
 ; CO2 and temperature effects on the carbon cycle
-beta=0.53 ; CO2 fertilization factor (unitless), calibrated to historical observations see Dorheim et al. in prep for details
+beta=0.53 ; CO2 fertilization factor (unitless), calibrated to historical observations Dorheim et al. 2024 for details
 ;pf.beta=0.53
 ;nonpf.beta=0.53
-q10_rh=1.76 ; Heterotrophic respiration temperature sensitivity factor (unitless), calibrated to historical observations see Dorheim et al. in prep for details
+q10_rh=1.76 ; Heterotrophic respiration temperature sensitivity factor (unitless), calibrated to historical observations Dorheim et al. 2024 for details
 ;pf.q10_rh=1.76
 ;nonpf.q10_rh=1.76
 
@@ -165,10 +165,10 @@ baseyear=1750 ; when to start reporting; by definition, all F=0 in this year
 delta_co2=0.05 ; (unitless) forcing tropospheric adjustments for CO2 (7.3.2.1 of IPCC AR6)
 delta_ch4=-.14 ; (unitless) forcing tropospheric adjustments for CH4 (7.3.2.2 of IPCC AR6)
 delta_n2o=0.07 ; (unitless) forcing tropospheric adjustments for N2O (7.3.2.3 of IPCC AR6)
-rho_bc=0.06386286 ; (W yr m–2 C Tg–1) see Dorheim et al. in prep
-rho_oc=-0.006407143 ; (W yr m–2 C Tg–1) see Dorheim et al. in prep
-rho_so2=-7.469841e-06 ; (W yr m–2 S Gg-1) see Dorheim et al. in prep
-rho_nh3=-0.002146032 ; (W yr m–2 NH3Tg–1) see Dorheim et al. in prep
+rho_bc=0.06386286 ; (W yr m–2 C Tg–1) Dorheim et al. 2024
+rho_oc=-0.006407143 ; (W yr m–2 C Tg–1) Dorheim et al. 2024
+rho_so2=-7.469841e-06 ; (W yr m–2 S Gg-1) Dorheim et al. 2024
+rho_nh3=-0.002146032 ; (W yr m–2 NH3Tg–1) Dorheim et al. 2024
 
 ; Miscellaneous radiative forcings are by default zero, but can read in from a input table to
 ; represent additional forcings not modeled by Hector (e.g. solar, bc on snow, jet contrails)
@@ -178,7 +178,7 @@ RF_misc[1750]=0
 ;------------------------------------------------------------------------
 [temperature]
 S=3.0 ; equilibrium climate sensitivity for 2xCO2 degC (A.4.4 of IPCC AR6)
-diff=2.38 ; ocean heat diffusivity, cm2/s calibrated to historical observations see Dorheim et al. in prep for details
+diff=2.38 ; ocean heat diffusivity, cm2/s calibrated to historical observations Dorheim et al. 2024 for details
 alpha=1.0 ; uncertainty scaling factor for aerosol forcing
 volscl=1.0 ; uncertainty scaling factor for volcanic forcing
 qco2=3.75 ; 2×CO2 RF (7.3.2 of IPCC AR6)

inst/input/hector_ssp245.ini

@@ -37,7 +37,7 @@ preind_interdeep_c=37100 ; intermediate and deep ocean C, IPCC AR6 Figure 5.12
 atmos_co2=590.33 ; initial atmospheric carbon pool Pg C of CO2 size used in spin up, consistent with C0
 C0=277.15 ; preindustrial CO2 from table 7.SM.1 IPCC AR6; CO2 radiative forcing is calibrated to this value
 npp_flux0=56.2 ; preindustrial net primary production, Pg C/yr from Ito et al. 2011
-;pf.npp_flux0=5.6 ; cf. Figure 3 in Chen et al. 2017 10.1088/1748-9326/aa8978 
+;pf.npp_flux0=5.6 ; cf. Figure 3 in Chen et al. 2017 10.1088/1748-9326/aa8978
 ;nonpf.npp_flux0=50.6
 
 veg_c=550 ; initial vegetation pool, Pg C
@@ -73,16 +73,16 @@ f_litterd=0.98 ; Fraction of litter flux to detritus (balance to soil)
 ;nonpf.f_litterd=0.98
 
 ; Anthropogenic contributions: emissions, direct air carbon capture and storage, and land use change, Pg C/yr
-ffi_emissions=csv:tables/ssp245_emiss-constraints_rf.csv 
+ffi_emissions=csv:tables/ssp245_emiss-constraints_rf.csv
 daccs_uptake=csv:tables/ssp245_emiss-constraints_rf.csv
 luc_emissions=csv:tables/ssp245_emiss-constraints_rf.csv
 luc_uptake=csv:tables/ssp245_emiss-constraints_rf.csv
 
