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Merged
strengejacke merged 26 commits into from
Jun 2, 2025
Merged

Better support for models of class sdmTMB #1075

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0a0c956
Better support for models of class `sdmTMB`
strengejacke May 22, 2025
db6446c
supported list
strengejacke May 22, 2025
e2cce55
supported model list
strengejacke May 22, 2025
b0f0423
readme
strengejacke May 22, 2025
23e26b6
more support
strengejacke May 22, 2025
ab90e51
fix
strengejacke May 22, 2025
10d60fe
fix
strengejacke May 22, 2025
59e3380
find_predictors
strengejacke May 22, 2025
3f48d10
find_predictors
strengejacke May 22, 2025
0cfa6f4
model info
strengejacke May 22, 2025
8608269
more
strengejacke May 22, 2025
4807dae
disable old tests
strengejacke May 22, 2025
4122dcf
get_predicted for sdmTMB
strengejacke May 23, 2025
5050787
docs
strengejacke May 23, 2025
9aaa956
remove unused code
strengejacke May 23, 2025
d487b2d
Merge branch 'main' into sdmTMB_support
strengejacke Jun 1, 2025
afaadda
add to suggest
strengejacke Jun 1, 2025
3b84994
styler
strengejacke Jun 1, 2025
d0a98d1
fix
strengejacke Jun 1, 2025
8fd0646
fix
strengejacke Jun 1, 2025
fe84cc2
new range option
strengejacke Jun 1, 2025
4dd2760
add getvarcov
strengejacke Jun 2, 2025
ad360a6
tests
strengejacke Jun 2, 2025
cc18323
fix
strengejacke Jun 2, 2025
49bc224
remove commented code
strengejacke Jun 2, 2025
3ef20c8
skip on ubuntu
strengejacke Jun 2, 2025
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2 changes: 1 addition & 1 deletion DESCRIPTION
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@@ -1,7 +1,7 @@
Type: Package
Package: insight
Title: Easy Access to Model Information for Various Model Objects
Version: 1.3.0
Version: 1.3.0.1
Authors@R:
c(person(given = "Daniel",
family = "Lüdecke",
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1 change: 1 addition & 0 deletions NAMESPACE
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Expand Up @@ -963,6 +963,7 @@ S3method(get_statistic,rq)
S3method(get_statistic,rqs)
S3method(get_statistic,rqss)
S3method(get_statistic,scam)
S3method(get_statistic,sdmTMB)
S3method(get_statistic,selection)
S3method(get_statistic,sem)
S3method(get_statistic,summary.lm)
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6 changes: 6 additions & 0 deletions NEWS.md
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@@ -1,3 +1,9 @@
# insight (devel)

## Changes

* Better support for models of class `sdmTMB`.

# insight 1.3.0

## Breaking Changes
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1 change: 1 addition & 0 deletions R/find_statistic.R
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Expand Up @@ -23,7 +23,7 @@
}

#' @export
find_statistic.default <- function(x, ...) {

Check warning on line 26 in R/find_statistic.R

View workflow job for this annotation

GitHub Actions / lint-changed-files / lint-changed-files 

file=R/find_statistic.R,line=26,col=1,[cyclocomp_linter] Reduce the cyclomatic complexity of this expression from 53 to at most 40.
# model object check --------------------------------------------------------

# check if the object is a model object; if not, quit early
Expand Down Expand Up @@ -140,6 +140,7 @@
"qr", "QRNLMM", "QRLMM",
"Rchoice", "riskRegression", "robmixglm", "rma", "rma.mv", "rma.uni", "rrvglm",
"Sarlm", "sem", "SemiParBIV", "serp", "slm", "slopes", "survreg", "svy_vglm",
"sdmTMB",
"test_mediation", "tobit",
"vglm",
"wbgee",
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17 changes: 17 additions & 0 deletions R/get_statistic.R
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Expand Up @@ -1394,6 +1394,23 @@ get_statistic.ergm <- function(x, verbose = TRUE, ...) {
}


#' @export
get_statistic.sdmTMB <- function(x, verbose = TRUE, ...) {
est <- stats::coef(x)
se <- sqrt(diag(get_varcov(x)))

out <- data.frame(
Parameter = names(est),
Statistic = est / se,
stringsAsFactors = FALSE,
row.names = NULL
)

attr(out, "statistic") <- find_statistic(x)
out
}


#' @export
get_statistic.btergm <- function(x, verbose = TRUE, ...) {
params <- x@coef
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6 changes: 4 additions & 2 deletions R/is_model.R
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Expand Up @@ -120,14 +120,15 @@ is_regression_model <- function(x) {
"mle", "mle2", "mlergm", "mlm", "mlma", "mlogit", "model_fit",
"multinom", "mvmeta", "mvord", "mvr", "marginaleffects",
"marginaleffects.summary", "mblogit", "mclogit", "mmrm", "mmrm_fit",
"mmrm_tmb", "multinom_weightit",
"mmrm_tmb", "multinom_weightit", "mmlogit", "med1way", "mcp12",

