Gadget3 global environment
aab_env.RdFunctions available to any gadget3 model
Details
g3_env is the top-level environment that any gadget3 model uses,
populated with utility functions.
NB: Several functions have _vec variants.
Due to TMB limitations these should be used when you have a vector not scalar input.
ADREPORT
TMB's ADREPORT function. See sdreport documentation
as_integer
C++ compatible equivalent to as.integer
as.numeric
R as.numeric or TMB asDouble
assert_msg
C++/R function that ensures expression is true, or stops model.
assert_msg(x > 0, "x must be positive")avoid_zero
Adds small value to input to ensure output is never zero
avoid_zero_vec is identical to avoid_zero, and is only present for backward compatibility.
bounded / bounded_vec
Ensures x is within limits b & a.
If x positive, return a.
If x negative, b.
If x -10..10, smoothly transition from b to a
bounded_vec(x, 200, 100)g3_matrix_vec
Apply matrix transformation tf to vector vec, return resultant vector.
g3_matrix_vec(tf, vec)lgamma_vec
Vector equivalent of lgamma
logspace_add
TMB's logspace_add, essentially a differentiable version of pmax.
normalize_vec
Divide vector a by it's sum, i.e. so it now sums to 1. If vector is all-zero, return an all-zero vector instead.
nvl
Return first non-null argument. NB: No C++ implementation.
print_array
Utility to pretty-print array ar
ratio_add_vec
Sum orig_vec & new_vec according to ratio of orig_amount & new_amount
nonconform_add / nonconform_mult / nonconform_div / nonconform_div_avz
Scalar sum/multiply/divide 2 non-conforming arrays, by treating the latter as a vector and repeating as many times as required. Results will be structured identically to the first array.
nonconform_div_avz(x, y) is equivalent to nonconform_div(x, avoid_zero_vec(y))
REPORT
TMB's REPORT function.
REprintf
Equivalent of RCpp REprintf
Rprintf
Equivalent of RCpp Rprintf
Examples
## avoid_zero
g3_eval(quote( c( avoid_zero(0), avoid_zero(10) ) ))
#> [1] 6.931472e-04 1.000000e+01
g3_eval(quote( avoid_zero(0:5) ))
#> [1] 0.0006931472 1.0000000000 2.0000000000 3.0000000000 4.0000000000
#> [6] 5.0000000000
## bounded / bounded_vec
curve(g3_eval(quote( bounded(x, 200, 100) ), x = x), -100, 100)
## logspace_add
curve(g3_eval(quote( logspace_add(x, 10) ), x = x), 0, 40)
## normalize_vec
g3_eval(quote( normalize_vec(c( 4, 4, 8, 2 )) ))
#> [1] 0.2222222 0.2222222 0.4444444 0.1111111
## nonconform_mult
g3_eval(quote( nonconform_mult(
array(seq(0, 4*5*6), dim = c(4,5,6)),
c(1e1, 1e2, 1e3, 1e4)) ))
#> , , 1
#>
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 0 40 80 120 160
#> [2,] 100 500 900 1300 1700
#> [3,] 2000 6000 10000 14000 18000
#> [4,] 30000 70000 110000 150000 190000
#>
#> , , 2
#>
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 200 240 280 320 360
#> [2,] 2100 2500 2900 3300 3700
#> [3,] 22000 26000 30000 34000 38000
#> [4,] 230000 270000 310000 350000 390000
#>
#> , , 3
#>
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 400 440 480 520 560
#> [2,] 4100 4500 4900 5300 5700
#> [3,] 42000 46000 50000 54000 58000
#> [4,] 430000 470000 510000 550000 590000
#>
#> , , 4
#>
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 600 640 680 720 760
#> [2,] 6100 6500 6900 7300 7700
#> [3,] 62000 66000 70000 74000 78000
#> [4,] 630000 670000 710000 750000 790000
#>
#> , , 5
#>
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 800 840 880 920 960
#> [2,] 8100 8500 8900 9300 9700
#> [3,] 82000 86000 90000 94000 98000
#> [4,] 830000 870000 910000 950000 990000
