## IWRES plots
ABS_IWRES_IPRED:
  ptype: SCATTER
  x: IPRED
  'y': IWRES
  is.title: TRUE
  labels:
    title: '|IWRES| vs IPRED'
    subtitle: ''
    'y': '|IWRES|'
    x: IPRED
  point:
    shape: 1.0
    colour: black
    size: 1.0
  is.hline: yes
  is.smooth: yes
  smooth_with_bloq: no
  smooth:
    se: no
    colour: red
    linetype: 1.0
    formula: y ~ x
  trans: abs_y
  bloq:
    show: yes
    cens: CENS
    limit: LIMIT
    colour: pink
    size: 2.0
    linewidth: 2.0
    alpha: 0.9

ABS_IWRES_TIME:
  ptype: SCATTER
  x: TIME
  'y': IWRES
  is.title: TRUE
  labels:
    title: '|IWRES| vs TIME'
    subtitle: ''
    'y': '|IWRES|'
    x: TIME
  point:
    shape: 1.0
    colour: black
    size: 1.0
  is.hline: yes
  is.smooth: yes
  smooth_with_bloq: no
  smooth:
    se: no
    colour: red
    linetype: 1.0
    formula: y ~ x
  trans: abs_y
  bloq:
    show: yes
    cens: CENS
    limit: LIMIT
    colour: pink
    size: 2.0
    linewidth: 2.0
    alpha: 0.9

IWRES_IPRED:
  ptype: SCATTER
  x: IPRED
  'y': IWRES
  is.title: TRUE
  labels:
    title: IWRES vs IPRED
    subtitle: ''
    x: IPRED
    'y': IWRES
  point:
    shape: 1.0
    colour: black
    size: 1.0
  is.hline: yes
  is.band: yes
  is.smooth: yes
  smooth_with_bloq: no
  smooth:
    se: no
    colour: red
    linetype: 1.0
    formula: y ~ x
  bloq:
    show: yes
    cens: CENS
    limit: LIMIT
    colour: pink
    size: 2.0
    linewidth: 2.0
    alpha: 0.9

IWRES_TIME:
  ptype: SCATTER
  x: TIME
  'y': IWRES
  is.title: TRUE
  labels:
    title: IWRES vs TIME
    subtitle: ''
    x: TIME
    'y': IWRES
  point:
    shape: 1.0
    colour: black
    size: 1.0
  is.hline: yes
  is.smooth: yes
  smooth_with_bloq: no
  is.band: yes
  smooth:
    se: no
    colour: red
    linetype: 1.0
    formula: y ~ x
  bloq:
    show: yes
    cens: CENS
    limit: LIMIT
    colour: pink
    size: 2.0
    linewidth: 2.0
    alpha: 0.9

IWRES_DENS:
  ptype: PMX_DENS
  x: IWRES
  is.title: FALSE
  dname: predictions
  labels:
    title: 'Density plot of IWRES'
    subtitle: ''
    x: IWRES
    'y': ' '

IWRES_QQ:
  ptype: PMX_QQ
  x: IWRES
  is.title: FALSE
  labels:
    title: ''
    subtitle: ''
    x: Standard Normal Quantiles
    'y': IWRES Quantiles
  is.reference_line: no
  reference_line:
    color: black
  is.identity_line: yes
  identity_line:
    intercept: 0
    colour: black

## NPDE plots

NPDE_TIME:
  ptype: SCATTER
  x: TIME
  'y': NPDE
  is.title: TRUE
  labels:
    title: NPDE vs TIME
    subtitle: ''
    x: TIME
    'y': NPDE
  point:
    shape: 1.0
    colour: black
    size: 1.0
  is.hline: yes
  is.band: yes
  is.smooth: yes
  smooth_with_bloq: no
  smooth:
    se: no
    colour: red
    linetype: 1.0
    formula: y ~ x
  bloq:
    show: yes
    cens: CENS
    limit: LIMIT
    colour: pink
    size: 2.0
    linewidth: 2.0
    alpha: 0.9

NPDE_PRED:
  ptype: SCATTER
  x: PRED
  'y': NPDE
  is.title: TRUE
  labels:
    title: NPDE vs PRED
    subtitle: ''
    x: PRED
    'y': NPDE
  point:
    shape: 1.0
    colour: black
    size: 1.0
  is.hline: yes
  hline:
    colour: black
  is.band: yes
  is.smooth: yes
  smooth_with_bloq: no
  smooth:
    se: no
    colour: red
    linetype: 1.0
    formula: y ~ x
  bloq:
    show: yes
    cens: CENS
    limit: LIMIT
    colour: pink
    linewidth: 2.0
    size: 2.0
    alpha: 0.9

NPDE_QQ:
  ptype: PMX_QQ
  x: NPDE
  is.title: TRUE
  labels:
    title: ''
    subtitle: ''
    x: Standard Normal Quantiles
    'y': NPDE Quantiles
  is.reference_line: yes
  reference_line:
    color: black

## DV plots

DV_PRED:
  ptype: SCATTER
  labels:
    title: DV vs PRED
    subtitle: ''
    x: PRED
    'y': DV
  x: PRED
  'y': DV
  is.title: TRUE
  point:
    shape: 1.0
    colour: black
    size: 1.0
  is.smooth: yes
  smooth_with_bloq: no
  smooth:
    se: no
    colour: red
    linetype: 1.0
    formula: y ~ x
  is.identity_line: yes
  identity_line:
    intercept: 0
    colour: black
  bloq:
    show: yes
    cens: CENS
    limit: LIMIT
    colour: pink
    size: 2.0
    linewidth: 2.0
    alpha: 0.9
  square_plot: yes
    
