Univariate 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

Uni-variate data is a set of pairs of values for an independent and associated dependent variable. (AmP data types.)

Codification of types univariate data

In the mydata file the author needs to specify which types of data are used in the entry. Labels for uni-variate data are packed as metaData.data_1. The codification generally follows DEB's notation rules. The table below presents the labels for the different types of univariate data found in the collection (dark yellow cells to the far right of each row in the species list). For the labels the independent and the dependent variables are separated by "-".

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

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

Several f or T might mean several constant values, but also that they vary in time. Various labels relate to life history events, as listed for zero-variate data. Trailing e means that data refers to embryo development. 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. Filtering rate also includes food-searching rate (for species that don't filter at all).

Data labels Description
t-Le time, embryo length
t-Le_T time, embryo length (several T)
t-Le_fT time, embryo length (several f, T)
t-L time, length
t-L_T time, length (several T)
t-L_f time, length (several f)
t-L_fT time, length (several f, T)
t-LR time, length including gonads
t-dL time, change in length
t-Ae time, surface area for embryo
t-A time, surface area
t-V time, volume
t-V_f time, volume (several f)
t-VYe time, embryo yolk volume
t-VY time, yolk volume
t-VY_T time, yolk volume (several T)
t-Wwe time, embryo wet weight
t-WwYe time, embryo yolk wet weight
t-WwVe time, embryo wet weight excluding yolk
t-Ww time, wet weight
t-Ww_f time, wet weight (several f)
t-Ww_T time, wet weight (several T)
t-Ww_fT time, wet weight (several f, T)
t-WwR time, gonad wet weight
t-WdVe time, embryo dry weight (excluding yolk)
t-WdYe time, embryo dry weight (yolk)
t-Wde time, embryo dry weight (total)
t-Wde_fT time, embryo dry weight (several f, T)
t-Wd time, dry weight
t-Wd_f time, dry weight (several f)
t-Wd_T time, dry weight (several T)
t-Wd_fT time, dry weight (several f, T)
t-WdR time, gonad dry weight
t-WC time, carbon weight
t-WC_T time, carbon weight (several T)
t-M_PLC time, mass of protein, lipid, carbohydrate
t-M_N time, mass of nitrogen
t-M_DNA time, mass of DNA
t-M_RNA time, mass of RNA
t-E time, energy content
t-pX time, food energy ingestion rate
t-p+ time, heat production
t-R_f time, reproduction rate (several f)
t-R_T time, reproduction rate (several T)
t-N time, number of offspring
t-N_f time, number of offspring (several f)
t-N_T time, number of offspring (several T)
t-N_fT time, number of offspring (several f, T)
t-JX_f time, ingestion rate (several f)
t-F_f time, filtering rate (several f)
t-JX time, ingestion rate
t-JX_T time, ingestion rate (several T)
t-JCe time, embryo CO_2 production
t-JOe time, embryo O_2 consumption
t-JOe_T time, embryo O_2 cons (several T)
t-JO time, O_2 consumption
t-JNe time, embryo NH_3 production
t-T time, body temperature
t-S time, surviving fraction
t-S_f time, surviving fraction (several f)
t-S_T time, surviving fraction (several T)
t-S_fT time, surviving fraction (several f, T)
t-dC time, condition factor
ax-Wwx_f age, weight at fledging (several f)
X-dL_L food dens., change in length (several L)
X-dWd_W food dens., change in dry w. (several W)
X-aj food density, age at j
X-ap food density, age at p
X-am food density, age at death
X-Lp food density, length at p
X-Li food dens., length at i
X-Vp food density, volume at p
X-Vi food density, volume at i
X-Ri food density, reproduction rate at i
X-JX food density, ingestion rate
X-JX_L food density, ingestion rate (several L)
X-JX_W food density, ingestion rate (several W)
X-JP_L food density, feaces production (several L)
X-JC_W food density, CO_2-production (several W)
L-L length, length (different length measures)
L-dL length, change in length
L0-Lt length at capture, length at recapture
L-V length, volume
L-Wwe length, embryo wet weight
L-Ww length, wet weight
L-Ww_f length, wet weight (several f)
L-Wde length, embryo dry weight
L-Wde_T length, embryo dry weight (several T)
L-Wd length, dry weight
L-Wd_f length, dry weight (several f)
L-WwR length, gonad wet weight
L-dWw length, change in wet weight
L-WC length, carbon weight
L-WN length, nitrogen weight
L-E length, total energy
L-N length, number of eggs/offspring
L-N_f length, number of eggs/offspring (several f)
L-N_T length, number of eggs/offspring (several T)
L-R length, reproduction rate
L-GSI length, gonado somatic in dex
L-F length, filtering rate
L-JX length, food consumption
L-X length, cumulated food ingested
L-JC length, CO_2 production
L-JO length, O_2 consumption
L-JO_T length, O_2 consumption (several T)
V-V volume at t_1, volume at t_2
Ww-dWw wet weight, change in wet weight
Ww0-Wwt wet weight at capture, wet weight at recapture
Ww-dWw_T wet weight, change in wet weight (several T)
Ww-N wet weight, number of eggs/offspring
Ww-N_T wet weight, number of eggs/offspring (several T)
Ww-R wet weight, reproduction rate
Ww-R_f wet weight, reproduction rate (several f)
Ww-JX wet weight, ingestion rate
Ww-JX_T wet weight, ingestion rate (several T)
Ww-JX_f wet weight, ingestion rate (several f)
Ww-X wet weight, cumulated food ingested
Ww-JO wet weight, O_2 consumption
Ww-JO_T wet weight, O_2 consumption (several T)
Ww-JO_f wet weight, O_2 consumption (several f)
Ww-JN_T wet weight, NH_3 consumption (several T)
Ww-p+_T wet weight, heat production (several T)
Ww-pX wet weight, food energy consumption
Wd-Wa dry weight, ash-free dry weight
Wd-Ww dry weight, wet weight
Wd-JC_T wet weight, CO_2 production (several T)
Wd-JO dry weight, O_2 consumption
Wd-JO_f dry weight, O_2 consumption (several f)
Wd-JO_T dry weight, O_2 consumption (several T)
Wd-JN dry weight, NH_3 production
Wd-JN_T dry weight, NH_3 production (several T)
WC-JX carbon weight,food consumption
JX-ap ingestion rate, age at p
JX-am ingestion rate, age at death
JX-Vp ingestion rate, volume at p
JX-Vi ingestion rate, volume at i
JX-Ri ingestion rate, reproduction rate at i
JX-JO_L ingestion rate, O_2 consumption (several L)
pX-pG ingestion power, growth power
T-ah temperature, age at h
T-ab temperature, age at b
T-aj temperature, age at j
T-ap temperature, age at p
T-am temperature, age at death
T-t temperature, time between stages
T-dWw temperature, change in wet weight
T-dWw_f temperature, change in wet weight (several f)
T-R temperature, reproduction rate
T-N temperature, number of eggs
T-JX temperature, food consumption
T-JC temperature, CO_2 production
T-JO temperature, O_2 consumption
T-JO_f temperature, O_2 consumption (several f)
T-JO_W temperature, O_2 consumption (several W)
T-JO_fW temperature, O_2 consumption (several f, W)
T-JN temperature, NH_3 production
T-JN_W temperature, NH_3 production (several W)