Test project - D70Montrave linetransect

[dill]

Here is a summary of the current state of this project's conversion:

> cc <- convert_project("inst/D70Montrave-lt/D70Montrave\\ linetransect")
Warning message:
In get_data(data_file) :
  Data contains transects with repeated visits, 'Sample.Label's will not match Distance for Windows
> lapply(cc, test_stats, 1:2)
$`robin half-normal hermite`
         Statistic Distance_value   mrds_value   Difference Pass
1       parameters              2            2            0    ✓
2              AIC     704.870728 -4360.534373     7.186289
3          Chi^2 p       0.467483            1     1.139115
4              P_a     0.62542713  -0.06019058     1.096239
5          CV(P_a)         0.1939    -4.614791     24.79985
6   log-likelihood      -350.4353    2182.2672            0    ✓
7            K-S p      0.2433462            0            1
8           C-vM p            0.5          0.5            0    ✓
9          density      0.6969193    -7.807282     12.20256
10     CV(density)         0.2204     -4.61538     21.94093
11     individuals             23   -259.20176     12.26964
12 CV(individuals)         0.2204     -4.61538     21.94093

$`robin FS`
         Statistic Distance_value     mrds_value     Difference Pass
1                n             80             80              0    ✓
2       parameters              2              2              0    ✓
3              AIC     704.226624 703.5538644419   0.0009553168    ✓
4          Chi^2 p      0.4338603      0.6593871      0.5198143
5              P_a      0.6359143      0.7306516      0.1489781
6          CV(P_a)      0.1618734      0.1871683      0.1562638
7   log-likelihood      -350.1133      -349.7769              0    ✓
8            K-S p      0.2814207      0.6546518       1.326239
9           C-vM p            0.6            0.8      0.3333333
10         density     0.68542612     0.64315853     0.06166612
11     CV(density)     0.19204509     0.20118036     0.04756831
12     individuals             23    21.35286316     0.07161465
13 CV(individuals)     0.19204509     0.20118036     0.04756831

$`robin haz rate`
         Statistic Distance_value       mrds_value       Difference Pass
1       parameters              2                2                0    ✓
2              AIC     704.801086 704.795374602854   0.000008103559    ✓
3          Chi^2 p    0.595224917      0.594403211      0.001380467    ✓
4              P_a    0.678749025      0.679068699     0.0004710121    ✓
5          CV(P_a)    0.077799998      0.077606563      0.002486335    ✓
6   log-likelihood      -350.4005        -350.3977                0    ✓
7            K-S p    0.464045703      0.465539624      0.003219346    ✓
8           C-vM p            0.8              0.7            0.125
9          density     0.64217001       0.69201365       0.07761754
10     CV(density)         0.1306        0.1070716        0.1801563
11     individuals             21      22.97485333       0.09404063
12 CV(individuals)         0.1306        0.1070716        0.1801563

Comments:

• mrds issue with Hermite polynomials -- something is clearly going wrong with this model.
• Multipliers are not supported properly (I just duplicate the transects accordingly) so there are discrepencies because of that. See Support multipliers #26.

[dill]

This looks slightly better after 8b1278c

> cc <- convert_project("inst/D70Montrave-lt/D70Montrave\\ linetransect")
Warning message:
In get_data(data_file) :
  Data contains transects with repeated visits, 'Sample.Label's will not match Distance for Windows
>  lapply(cc, test_stats, 1:2)
$`robin half-normal hermite`
         Statistic Distance_value   mrds_value   Difference Pass
1       parameters              2            2            0    ✓
2              AIC     704.870728 704.06360892   0.00114506    ✓
3          Chi^2 p       0.467483    0.3918724    0.1617398
4              P_a     0.62542713   0.57725915   0.07701609
5          CV(P_a)         0.1939    0.1029525    0.4690431
6   log-likelihood      -350.4353    -350.0318            0    ✓
7            K-S p      0.2433462           NA           NA    ✓
8           C-vM p            0.5          0.2          0.6
9          density      0.6969193    0.8140621    0.1680866
10     CV(density)         0.2204    0.1266522    0.4253531
11     individuals             23    27.026863     0.175081
12 CV(individuals)         0.2204    0.1266522    0.4253531

