test_that("generics work ssn_lm point data", { # Copy the mf04p .ssn data to a local directory and read it into R # When modeling with your .ssn object, you will load it using the relevant # path to the .ssn data on your machine copy_lsn_to_temp() temp_path <- paste0(tempdir(), "/MiddleFork04.ssn") mf04p <- ssn_import( temp_path, predpts = c("pred1km", "CapeHorn", "Knapp"), overwrite = TRUE ) ssn_mod1 <- ssn_lm(Summer_mn ~ ELEV_DEM, mf04p, tailup_type = "exponential", taildown_type = "exponential", euclid_type = "exponential", nugget_type = "nugget", additive = "afvArea" ) ssn_mod2 <- ssn_lm(Summer_mn ~ ELEV_DEM, mf04p, tailup_type = "exponential", taildown_type = "none", euclid_type = "none", nugget_type = "nugget", additive = "afvArea" ) # AIC expect_vector(AIC(ssn_mod1)) expect_s3_class(AIC(ssn_mod1, ssn_mod2), "data.frame") # turn reml fixed effects warning off # anova expect_s3_class(anova(ssn_mod1), "data.frame") expect_s3_class(anova(ssn_mod1), "anova.ssn_lm") expect_s3_class(tidy(anova(ssn_mod1)), "data.frame") expect_s3_class(anova(ssn_mod1, ssn_mod2), "data.frame") expect_s3_class(anova(ssn_mod1, ssn_mod2), "anova.ssn_lm") expect_s3_class(tidy(anova(ssn_mod1, ssn_mod2)), "data.frame") # augment expect_s3_class(augment(ssn_mod1), "data.frame") expect_s3_class(augment(ssn_mod1, newdata = "pred1km"), "data.frame") # coef expect_vector(coef(ssn_mod1)) expect_s3_class(coef(ssn_mod1, type = "tailup"), "tailup_exponential") expect_s3_class(coef(ssn_mod1, type = "euclid"), "euclid_exponential") expect_type(coef(ssn_mod1, type = "ssn"), "list") expect_null(coef(ssn_mod1, type = "randcov")) expect_vector(coefficients(ssn_mod1)) expect_s3_class(coefficients(ssn_mod1, type = "taildown"), "taildown_exponential") expect_s3_class(coef(ssn_mod1, type = "nugget"), "nugget_nugget") expect_null(coefficients(ssn_mod1, type = "randcov")) # confint expect_true(inherits(confint(ssn_mod1), "matrix")) expect_true(inherits(confint(ssn_mod1, parm = c("x"), level = 0.9), "matrix")) # cooks.distance expect_vector(cooks.distance(ssn_mod1)) # covmatrix expect_true(inherits(covmatrix(ssn_mod1), "matrix")) expect_true(inherits(covmatrix(ssn_mod1, "pred1km"), "matrix")) expect_true(inherits(covmatrix(ssn_mod1, "pred1km", type = "obs.pred"), "matrix")) expect_true(inherits(covmatrix(ssn_mod1, "pred1km", cov_type = "pred.pred"), "matrix")) # deviance expect_vector(deviance(ssn_mod1)) # fitted expect_vector(fitted(ssn_mod1)) expect_vector(fitted(ssn_mod1, type = "tailup")) expect_vector(fitted(ssn_mod1, type = "taildown")) expect_null(fitted(ssn_mod1, type = "randcov")) expect_vector(fitted.values(ssn_mod1)) expect_vector(fitted.values(ssn_mod1, type = "euclid")) expect_vector(fitted.values(ssn_mod1, type = "nugget")) expect_null(fitted.values(ssn_mod1, type = "randcov")) # formula expect_type(formula(ssn_mod1), "language") # getCall expect_type(getCall(ssn_mod1), "language") # glance expect_s3_class(glance(ssn_mod1), "data.frame") # glances expect_s3_class(glances(ssn_mod1), "data.frame") expect_s3_class(glances(ssn_mod1, ssn_mod2), "data.frame") # hatvalues expect_vector(hatvalues(ssn_mod1)) # influence expect_s3_class(influence(ssn_mod1), "data.frame") # labels expect_type(labels(ssn_mod1), "character") # logLik expect_vector(logLik(ssn_mod1)) # loocv expect_s3_class(loocv(ssn_mod1), "data.frame") expect_type(loocv(ssn_mod1, cv_predict = TRUE, se.fit = TRUE), "list") # model.frame expect_s3_class(model.frame(ssn_mod1), "data.frame") # model.matrix expect_true(inherits(model.matrix(ssn_mod1), "matrix")) # model.offset expect_null(model.offset(model.frame(ssn_mod1))) # model.response expect_vector(model.response(model.frame(ssn_mod1))) # plot expect_invisible(plot(ssn_mod1, which = 1)) expect_invisible(plot(ssn_mod1, which = 2)) expect_invisible(plot(ssn_mod1, which = 3)) expect_invisible(plot(ssn_mod1, which = 4)) expect_invisible(plot(ssn_mod1, which = 5)) expect_invisible(plot(ssn_mod1, which = 6)) # predict expect_vector(predict(ssn_mod1, newdata = "pred1km")) expect_type(predict(ssn_mod1, newdata = "pred1km", se.fit = TRUE), "list") expect_type(predict(ssn_mod1, newdata = "pred1km", interval = "prediction", se.fit = TRUE), "list") expect_true(inherits(predict(ssn_mod1, newdata = "pred1km", interval = "confidence", level = 0.9), "matrix")) expect_vector(predict(ssn_mod1, newdata = "pred1km", block = TRUE)) expect_type(predict(ssn_mod1, newdata = "pred1km", block = TRUE, se.fit = TRUE), "list") expect_true(inherits(predict(ssn_mod1, newdata = "pred1km", block = TRUE, interval = "confidence"), "matrix")) expect_true(inherits(predict(ssn_mod1, newdata = "pred1km", block = TRUE, interval = "prediction"), "matrix")) # print expect_output(print(ssn_mod1)) expect_output(print(summary(ssn_mod1))) expect_output(print(anova(ssn_mod1))) # pseudoR2 expect_vector(pseudoR2(ssn_mod1)) # residuals expect_vector(residuals(ssn_mod1)) expect_vector(residuals(ssn_mod1, type = "pearson")) expect_vector(residuals(ssn_mod1, type = "standardized")) expect_vector(resid(ssn_mod1)) expect_vector(resid(ssn_mod1, type = "pearson")) expect_vector(resid(ssn_mod1, type = "standardized")) expect_vector(rstandard(ssn_mod1)) # summary expect_type(summary(ssn_mod1), "list") # terms expect_type(terms(ssn_mod1), "language") # tidy expect_s3_class(tidy(ssn_mod1), "data.frame") expect_s3_class(tidy(ssn_mod1, conf.int = TRUE, level = 0.9), "data.frame") expect_s3_class(tidy(ssn_mod1, effects = "ssn"), "data.frame") expect_s3_class(tidy(ssn_mod1, effects = "tailup"), "data.frame") expect_s3_class(tidy(ssn_mod1, effects = "taildown"), "data.frame") expect_s3_class(tidy(ssn_mod1, effects = "euclid"), "data.frame") expect_s3_class(tidy(ssn_mod1, effects = "nugget"), "data.frame") # update expect_s3_class(update(ssn_mod2), "ssn_lm") # varcomp expect_s3_class(varcomp(ssn_mod1), "data.frame") # vcov expect_true(inherits(vcov(ssn_mod1), "matrix")) })