 ; CO2 and temperature effects on the carbon cycle
-beta=0.53 ; CO2 fertilization factor (unitless), calibrated to historical observations see Dorheim et al. in prep for details
+beta=0.53 ; CO2 fertilization factor (unitless), calibrated to historical observations Dorheim et al. 2024 for details
 ;pf.beta=0.53
 ;nonpf.beta=0.53
-q10_rh=1.76 ; Heterotrophic respiration temperature sensitivity factor (unitless), calibrated to historical observations see Dorheim et al. in prep for details
+q10_rh=1.76 ; Heterotrophic respiration temperature sensitivity factor (unitless), calibrated to historical observations Dorheim et al. 2024 for details
 ;pf.q10_rh=1.76
 ;nonpf.q10_rh=1.76
 
@@ -165,10 +165,10 @@ baseyear=1750 ; when to start reporting; by definition, all F=0 in this year
 delta_co2=0.05 ; (unitless) forcing tropospheric adjustments for CO2 (7.3.2.1 of IPCC AR6)
 delta_ch4=-.14 ; (unitless) forcing tropospheric adjustments for CH4 (7.3.2.2 of IPCC AR6)
 delta_n2o=0.07 ; (unitless) forcing tropospheric adjustments for N2O (7.3.2.3 of IPCC AR6)
-rho_bc=0.06386286 ; (W yr m–2 C Tg–1) see Dorheim et al. in prep
-rho_oc=-0.006407143 ; (W yr m–2 C Tg–1) see Dorheim et al. in prep
-rho_so2=-7.469841e-06 ; (W yr m–2 S Gg-1) see Dorheim et al. in prep
-rho_nh3=-0.002146032 ; (W yr m–2 NH3Tg–1) see Dorheim et al. in prep
+rho_bc=0.06386286 ; (W yr m–2 C Tg–1) Dorheim et al. 2024
+rho_oc=-0.006407143 ; (W yr m–2 C Tg–1) Dorheim et al. 2024
+rho_so2=-7.469841e-06 ; (W yr m–2 S Gg-1) Dorheim et al. 2024
+rho_nh3=-0.002146032 ; (W yr m–2 NH3Tg–1) Dorheim et al. 2024
 
 ; Miscellaneous radiative forcings are by default zero, but can read in from a input table to
 ; represent additional forcings not modeled by Hector (e.g. solar, bc on snow, jet contrails)
@@ -178,7 +178,7 @@ RF_misc[1750]=0
 ;------------------------------------------------------------------------
 [temperature]
 S=3.0 ; equilibrium climate sensitivity for 2xCO2 degC (A.4.4 of IPCC AR6)
-diff=2.38 ; ocean heat diffusivity, cm2/s calibrated to historical observations see Dorheim et al. in prep for details
+diff=2.38 ; ocean heat diffusivity, cm2/s calibrated to historical observations Dorheim et al. 2024 for details
 alpha=1.0 ; uncertainty scaling factor for aerosol forcing
 volscl=1.0 ; uncertainty scaling factor for volcanic forcing
 qco2=3.75 ; 2×CO2 RF (7.3.2 of IPCC AR6)
@@ -232,7 +232,7 @@ delta_HFC32=0.0 ; tropospheric adjustments scalar unitless (7.3.2.4 IPCC AR6
 molarMass=52.0 ; grams
 HFC32_emissions=csv:tables/ssp245_emiss-constraints_rf.csv
 
-[HFC4310_halocarbon] 
+[HFC4310_halocarbon]
 ; This is equivalent to HFC-43-10mee
 tau=17.0 ; lifetime in years (Table 7.SM.7 IPPC AR6)
 rho_HFC4310=0.000357 ; radiative efficiencies W/m2/ppt (Table 7.SM.7 IPPC AR6)

inst/input/hector_ssp370.ini

@@ -37,7 +37,7 @@ preind_interdeep_c=37100 ; intermediate and deep ocean C, IPCC AR6 Figure 5.12
 atmos_co2=590.33 ; initial atmospheric carbon pool Pg C of CO2 size used in spin up, consistent with C0
 C0=277.15 ; preindustrial CO2 from table 7.SM.1 IPCC AR6; CO2 radiative forcing is calibrated to this value
 npp_flux0=56.2 ; preindustrial net primary production, Pg C/yr from Ito et al. 2011
-;pf.npp_flux0=5.6 ; cf. Figure 3 in Chen et al. 2017 10.1088/1748-9326/aa8978 
+;pf.npp_flux0=5.6 ; cf. Figure 3 in Chen et al. 2017 10.1088/1748-9326/aa8978
 ;nonpf.npp_flux0=50.6
 
 veg_c=550 ; initial vegetation pool, Pg C
@@ -73,16 +73,16 @@ f_litterd=0.98 ; Fraction of litter flux to detritus (balance to soil)
 ;nonpf.f_litterd=0.98
 