#>
#> , , 6
#>
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 1000 1040 1080 1120 1160
#> [2,] 10100 10500 10900 11300 11700
#> [3,] 102000 106000 110000 114000 118000
#> [4,] 1030000 1070000 1110000 1150000 1190000
#>
## nonconform_div_avz
g3_eval(quote( nonconform_div_avz(
array(seq(0, 4*5*6), dim = c(4,5,6)),
c(1e1, 1e2, 0, 1e4)) ))
#> , , 1
#>
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 0.0000 0.4000 0.8000 1.2000 1.6000
#> [2,] 0.0100 0.0500 0.0900 0.1300 0.1700
#> [3,] 2885.3901 8656.1702 14426.9504 20197.7306 25968.5107
#> [4,] 0.0003 0.0007 0.0011 0.0015 0.0019
#>
#> , , 2
#>
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 2.0000 2.4000 2.8000 3.2000 3.6000
#> [2,] 0.2100 0.2500 0.2900 0.3300 0.3700
#> [3,] 31739.2909 37510.0711 43280.8512 49051.6314 54822.4116
#> [4,] 0.0023 0.0027 0.0031 0.0035 0.0039
#>
#> , , 3
#>
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 4.0000 4.4000 4.8000 5.2000 5.6000
#> [2,] 0.4100 0.4500 0.4900 0.5300 0.5700
#> [3,] 60593.1917 66363.9719 72134.7520 77905.5322 83676.3124
#> [4,] 0.0043 0.0047 0.0051 0.0055 0.0059
#>
#> , , 4
#>
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 6.0000 6.4000 6.8000 7.2000 7.6000
#> [2,] 0.6100 0.6500 0.6900 0.7300 0.7700
#> [3,] 89447.0925 95217.8727 100988.6529 106759.4330 112530.2132
#> [4,] 0.0063 0.0067 0.0071 0.0075 0.0079
#>
#> , , 5
#>
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 8.0000 8.4000 8.8000 9.2000 9.6000
#> [2,] 0.8100 0.8500 0.8900 0.9300 0.9700
#> [3,] 118300.9934 124071.7735 129842.5537 135613.3338 141384.1140
#> [4,] 0.0083 0.0087 0.0091 0.0095 0.0099
#>
#> , , 6
#>
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 10.0000 10.4000 10.8000 11.2000 11.6000
#> [2,] 1.0100 1.0500 1.0900 1.1300 1.1700
#> [3,] 147154.8942 152925.6743 158696.4545 164467.2347 170238.0148
#> [4,] 0.0103 0.0107 0.0111 0.0115 0.0119
#>
g3_eval(quote( nonconform_div(
array(seq(0, 4*5*6), dim = c(4,5,6)),
avoid_zero(c(1e1, 1e2, 0, 1e4))) ))
#> , , 1
#>
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 0.0000 0.4000 0.8000 1.2000 1.6000
#> [2,] 0.0100 0.0500 0.0900 0.1300 0.1700
#> [3,] 2885.3901 8656.1702 14426.9504 20197.7306 25968.5107
#> [4,] 0.0003 0.0007 0.0011 0.0015 0.0019
#>
#> , , 2
#>
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 2.0000 2.4000 2.8000 3.2000 3.6000
#> [2,] 0.2100 0.2500 0.2900 0.3300 0.3700
#> [3,] 31739.2909 37510.0711 43280.8512 49051.6314 54822.4116
#> [4,] 0.0023 0.0027 0.0031 0.0035 0.0039
#>
#> , , 3
#>
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 4.0000 4.4000 4.8000 5.2000 5.6000
#> [2,] 0.4100 0.4500 0.4900 0.5300 0.5700
#> [3,] 60593.1917 66363.9719 72134.7520 77905.5322 83676.3124
#> [4,] 0.0043 0.0047 0.0051 0.0055 0.0059
#>
#> , , 4
#>
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 6.0000 6.4000 6.8000 7.2000 7.6000
#> [2,] 0.6100 0.6500 0.6900 0.7300 0.7700
#> [3,] 89447.0925 95217.8727 100988.6529 106759.4330 112530.2132
#> [4,] 0.0063 0.0067 0.0071 0.0075 0.0079
#>
#> , , 5
#>
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 8.0000 8.4000 8.8000 9.2000 9.6000
#> [2,] 0.8100 0.8500 0.8900 0.9300 0.9700
#> [3,] 118300.9934 124071.7735 129842.5537 135613.3338 141384.1140
#> [4,] 0.0083 0.0087 0.0091 0.0095 0.0099
#>
#> , , 6
#>
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 10.0000 10.4000 10.8000 11.2000 11.6000
#> [2,] 1.0100 1.0500 1.0900 1.1300 1.1700
#> [3,] 147154.8942 152925.6743 158696.4545 164467.2347 170238.0148
#> [4,] 0.0103 0.0107 0.0111 0.0115 0.0119
#>