# n --------------------
"negbin", "negbinmfx", "negbinirr", "nlreg", "nlrq", "nls",
"nparLD", "nestedLogit",

# o --------------------
"objectiveML", "ols", "osrt", "orcutt", "ordinal_weightit", "oohbchoice",
"onesampb", "orm",

# p --------------------
"pairwise.htest", "pb1", "pb2", "pgmm", "plm", "plmm", "PMCMR",
Expand All @@ -146,7 +147,8 @@ is_regression_model <- function(x) {
"Sarlm", "scam", "selection", "sem", "SemiParBIV", "serp", "slm", "speedlm",
"speedglm", "splmm", "spml", "stanmvreg", "stanreg", "summary.lm",
"survfit", "survreg", "survPresmooth", "svychisq", "svyglm", "svy_vglm",
"svyolr", "svytable", "systemfit", "svy2lme", "seqanova.svyglm",
"svyolr", "svytable", "systemfit", "svy2lme", "seqanova.svyglm", "sdmTMB",
"stanfit", "semLME",

# t --------------------
"t1way", "t2way", "t3way", "test_mediation", "tobit", "trendPMCMR",
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9 changes: 6 additions & 3 deletions R/is_model_supported.R
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Expand Up @@ -35,7 +35,7 @@ is_model_supported <- function(x) {
#' @rdname is_model_supported
#' @export
supported_models <- function() {
sort(.supported_models_list())
sort(unique(.supported_models_list()))
}


Expand Down Expand Up @@ -79,6 +79,9 @@ supported_models <- function() {
# i ----------------------------
"ivFixed", "iv_robust", "ivreg", "ivprobit",

# j ----------------------------
"joint",

# l ----------------------------
"lavaan", "lm", "lm_robust", "lme", "lmrob", "lmRob", "lmerMod",
"lmerModLmerTest", "lmodel2", "logitmfx", "logitor", "logistf", "logitr",
Expand All @@ -103,14 +106,14 @@ supported_models <- function() {
"probitmfx", "phyloglm", "phylolm",

# r ----------------------------
"Rchoice", "ridgelm", "riskRegression", "rjags", "rlm", "rlmerMod",
"Rchoice", "ridgelm", "riskRegression", "rjags", "rlm", "rlmerMod", "rms",
"robtab", "RM", "rma", "rma.uni", "robmixglm", "rq", "rqs", "rqss", "rvar",

# s ----------------------------
"Sarlm", "scam", "selection", "sem", "semLm", "semLme", "SemiParBIV", "serp",
"slm", "speedlm", "speedglm", "stanfit", "stanmvreg", "stanreg", "summary.lm",
"survfit", "survreg", "svy_vglm", "svychisq", "svyglm", "svyolr", "svy2lme",
"seqanova.svyglm",
"seqanova.svyglm", "sdmTMB", "systemfit",

# t ----------------------------
"t1way", "tobit", "trimcibt", "truncreg",
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136 changes: 69 additions & 67 deletions README.md
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Expand Up @@ -281,7 +281,7 @@ email or also file an issue.

