{"stage":"timepoints","label":"Requested timepoints","description":"Requested timepoints","scale":"time","plot.order":1,"plotting.colour":"Black","plotting.alpha":1}
{"stage":"clim.signal.ann","label":"(1) Input climate","description":"Input climate signal at requested timepoints at annual resolution","scale":"Climate units","plot.order":1,"plotting.colour":"#018571","plotting.alpha":1}
{"stage":"clim.signal.smoothed","label":"(1) Input climate","description":"Input climate signal at regular time intervals and resolution = plot.sig.res","scale":"Climate units","plot.order":2,"plotting.colour":"#018571","plotting.alpha":1}
{"stage":"clim.timepoints.ssr","label":"(1) Input climate","description":"Input climate signal at requested timepoints, smoothed to resolution = plot.sig.res","scale":"Climate units","plot.order":3,"plotting.colour":"#018571","plotting.alpha":1}
{"stage":"proxy.bt","label":"(2) +Bioturbation","description":"Climate signal after bioturbation","scale":"Proxy units","plot.order":4,"plotting.colour":"Green","plotting.alpha":1}
{"stage":"proxy.bt.sb","label":"(3) +Habitat bias","description":"Climate signal after bioturbation and habitat bias","scale":"Proxy units","plot.order":5,"plotting.colour":"Gold","plotting.alpha":1}
{"stage":"proxy.bt.sb.inf.b","label":"(.) +Bias","description":"Climate signal after bioturbation, habitat bias, and bias","scale":"Proxy units","plot.order":10,"plotting.colour":"Pink","plotting.alpha":0.5}
{"stage":"proxy.bt.sb.inf.b.n","label":"(5) +Independent error","description":"Climate signal after bioturbation, habitat bias, and measurement error","scale":"Proxy units","plot.order":6,"plotting.colour":"#7570b3","plotting.alpha":0.5}
{"stage":"proxy.bt.sb.sampY","label":"(4) +Aliasing Y","description":"Climate signal after bioturbation, habitat bias, and aliasing of inter-annual variation","scale":"Proxy units","plot.order":7,"plotting.colour":"#d95f02","plotting.alpha":0.5}
{"stage":"proxy.bt.sb.sampYM","label":"(4) +Aliasing YM","description":"Climate signal after bioturbation, habitat bias, and aliasing of inter-annual and intra-annual variation such as monthly temperatures or depth habitats","scale":"Proxy units","plot.order":8,"plotting.colour":"#d95f02","plotting.alpha":1}
{"stage":"proxy.bt.sb.sampYM.b","label":"(.) +Bias","description":"Climate signal after bioturbation, habitat bias, and aliasing of inter-annual and intra-annual variation such as monthly temperatures or depth habitats, and bias","scale":"Proxy units","plot.order":9,"plotting.colour":"Pink","plotting.alpha":0.5}
{"stage":"proxy.bt.sb.sampYM.b.n","label":"(5) +Independent error","description":"Climate signal after bioturbation, habitat bias, aliasing, and measurement error","scale":"Proxy units","plot.order":11,"plotting.colour":"#7570b3","plotting.alpha":0.5}
{"stage":"simulated.proxy","label":"(5) +Independent error","description":"Final simulated pseudo-proxy, this will be same as proxy.bt.sb.inf.b.n when n.samples = Inf, and proxy.bt.sb.sampYM.b.n when n.samples is finite","scale":"Proxy units","plot.order":12,"plotting.colour":"#7570b3","plotting.alpha":1}
{"stage":"simulated.proxy.cal.err","label":"(6) +Calibration uncertainty","description":"Final simulated pseudo-proxy + uncertainty in true relationship to the climate variable (calibration error)","scale":"Proxy units","plot.order":13,"plotting.colour":"Red","plotting.alpha":1}
{"stage":"reconstructed.climate","label":"(7) Reconstructed climate","description":"Final pseudo-proxy calibrated to temperature","scale":"Climate units","plot.order":14,"plotting.colour":"Blue","plotting.alpha":0.5}
{"stage":"observed.proxy","label":"(*) Observed proxy","description":"True observed proxy (when supplied)","plot.order":15,"plotting.colour":"Red","plotting.alpha":0.5}