$`robin FS`
         Statistic Distance_value     mrds_value     Difference Pass
1                n             80             80              0    ✓
2       parameters              2              2              0    ✓
3              AIC     704.226624 703.5538644419   0.0009553168    ✓
4          Chi^2 p      0.4338603      0.6593871      0.5198143
5              P_a      0.6359143      0.7306516      0.1489781
6          CV(P_a)      0.1618734      0.1871683      0.1562638
7   log-likelihood      -350.1133      -349.7769              0    ✓
8            K-S p      0.2814207             NA             NA    ✓
9           C-vM p            0.6            0.8      0.3333333
10         density     0.68542612     0.64315853     0.06166612
11     CV(density)     0.19204509     0.20118036     0.04756831
12     individuals             23    21.35286316     0.07161465
13 CV(individuals)     0.19204509     0.20118036     0.04756831

$`robin haz rate`
         Statistic Distance_value       mrds_value       Difference Pass
1       parameters              2                2                0    ✓
2              AIC     704.801086 704.795374602854   0.000008103559    ✓
3          Chi^2 p     0.59522492        0.5960077       0.00131514    ✓
4              P_a    0.678749025       0.67909155     0.0005046784    ✓
5          CV(P_a)    0.077799998      0.077698765      0.001301218    ✓
6   log-likelihood      -350.4005        -350.3977                0    ✓
7            K-S p      0.4640457               NA               NA    ✓
8           C-vM p            0.8              0.7            0.125
9          density     0.64217001       0.69199037       0.07758128
10     CV(density)         0.1306        0.1071384        0.1796444
11     individuals             21      22.97408024       0.09400382
12 CV(individuals)         0.1306        0.1071384        0.1796444

Warning messages:
1: In ticks[as.numeric(res_text) >= tolerance] <- "" :
  NAs introduced by coercion
2: In data.frame(Statistic = stats$Name, Distance_value = as.numeric(stats$Value),  :
  NAs introduced by coercion

[dill]

Issue in 9c0c512 where the $summary table is of length 1 and doesn't have a "Total" row... need to write some better code for abundance estimation... Maybe we can just use the bottom row? See 27aa599

[dill]

Now we have:

>  cc <- convert_project("inst/D70Montrave-lt/D70Montrave\\ linetransect")
Warning message:
In get_data(data_file) :
  Data contains transects with repeated visits, 'Sample.Label's will not match Distance for Windows
> lapply(cc, test_stats, 1:2)
$`robin half-normal hermite`
         Statistic Distance_value   mrds_value   Difference Pass
1       parameters              2            2            0    ✓
2              AIC     704.870728 -4360.534373     7.186289
3          Chi^2 p       0.467483            1     1.139115
4              P_a     0.62542713  -0.06019058     1.096239
5          CV(P_a)         0.1939     -4.61477     24.79974
6   log-likelihood      -350.4353    2182.2672            0    ✓
7           C-vM p            0.5          0.5            0    ✓
8          density      0.6969193    -7.807282     12.20256
9      CV(density)         0.2204     -4.61536     21.94083
10     individuals             23   -259.20176     12.26964
11 CV(individuals)         0.2204     -4.61536     21.94083

$`robin FS`
         Statistic Distance_value     mrds_value     Difference Pass
1                n             80             80              0    ✓
2       parameters              2              2              0    ✓
3              AIC     704.226624 703.5538644419   0.0009553168    ✓
4          Chi^2 p      0.4338603      0.6593871      0.5198143
5              P_a      0.6359143      0.7306516      0.1489781
6          CV(P_a)      0.1618734      0.1871683      0.1562638
7   log-likelihood      -350.1133      -349.7769              0    ✓
8           C-vM p            0.6            0.8      0.3333333
9          density     0.68542612     0.64315853     0.06166612
10     CV(density)     0.19204509     0.20118036     0.04756831
11     individuals             23    21.35286316     0.07161465
12 CV(individuals)     0.19204509     0.20118036     0.04756831

$`robin haz rate`
         Statistic Distance_value       mrds_value       Difference Pass
1       parameters              2                2                0    ✓
2              AIC     704.801086 704.795374602854   0.000008103559    ✓
3          Chi^2 p     0.59522492        0.5960077       0.00131514    ✓
4              P_a    0.678749025       0.67909155     0.0005046784    ✓
5          CV(P_a)    0.077799998      0.077698765      0.001301218    ✓
6   log-likelihood      -350.4005        -350.3977                0    ✓
7           C-vM p            0.8              0.7            0.125
8          density     0.64217001       0.69199037       0.07758128
9      CV(density)         0.1306        0.1071384        0.1796444
10     individuals             21      22.97408024       0.09400382
11 CV(individuals)         0.1306        0.1071384        0.1796444

NB lack of warnings!