 ; Anthropogenic contributions: emissions, direct air carbon capture and storage, and land use change, Pg C/yr
-ffi_emissions=csv:tables/ssp370_emiss-constraints_rf.csv 
+ffi_emissions=csv:tables/ssp370_emiss-constraints_rf.csv
 daccs_uptake=csv:tables/ssp370_emiss-constraints_rf.csv
 luc_emissions=csv:tables/ssp370_emiss-constraints_rf.csv
 luc_uptake=csv:tables/ssp370_emiss-constraints_rf.csv
 
 ; CO2 and temperature effects on the carbon cycle
-beta=0.53 ; CO2 fertilization factor (unitless), calibrated to historical observations see Dorheim et al. in prep for details
+beta=0.53 ; CO2 fertilization factor (unitless), calibrated to historical observations Dorheim et al. 2024 for details
 ;pf.beta=0.53
 ;nonpf.beta=0.53
-q10_rh=1.76 ; Heterotrophic respiration temperature sensitivity factor (unitless), calibrated to historical observations see Dorheim et al. in prep for details
+q10_rh=1.76 ; Heterotrophic respiration temperature sensitivity factor (unitless), calibrated to historical observations Dorheim et al. 2024 for details
 ;pf.q10_rh=1.76
 ;nonpf.q10_rh=1.76
 
@@ -165,10 +165,10 @@ baseyear=1750 ; when to start reporting; by definition, all F=0 in this year
 delta_co2=0.05 ; (unitless) forcing tropospheric adjustments for CO2 (7.3.2.1 of IPCC AR6)
 delta_ch4=-.14 ; (unitless) forcing tropospheric adjustments for CH4 (7.3.2.2 of IPCC AR6)
 delta_n2o=0.07 ; (unitless) forcing tropospheric adjustments for N2O (7.3.2.3 of IPCC AR6)
-rho_bc=0.06386286 ; (W yr m–2 C Tg–1) see Dorheim et al. in prep
-rho_oc=-0.006407143 ; (W yr m–2 C Tg–1) see Dorheim et al. in prep
-rho_so2=-7.469841e-06 ; (W yr m–2 S Gg-1) see Dorheim et al. in prep
-rho_nh3=-0.002146032 ; (W yr m–2 NH3Tg–1) see Dorheim et al. in prep
+rho_bc=0.06386286 ; (W yr m–2 C Tg–1) Dorheim et al. 2024
+rho_oc=-0.006407143 ; (W yr m–2 C Tg–1) Dorheim et al. 2024
+rho_so2=-7.469841e-06 ; (W yr m–2 S Gg-1) Dorheim et al. 2024
+rho_nh3=-0.002146032 ; (W yr m–2 NH3Tg–1) Dorheim et al. 2024
 
 ; Miscellaneous radiative forcings are by default zero, but can read in from a input table to
 ; represent additional forcings not modeled by Hector (e.g. solar, bc on snow, jet contrails)
@@ -178,7 +178,7 @@ RF_misc[1750]=0
 ;------------------------------------------------------------------------
 [temperature]
 S=3.0 ; equilibrium climate sensitivity for 2xCO2 degC (A.4.4 of IPCC AR6)
-diff=2.38 ; ocean heat diffusivity, cm2/s calibrated to historical observations see Dorheim et al. in prep for details
+diff=2.38 ; ocean heat diffusivity, cm2/s calibrated to historical observations Dorheim et al. 2024 for details
 alpha=1.0 ; uncertainty scaling factor for aerosol forcing
 volscl=1.0 ; uncertainty scaling factor for volcanic forcing
 qco2=3.75 ; 2×CO2 RF (7.3.2 of IPCC AR6)
@@ -232,7 +232,7 @@ delta_HFC32=0.0 ; tropospheric adjustments scalar unitless (7.3.2.4 IPCC AR6
 molarMass=52.0 ; grams
 HFC32_emissions=csv:tables/ssp370_emiss-constraints_rf.csv
 
-[HFC4310_halocarbon] 
+[HFC4310_halocarbon]
 ; This is equivalent to HFC-43-10mee
 tau=17.0 ; lifetime in years (Table 7.SM.7 IPPC AR6)
 rho_HFC4310=0.000357 ; radiative efficiencies W/m2/ppt (Table 7.SM.7 IPPC AR6)