Is your feature request related to a problem? Please describe.
Not a separate function. Basic calculation.
The HC05 is the 5th percentile hazardous concentration of a set of related 95th percentile extirpation concentration values (XC95). The HC05 is the estimated value of the stressor at which 5% of species will be extirpated.
Describe the solution you'd like
Pulled from BC paper code, March 2017 and some other files from June 2016.
Describe alternatives you've considered
Add as an example
Additional context
Run example for fish.wt.cdf to get XC95 values.
# data
data(dta.do)
data(ss.sites)
# run function (~20 seconds)
dftv.do <- fish.wt.cdf(datafile = dta.do, ss = ss.sites, plot = T, dogam = T
, SampleID = "Station_Date", tag = "wt", sortvect = NULL
, np = 61, nt = 25, addtrend = T
, wd = getwd(), groups = c("BigHUC","ECOREGL3","WS_AREA")
, xvar = "cond")
View(dftv.do)
knitr::kable(head(dftv.do))
GENUS
XC95.cdf
trend
XC95.gam
total.n
total.N
HUC
eco3
wtshed
26
Etheostoma baileyi
322
=
501
38
1729
500
70_69_68
1.8_353
78
Noturus insignis
351
=
347
208
3259
204_205_207_208_301_500_601
67_69
19.597_8336.5394
22
Erimyzon oblongus
382
=
443
26
3232
204_205_207_208_500
70_67_69
4.3934_493.1524
25
Esox niger
467
~
672
63
1503
204_205_207_208
67_69
3.4644_742.9773
98
Salvelinus fontinalis
508
=
639
1361
3215
204_205_207_500
67_69_70
1.4111_395.4895
16
Cottus girardi
518
~
672
31
1085
205_207
67
2.0236_594.457
Then calculate the 5th quantile.
hc05_cdf <- quantile(dftv.do$XC95.cdf, probs = 0.05, na.rm = TRUE, type = 6)
hc05_gam <- quantile(dftv.do$XC95.gam, probs = 0.05, na.rm = TRUE, type = 6)
# both at once
hc05_both <- apply(dftv.do[, c("XC95.cdf", "XC95.gam")], 2
, quantile, probs=0.05, na.rm=TRUE, type=6)
leppott
commented
4 years ago
Is your feature request related to a problem? Please describe. Not a separate function. Basic calculation.
The HC05 is the 5th percentile hazardous concentration of a set of related 95th percentile extirpation concentration values (XC95). The HC05 is the estimated value of the stressor at which 5% of species will be extirpated.
Describe the solution you'd like Pulled from BC paper code, March 2017 and some other files from June 2016.
Describe alternatives you've considered Add as an example
Additional context Run example for fish.wt.cdf to get XC95 values.
Then calculate the 5th quantile.