Zero-variate data

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AmP estimation
Concepts

Data and completeness
Parameter estimation
Goodness-of-fit: SMSE / MRE
AmP Literature

Practice - essentials

Starting an estimation for a new species
Setting initial parameter values
Setting weight coefficients
Computing implied properties
Submitting to the collection

Practice - extra modules
Code specification
User-defined files: run, mydata, pars_init, predict
Data: Zero-variate, Univariate, Pseudo-data

Typified models
Estimation options

Zero-variate data is a scalar that quantifies a feature of the organism at a given moment. (See more about AmP data types.)

Codification of types zero-variate data

In the mydata file the author needs to specify which types of data are used in the entry. Labels for zero-variate data are packed as metaData.data_0. The codification generally follows DEB's notation rules. The leading character indicates the type of variable, followed by a marker for the life history event.

Indices symbolising different life history events
0 start of development j end of acceleration R first breeding
h hatching (leaving egg) p puberty (start of allocation to reproduction) e emergence (imago)
b birth (start of feeding) i ultimate state s start of acceleration
x weaning (or fledging) m death (life span)

Optionally this can be followed by an underscore ("_"), indicating several values of a modifying factor:

  • f, functional response
  • T, temperature
  • t, time
  • L, length
  • W, weight

The labels are stylized, meaning e.g. that label ap stands for age-at-puberty, while actually time since birth at puberty, tp, might be used as a data-point. The rationale is that delays in the start of development can occur, which would affect ap, but not tp. Data might relate to males and females; this is not indicated in the data labels, but comments in such entries specify the parameters in which they differ.

Data Labels Description
ah age at h
ah_T age at h (several T))
ab age at birth
ab_T age at birth (several T)
ab_f age at birth (several f)
tg gestation time
ax age at x
as age at s
aj age at j
aj_T age at j (several T)
ap age (or time since birth) at p
ap_T age at p (several T)
ap_f age at p (several f)
aR age at R
ae age at e
am age at death (life span)
am_f age at death (several f)
am_T age at death (several T)
L0 length at 0
Lh length at h
Lb length at b
Lb_f length at b (several f)
Lx length at x
Ls length at s
Lj length at j
Lp length at p
Lp_f length at p (several f)
LR length at R
Li length at i
Li_f length at i (several f)
L_t length at time t
L_W length at time weight
dLb change in length at b
dLp change in length at p
dLj change in length at j
Ab surface area at b
Ap surface area at p
Ai surface area at i
V0 volume at 0
Vb volume at b
Vb_f volume at b (several f)
Vp volume at p
Vp_f volume at p (several f)
Vi volume at i
Vi_f volume at i (several f)
Ww0 wet weight at 0
Wwh wet weight at h
Wwb wet weight at b
Wwb_f wet weight at b (several f)
Wwx wet weight at x
Wws wet weight at s
Wwj wet weight at j
WwR wet weight at R
Wwp wet weight at p
Wwe wet weight at e
Wwi wet weight at i
Ww_L wet weight at length
Ww_t wet weight at time
dWw_W change in wet weight at W
Wd0 dry weight at 0
Wdh dry weight at h
Wdb dry weight at b
Wdb_f dry weight at b (several f)
Wdx dry weight at x
Wds dry weight at s
Wdj dry weight at j
Wdp dry weight at p
Wde dry weight at e
Wdi dry weight at i
Wd_t dry weight at t
Wd_L dry weight at length
WdR_L gonad dry weight at L
WdR_Wd gonad dry weight at Wd
WC0 carbon weight at 0
WN0 nitrogen weight at 0
dWdb change in dry weight at b
dWd decrease in dry weight during starvation
E_L total energy at L
E0 reserve energy at 0
Eh reserve energy at h
Eb reserve energy at b
Ej reserve energy at j
EbE0 ratio of reserve energy at b and 0
EXx cumulated food energy at x
r specific growth rate
rB von Bertalanffy growth rate
rB_T von Bertalanffy growth rate (several T)
Ri reproduction rate at i
Ri_f reproduction rate at i (several f)
R_L reproduction rate at length
R_W reproduction rate at weight
GSI gonado-somatic index
Ni (total) number of offspring at i
Ni_f (total) number of offspring at i (several f)
Fm maximum clearance (filtering) rate
K half saturation coefficient
pXi maximum ingestion rate (energy)
pXi_Wd maximum ingestion rate at Wd (energy)
pX_t food energy ingestion rate at t
pAi maximum assimilation rate (energy)
pL lactation flux (energy)
kapX digestion efficiency
RQ respiration quotient: JC/JO
JXi food consumption at i
JX_L food consumption at L
JX_W food consumption at W
JLi milk production at i
JOb O2 consumption at b
JOi O2 consumption at i
JO_W O2 consumption at W
JCi CO2 production at i
ss supply stress
xi_WE energy density of dry mass excluding the reproduction buffer