## List of Supported Models by Class

Currently, about 239 model classes are supported.
Currently, about 243 model classes are supported.

``` r
supported_models()
Expand Down Expand Up @@ -339,72 +339,74 @@ supported_models()
#> [103] "HLfit" "htest"
#> [105] "hurdle" "iv_robust"
#> [107] "ivFixed" "ivprobit"
#> [109] "ivreg" "lavaan"
#> [111] "lm" "lm_robust"
#> [113] "lme" "lmerMod"
#> [115] "lmerModLmerTest" "lmodel2"
#> [117] "lmrob" "lmRob"
#> [119] "logistf" "logitmfx"
#> [121] "logitor" "logitr"
#> [123] "LORgee" "lqm"
#> [125] "lqmm" "lrm"
#> [127] "manova" "MANOVA"
#> [129] "marginaleffects" "marginaleffects.summary"
#> [131] "margins" "maxLik"
#> [133] "mblogit" "mclogit"
#> [135] "mcmc" "mcmc.list"
#> [137] "MCMCglmm" "mcp1"
#> [139] "mcp12" "mcp2"
#> [141] "med1way" "mediate"
#> [143] "merMod" "merModList"
#> [145] "meta_bma" "meta_fixed"
#> [147] "meta_random" "metaplus"
#> [149] "mhurdle" "mipo"
#> [151] "mira" "mixed"
#> [153] "MixMod" "mixor"
#> [155] "mjoint" "mle"
#> [157] "mle2" "mlm"
#> [159] "mlogit" "mmclogit"
#> [161] "mmlogit" "mmrm"
#> [163] "mmrm_fit" "mmrm_tmb"
#> [165] "model_fit" "multinom"
#> [167] "multinom_weightit" "mvord"
#> [169] "negbinirr" "negbinmfx"
#> [171] "nestedLogit" "ols"
#> [173] "onesampb" "oohbchoice"
#> [175] "ordinal_weightit" "orm"
#> [177] "pgmm" "phyloglm"
#> [179] "phylolm" "plm"
#> [181] "PMCMR" "poissonirr"
#> [183] "poissonmfx" "polr"
#> [185] "probitmfx" "psm"
#> [187] "Rchoice" "ridgelm"
#> [189] "riskRegression" "rjags"
#> [191] "rlm" "rlmerMod"
#> [193] "RM" "rma"
#> [195] "rma.uni" "robmixglm"
#> [197] "robtab" "rq"
#> [199] "rqs" "rqss"
#> [201] "rvar" "Sarlm"
#> [203] "scam" "selection"
#> [205] "sem" "SemiParBIV"
#> [207] "semLm" "semLme"
#> [209] "seqanova.svyglm" "serp"
#> [211] "slm" "speedglm"
#> [213] "speedlm" "stanfit"
#> [215] "stanmvreg" "stanreg"
#> [217] "summary.lm" "survfit"
#> [219] "survreg" "svy_vglm"
#> [221] "svy2lme" "svychisq"
#> [223] "svyglm" "svyolr"
#> [225] "t1way" "tobit"
#> [227] "trimcibt" "truncreg"
#> [229] "vgam" "vglm"
#> [231] "wbgee" "wblm"
#> [233] "wbm" "wmcpAKP"
#> [235] "yuen" "yuend"
#> [237] "zcpglm" "zeroinfl"
#> [239] "zerotrunc"
#> [109] "ivreg" "joint"
#> [111] "lavaan" "lm"
#> [113] "lm_robust" "lme"
#> [115] "lmerMod" "lmerModLmerTest"
#> [117] "lmodel2" "lmrob"
#> [119] "lmRob" "logistf"
#> [121] "logitmfx" "logitor"
#> [123] "logitr" "LORgee"
#> [125] "lqm" "lqmm"
#> [127] "lrm" "manova"
#> [129] "MANOVA" "marginaleffects"
#> [131] "marginaleffects.summary" "margins"
#> [133] "maxLik" "mblogit"
#> [135] "mclogit" "mcmc"
#> [137] "mcmc.list" "MCMCglmm"
#> [139] "mcp1" "mcp12"
#> [141] "mcp2" "med1way"
#> [143] "mediate" "merMod"
#> [145] "merModList" "meta_bma"
#> [147] "meta_fixed" "meta_random"
#> [149] "metaplus" "mhurdle"
#> [151] "mipo" "mira"
#> [153] "mixed" "MixMod"
#> [155] "mixor" "mjoint"
#> [157] "mle" "mle2"
#> [159] "mlm" "mlogit"
#> [161] "mmclogit" "mmlogit"
#> [163] "mmrm" "mmrm_fit"
#> [165] "mmrm_tmb" "model_fit"
#> [167] "multinom" "multinom_weightit"
#> [169] "mvord" "negbinirr"
#> [171] "negbinmfx" "nestedLogit"
#> [173] "ols" "onesampb"
#> [175] "oohbchoice" "ordinal_weightit"
#> [177] "orm" "pgmm"
#> [179] "phyloglm" "phylolm"
#> [181] "plm" "PMCMR"
#> [183] "poissonirr" "poissonmfx"
#> [185] "polr" "probitmfx"
#> [187] "psm" "Rchoice"
#> [189] "ridgelm" "riskRegression"
#> [191] "rjags" "rlm"
#> [193] "rlmerMod" "RM"
#> [195] "rma" "rma.uni"
#> [197] "rms" "robmixglm"
#> [199] "robtab" "rq"
#> [201] "rqs" "rqss"
#> [203] "rvar" "Sarlm"
#> [205] "scam" "sdmTMB"
#> [207] "selection" "sem"
#> [209] "SemiParBIV" "semLm"
#> [211] "semLme" "seqanova.svyglm"
#> [213] "serp" "slm"
#> [215] "speedglm" "speedlm"
#> [217] "stanfit" "stanmvreg"
#> [219] "stanreg" "summary.lm"
#> [221] "survfit" "survreg"
#> [223] "svy_vglm" "svy2lme"
#> [225] "svychisq" "svyglm"
#> [227] "svyolr" "systemfit"
#> [229] "t1way" "tobit"
#> [231] "trimcibt" "truncreg"
#> [233] "vgam" "vglm"
#> [235] "wbgee" "wblm"
#> [237] "wbm" "wmcpAKP"
#> [239] "yuen" "yuend"
#> [241] "zcpglm" "zeroinfl"
#> [243] "zerotrunc"
```

- **Didn’t find a model?** [File an
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