DV_IPRED:
  ptype: SCATTER
  labels:
    title: DV vs IPRED
    subtitle: ''
    x: IPRED
    'y': DV
  x: IPRED
  'y': DV
  is.title: TRUE
  point:
    shape: 1.0
    colour: black
    size: 1.0
  is.smooth: yes
  smooth_with_bloq: no
  smooth:
    se: no
    colour: red
    linetype: 1.0
    formula: y ~ x
  is.identity_line: yes
  identity_line:
    intercept: 0
    colour: black
  bloq:
    show: yes
    cens: CENS
    limit: LIMIT
    colour: pink
    linewidth: 2.0
    size: 2.0
    alpha: 0.9

## Individual plots

INDIVIDUAL:
  ptype: IND
  dname: IND
  ranges: ~
  is.smooth: no
  smooth_with_bloq: no
  is.title: TRUE
  ipred_line:
    colour: black
    linewidth: 1
    linetype: 2
  pred_line:
    colour: black
    linewidth: 1
    linetype: 1
  point:
    colour: black
    shape : 21
    size: 1.5
  facets:
    ncol: 3
    nrow: 4
    scales: free
  labels:
    title: Individual fits
    subtitle: ''
    x: TIME
    'y': DV
  use.finegrid: yes
  bloq:
    show: yes
    cens: CENS
    limit: LIMIT
    colour: pink
    linewidth: 2.0
    size: 2.0
    alpha: 0.9
  is.legend: yes
  legend.position: top
    
## Eta plots
    
ETA_HIST:
  ptype: DIS
  type: hist
  dname: eta
  is.title: TRUE
  facets:
    scales: free_x
    nrow: 3.0
  is.shrink: yes
  shrink:
    fun: var
    size: 4.0
    colour: black
    hjust: -1
    vjust: 2
    annotation: shrinkage
  histogram:
    binwidth: 0.034
    position: dodge
    fill: white
    colour: black
  labels:
    title: EBE distribution
    subtitle: ''
    x: 'Estimated eta'
    'y': 'Histogram'
    legend: Random effect

ETA_BOX:
  ptype: DIS
  dname: eta
  type: box
  is.title: TRUE
  is.jitter: yes
  jitter:
    shape: 1.0
    colour: black
    width: 0.1
    height: 0.1
    alpha: 0.6
  is.shrink: yes
  shrink:
    fun: var
    size: 4.0
    colour: black
    hjust: 0.5
    vjust: 2.0
    annotation: shrinkage
  labels:
    title: EBE distribution
    subtitle: ''
    x: 'Model parameters'
    'y': 'EBEs'
    legend: Random effect
  facets:
    scales: free_x
    nrow: 3.0
  is.band: yes
  band:
    'yintercept':
    - 0
    - 0
    linetype: 2.0
    color: grey50

ETA_MATRIX:
  ptype: ETA_PAIRS
  title: Correlations of random effects
  dname: eta
  type.eta: mode
  text_color: black
  is.smooth: yes
  smooth_with_bloq: no
  is.hline: yes
  is.title: TRUE
  hline: 
    linetype: 2.0
  point:
    size: 1
    colour: black
    shape: 21
  smooth:
    se: FALSE
    linetype: 1
    linewidth: 1.5
    method: loess
    colour: red
    formula: y ~ x
  is.shrink: TRUE
  shrink:
    fun : var
    size: 5
  
ETA_CATS:
  ptype: ETA_COV
  is.title: TRUE
  type: cats
  
ETA_CONTS:
  ptype: ETA_COV
  type: conts
  is.title: TRUE
  facets:
    scales: free
  point:
    shape: 21
    color: black
  correl:
    colour: red
    size: 4
  is.smooth: yes
  smooth_with_bloq: no
  smooth:
    se: no
    linewidth: 1
    color: black
    linetype: 1.0
    method: lm
    formula: y ~ x
  is.band: yes
  band:
    'yintercept':
    - 0
    - 0
    linetype: 2.0

  
ETA_QQ:
  ptype: PMX_QQ
  x: VALUE
  dname: eta
  is.title: TRUE
  labels:
    title: ''
    subtitle: ''
    x: Standard Normal Quantiles
    'y': ETA Quantiles
  facets:
    scales: free_y
    nrow: 2
  is.reference_line: yes
  reference_line:
    color: black
  xmax: no
  is.shrink: yes
  shrink:
    fun: var
    size: 4.0
    colour: black
    hjust: -1
    vjust: 2
    annotation: shrink
  is.hline: yes
  hline:
    colour: black
## VPC plots
    
PMX_VPC:
  ptype: VPC
  type: percentile
  dname: sim
  is.title: TRUE
  labels:
    title: 'Percentile VPC'
    subtitle: '(with observations)'
    x: TIME
    'y': DV
  is.smooth: no
  smooth_with_bloq: no

## SAEM plots
    
SAEM_CONVERGENCE:
  ptype: PARAM_HISTORY
  dname: saem
  is.title: TRUE
  is.smooth: no
  is.reference_line: yes
  parameter_line:
    colour: blue
    linetype: solid
  convergence_line:
    colour: violet
    linetype: solid
  reference_line:
    colour: red
    linetype: solid
  smooth_with_bloq: no
  labels:
    title: 'SAEM Convergence Plot by Parameter'
    subtitle: ''
    x: 'Iteration'
    'y': 'Parameter Value'
  facets:
    ncol: 3
    scales: free_y
